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Kumar, Santosh, Travis W. Banks, and Sylvie Cloutier. "SNP Discovery through Next-Generation Sequencing and Its Applications." International Journal of Plant Genomics 2012 (November 22, 2012): 1–15. http://dx.doi.org/10.1155/2012/831460.
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The decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in partially or completely sequenced genomes. Although excellent reviews have been published on next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic studies, a comprehensive review connecting these three intertwined research areas is needed. This paper touches upon various aspects of SNP discovery, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses. The use of next-generation sequencing methodologies in many non-model crops leading to discovery and implementation of SNPs in various genetic studies is discussed. Development and improvement of bioinformatics software that are open source and freely available have accelerated the SNP discovery while reducing the associated cost. Key considerations for SNP filtering and associated pipelines are discussed in specific topics. A list of commonly used software and their sources is compiled for easy access and reference.
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Spencer, Amy Victoria, Angela Cox, and Kevin Walters. "Comparing the Efficacy of SNP Filtering Methods for Identifying a Single Causal SNP in a Known Association Region." Annals of Human Genetics 78, no. 1 (November 11, 2013): 50–61. http://dx.doi.org/10.1111/ahg.12043.
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Lakhssassi, Kenza, and Oscar González-Recio. "A haplotype regression approach for genetic evaluation using sequences from the 1000 bull genomes Project." Spanish Journal of Agricultural Research 15, no. 4 (February 7, 2018): e0407. http://dx.doi.org/10.5424/sjar/2017154-11736.
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Haplotypes from sequencing data may improve the prediction accuracy in genomic evaluations as haplotypes are in stronger linkage disequilibrium with quantitative trait loci than markers from SNP chips. This study focuses first, on the creation of haplotypes in a population sample of 450 Holstein animals, with full-sequence data from the 1000 bull genomes project; and second, on incorporating them into the whole genome prediction model. In total, 38,319,258 SNPs (and indels) from Next Generation Sequencing were included in the analysis. After filtering variants with minor allele frequency (MAF< 0.025) 13,912,326 SNPs were available for the haplotypes extraction with findhap.f90. The number of SNPs in the haploblocks was on average 924 SNP (166,552 bp). Unique haplotypes were around 97% in all chromosomes and were ignored leaving 153,428 haplotypes. Estimated haplotypes had a large contribution to the total variance of genomic estimated breeding values for kilogram of protein, Global Type Index, Somatic Cell Score and Days Open (between 32 and 99.9%). Haploblocks containing haplotypes with large effects were selected by filtering for each trait, haplotypes whose effect was larger/lower than the mean plus/minus 3 times the standard deviation (SD) and 1 SD above the mean of the haplotypes effect distribution. Results showed that filtering by 3 SD would not be enough to capture a large proportion of genetic variance, whereas filtering by 1 SD could be useful but model convergence should be considered. Additionally, sequence haplotypes were able to capture additional genetic variance to the polygenic effect for traits undergoing lower selection intensity like fertility and health traits.
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Toghiani, S., L. Y. Chang, S. E. Aggrey, and R. Rekaya. "0300 SNP filtering using Fst and implications for genome wide association and phenotype prediction." Journal of Animal Science 94, suppl_5 (October 1, 2016): 143. http://dx.doi.org/10.2527/jam2016-0300.
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Markello, Thomas C., Ted Han, Hannah Carlson-Donohoe, Chidi Ahaghotu, Ursula Harper, MaryPat Jones, Settara Chandrasekharappa, et al. "Recombination mapping using Boolean logic and high-density SNP genotyping for exome sequence filtering." Molecular Genetics and Metabolism 105, no. 3 (March 2012): 382–89. http://dx.doi.org/10.1016/j.ymgme.2011.12.014.
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Friedman, Sam, Laura Gauthier, Yossi Farjoun, and Eric Banks. "Lean and deep models for more accurate filtering of SNP and INDEL variant calls." Bioinformatics 36, no. 7 (December 12, 2019): 2060–67. http://dx.doi.org/10.1093/bioinformatics/btz901.
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Abstract Summary We investigate convolutional neural networks (CNNs) for filtering small genomic variants in short-read DNA sequence data. Errors created during sequencing and library preparation make variant calling a difficult task. Encoding the reference genome and aligned reads covering sites of genetic variation as numeric tensors allows us to leverage CNNs for variant filtration. Convolutions over these tensors learn to detect motifs useful for classifying variants. Variant filtering models are trained to classify variants as artifacts or real variation. Visualizing the learned weights of the CNN confirmed it detects familiar DNA motifs known to correlate with real variation, like homopolymers and short tandem repeats (STR). After confirmation of the biological plausibility of the learned features we compared our model to current state-of-the-art filtration methods like Gaussian Mixture Models, Random Forests and CNNs designed for image classification, like DeepVariant. We demonstrate improvements in both sensitivity and precision. The tensor encoding was carefully tailored for processing genomic data, respecting the qualitative differences in structure between DNA and natural images. Ablation tests quantitatively measured the benefits of our tensor encoding strategy. Bayesian hyper-parameter optimization confirmed our notion that architectures designed with DNA data in mind outperform off-the-shelf image classification models. Our cross-generalization analysis identified idiosyncrasies in truth resources pointing to the need for new methods to construct genomic truth data. Our results show that models trained on heterogenous data types and diverse truth resources generalize well to new datasets, negating the need to train separate models for each data type. Availability and implementation This work is available in the Genome Analysis Toolkit (GATK) with the tool name CNNScoreVariants (https://github.com/broadinstitute/gatk). Supplementary information Supplementary data are available at Bioinformatics online.
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O'Leary, Shannon J., Jonathan B. Puritz, Stuart C. Willis, Christopher M. Hollenbeck, and David S. Portnoy. "These aren’t the loci you’e looking for: Principles of effective SNP filtering for molecular ecologists." Molecular Ecology 27, no. 16 (July 27, 2018): 3193–206. http://dx.doi.org/10.1111/mec.14792.
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Lyu, Pin, Jianhua Hou, Haifeng Yu, and Huimin Shi. "High-density Genetic Linkage Map Construction in Sunflower (Helianthus annuus L.) Using SNP and SSR Markers." Current Bioinformatics 15, no. 8 (January 1, 2021): 889–97. http://dx.doi.org/10.2174/1574893615666200324134725.
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Background: Sunflower (Helianthus annuus L.) is an important oil crop only after soybean, canola and peanuts. A high-quality genetic map is the foundation of marker-assisted selection (MAS). However, for this species, the high-density maps have been reported limitedly. Objective: In this study, we proposed the construction of a high-density genetic linkage map by the F7 population of sunflowers using SNP and SSR Markers. Methods: The SLAF-seq strategy was employed to further develop SNP markers with SSR markers to construct the high-density genetic map by the HighMap software. Results: A total of 1,138 million paired-end reads (226Gb) were obtained and 518,900 SLAFs were detected. Of the polymorphic SLAFs, 2,472,245 SNPs were developed and finally, 5,700 SNPs were found to be ideal to construct a genetic map after filtering. The final high-density genetic map included 4,912 SNP and 93 SSR markers distributed in 17 linkage groups (LGs) and covered 2,425.05 cM with an average marker interval of 0.49 cM. Conclusion: The final result demonstrated that the SLAF-seq strategy is suitable for SNP markers detection. The genetic map reported in this study can be considered as one of the most highdensity genetic linkage maps of sunflower and could lay a foundation for quantitative trait loci (QTLs) fine mapping or map-based gene cloning.
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Vossen, David M., Caroline V. M. Verhagen, Reidar Grénman, Roelof J. C. Kluin, Marcel Verheij, Michiel W. M. van den Brekel, Lodewyk F. A. Wessels, and Conchita Vens. "Role of variant allele fraction and rare SNP filtering to improve cellular DNA repair endpoint association." PLOS ONE 13, no. 11 (November 8, 2018): e0206632. http://dx.doi.org/10.1371/journal.pone.0206632.
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Ulaszewski, Bartosz, Joanna Meger, and Jaroslaw Burczyk. "Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods." Forests 12, no. 2 (February 15, 2021): 222. http://dx.doi.org/10.3390/f12020222.
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Next-generation sequencing of reduced representation genomic libraries (RRL) is capable of providing large numbers of genetic markers for population genetic studies at relatively low costs. However, one major concern of these types of markers is the precision of genotyping, which is related to the common problem of missing data, which appears to be particularly important in association and genomic selection studies. We evaluated three RRL approaches (GBS, RADseq, ddRAD) and different SNP identification methods (de novo or based on a reference genome) to find the best solutions for future population genomics studies in two economically and ecologically important broadleaved tree species, namely F. sylvatica and Q. robur. We found that the use of ddRAD method coupled with SNP calling based on reference genomes provided the largest numbers of markers (28 k and 36 k for beech and oak, respectively), given standard filtering criteria. Using technical replicates of samples, we demonstrated that more than 80% of SNP loci should be considered as reliable markers in GBS and ddRAD, but not in RADseq data. According to the reference genomes’ annotations, more than 30% of the identified ddRAD loci appeared to be related to genes. Our findings provide a solid support for using ddRAD-based SNPs for future population genomics studies in beech and oak.
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Reinbolt, Raquel E., Stephen T. Sonis, Cynthia Dawn Timmers, Juan Luis Fernández-Martínez, Enrique J. deAndrés-Galiana, Sepehr Hashemi, Karin Miller, et al. "Genomic risk prediction of aromatase inhibitor-related arthralgias (AIA) in breast cancer (BC) patients using a novel analytical algorithm (NAA)." Journal of Clinical Oncology 35, no. 15_suppl (May 20, 2017): 10102. http://dx.doi.org/10.1200/jco.2017.35.15_suppl.10102.
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10102 Background: Many BC patients treated with aromatase inhibitors (AIs) develop AIA; 20% have symptoms severe enough to effect treatment compliance. Results of candidate gene studies to identify AIA risk are limited in scope. In this case-controlled study, we evaluated the potential of a NAA to predict AIA using germline single nucleotide polymorphism (SNP) data obtained prior to treatment initiation. Methods: Systematic chart review of 700 AI-treated patients with stage I-III BC between 2003-2012 identified asymptomatic patients (n = 39) and those with clinically significant AIA resulting in AI termination or therapy switch (n = 123). Germline DNA was obtained from peripheral blood cells and SNP genotyping performed using the Affymetrix UK BioBank Axiom Array to yield 695,277 SNPs. The identity of the cluster of SNPs that most closely defined AIA risk was discovered using an NAA that sequentially combined statistical filtering and a machine learning algorithm. NCBI PhenGenI and Ensemble databases were used to define gene attribution of the 200 most discriminating SNPs. Phenotype, pathway, and ontologic analyses assessed functional and mechanistic validity. Results: Cases and controls were similar in demographic characteristics. A cluster of 70 SNPs, correlated to 57 genes (accounting for linkage disequilibrium), was identified. This SNP group predicted AIA occurrence with a maximum accuracy of 75.93%. Strong associations with arthralgia, breast cancer, and estrogen phenotypes were seen in 19/57 genes (33%) and were functionally and ontologically consistent. Conclusions: Using a NAA, we identified a 70 SNP cluster that predicted AIA risk with fair accuracy. Phenotype, functional, and pathway analysis of attributed genes was consistent with clinical phenotypes. This study is the first to link a specific SNP/gene cluster to AIA risk independent of candidate gene bias. An ongoing prospective companion study will be used to validate and to expand upon results.
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Yu, Xiaoxia, Mingfei Zhang, Zhuo Yu, Dongsheng Yang, Jingwei Li, Guofang Wu, and Jiaqi Li. "An SNP-Based High-Density Genetic Linkage Map for Tetraploid Potato Using Specific Length Amplified Fragment Sequencing (SLAF-Seq) Technology." Agronomy 10, no. 1 (January 13, 2020): 114. http://dx.doi.org/10.3390/agronomy10010114.
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Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for the discovery of large-scale de novo genotyping of single nucleotide polymorphism (SNP) markers. In the present research, in order to facilitate genome-guided breeding in potato, this strategy was used to develop a large number of SNP markers and construct a high-density genetic linkage map for tetraploid potato. The genomic DNA extracted from 106 F1 individuals derived from a cross between two tetraploid potato varieties YSP-4 × MIN-021 and their parents was used for high-throughput sequencing and SLAF library construction. A total of 556.71 Gb data, which contained 2269.98 million pair-end reads, were obtained after preprocessing. According to bioinformatics analysis, a total of 838,604 SLAF labels were developed, with an average sequencing depth of 26.14-fold for parents and 15.36-fold for offspring of each SLAF, respectively. In total, 113,473 polymorphic SLAFs were obtained, from which 7638 SLAFs were successfully classified into four segregation patterns. After filtering, a total of 7329 SNP markers were detected for genetic map construction. The final integrated linkage map of tetraploid potato included 3001 SNP markers on 12 linkage groups, and covered 1415.88 cM, with an average distance of 0.47 cM between adjacent markers. To our knowledge, the integrated map described herein has the best coverage of the potato genome and the highest marker density for tetraploid potato. This work provides a foundation for further quantitative trait loci (QTL) location, map-based gene cloning of important traits and marker-assisted selection (MAS) of potato.
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Li, Zitong, Ari Löytynoja, Antoine Fraimout, and Juha Merilä. "Effects of marker type and filtering criteria on Q ST - F ST comparisons." Royal Society Open Science 6, no. 11 (November 2019): 190666. http://dx.doi.org/10.1098/rsos.190666.
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Comparative studies of quantitative and neutral genetic differentiation ( Q ST - F ST tests) provide means to detect adaptive population differentiation. However, Q ST - F ST tests can be overly liberal if the markers used deflate F ST below its expectation, or overly conservative if methodological biases lead to inflated F ST estimates. We investigated how marker type and filtering criteria for marker selection influence Q ST - F ST comparisons through their effects on F ST using simulations and empirical data on over 18 000 in silico genotyped microsatellites and 3.8 million single-locus polymorphism (SNP) loci from four populations of nine-spined sticklebacks ( Pungitius pungitius ). Empirical and simulated data revealed that F ST decreased with increasing marker variability, and was generally higher with SNPs than with microsatellites. The estimated baseline F ST levels were also sensitive to filtering criteria for SNPs: both minor alleles and linkage disequilibrium (LD) pruning influenced F ST estimation, as did marker ascertainment. However, in the case of stickleback data used here where Q ST is high, the choice of marker type, their genomic location, ascertainment and filtering made little difference to outcomes of Q ST - F ST tests. Nevertheless, we recommend that Q ST - F ST tests using microsatellites should discard the most variable loci, and those using SNPs should pay attention to marker ascertainment and properly account for LD before filtering SNPs. This may be especially important when level of quantitative trait differentiation is low and levels of neutral differentiation high.
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Melak, Sherif, Qin Wang, Ye Tian, Wei Wei, Lifan Zhang, Ahmed Elbeltagy, and Jie Chen. "Identification and Validation of Marketing Weight-Related SNP Markers Using SLAF Sequencing in Male Yangzhou Geese." Genes 12, no. 8 (August 3, 2021): 1203. http://dx.doi.org/10.3390/genes12081203.
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Growth performance is a complex economic trait for avian production. The swan goose (Anser cygnoides) has never been exploited genetically like chickens or other waterfowl species such as ducks. Traditional phenotypic selection is still the main method for genetic improvement of geese body weight. In this study, specific locus amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) was conducted for discovering and genotyping single nucleotide polymorphisms (SNPs) associated with marketing weight trait in male geese. A total of 149,045 SNPs were obtained from 427,093 SLAF tags with an average sequencing depth of 44.97-fold and a Q30 value of 93.26%. After SNPs’ filtering, a total of 12,917 SNPs were included in the study. The 31 highest significant SNPs—which had different allelic frequencies—were further validated by individual-based AS-PCR genotyping in two populations. The association between 10 novel SNPs and the marketing weight of male geese was confirmed. The 10 significant SNPs were involved in linear regression model analysis, which confirmed single-SNP associations and revealed three types of SNP networks for marketing weight. The 10 significant SNPs were located within or close to 10 novel genes, which were identified. The qPCR analysis showed significant difference between genotypes of each SNP in seven genes. Developed SLAF-seq and identified genes will enrich growth performance studies, promoting molecular breeding applications to boost the marketing weight of Chinese geese.
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Cagirici, H. Busra, Bala Ani Akpinar, Taner Z. Sen, and Hikmet Budak. "Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing." International Journal of Molecular Sciences 22, no. 19 (September 27, 2021): 10400. http://dx.doi.org/10.3390/ijms221910400.
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The highly challenging hexaploid wheat (Triticum aestivum) genome is becoming ever more accessible due to the continued development of multiple reference genomes, a factor which aids in the plight to better understand variation in important traits. Although the process of variant calling is relatively straightforward, selection of the best combination of the computational tools for read alignment and variant calling stages of the analysis and efficient filtering of the false variant calls are not always easy tasks. Previous studies have analyzed the impact of methods on the quality metrics in diploid organisms. Given that variant identification in wheat largely relies on accurate mining of exome data, there is a critical need to better understand how different methods affect the analysis of whole exome sequencing (WES) data in polyploid species. This study aims to address this by performing whole exome sequencing of 48 wheat cultivars and assessing the performance of various variant calling pipelines at their suggested settings. The results show that all the pipelines require filtering to eliminate false-positive calls. The high consensus among the reference SNPs called by the best-performing pipelines suggests that filtering provides accurate and reproducible results. This study also provides detailed comparisons for high sensitivity and precision at individual and population levels for the raw and filtered SNP calls.
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Seo, Eunju, Kipoong Kim, Tae-Hwan Jun, Jinsil Choi, Seong-Hoon Kim, María Muñoz-Amatriaín, Hokeun Sun, and Bo-Keun Ha. "Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers." Plants 9, no. 9 (September 12, 2020): 1190. http://dx.doi.org/10.3390/plants9091190.
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Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.
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Lavrichenko, Ksenia, Øyvind Helgeland, Pål R. Njølstad, Inge Jonassen, and Stefan Johansson. "SeeCiTe: a method to assess CNV calls from SNP arrays using trio data." Bioinformatics 37, no. 13 (January 18, 2021): 1876–83. http://dx.doi.org/10.1093/bioinformatics/btab028.
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Abstract Motivation Single nucleotide polymorphism (SNP) genotyping arrays remain an attractive platform for assaying copy number variants (CNVs) in large population-wide cohorts. However, current tools for calling CNVs are still prone to extensive false positive calls when applied to biobank scale arrays. Moreover, there is a lack of methods exploiting cohorts with trios available (e.g. nuclear family) to assist in quality control and downstream analyses following the calling. Results We developed SeeCiTe (Seeing CNVs in Trios), a novel CNV-quality control tool that postprocesses output from current CNV-calling tools exploiting child-parent trio data to classify calls in quality categories and provide a set of visualizations for each putative CNV call in the offspring. We apply it to the Norwegian Mother, Father and Child Cohort Study (MoBa) and show that SeeCiTe improves the specificity and sensitivity compared to the common empiric filtering strategies. To our knowledge, it is the first tool that utilizes probe-level CNV data in trios (and singletons) to systematically highlight potential artifacts and visualize signal intensities in a streamlined fashion suitable for biobank scale studies. Availability and implementation The software is implemented in R with the source code freely available at https://github.com/aksenia/SeeCiTe Supplementary information Supplementary data are available at Bioinformatics online.
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Mehravi, Shaghayegh, Gholam Ali Ranjbar, Ghader Mirzaghaderi, Anita Alice Severn-Ellis, Armin Scheben, David Edwards, and Jacqueline Batley. "De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing." Agronomy 11, no. 7 (June 30, 2021): 1342. http://dx.doi.org/10.3390/agronomy11071342.
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The species of Pimpinella, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide polymorphisms (SNPs) in eight Pimpinella species from Iran. After double-digestion with the enzymes HpyCH4IV and HinfI, a total of 334,702,966 paired-end reads were de novo assembled into 1,270,791 loci with an average of 28.8 reads per locus. After stringent filtering, 2440 high-quality SNPs were identified for downstream analysis. Analysis of genetic relationships and population structure, based on these retained SNPs, indicated the presence of three major groups. Gene ontology and pathway analysis were determined by using comparison SNP-associated flanking sequences with a public non-redundant database. Due to the lack of genomic resources in this genus, our present study is the first report to provide high-quality SNPs in Pimpinella based on a de novo analysis pipeline using ddRAD-seq. This data will enhance the molecular knowledge of the genus Pimpinella and will provide an important source of information for breeders and the research community to enhance breeding programs and support the management of Pimpinella genomic resources.
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Grzegorczyk, Joanna, Artur Gurgul, Maria Oczkowicz, Tomasz Szmatoła, Agnieszka Fornal, and Monika Bugno-Poniewierska. "Single Nucleotide Polymorphism Discovery and Genetic Differentiation Analysis of Geese Bred in Poland, Using Genotyping-by-Sequencing (GBS)." Genes 12, no. 7 (July 14, 2021): 1074. http://dx.doi.org/10.3390/genes12071074.
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Poland is the largest European producer of goose, while goose breeding has become an essential and still increasing branch of the poultry industry. The most frequently bred goose is the White Kołuda® breed, constituting 95% of the country’s population, whereas geese of regional varieties are bred in smaller, conservation flocks. However, a goose’s genetic diversity is inaccurately explored, mainly because the advantages of the most commonly used tools are strongly limited in non-model organisms. One of the most accurate used markers for population genetics is single nucleotide polymorphisms (SNP). A highly efficient strategy for genome-wide SNP detection is genotyping-by-sequencing (GBS), which has been already widely applied in many organisms. This study attempts to use GBS in 12 conservative goose breeds and the White Kołuda® breed maintained in Poland. The GBS method allowed for the detection of 3833 common raw SNPs. Nevertheless, after filtering for read depth and alleles characters, we obtained the final markers panel used for a differentiation analysis that comprised 791 SNPs. These variants were located within 11 different genes, and one of the most diversified variants was associated with the EDAR gene, which is especially interesting as it participates in the plumage development, which plays a crucial role in goose breeding.
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Knight, Samantha JL, Ruth Clifford, Pauline Robbe, Sara DC Ramos, Adam Burns, Adele T. Timbs, Reem Alsolami, et al. "The Identification of Further Minimal Regions of Overlap in Chronic Lymphocytic Leukemia Using High-Resolution SNP Arrays." Blood 124, no. 21 (December 6, 2014): 3315. http://dx.doi.org/10.1182/blood.v124.21.3315.3315.
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Abstract Background:Historically, the identification of minimal deleted regions (MDRs) has been a useful approach for pinpointing genes involved in the pathogenesis of human malignancies and constitutional disorders. Microarray technology has offered increased capability for newly identifying or refining existing MDRs and minimal overlapping regions (MORs) in cancer. Despite this, in chronic lymphocytic leukemia (CLL), published MORs that pinpoint only a few candidate genes have been limited and with the advent of NGS, the utility of high resolution array work as a discovery tool has become uncertain. Here, we show that profiling copy number abnormalities (CNAs) and cnLOH using arrays in a large patient series can still be a valuable approach for the identification of genes that are disrupted or mutated in CLL and have a role in CLL development and/or progression. Methods: 250 CLL patient DNAs from individuals enrolled in two UK-based Phase II randomised controlled trials (AdMIRe and ARCTIC trials) were tested using Infinium HumanOmni2.5-8 v1.1 according to manufacturer’s guidelines (Illumina Inc, San Diego, CA). Data were processed using GenomeStudioV2009.2 (Illumina Inc.) and analysed using Nexus Discovery Edition v6.1 (BioDiscovery, Hawthorne, CA). All Nexus plots were inspected visually to verify calls made, identify uncalled events and exclude likely false positives. To exclude common germline CNVs, the Database of Genomic Variants (DGV), a comprehensive catalog of structural variation in control data, was used. Copy number (CN) changes that encompassed fully changes noted in the DGV were excluded from further analysis. Regions of copy neutral loss of heterozygosity (cnLOH) were recorded if >1Mb in size, but were not used to define or refine MORs. Data from 1275 age-appropriate control samples minimised the reporting of common cnLOH events. All genomic coordinates were noted with reference to the GRCh37, hg19 assembly. MORs were investigated using Microsoft Excel filtering functions. A subset of genes (n=91) selected from MORs mainly on the basis of event frequency and/or number of genes within the MOR and/or literature interest were taken forward for targeted sequencing (exons only) of appropriate samples with/without CN Losses or cnLOH (Set 1 n=124; Set 2 n=126). These were tested using custom designed TruSeq Custom Amplicon panels (Illumina Inc) and processed according to manufacturer’s instructions. SAMHD1 was excluded from these panels since it had been studied separately within our laboratory. The data were analysed using an in-house bioinformatics pipeline that uses the sequence aligners MSR and Stampy and the variant callers GATK and Platypus, followed by stringent filtering. Results: Using our datasets we have identified >50 MORs previously unreported in the literature. Six of these showed copy number (CN) losses in >3% of patients studied. Furthermore, we have refined 14 MORs that overlapped with regions described previously and that had also a CN loss frequency of >3%. Thirteen MORs involved only a single reference gene, often a gene implicated previously in cancer (eg. SAMHD1, MTSS1, DCC and RFC1). Of the 91 genes taken forward for targeted sequencing, stringent data filtering led to a subset of 19 genes of interest harbouring exonic mutations. Genes with mutations identified include DCC, BAP1 and FBXW7, also implicated previously in cancer. Conclusion: We have generated high resolution CNA and cnLOH profiles for 250 first-line chemo-immunotherapy treated CLL patients and used this information to document newly identified MORs, to refine MORs reported previously and to identify mutation harbouring genes using targeted NGS. Functional knowledge supports our hypothesis that these genes may have a contributory role in CLL. For two genes, SAMHD1 and FBXW7, relevance in CLL has been established already. Taken together, our data validate the utility of high resolution arrays studies for the identification of candidate genes that may be involved in CLL development or progression when disrupted. Further studies are required to confirm a role for these genes in CLL and to elucidate the nature of the underlying biological mechanisms. Disclosures No relevant conflicts of interest to declare.
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Deniskova, Tatiana Evgenievna, Arsen V. Dotsev, Marina I. Selionova, Margaret S. Fornara, Henry Reyer, Klaus Wimmers, Gottfried Brem, and Natalia A. Zinovieva. "PSX-17 Genome-wide diversity and demographic history of Russian native goat breeds." Journal of Animal Science 98, Supplement_4 (November 3, 2020): 450. http://dx.doi.org/10.1093/jas/skaa278.783.
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Abstract Specific environmental conditions and local livestock management systems resulted in creation of valuable native breeds. The timely monitoring of genetic diversity within native breeds based on using high-throughput DNA arrays will prevent their irreparable loss. In this regard, we aimed to assess genome-wide diversity and to study demographic history of Russian native goat breeds (Altai Mountain, Orenburg, Soviet Mohair, Dagestan Milk, Dagestan Local, Dagestan Fluff and Karachaev) based on SNP-data. A total of 200 goats were genotyped using Goat 50K SNP BeadChip (Illumina, USA). Quality control and SNP-filtering were performed in PLINKv1.9. R package ‘diveRsity’ was used to calculate observed heterozygosity (Ho), expected heterozygosity (He), and inbreeding coefficient (Fis). Effective population sizes (Ne) were estimated in SneP software. Observed heterozygosity was high and exceeded 0.402 in five out of seven breeds. Orenburg, Soviet Mohair, Dagestan Milk, and Karachaev breeds showed slight excess of heterozygotes varied from 0.6% (Fis= -0.015) in Orenburg to 1.7% (Fis= -0.04) in Karachaev breed. The traces of insignificant inbreeding were found in Dagestan Local (Fis=0.005) and Dagestan Fluff (Fis= 0.01) breeds. The recent effective population sizes estimated for four generations ago varied from 140 in Karachaev to 472 in Orenburg breed. Analysis of historical trends in effective population sizes estimated for sixty generations ago revealed obvious decrease ranging from 10.25% in Dagestan Local to 34.65% in Orenburg breed. However, recent effective sizes in Russian native goats are higher than critical threshold (Ne= 100) that is essential to breed maintenance in the future. Our research findings provide an evidence that Russian native goat breeds are not in endangered status, but development of the effective utilization programs is highly recommended. The genotyping of 96 goats was funded by RSF No. 19-76-20006. The reported study was funded by RFBR according to the research project № 18-316-20006.
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Alonso, Inés, Noelia Ibáñez-Escriche, José L. Noguera, Joaquim Casellas, Melani Martín de Hijas-Villalba, María J. Gracia-Santana, and Luis Varona. "Genomic differentiation among varieties of Iberian pig." Spanish Journal of Agricultural Research 18, no. 1 (April 22, 2020): e0401. http://dx.doi.org/10.5424/sjar/2020181-15411.
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Aim of study: The objective of this study was to identify the autosomal genomic regions associated with genetic differentiation between three commercial strains of Iberian pig.Area of study: Extremadura (Spain).Material and methods: We used the Porcine v2 BeadChip to genotype 349 individuals from three varieties of Iberian pig (EE, Entrepelado; RR, Retinto; and TT, Torbiscal) and their crosses. After standard filtering of the Single Nucleotide Polymorphism (SNP) markers, 47, 67, and 123 haplotypic phases from EE, RR, and TT origins were identified. The allelic frequencies of 31,180 SNP markers were used to calculate the fixation index (FST) that were averaged in sliding windows of 2Mb.Main results: The results confirmed the greater genetic closeness of the EE and RR varieties, and we were able to identify several genomic regions with a divergence greater than expected. The genes present in those genomic regions were used to perform an Overrepresentation Enrichment Analysis (ORA) for the Gene Ontology (GO) terms for biological process. The ORA indicated that several groups of biological processes were overrepresented: a large group involving morphogenesis and development, and others associated with neurogenesis, cellular responses, or metabolic processes. These results were reinforced by the presence of some genes within the genomic regions that had the highest genomic differentiation.Research highlights: The genomic differentiation among varieties of the Iberian pig is heterogeneous along the genome. The genomic regions with the highest differentiation contain an overrepresentation of genes related with morphogenesis and development, neurogenesis, cellular responses and metabolic processes.
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Wong, Li Lian, Zulaikha Mat Deris, Yoji Igarashi, Songqian Huang, Shuichi Asakawa, Qasim Ayub, Shu Yong Lim, et al. "Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region." Biology 9, no. 9 (September 7, 2020): 277. http://dx.doi.org/10.3390/biology9090277.
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The domestication of a wild-caught aquatic animal is an evolutionary process, which results in genetic discrimination at the genomic level in response to strong artificial selection. Although black tiger shrimp (Penaeus monodon) is one of the most commercially important aquaculture species, a systematic assessment of genetic divergence and structure of wild-caught and domesticated broodstock populations of the species is yet to be documented. Therefore, we used skim sequencing (SkimSeq) based genotyping approach to investigate the genetic structure of 50 broodstock individuals of P. monodon species, collected from five sampling sites (n = 10 in each site) across their distribution in Indo-Pacific regions. The wild-caught P. monodon broodstock population were collected from Malaysia (MS) and Japan (MJ), while domesticated broodstock populations were collected from Madagascar (MMD), Hawaii, HI, USA (MMO), and Thailand (MT). After various filtering process, a total of 194,259 single nucleotide polymorphism (SNP) loci were identified, in which 4983 SNP loci were identified as putatively adaptive by the pcadapt approach. In both datasets, pairwise FST estimates high genetic divergence between wild and domesticated broodstock populations. Consistently, different spatial clustering analyses in both datasets categorized divergent genetic structure into two clusters: (1) wild-caught populations (MS and MJ), and (2) domesticated populations (MMD, MMO and MT). Among 4983 putatively adaptive SNP loci, only 50 loci were observed to be in the coding region. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that non-synonymous mutated genes might be associated with the energy production, metabolic functions, respiration regulation and developmental rates, which likely act to promote adaptation to the strong artificial selection during the domestication process. This study has demonstrated the applicability of SkimSeq in a highly duplicated genome of P. monodon specifically, across a range of genetic backgrounds and geographical distributions, and would be useful for future genetic improvement program of this species in aquaculture.
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Genievskaya, Y., Y. Fedorenko, A. Sarbayev, A. Amalova, S. Abugalieva, S. Griffiths, and Y. Turuspekov. "Identification of QTLs for resistance to leaf and stem rusts in bread wheat (Triticum aestivum L.) using a mapping population of ‘Pamyati Azieva × Paragon’." Vavilov Journal of Genetics and Breeding 23, no. 7 (November 24, 2019): 887–95. http://dx.doi.org/10.18699/vj19.563.
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Leaf rust (LR) and stem rust (SR) are harmful fungal diseases of bread wheat (Triticum aestivum L.). The purpose of this study was to identify QTLs for resistance to LR and SR that are effective in two wheat-growing regions of Kazakhstan. To accomplish this task, a population of recombinant inbred lines (RILs) of ‘Pamyati Azieva × Paragon’ was grown in the northern and southeastern parts of Kazakhstan, phenotyped for LR/SR severities, and analyzed for key yield components. The study revealed a negative correlation between disease severity and plant productivity in both areas. The mapping population was genotyped using a 20,000 Illumina SNP array. A total of 4595 polymorphic SNP markers were further selected for linkage analysis after filtering based on missing data percentage and segregation distortion. Windows QTL Cartographer was applied to identify QTLs associated with LR and SR resistances in the RIL mapping population studied. Two QTLs for LR resistance and eight for SR resistance were found in the north, and the genetic positions of eight of them have matched the positions of the known Lr and Sr genes, while two QTLs for SR were novel. In the southeast, eight QTLs for LR and one for SR were identified in total. The study is an initial step of the genetic mapping of LR and SR resistance loci of bread wheat in Kazakhstan. Field trials in two areas of the country and the genotyping of the selected mapping population have allowed identification of key QTLs that will be effective in regional breeding projects for better bread wheat productivity.
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Martinez-Castillero, Maria, Carlos Then, Juan Altarriba, Houssemeddine Srihi, David López-Carbonell, Clara Díaz, Paulino Martinez, Miguel Hermida, and Luis Varona. "Detection of Genomic Regions with Pleiotropic Effects for Growth and Carcass Quality Traits in the Rubia Gallega Cattle Breed." Animals 11, no. 6 (June 4, 2021): 1682. http://dx.doi.org/10.3390/ani11061682.
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The breeding scheme in the Rubia Gallega cattle population is based upon traits measured in farms and slaughterhouses. In recent years, genomic evaluation has been implemented by using a ssGBLUP (single-step Genomic Best Linear Unbiased Prediction). This procedure can reparameterized to perform ssGWAS (single-step Genome Wide Association Studies) by backsolving the SNP (single nucleotide polymorphisms) effects. Therefore, the objective of this study was to identify genomic regions associated with the genetic variability in growth and carcass quality traits. We implemented a ssGBLUP by using a database that included records for Birth Weight (BW -327,350 records-), Weaning Weight (WW -83,818-), Cold Carcass Weight (CCW -91,621-), Fatness (FAT -91,475-) and Conformation (CON-91,609-). The pedigree included 464,373 individuals, 2,449 of which were genotyped. After a process of filtering, we ended up using 43,211 SNP markers. We used the GBLUP and SNPBLUP model equivalences to obtain the effects of the SNPs and then calculated the percentage of variance explained by the regions of the genome between 1 Mb. We identified 7 regions of the genome for CCW; 8 regions for BW, WW, FAT and 9 regions for CON, which explained the percentage of variance above 0.5%. Furthermore, a number of the genome regions had pleiotropic effects, located at: BTA1 (131-132 Mb), BTA2 (1-11 Mb), BTA3 (32-33 Mb), BTA6 (36-38 Mb), BTA16 (24-26 Mb), and BTA 21 (56-57 Mb). These regions contain, amongst others, the following candidate genes: NCK1, MSTN, KCNA3, LCORL, NCAPG, and RIN3.
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Johannesen, Jes, Armin G. Fabritzek, Bettina Ebner, and Sven-Ernö Bikar. "Characterisation of microsatellite and SNP markers from Miseq and genotyping-by-sequencing data among parapatric Urophora cardui (Tephritidae) populations." PeerJ 5 (August 14, 2017): e3582. http://dx.doi.org/10.7717/peerj.3582.
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Phylogeographic analyses of the gall fly Urophora cardui have in earlier studies based on allozymes and mtDNA identified small-scale, parapatrically diverged populations within an expanding Western Palearctic population. However, the low polymorphism of these markers prohibited an accurate delimitation of the evolutionary origin of the parapatric divergence. Urophora cardui from the Western Palearctic have been introduced into Canada as biological control agents of the host plant Cirsium arvense. Here, we characterise 12 microsatellite loci with hexa-, penta- and tetra-nucleotide repeat motifs and report a genotyping-by-sequencing SNP protocol. We test the markers for genetic variation among three parapatric U. cardui populations. Microsatellite variability (N = 59 individuals) was high: expected heterozygosity/locus/population (0.60–0.90), allele number/locus/population (5–21). One locus was alternatively sex-linked in males or females. Cross-species amplification in the sister species U. stylata was successful or partially successful for seven loci. For genotyping-by-sequencing (N = 18 individuals), different DNA extraction methods did not affect data quality. Depending on sequence sorting criteria, 1,177–2,347 unlinked SNPs and 1,750–4,469 parsimony informative sites were found in 3,514–5,767 loci recovered after paralog filtering. Both marker systems quantified the same population partitions with high probabilities. Many and highly differentiated loci in both marker systems indicate genome-wide diversification and genetically distinct populations.
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Sater, Mohamad, Timothy Farrell, Febriana Pangestu, Ian Herriott, Melis Anahtar, Doug Kwon, Erica Shenoy, David Hooper, and Miriam Huntley. "Democratizing Sequencing for Infection Control: A Scalable, Automated Pipeline for WGS Analysis for Outbreak Detection." Infection Control & Hospital Epidemiology 41, S1 (October 2020): s442—s443. http://dx.doi.org/10.1017/ice.2020.1111.
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Background: Whole-genome sequencing (WGS) is well established as a high-resolution method for measuring bacterial relatedness to better understand infection transmission in cases of healthcare-associated infections (HAIs). However, sequencing is still rarely used in HAI investigations due to a lack of access to computational analysis platforms with actionable turnaround times. Single-nucleotide polymorphism (SNP) analysis is typically used to determine bacterial relatedness. However, SNP-based methods often require a suite of bioinformatics tools that can be difficult to use and interpret without the expertise of a trained computational biologist. These obstacles become more significant in the case of prospective, real-time surveillance of HAIs, which can require the analysis of a large number of isolates. To enable the use of WGS for proactive determination of infection outbreaks, a rapid, automated method that can scale to large data sets is needed. Methods: Here, we demonstrate the capabilities of ksim, a novel automated algorithm to determine the clonality of bacterial samples using WGS. ksim measures the number of shared kmers (genomic subsequences of length k) between bacterial samples to determine their relatedness. ksim also filters out accessory genomic regions, such as plasmids, that can confound genetic relatedness estimates. We benchmarked the accuracy and speed of ksim relative to an SNP-based pipeline on simulated data sets (with sequencing reads generated in silico) and on 9 clinical-cluster data sets (6 publicly available and 3 real-time data sets from Massachusetts General Hospital [MGH]). We also used ksim to determine the relatedness of >5,000 historical clinical bacterial isolates from MGH, collected between 2015 and 2019. Results: ksim first preprocesses raw sequencing data to generate a common data structure, after which it computes the genomic distance between bacterial samples in ∼0.2 seconds in simple cases and in ∼4 seconds in complex cases when accessory genome filtering is required. In simulations across 5 species, ksim determined clonality (defined as <40 SNPs) with high accuracy (sensitivity, 99.7% and specificity, 99.6%). ksim performance on 9 clinical HAI data sets demonstrated its sensitivity (99.4%) and specificity (90.8%) compared to an SNP-based pipeline. ksim efficiently analyzed >5,000 clinical samples from MGH and found previously unidentified transmission clusters. Conclusions:ksim shows promise for rapid clonality determination in HAI outbreaks and has the potential to scale to tens of thousands of samples. This method could enable infection control teams to use WGS for prospective outbreak detection via an automated computational pipeline without the need for specialized computational biology training.Funding: Day Zero Diagnostics and the NIH provided Funding: for this study.Disclosures: Mohamad Sater reports salary from Day Zero Diagnostics.
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Stone, Brad, Scott Graves, Arnold Kas, Alexander Ford, Nathan Standifer, Crystal Rawlings, Steven Rosinski, Susan Masewicz, Maynard Olson, and Rainer F. Storb. "Direct Genotyping of Coding Non-Synonymous SNPs for Identification of Novel Minor Histocompatibility Antigens." Blood 108, no. 11 (November 16, 2006): 3237. http://dx.doi.org/10.1182/blood.v108.11.3237.3237.
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Abstract Traditional methods for identifying minor histocompatibility antigens (mHags) are technically challenging and biased against discovery of mHags not expressed in the peripheral blood. In this work, we propose a rapid, unbiased, genetic approach for identification minor antigens resulting from disparities in coding non-synonymous SNPs (“C SNPS”). This approach is capable of testing for responses to candidate minor antigens expressed in virtually any tissue, including those expressed exclusively in tissues targeted by GVHD. The first step in our approach begins with comparison of donor and recipient C SNP genotypes generated using C SNP microarrays. These arrays interrogate approximately 80% of human C SNPs predicted to occur in greater than 5% of the population. Comparison of C SNP genotypes directly identifies protein-altering alleles present in the recipient but not the donor (hereafter referred to as “recipient-restricted” alleles), thereby identifying a transplant-specific set of candidate minor antigens. The second step utilizes conventional HLA-class I epitope prediction performed on all linear peptides that include amino-acid residues defined by a recipient-restricted allele. This two step filtering process identifies a small, “testable” number candidate minor peptide epitopes for an individual expressed HLA-class I allele. Candidate epitopes can then be synthesized, pooled and tested at diagnosis of GVHD using a commercial Granzyme B ELISPOT assay. As proof-of-principal for a direct genotyping approach, we have analyzed C SNP genotypes, performed epitope prediction and generated T-cell lines specific for candidate minor antigens using DNA and PBL from a pair of disease-free HLA-identical siblings. Analysis of 10,000 C SNPs shows that approximately 2,000 C SNP alleles are restricted to one sibling within the pair. BIMAS epitope prediction of short unique peptide sequences determined by each sibling-restricted allele identifies approximately 100 candidate minor epitopes predicted to bind HLA-A*0201. These candidate minor epitopes were ranked using expression microarrays performed on EBV-transformed LCL derived from each sibling, with candidates derived from highly expressed genes ranked above those from genes with lower expression levels. A pool of 12 candidate minor epitopes that were both unique to sibling “A” and derived from genes highly expressed in LCL were synthesized and used to generate CD8+ T-cell lines from sibling “B”. Stimulation utilized autologous (sibling “B”-derived) mature dendritic cells loaded with candidate minor epitopes. After several rounds of in-vitro stimulation, each T-cell line was tested for responses to EBV-LCL from sibling “B” and sibling “A” using a Granzyme B ELISPOT kit. Five out of sixteen lines responded to LCL from sibling A while no line responded to autologous LCL. Thus we show that this approach frequently generates CD8+ T-cell lines specific for sibling-derived target cells, suggesting that this approach efficiently identifies genuine, novel, endogenously processed and presented minor epitopes. Deconvolution of the peptide pool suggests that at least two out of the twelve candidate minor epitopes are naturally processed and presented.
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Mudassar Imran Bukhari, Syed, Kiu Kwong Yew, Rajasunthari Thambiraja, Sarina Sulong, Aida Hanum Ghulam Rasool, and Liza-Sharmini Ahmad Tajudin. "Microvascular endothelial function and primary open angle glaucoma." Therapeutic Advances in Ophthalmology 11 (January 2019): 251584141986810. http://dx.doi.org/10.1177/2515841419868100.
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Purpose: To determine the role of microvascular endothelial dysfunction as risk factor for primary open angle glaucoma. Methods: A cross-sectional study was conducted involving 114 Malay patients with POAG seen at the eye clinic of Hospital Universiti Sains Malaysia. Patients aged between 40 and 80 years who were diagnosed with other types of glaucoma, previous glaucoma filtering surgery or other surgeries except uncomplicated cataract surgery and pterygium surgery were excluded. A total of 101 patients who were followed up for dry eyes, age-related cataracts or post cataracts extraction surgery were recruited as control subjects. Those with family history of glaucoma or glaucoma suspect were excluded. Microvascular endothelial function was assessed using laser Doppler fluximetry and the process of iontophoresis. Iontophoresis with acetylcholine (ACh) and sodium nitroprusside (SNP) was used to measure microvascular endothelium-dependent and endothelium-independent vasodilatations, respectively. Results: In general, POAG patients demonstrated lower ACh% and AChmax values compared with controls. There was significant difference in microvascular endothelial function [ACh%: mean, 95% confidence interval = 503.1 (378.0, 628.3), and AChmax: mean, 95% confidence interval = 36.8 (30.2, 43.5)] between primary open angle glaucoma cases ( p < 0.001) and controls [ACh%: mean, 95% confidence interval = 1378.4 (1245.4, 1511.3), and AChmax: mean, 95% confidence interval = 79.2 (72.1, 86.2)]; this difference remained significant even after controlling for potential confounders. Similar difference was also found in SNP% and SNPmax between POAG and controls ( p < 0.001). Age and diastolic blood pressure were inversely correlated with microvascular endothelial function. Conclusion: There was an impairment of microvascular endothelial function and endothelial-independent vasodilatation in POAG patients. Microvascular endothelial function is a potential risk factor for POAG.
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Do, Duy Ngoc, Nathalie Bissonnette, Pierre Lacasse, Filippo Miglior, Xin Zhao, and Eveline M. Ibeagha-Awemu. "A targeted genotyping approach to enhance the identification of variants for lactation persistency in dairy cows." Journal of Animal Science 97, no. 10 (October 2019): 4066–75. http://dx.doi.org/10.1093/jas/skz279.
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Abstract Lactation persistency (LP), defined as the ability of a cow to maintain milk production at a high level after milk peak, is an important phenotype for the dairy industry. In this study, we used a targeted genotyping approach to scan for potentially functional single nucleotide polymorphisms (SNPs) within 57 potential candidate genes derived from our previous genome wide association study on LP and from the literature. A total of 175,490 SNPs were annotated within 10-kb flanking regions of the selected candidate genes. After applying several filtering steps, a total of 105 SNPs were retained for genotyping using target genotyping arrays. SNP association analyses were performed in 1,231 Holstein cows with 69 polymorphic SNPs using the univariate liner mixed model with polygenic effects using DMU package. Six SNPs including rs43770847, rs208794152, and rs208332214 in ADRM1; rs209443540 in C5orf34; rs378943586 in DDX11; and rs385640152 in GHR were suggestively significantly associated with LP based on additive effects and associations with 4 of them (rs43770847, rs208794152, rs208332214, and rs209443540) were based on dominance effects at P < 0.05. However, none of the associations remained significant at false discovery rate adjusted P (FDR) < 0.05. The additive variances explained by each suggestively significantly associated SNP ranged from 0.15% (rs43770847 in ADRM1) to 5.69% (rs209443540 in C5orf34), suggesting that these SNPs might be used in genetic selection for enhanced LP. The percentage of phenotypic variance explained by dominance effect ranged from 0.24% to 1.35% which suggests that genetic selection for enhanced LP might be more efficient by inclusion of dominance effects. Overall, this study identified several potentially functional variants that might be useful for selection programs for higher LP. Finally, a combination of identification of potentially functional variants followed by targeted genotyping and association analysis is a cost-effective approach for increasing the power of genetic association studies.
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Rumpf, Robert Wolfgang, Samuel L. Wolock, and William C. Ray. "StickWRLD as an Interactive Visual Pre-Filter for Canceromics-Centric Expression Quantitative Trait Locus Data." Cancer Informatics 13s3 (January 2014): CIN.S14024. http://dx.doi.org/10.4137/cin.s14024.
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As datasets increase in complexity, the time required for analysis (both computational and human domain-expert) increases. One of the significant impediments introduced by such burgeoning data is the difficulty in knowing what features to include or exclude from statistical models. Simple tables of summary statistics rarely provide an adequate picture of the patterns and details of the dataset to enable researchers to make well-informed decisions about the adequacy of the models they are constructing. We have developed a tool, StickWRLD, which allows the user to visually browse through their data, displaying all possible correlations. By allowing the user to dynamically modify the retention parameters (both P and the residual, r), StickWRLD allows the user to identify significant correlations and disregard potential correlations that do not meet those same criteria – effectively filtering through all possible correlations quickly and identifying possible relationships of interest for further analysis. In this study, we applied StickWRLD to a semi-synthetic dataset constructed from two published human datasets. In addition to detecting high-probability correlations in this dataset, we were able to quickly identify gene–SNP correlations that would have gone undetected using more traditional approaches due to issues of low penetrance.
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Tian, Wenlan, Dev Paudel, Wagner Vendrame, and Jianping Wang. "Enriching Genomic Resources and Marker Development from Transcript Sequences ofJatropha curcasfor Microgravity Studies." International Journal of Genomics 2017 (2017): 1–14. http://dx.doi.org/10.1155/2017/8614160.
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Jatropha (Jatropha curcasL.) is an economically important species with a great potential for biodiesel production. To enrich the jatropha genomic databases and resources for microgravity studies, we sequenced and annotated the transcriptome of jatropha and developed SSR and SNP markers from the transcriptome sequences. In total 1,714,433 raw reads with an average length of 441.2 nucleotides were generated. De novo assembling and clustering resulted in 115,611 uniquely assembled sequences (UASs) including 21,418 full-length cDNAs and 23,264 new jatropha transcript sequences. The whole set of UASs were fully annotated, out of which 59,903 (51.81%) were assigned with gene ontology (GO) term, 12,584 (10.88%) had orthologs in Eukaryotic Orthologous Groups (KOG), and 8,822 (7.63%) were mapped to 317 pathways in six different categories in Kyoto Encyclopedia of Genes and Genome (KEGG) database, and it contained 3,588 putative transcription factors. From the UASs, 9,798 SSRs were discovered with AG/CT as the most frequent (45.8%) SSR motif type. Further 38,693 SNPs were detected and 7,584 remained after filtering. This UAS set has enriched the current jatropha genomic databases and provided a large number of genetic markers, which can facilitate jatropha genetic improvement and many other genetic and biological studies.
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Rovelli, Valentina, Aritz Ruiz-González, Leonardo Vignoli, Daniele Macale, Vincenzo Buono, Francesca Davoli, David R. Vieites, Nadav Pezaro, and Ettore Randi. "Genotyping-by-Sequencing (GBS) of large amphibian genomes: a comparative study of two non-model species endemic to Italy." Animal Biology 69, no. 3 (2019): 307–26. http://dx.doi.org/10.1163/15707563-00001094.
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Abstract Next Generation Sequencing (NGS) and related technologies have revolutionized the field of conservation and population genetics, providing novel tools and the capacity to discover thousands of new Single Nucleotide Polymorphisms (SNPs) for the analysis of population parameters. However, gathering NGS data for organisms with very large genomes, such as amphibians, remains challenging because it is still unclear how the current methods perform. Here, we use the Genotyping-by-Sequencing (GBS) approach to generate SNP data for the genotyping of two amphibian species that are of conservation concern, the Sardinian brook salamander (Euproctus platycephalus) and the Italian stream frog (Rana italica). Both E. platycephalus and R. italica have very large genomes (5.53 Gb and >20 Gb, respectively) so genomic data are not available for either of them. We used 95 individual samples and one Illumina lane for each species, with an additional lane for E. platycephalus. After filtering, we obtained 961 and 854 high-coverage SNPs for E. platycephalus and R. italica, respectively. Our results suggest that GBS can serve as a reliable and cost-effective method for genotyping large amphibian genomes, including non-model species.
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Bitaraf Sani, Morteza, Javad Zare Harofte, Ahmad Bitaraf, Saeid Esmaeilkhanian, Mohammad Hossein Banabazi, Nader Salim, Abbas Teimoori, et al. "Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran." Genes 11, no. 6 (May 29, 2020): 599. http://dx.doi.org/10.3390/genes11060599.
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The development of camel husbandry for good production in a desert climate is very important, thus we need to understand the genetic basis of camels and give attention to genomic analysis. We assessed genome-wide diversity, linkage disequilibrium (LD), effective population size (Ne) and relatedness in 96 dromedaries originating from five different regions of the central desert of Iran using genotyping-by-sequencing (GBS). A total of 14,522 Single Nucleotide Polymorphisms (SNPs) with an average minor allele frequency (MAF) of 0.19 passed quality control and filtering steps. The average observed heterozygosity in the population was estimated at 0.25 ± 0.03. The mean of LD at distances shorter than 40 kb was low (r2 = 0.089 ± 0.234). The camels sampled from the central desert of Iran exhibited higher relatedness than Sudanese and lower than Arabian Peninsula dromedaries. Recent Ne of Iran’s camels was estimated to be 89. Predicted Tajima’s D (1.28) suggested a bottleneck or balancing selection in dromedary camels in the central desert of Iran. A general decrease in effective and census population size poses a threat for Iran’s dromedaries. This report is the first SNP calling report on nearly the chromosome level and a first step towards understanding genomic diversity, population structure and demography in Iranian dromedaries.
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Lozada, Dennis N., and Arron H. Carter. "Genomic Selection in Winter Wheat Breeding Using a Recommender Approach." Genes 11, no. 7 (July 11, 2020): 779. http://dx.doi.org/10.3390/genes11070779.
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Achieving optimal predictive ability is key to increasing the relevance of implementing genomic selection (GS) approaches in plant breeding programs. The potential of an item-based collaborative filtering (IBCF) recommender system in the context of multi-trait, multi-environment GS has been explored. Different GS scenarios for IBCF were evaluated for a diverse population of winter wheat lines adapted to the Pacific Northwest region of the US. Predictions across years through cross-validations resulted in improved predictive ability when there is a high correlation between environments. Using multiple spectral traits collected from high-throughput phenotyping resulted in better GS accuracies for grain yield (GY) compared to using only single traits for predictions. Trait adjustments through various Bayesian regression models using genomic information from SNP markers was the most effective in achieving improved accuracies for GY, heading date, and plant height among the GS scenarios evaluated. Bayesian LASSO had the highest predictive ability compared to other models for phenotypic trait adjustments. IBCF gave competitive accuracies compared to a genomic best linear unbiased predictor (GBLUP) model for predicting different traits. Overall, an IBCF approach could be used as an alternative to traditional prediction models for important target traits in wheat breeding programs.
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Li, Shiming, Xuemei Ni, Qiuju Xia, Yunfei Li, Xiao Dong, Junliang Hou, Zehua Li, et al. "Rapid Characterization of the Genetic Loci Controlling Commodity Traits of Chinese Hami Melon (Cucumis melo var. Saccharinensis Naud.) through Multiplexed Shotgun Genotyping." Agronomy 9, no. 8 (August 4, 2019): 430. http://dx.doi.org/10.3390/agronomy9080430.
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The genetic architecture and the genetic loci controlling commodity traits in this Hami melon have not been characterized. Multiplexed shotgun genotyping (MSG) was used to genotype an F2 population of 370 Chinese Hami melon progeny. A total of 47,609 single nucleotide polymorphism (SNP) markers were obtained after strict filtering. Thebins were used to construct a genetic linkage map with a total length of 1572.954 cM. Quantitative trait locus (QTL) analysis revealed that fruit color was controlled by one major gene about 2 Mb region on chr09, while exocarp color (EC) was controlled by one major gene about 1.9 Mb on chr04, and skin spotting was controlled by two dominant genes, one in the same region of chr04as the EC QTL and the other in the 1031.05 kb region on chr02. Two major QTLs on chr03 and chr05 were related pleiotropically to several quantitative fruit traits, namely, edge sugar content (ES), center sugar content (CS), fruit weight (FW), and fruit length (FL). A further QTL on chr09 also influenced ES, while five other QTLs affected FL. This study was the first to conduct genetic architecture analysis and QTL mapping in Chinese Hami melon with high-density markers and a large target population.
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Choudhary, Shruti, Sapna Thakur, Raoof Ahmad Najar, Aasim Majeed, Amandeep Singh, and Pankaj Bhardwaj. "Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)." Genome 61, no. 6 (June 2018): 417–28. http://dx.doi.org/10.1139/gen-2017-0143.
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Rhododendron arboreum is an ecologically prominent species, which also lends commercial and medicinal benefits in the form of palatable juices and useful herbal drugs. Local abundance and survival of the species under a highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina’s platform facilitated the generation of ∼100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out of shorter transcripts predicted 113 167 non-redundant transcripts with an average length of 1164.6 bases. Of these, 71 961 transcripts were categorized based on functional annotations in the Gene Ontology database, whereby 5710 were grouped into 141 pathways and 23 746 encoded for different transcription factors. Transcriptome screening further identified 35 419 microsatellite regions, of which, 43 polymorphic loci were characterized on 30 genotypes. Seven hundred and nineteen transcripts had 811 high-quality single-nucleotide polymorphic variants with a minimum coverage of 10, a total score of 20, and SNP% of 50.
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Jeon, Hajin, Jeongmin Bae, Sang-Hyun Hwang, Kyu-Young Whang, Hyun-Seob Lee, Hyerin Kim, and Min-Soo Kim. "MRPrimerW2: an enhanced tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments." Nucleic Acids Research 47, W1 (May 2, 2019): W614—W622. http://dx.doi.org/10.1093/nar/gkz323.
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Abstract For the best results in quantitative polymerase chain reaction (qPCR) experiments, it is essential to design high-quality primers considering a multitude of constraints and the purpose of experiments. The constraints include many filtering constraints, homology test on a huge number of off-target sequences, the same constraints for batch design of primers, exon spanning, and avoiding single nucleotide polymorphism (SNP) sites. The target sequences are either in database or given as FASTA sequences, and the experiment is for amplifying either each target sequence with each corresponding primer pairs designed under the same constraints or all target sequences with a single pair of primers. Many websites have been proposed, but none of them including our previous MRPrimerW fulfilled all the above features. Here, we describe the MRPrimerW2, the update version of MRPrimerW, which fulfils all the features by maintaining the advantages of MRPrimerW in terms of the kinds and sizes of databases for valid primers and the number of search modes. To achieve it, we exploited GPU computation and a disk-based key-value store using PCIe SSD. The complete set of 3 509 244 680 valid primers of MRPrimerW2 covers 99% of nine important organisms in an exhaustive manner. Free access: http://MRPrimerW2.com
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Letko, Anna, Alexandria Marie Schauer, Martijn F. L. Derks, Llorenç Grau-Roma, Cord Drögemüller, and Alexander Grahofer. "Phenotypic and Genomic Analysis of Cystic Hygroma in Pigs." Genes 12, no. 2 (January 31, 2021): 207. http://dx.doi.org/10.3390/genes12020207.
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Cystic hygroma is a malformation of the lymphatic and vascular system and is recognized as a benign congenital tumor that affects humans and animals in the perinatal period. This congeni-tal disorder is rarely described in animals, and until today, cystic hygroma in pigs has not been described in the literature. In a purebred Piètrain litter with twelve live-born piglets, cystic hy-groma was noticed on the rump of two male pigs within the first week of life. In addition, a third case of a crossbred weaner (Large White × Landrace) was detected during a herd examina-tion. To rule out common differential diagnoses, e.g., abscess or hematoma, further clinical and pathological investigations were conducted. During clinical examination, a painless and soft mass, which was compressible, was detected on the rump of all affected animals. The ultra-sonographic examination revealed a fluid-filled and cavernous subcutaneous structure. In addi-tion, a puncture of the cyst was conducted, revealing a serosanguinous fluid with negative bacte-riological culture. In all cases, a necropsy was performed, showing that the animals had fluid-filled cysts lined by well-differentiated lymphatic endothelium. Based on the clinicopathological examination, cystic hygroma was diagnosed. Furthermore, SNP array genotyping and whole-genome sequencing was performed and provided no evidence for a chromosomal disorder. In the Piètrain family, several genome regions were homozygous in both affected piglets. None-theless, a dominant acting de novo germline variant could not be ruled out, and therefore differ-ent filtering strategies were used to find pathogenic variants. The herein presented lists of pri-vate variants after filtering against hundreds of control genomes provide no plausible candidate and no shared variants among the two sequenced cases. Therefore, further studies are needed to evaluate possible genetic etiology. In general, systematic surveillance is needed to identify ge-netic defects as early as possible and to avoid the occurrence of losses in the pig population.
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Khatri, Bhuwan, Ashley M. Hayden, Nicholas B. Anthony, and Byungwhi C. Kong. "Whole Genome Resequencing of Arkansas Progressor and Regressor Line Chickens to Identify SNPs Associated with Tumor Regression." Genes 9, no. 10 (October 19, 2018): 512. http://dx.doi.org/10.3390/genes9100512.
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Arkansas Regressor (AR) chickens, unlike Arkansas Progressor (AP) chickens, regress tumors induced by the v-src oncogene. To better understand the genetic factors responsible for this tumor regression property, whole genome resequencing was conducted using Illumina Hi-Seq 2 × 100 bp paired-end read method (San Diego, CA, USA) with AR (confirmed tumor regression property) and AP chickens. Sequence reads were aligned to the chicken reference genome (galgal5) and produced coverage of 11× and 14× in AR and AP, respectively. A total of 7.1 and 7.3 million single nucleotide polymorphisms (SNPs) were present in AR and AP genomes, respectively. Through a series of filtration processes, a total of 12,242 SNPs were identified in AR chickens that were associated with non-synonymous, frameshift, nonsense, no-start and no-stop mutations. Further filtering of SNPs based on read depth ≥ 10, SNP% ≥ 0.75, and non-synonymous mutations identified 63 reliable marker SNPs which were chosen for gene network analysis. The network analysis revealed that the candidate genes identified in AR chickens play roles in networks centered to ubiquitin C (UBC), phosphoinositide 3-kinases (PI3K), and nuclear factor kappa B (NF-kB) complexes suggesting that the tumor regression property in AR chickens might be associated with ubiquitylation, PI3K, and NF-kB signaling pathways. This study provides an insight into genetic factors that could be responsible for the tumor regression property.
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Kim, Byung Chul, Eun-Hye Kim, Byoung-Chul Ghim, So-Jung Choi, Jinseon Lee, and Jhingook Kim. "High-throughput targeted resequencing of lung adenocarcinoma." Journal of Clinical Oncology 30, no. 15_suppl (May 20, 2012): 7053. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.7053.
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7053 Background: The mutational profiles are crucial for cancer diagnosis and classification, which lead to tailoring the best therapeutic strategy to each patient. Here, we present target sequencing of 30 hot spot genes in lung adenocarcinoma to identify new hot spot mutations in never-smoker, female lung adenocarcinoma patients. Methods: We targeted 30 genes that are known to be mutated frequently in lung adenocarcinoma. The exome capture was done using selector technology and sequencing was done using Illumina GA IIx Genome Analyzer. Exomic short reads from Illumina Pipeline 1.4 were aligned to human genome (NCBI build 36) with BWA 0.5.0. Variations and small indels were called by Samtools 0.1.7 and filtered by custom R scripts. Potential effects of these identified alterations were assessed with sequence analysis. Results: On average, 1.5 billion bases were uniquely mapped, and mean depth and coverage of exon regions were 38X and 96%, respectively. Filtering of data against public SNP database (dbSNP130), resulted in ~2,000 novel genetic alterations per sample, including single nucleotide variations, and small insertion and deletions in protein-coding regions. Among them, there were novel variants in LTK and EPHA5 genes. Conclusions: Our results demonstrated the feasibility of high-throughput mutation profiling with lung adenocarcinoma samples. We identified novel variants in hot target genes, which may provide an insight into the tumorigenesis signaling of lung adenocarcinoma.
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Lestringant, Valentin, Nicolas Duployez, Dominique Penther, Nathalie Grardel, Anne Lutun, Claude Preudhomme, Michaela West, et al. "Optical Mapping, a Promising Alternative to Gold Standard Cytogenetic Approaches in Acute Lymphoblastic Leukemias: A Blind Comparison on 10 Patients." Blood 136, Supplement 1 (November 5, 2020): 39–40. http://dx.doi.org/10.1182/blood-2020-136257.
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Acute lymphoblastic leukemias (ALL) are characterized by a large number of genetic abnormalities of prognostic and theranostic interest. Their detection requires the use of several conventional and molecular cytogenetic techniques in order to establish the most exhaustive genetic profile: conventional karyotype, FISH, SNP-Array and RT-MLPA for detection of fusion transcripts. Optical genome mapping technique is based on analysis of ultra-high molecular weight DNA (UHMW: 150 kbp-2.5 Mbp). It allows an automatic, high resolution, genome-wide detection of structural anomalies, including balanced translocations and copy number anomalies, making this technology a promising tool in ALL. However, very few data are available in ALL so far. Our objective was to compare optical mapping (Bionano Genomics) to standard techniques performed routinely (combination of karyotype, FISH, SNP-array and RT-MLPA) in 10 selected B or T-ALL patients carrying at least one major genetic abnormality including t(10;14) TLX1-TRA, t(9;22) BCR-ABL1 (e1a2 and e14a2 transcripts), t(10;11) MLLT10-PICALM, t(11;19) KMT2A-MLLT1, typical hyperdiploid profile, iAMP21, SET-NUP214 fusion, various deletions involving CDKN2A/CDKN2B, IKZF1, PAX5, PTEN, ERG and FBXW7. Abnormalities on SNP-array were retained when allele fraction was > 10% and larger than 1Mbp or > 20 kbp and involving one of the 186 genes defined as potentially relevant in leukemogenesis. A total of 79 anomalies meeting these criteria in SNP-array, and/or found by other standard techniques were identified (45 deletions, 16 whole chromosome gains, 10 duplications or partial gains, and 8 translocations). Bone marrow DMSO pellets from the 10 patients, all treated at the CHU Amiens-Picardie, were used for this study. The UHMW DNA extraction technique provided molecules with an average N50 (≥ 150 kbp) of 286 kbp, and an average coverage of 339x. Direct imaging of the DNA molecules was performed on the Bionano Saphyr system and structural variants were automatically detected using the Rare Variant Pipeline. Abnormalities analysis was blindly performed by two independent operators on the Bionano Access software (v 1.5.2.), one cytogeneticist with no training in optical mapping (operator 1) and the other optical mapping technician without training in cytogenetics (operator 2). Among the 79 relevant anomalies, 72 (91.1%) were found by operator 1 and 71 (89.9%) by operator 2. All (8/8) translocations, 43/45 (95.6%) of deletions, 8/10 (80%) of gains were found by both operators whereas 13/16 (81.25%) and 12/16 (75%) of chromosomal gains were found by operator 1 and 2 respectively. Concerning the 8 discrepancies between optical mapping and standard techniques, 4 of them were filtering issues. Three were low allelic frequency large gains clearly visible in raw data but rejected by software's CNV filters, totally, or partially for a trisomy 3 that caused the discrepancy between the two observers. The fourth was a deletion of VPREB1 gene, erroneously eliminated by operators because included in recurrent deletion zones of IGL locus. The 4 others discrepancies were non detected anomalies. Two of them were copy number variations in Xp22.33 (pseudoautosomal region), a non-covered area with the optical mapping technology, one of which was a P2RY8-CRLF2 fusion. Another sub-clonal gain (trisomy 21) found by karyotype and FISH (quantified at 7% of all nuclei) but not by SNP-array, was missed, even in raw data. The last was a near-tetraploid subclone, found only on karyotype, that might be strictly tetraploid and by definition undetectable by quantitative techniques. Interestingly, new anomalies, not detected by standard techniques, were revealed, including a translocation t(11;14)(p13;q11.2) LMO2-TRA, a translocation with inversion t(7;8)(q34;q24.1) TRB-MYC and a translocation t(14;20)(q32.33;q13.13) IGH-CEBPB. At last, in 3 cases, unidentified complex rearrangements by cytogenetics could be resolved using optical mapping. Thus, optical mapping represents an innovative, time and cost effective alternative to the different cytogenetic techniques currently performed routinely for ALL genetic characterization. It enables identification of complex cytogenetic events, including those currently inaccessible to standard techniques such as chromotripsis or certain complex translocations. Disclosures Lee: Bionano Genomics, San Diego: Current Employment. Ferret:Bionano Genomics: Research Funding.
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Lioi, Lucia, Diana L. Zuluaga, Stefano Pavan, and Gabriella Sonnante. "Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces." Diversity 11, no. 9 (September 3, 2019): 154. http://dx.doi.org/10.3390/d11090154.
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The common bean (Phaseolus vulgaris L.) is one of the main legumes worldwide and represents a valuable source of nutrients. Independent domestication events in the Americas led to the formation of two cultivated genepools, namely Mesoamerican and Andean, to which European material has been brought back. In this study, Italian common bean landraces were analyzed for their genetic diversity and structure, using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS) technology. After filtering, 11,866 SNPs were obtained and 798 markers, pruned for linkage disequilibrium, were used for structure analysis. The most probable number of subpopulations (K) was two, consistent with the presence of the two genepools, identified through the phaseolin diagnostic marker. Some landraces were admixed, suggesting probable hybridization events between Mesoamerican and Andean material. When increasing the number of possible Ks, the Andean germplasm appeared to be structured in two or three subgroups. The subdivision within the Andean material was also observed in a principal coordinate analysis (PCoA) plot and a dendrogram based on genetic distances. The Mesoamerican landraces showed a higher level of genetic diversity compared to the Andean landraces. Calculation of the fixation index (FST) at individual SNPs between the Mesoamerican and Andean genepools and within the Andean genepool evidenced clusters of highly divergent loci in specific chromosomal regions. This work may help to preserve landraces of the common bean from genetic erosion, and could represent a starting point for the identification of interesting traits that determine plant adaptation.
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Jamieson, Aidan, Spencer J. Anderson, Jérémie Fuller, Steeve D. Côté, Joseph M. Northrup, and Aaron B. A. Shafer. "Heritability Estimates of Antler and Body Traits in White-Tailed Deer (Odocoileus virginianus) From Genomic-Relatedness Matrices." Journal of Heredity 111, no. 5 (July 2020): 429–35. http://dx.doi.org/10.1093/jhered/esaa023.
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Abstract Estimating heritability (h2) is required to predict the response to selection and is useful in species that are managed or farmed using trait information. Estimating h2 in free-ranging populations is challenging due to the need for pedigrees; genomic-relatedness matrices (GRMs) circumvent this need and can be implemented in nearly any system where phenotypic and genome-wide single-nucleotide polymorphism (SNP) data are available. We estimated the heritability of 5 body and 3 antler traits in a free-ranging population of white-tailed deer (Odocoileus virginianus) on Anticosti Island, Quebec, Canada. We generated classic and robust GRMs from >10,000 SNPs: hind foot length, dressed body mass, and peroneus muscle mass had high h2 values of 0.62, 0.44, and 0.55, respectively. Heritability in male-only antler features ranged from 0.07 to 0.33. We explored the influence of filtering by minor allele frequency and data completion on h2: GRMs derived from fewer SNPs had reduced h2 estimates and the relatedness coefficients significantly deviated from those generated with more SNPs. As a corollary, we discussed limitations to the application of GRMs in the wild, notably how skewed GRMs, specifically many unrelated individuals, can increase variance around h2 estimates. This is the first study to estimate h2 on a free-ranging population of white-tailed deer and should be informative for breeding designs and management as these traits could respond to selection.
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Chew, Tracy, Bianca Haase, Roslyn Bathgate, Cali E. Willet, Maria K. Kaukonen, Lisa J. Mascord, Hannes T. Lohi, and Claire M. Wade. "A Coding Variant in the Gene Bardet-Biedl Syndrome 4 (BBS4) Is Associated with a Novel Form of Canine Progressive Retinal Atrophy." G3 Genes|Genomes|Genetics 7, no. 7 (July 1, 2017): 2327–35. http://dx.doi.org/10.1534/g3.117.043109.
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Abstract Progressive retinal atrophy is a common cause of blindness in the dog and affects >100 breeds. It is characterized by gradual vision loss that occurs due to the degeneration of photoreceptor cells in the retina. Similar to the human counterpart retinitis pigmentosa, the canine disorder is clinically and genetically heterogeneous and the underlying cause remains unknown for many cases. We use a positional candidate gene approach to identify putative variants in the Hungarian Puli breed using genotyping data of 14 family-based samples (CanineHD BeadChip array, Illumina) and whole-genome sequencing data of two proband and two parental samples (Illumina HiSeq 2000). A single nonsense SNP in exon 2 of BBS4 (c.58A > T, p.Lys20*) was identified following filtering of high quality variants. This allele is highly associated (PCHISQ = 3.425e−14, n = 103) and segregates perfectly with progressive retinal atrophy in the Hungarian Puli. In humans, BBS4 is known to cause Bardet–Biedl syndrome which includes a retinitis pigmentosa phenotype. From the observed coding change we expect that no functional BBS4 can be produced in the affected dogs. We identified canine phenotypes comparable with Bbs4-null mice including obesity and spermatozoa flagella defects. Knockout mice fail to form spermatozoa flagella. In the affected Hungarian Puli spermatozoa flagella are present, however a large proportion of sperm are morphologically abnormal and <5% are motile. This suggests that BBS4 contributes to flagella motility but not formation in the dog. Our results suggest a promising opportunity for studying Bardet–Biedl syndrome in a large animal model.
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Youssef, Helmy M., Mohamed Allam, Faiza Boussora, Axel Himmelbach, Sara G. Milner, Martin Mascher, and Thorsten Schnurbusch. "Dissecting the Genetic Basis of Lateral and Central Spikelet Development and Grain Traits in Intermedium-Spike Barley (Hordeum vulgare Convar. Intermedium)." Plants 9, no. 12 (November 26, 2020): 1655. http://dx.doi.org/10.3390/plants9121655.
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Barley (Hordeum vulgare L.) is one of the major grain crops worldwide and considered as a model plant for temperate cereals. One of the barley row-type groups, named intermedium-barley, was used in our previous study where we reported that other genetic loci rather than vrs1 and Int-c could play a role in lateral spikelet development and even in setting grains. To continue this work, we used phenotypic and genotypic data of 254 intermedium-spike barley accessions aimed at dissecting the genetic basis of development and grain traits of lateral and central spikelet using genome wide association (GWAS) analysis. After genotypic data filtering, 8,653 single-nucleotide polymorphism (SNPs) were used for GWAS analysis. A total of 169 significant associations were identified and we focused only on the subset of associations that exceeded the p < 10−4 threshold. Thirty-three highly significant marker-trait-associations (MTAs), represented in 28 different SNPs on all seven chromosomes for the central and/or lateral spikelet traits; such as kernel length, width, area, weight, unfilled spikelet and 1000-kernel weight, were detected. Highly significant associated markers were anchored physically using barley genome sequencing to identify candidate genes to either contain the SNPs or the closest gene to the SNP position. The results showed that 12 MTAs were specific for lateral spikelet traits, nine MTAs were specific for central spikelet traits and seven MTAs for both central and lateral traits. All together, the GWAS and candidate gene results support our hypothesis that lateral spikelet development could be regulated by loci different from those regulating central spikelet development.
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Лун, Сюй, Xu Long, Йан Йихуа, Yan Yihua, Чэн Цзюнь, and Cheng Jun. "Guided filtering for solar image/video processing." Solar-Terrestrial Physics 3, no. 2 (August 9, 2017): 9–15. http://dx.doi.org/10.12737/stp-3220172.
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A new image enhancement algorithm employing guided filtering is proposed in this work for enhancement of solar images and videos, so that users can easily figure out important fine structures imbedded in the recorded images/movies for solar observation. The proposed algorithm can efficiently remove image noises, including Gaussian and impulse noises. Meanwhile, it can further highlight fibrous structures on/beyond the solar disk. These fibrous structures can clearly demonstrate the progress of solar flare, prominence coronal mass emission, magnetic field, and so on. The experimental results prove that the proposed algorithm gives significant enhancement of visual quality of solar images beyond original input and several classical image en-hancement algorithms, thus facilitating easier determi-nation of interesting solar burst activities from recorded images/movies.
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Leone, Paola E., Brian A. Walker, Nicholas J. Dickens, Matthew W. Jenner, David C. Johnson, Fiona M. Ross, Faith E. Davies, and Gareth J. Morgan. "Screening of Homozygous Deletions Identifies Key Deregulated Genes and Pathways in Multiple Myeloma." Blood 110, no. 11 (November 16, 2007): 2474. http://dx.doi.org/10.1182/blood.v110.11.2474.2474.
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Abstract Homozygous deletions (HD) are important in cancer cell lines and have a non-random distribution in the genome. We have determined the frequency and distribution of HD, along with the genes affected, in 84 presenting multiple myeloma cases using the Affymetrix 500K SNP GeneChip mapping arrays. Initially we took a highly sensitive approach identifying regions with a copy number (CN) <1.0 in at least 4 adjacent SNPs. The analysis was done both manually, in dChip, and using an in-house algorithm. To reduce the complexity of the data generated we removed deletions that only occurred in one sample and further filtered the data using U133 Plus 2.0 expression array analysis. Genes passed expression filtering criteria by having a lower expression than the median expression of all samples. HD in plasma cells occur during IgH and IgL chain rearrangements and were used as internal controls to validate our approach. We found that regions of homozygous deletion were not randomly distributed. At the CN<1.0 level, we identified 1761 regions containing 6650 genes. After expression filtering 129 genes were identified (with an additional 116 genes which did not have expression array probesets) which fell in chromosomal regions 1p, 6q, 8p, 11q, 12p, 13q, 14q, 16q, 20q, and 22q, which are also the regions that most frequently have loss of heterozygosity (LOH). The distribution of deletions was even between different myeloma molecular groups. We then applied a more stringent copy number cut-off of 0.65 and identified 18/84 cases with HD (21%, median size 18 kb) and most cases had only one homozygous deletion. In this analysis the number of genomic regions falls to 29 spread over 10 chromosomes, including 241 genes of which only 20 genes survived expression filtering. Of these regions 3 are in known fragile sites and only 1p, 11q, 13q, and 22q showed HD containing genes with a decreased expression. Although deletions were seen on chromosome 13, none involved the RB1 locus. Several microRNA were also noted to be deleted on chromosomes 6, 13, and 22 indicating that these may also be important in myeloma and are being explored further. The NF-kB pathway inhibitors BIRC2 and BIRC3, on 11q, were homozygously deleted in 4 cases as were the neighbouring loci ANGPTL5 and TMEM123. Interestingly, the 11q region was the exception to the rule that HD occur only in regions of LOH. The most frequent regions of homozygous deletion involved CDKN2C (p18) and FAF1 on 1p32.3, which were deleted in 6 cases (CN<1.0). In addition we have demonstrated that deletion of this region is an important prognostic marker (median survival 19 months vs 33 months). We and others have suggested that p18 is the important event at this locus but in this study when stringent criteria (CN<0.65) were applied more frequent deletions were found at the FAF1 locus. To define the critical lesion we carried out mutation and methylation analysis on both these genes and did not find any abnormalities at p18 and are using this approach to analyse FAF1. FAF1 is potentially relevant to myeloma as it is a regulator of NF-kB which also induces apoptosis via the FAS pathway. Loss of FAF1 could enable cells to tolerate DNA damage better than when it is intact. We have attempted to differentiate these two roles further through correlation with downstream deregulated genes using global expression arrays.
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Karaesmen, Ezgi, Abbas A. Rizvi, Junke Wang, Michael Sovic, Qianqian Zhu, Li Yan, Leah Preus, et al. "Genome Wide Interaction Analysis Identifies Expression Quantitative Trait Loci Associated with Reduced Survival after Reduced Intensity Conditioning HLA-Matched Unrelated Donor Allogeneic Hematopoietic Cell Transplant." Blood 134, Supplement_1 (November 13, 2019): 4595. http://dx.doi.org/10.1182/blood-2019-129182.
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Conditioning regimen intensity before allogeneic blood or marrow transplant (BMT) can be modified from myeloablative (MAC) to reduced intensity (RIC) to promote a graft versus tumor effect or minimize toxicity in older patients or those with comorbidities. However, the benefits of using RIC over MAC remain inconclusive as overall survival (OS) rates are similar. Prior genome wide association studies (GWAS) in solid tumor and autoimmune patients have shown that single nucleotide polymorphisms (SNPs) can affect patient response and toxicity after treatment with cyclophosphamide, busulfan and melphalan. Thus, it is possible SNPs may also affect patient response or toxicity to a given conditioning regimen or regimen intensity, guide regimen selection for a given patient or determine if disease recurrence is more likely for a given regimen or intensity. SNPs associated with patient response are significantly enriched for expression quantitative trait loci (eQTLs). eQTLs are genomic loci that explain significant proportions of inter-individual variability in mRNA levels in a given tissue for one or more genes. This suggests that selecting eQTLs a priori for the identification of genetic predictors for patient response could provide important insights into the likely function of identified SNPs. We hypothesized that recipient eQTL SNPs may interact with conditioning intensity to impact post-BMT OS and performed a genome wide interaction study (GWIS) to test the interaction of eQTL SNPs with conditioning intensity (MAC or RIC) and post-BMT OS in a large cohort of AML, MDS and ALL patients. Our GWIS included European ancestry patients from the DISCOVeRY-BMT study, a GWAS of >3,000 ALL, AML or MDS patients and their 8/8 HLA-matched unrelated donors reported to the CIBMTR between 2000-2011 (Table 1). SNPs were selected for inclusion in OS models if there was significant evidence that they modified expression in whole blood tissue in an independent study of over 30,000 samples (eQTLGen). After quality control and filtering (minor allele frequency >1% and info score > .8) 1,401,296 recipient eQTL SNPs were tested for interaction with MAC/RIC in the two DISCOVeRY-BMT cohorts; multiple test correction for the number of independent eQTLs (R2 < .2) was P < 9.41×10-7. We constructed Cox proportional hazard models for OS with clinical covariates including patient age, disease status at transplant, source of graft (bone marrow or peripheral blood) and an interaction term for each eQTL SNP and conditioning intensity (SNP×MAC/RIC). For significant interactions, we performed stratified analyses by conditioning regimen (Table 1) and by the causes of death which comprise OS, disease related mortality (DRM) and transplant related mortality (TRM). Meta analyses of the two cohorts identified two correlated (R2=1) eQTL SNPs: rs10437630 (imputed) and rs3911014 (typed) with GWIS meta p-values of 8.4x10-7 and 9.3x10-7, respectively in a ~25kb haplotype block located adjacent to TRIM44 (Chromosome 11) (Fig.1). This SNP is in a ~2 kb enhancer region that shows chromatin looping interactions with the transcription start site of TRIM44. TRIM44 has been shown to promote cancer cell survival in multiple cancers, including multiple myeloma. To better understand the interaction between rs3911014 and conditioning regimen intensity, we conducted stratified analyses of rs3911014 by MAC and RIC. Analyses of MAC regimen group (Table 1) with rs3911014 was not significantly associated with OS, DRM or TRM (Pmeta >.2). Among patients who received RIC, the C allele in rs3911014 associated with 1 year post-BMT OS (Pmeta= 1.0×10-5, HRmeta = 1.4, [1.2-1.6]) and was driven by a higher risk of death due to disease (Pmeta= 3.7×10-6, HRmeta = 1.6, [1.3-1.9]) and not TRM (Figs 2 and 3). The rs3911014 C allele associated with increased risk of DRM in RIC regimens (Table 1) A (P=.12), B (P=7.8x10-5), C (P=.03) and D (P=.012). TRIM44 involvement with cancer cell survival suggests the SNP association in RIC patients could be attributable to partial ablation of tumor cells which is supported by the observation that most RIC patients with this variant die of disease in the first few months after BMT. In contrast, the variant posed no increased risk in MAC patients due to a higher degree of myeloablation and tumor cell killing. Further analyses may be able to identify RIC or MAC regimens that are not associated with worse survival in patients with this genotype. Disclosures Pasquini: Medigene: Consultancy; Novartis: Research Funding; Kit Pharma: Research Funding; BMS: Research Funding; Pfizer: Other: Advisory Board; Amgen: Consultancy.
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Romoli, Jacopo, and Paolo Santorio. "Filtering free choice." Semantics and Pragmatics 12, no. 12 (November 18, 2019): 1–27. http://dx.doi.org/10.3765/sp.12.12.
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