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Journal articles on the topic 'Genotype data'
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Have, Christian Theil, Emil Vincent Appel, Niels Grarup, Torben Hansen, and Bork-Jensen Jette. "Identification of Mislabeled Samples and Sample Mix-ups in Genotype Data Using Barcode Genotypes." International Journal of Bioscience, Biochemistry and Bioinformatics 4, no. 5 (2014): 355–60. http://dx.doi.org/10.7763/ijbbb.2014.v4.370.
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Yan, Weikai, and Duane E. Falk. "Biplot Analysis of Host-by-Pathogen Data." Plant Disease 86, no. 12 (December 2002): 1396–401. http://dx.doi.org/10.1094/pdis.2002.86.12.1396.
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Effective breeding for disease resistance relies on a thorough understanding of host-by-pathogen relations. Achieving such understanding can be difficult and challenging, particularly for large data sets with complex host genotype-by-pathogen strain interactions. This paper presents a biplot approach that facilitates visual analysis of host-by-pathogen data. A biplot displays both host genotypes and pathogen isolates in a single scatter plot; each genotype or isolate is displayed as a point defined by its scores on the first two principal components derived from subjecting genotype- or strain-centered data to singular value decomposition. From a biplot, clusters of host genotypes and clusters of pathogen strains can be simultaneously visualized. Moreover, the basis for genotype and strain classifications, i.e., interactions between individual genotypes and strains, can be visualized at the same time. A biplot based on genotype-centered data and that based on strain-centered data are appropriate for visual evaluation of susceptibility/resistance of genotypes and virulence/avirulence of strains, respectively. Biplot analysis of genotype-by-strain is illustrated with published response scores of 13 barley line groups to 8 net blotch isolate groups.
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Whalen, Andrew, Gregor Gorjanc, and John M. Hickey. "AlphaFamImpute: high-accuracy imputation in full-sib families from genotype-by-sequencing data." Bioinformatics 36, no. 15 (May 28, 2020): 4369–71. http://dx.doi.org/10.1093/bioinformatics/btaa499.
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Abstract Summary AlphaFamImpute is an imputation package for calling, phasing and imputing genome-wide genotypes in outbred full-sib families from single nucleotide polymorphism (SNP) array and genotype-by-sequencing (GBS) data. GBS data are increasingly being used to genotype individuals, especially when SNP arrays do not exist for a population of interest. Low-coverage GBS produces data with a large number of missing or incorrect naïve genotype calls, which can be improved by identifying shared haplotype segments between full-sib individuals. Here, we present AlphaFamImpute, an algorithm specifically designed to exploit the genetic structure of full-sib families. It performs imputation using a two-step approach. In the first step, it phases and imputes parental genotypes based on the segregation states of their offspring (i.e. which pair of parental haplotypes the offspring inherited). In the second step, it phases and imputes the offspring genotypes by detecting which haplotype segments the offspring inherited from their parents. With a series of simulations, we find that AlphaFamImpute obtains high-accuracy genotypes, even when the parents are not genotyped and individuals are sequenced at <1x coverage. Availability and implementation AlphaFamImpute is available as a Python package from the AlphaGenes website http://www.AlphaGenes.roslin.ed.ac.uk/AlphaFamImpute. Supplementary information Supplementary data are available at Bioinformatics online.
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Lewis, R. M., B. Grundy, and L. A. Kuehn. "Predicting population gene frequency from sample data." Animal Science 78, no. 1 (February 2004): 03–11. http://dx.doi.org/10.1017/s1357729800053789.
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AbstractWith an increase in the number of candidate genes for important traits in livestock, effective strategies for incorporating such genes into selection programmes are increasingly important. Those strategies in part depend on the frequency of a favoured allele in a population. Since comprehensive genotyping of a population is seldom possible, we investigate the consequences of sampling strategies on the reliability of the gene frequency estimate for a bi-allelic locus. Even within a subpopulation or line, often only a proportion of individuals will be genotype tested. However, through segregation analysis, probable genotypes can be assigned to individuals that themselves were not tested, using known genotypes on relatives and a starting (presumed) gene frequency. The value of these probable genotypes in estimation of gene frequency was considered. A subpopulation or line was stochastically simulated and sampled at random, over a cluster of years or by favouring a particular genotype. Line was simulated (replicated) 1000 times. The reliability of gene frequency estimates depended on the sampling strategy used. With random sampling, even when a small proportion of a line was genotyped (0·10), the gene frequency of the population was well estimated from the across-line mean. When information on probable genotypes on untested individuals was combined with known genotypes, the between-line variance in gene frequency was estimated well; including probable genotypes overcame problems of statistical sampling. When the sampling strategy favoured a particular genotype, unsurprisingly the estimate of gene frequency was biased towards the allele favoured. In using probable genotypes the bias was lessened but the estimate of gene frequency still reflected the sampling strategy rather than the true population frequency. When sampling was confined to a few clustered years, the estimation of gene frequency was biased for those generations preceding the sampling event, particularly when the presumed starting gene frequency differed from the true population gene frequency. The potential risks of basing inferences about a population from a potentially biased sample are discussed.
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Broman, Karl W. "Cleaning genotype data." Genetic Epidemiology 17, S1 (1999): S79—S83. http://dx.doi.org/10.1002/gepi.1370170714.
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de Vries, F., H. Hamann, C. Drögemüller, M. Ganter, and O. Distl. "Analysis of associations between the prion protein genotype and reproduction traits in meat sheep breeds." Animal Science 79, no. 3 (December 2004): 397–404. http://dx.doi.org/10.1017/s1357729800090263.
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AbstractThe objective of this study was to analyse the associations between ovine prion protein (PrP) genotypes and reproduction traits in three German meat sheep breeds. Reproduction traits were age at first early lambing, age at first late lambing, first lambing interval, second lambing interval and total number of lambs born. The data set included 595 genotyped German Texel sheep among 5225 recorded sheep, 351 genotyped German Black-Headed Mutton among 10 177 sheep and 282 genotyped Suffolk sheep among 2849 sheep. Linear animal models were employed for the analysis of the PrP-genotype effect. The PrP-genotype effect was analysed by comparing the most frequent PrP genotypes ARR/ARR, ARR/ARQ, and ARQ/ARQ. In a more general analysis three PrP genotype classes of animals with two, one or no copy of the ARR allele were compared.In most cases, no significant associations were found between the PrP genotypes and the reproduction traits investigated. Only for the traits age at first early lambing in German Texel and second lambing interval in German Black-Headed Mutton and Suffolk could a significant association with the PrP genotype be observed.
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Velkov, Stoyan, Jördis Ott, Ulrike Protzer, and Thomas Michler. "The Global Hepatitis B Virus Genotype Distribution Approximated from Available Genotyping Data." Genes 9, no. 10 (October 15, 2018): 495. http://dx.doi.org/10.3390/genes9100495.
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Hepatitis B virus (HBV) is divided into nine genotypes, A to I. Currently, it remains unclear how the individual genotypes contribute to the estimated 250 million chronic HBV infections. We performed a literature search on HBV genotyping data throughout the world. Over 900 publications were assessed and data were extracted from 213 records covering 125 countries. Using previously published HBV prevalence, and population data, we approximated the number of infections with each HBV genotype per country and the genotype distribution among global chronic HBV infections. We estimated that 96% of chronic HBV infections worldwide are caused by five of the nine genotypes: genotype C is most common (26%), followed by genotype D (22%), E (18%), A (17%) and B (14%). Genotypes F to I together cause less than 2% of global chronic HBV infections. Our work provides an up-to-date analysis of global HBV genotyping data and an initial approach to estimate how genotypes contribute to the global burden of chronic HBV infection. Results highlight the need to provide HBV cell culture and animal models that cover at least genotypes A to E and represent the vast majority of global HBV infections to test novel treatment strategies.
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Genç, Serpil, Mediha Uğur, Emel Uzunoğlu Karagöz, and Esin Avcı. "Giresun İli Hepatit C Hastalarında Genotip Dağılımının Araştırılması." Flora the Journal of Infectious Diseases and Clinical Microbiology 25, no. 4 (December 30, 2020): 549–54. http://dx.doi.org/10.5578/flora.69198.
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Introduction: HCV infections are an important public health problem due to their high chronicity, cirrhosis and advanced complications like hepatocellular carcinoma. In HCV infections, it is important and necessary to determine genotypes before treatment because treatment times and protocols vary according to genotypes. The aim of this study was to determine the distribution of HCV genotypes in HCV-RNA positive individuals in Giresun province and to investigate whether there was a statistically significant difference between genotypes and patient ages. Materials and Methods: HCV-RNA level and HCV genotype of 147 patients were included in the study. HCV RNA levels of the samples were studied by QIAsymphony SP (Qiagen) automated device, genotype determination by Rotor Gene Q (Qiagen) automated device by “real-time polymerase chain reaction (PCR)” method. Each sample was tested for HCV genotypes 1a, 1b, 2, 3, 4, 5a and 6. Results: Of the 147 patients genotyped; 128 (87%) genotype 1b, 9 (6%) genotype 1a, 8 (6%) genotype 3, 2 (1%) genotype 2 were detected. Genotypes 4, 5a and 6 were not detected. According to the HCV genotype distribution, median age and range (min.-max.) of the patients weren50 (30-83) for 1a, 70 (22-87) for 1b, 48.5 (36-61) for 2 and 33 (25-52) for 3. HCV RNA levels were between 37 and 12.630.170 IU/mL. Conclusion: The predominant genotype in the world and Turkey is genotype 1b. In our study, the most common genotype was also genotype 1b (87%), consistent with other studies in our country. This study contributed to HCV genotype distribution data in our region and country.
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Du, F.-X., and I. Hoeschele. "A Note on Algorithms for Genotype and Allele Elimination in Complex Pedigrees With Incomplete Genotype Data." Genetics 156, no. 4 (December 1, 2000): 2051–62. http://dx.doi.org/10.1093/genetics/156.4.2051.
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Abstract Elimination of genotypes or alleles for each individual or meiosis, which are inconsistent with observed genotypes, is a component of various genetic analyses of complex pedigrees. Computational efficiency of the elimination algorithm is critical in some applications such as genotype sampling via descent graph Markov chains. We present an allele elimination algorithm and two genotype elimination algorithms for complex pedigrees with incomplete genotype data. We modify all three algorithms to incorporate inheritance restrictions imposed by a complete or incomplete descent graph such that every inconsistent complete descent graph is detected in any pedigree, and every inconsistent incomplete descent graph is detected in any pedigree without loops with the genotype elimination algorithms. Allele elimination requires less CPU time and memory, but does not always eliminate all inconsistent alleles, even in pedigrees without loops. The first genotype algorithm produces genotype lists for each individual, which are identical to those obtained from the Lange-Goradia algorithm, but exploits the half-sib structure of some populations and reduces CPU time. The second genotype elimination algorithm deletes more inconsistent genotypes in pedigrees with loops and detects more illegal, incomplete descent graphs in such pedigrees.
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Idris, Idris. "Analisis Data Hasil Pengujian Multilokasi Padi Sawah dengan Menggunakan Model AMMI." Informatika Pertanian 24, no. 1 (July 1, 2015): 17. http://dx.doi.org/10.21082/ip.v24n1.2015.p17-30.
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Various study of multi-location test of rice genotypes was strongly influenced by field and environmental factors. This study aimed to implement and to identify wetland rice genotypes. Multi-location test was conducted on some rice genotypes in Southeast Sulawesi in 2010 at various locations. Randomized block design was used with three replications in different locations. Data were analyzed using AMMI model. Results showed that rice production had the main effect with the genotype of KUI 1 and KUI 2. Moreover, BIPLOT test found that the genotype 2 of S3393-2F-17-1-1 was the only one of unstable genotype, and the rest were stable genotype. Not surprisingly, genotype (G) 4 (S3382-2D-PN-4-1), G 5 (S3382-2D-PN-6-3-3), G 7 (S3382-2D-PN-2D-1-1), G 11 (S3382-2D-1-1), G13 (Ciherang) and G 14 (Cisantana) were relatively stable. Those genotypes could be recommended as the high potential yield due to higher average production compared with general average. This study also indicated that G 3 (S3381-2D-PN-27-2), G 9 (S4359-E-11-2), and G 12 (IR64) are very suitable for growing in location A at Ladongi. Moreover, in location B study suggested that G 11 (OBS-9595) should be recommended at Wundulako. Finally, in Lambuya, particularly in location C, study indicated that some genotypes can grow well, viz. G 6 (S3382-2D-PN-17-3), G 8 (S4690 G-KN-4-3) and G 14 (Cisantana).
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Kovács, K., J. Völgyi-Csík, A. Zsolnai, I. Györkös, and L. Fésüs. "Associations between the AluI polymorphism of growth hormone gene and production and reproduction traits in a Hungarian Holstein-Friesian bull dam population." Archives Animal Breeding 49, no. 3 (October 10, 2006): 236–49. http://dx.doi.org/10.5194/aab-49-236-2006.
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Abstract. The aim of this paper was to study the polymorphisms of bovine growth hormone gene. The authors genotyped 363 Hungarian Holstein-Friesian bull dams from 6 farms all over the country. Two variants (L and V) of the bovine growth hormone gene digested with AluI enzyme were identified in the experiment. Genotyping was carried out by PCR-RFLP method. The frequency data of L and V allele was 0.93 and 0.07 respectively. Distribution of the three genotypes were 87.05% (LL), 12.40% (LV) and 0.55% (VV). The studied population was in H-W equilibrium considering the genotype distribution. SPSS 11.0 for Windows was used to reveal the possible correlations between GH genotypes and production and reproduction traits and further statistical analyses. On the basis of statistical analyses it can be found that VV genotype cows had the longest milking period and LL had the shortest dry period. Both differences were significant. Cows with LV genotype had significantly higher test milking data than LL cows. Furthermore, LV genotype seemed to be advantageous for 305 days lactation milk yield. While milk composition traits, as 305 days milk fat and protein percent showed the opposite tendency, since LL genotyped dams produced significantly higher values in these traits.
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Friesen, Lyle F., Anita L. Brûlé-Babel, Gary H. Crow, and Patricia A. Rothenburger. "Mixed model and stability analysis of spring wheat genotype yield evaluation data from Manitoba, Canada." Canadian Journal of Plant Science 96, no. 2 (April 1, 2016): 305–20. http://dx.doi.org/10.1139/cjps-2015-0252.
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In western Canada and in many agricultural areas around the world, new crop genotypes are evaluated over a number of locations and years in multi-environment trials (MET) to investigate yield, yield stability, agronomic, and quality characteristics, with the ultimate goal to predict future genotype performance in commercial fields. This evaluation informs decisions about the commercial value of new crop genotypes, with a primary user of this information being farmers. Currently in many regions of Canada as the first step in analysis of this MET data, values usually are expressed as a percentage of a designated check genotype value at each site-year (trial), usually followed by a relatively simplistic statistical analysis of this percentage data. There are a number of problems with this traditional approach including selection of an appropriate check genotype or genotypes, and the necessary consistent performance of the check genotype over a number of locations and years. Following the recent approach of other countries and jurisdictions, MET spring wheat genotype yield data (kg ha−1) that had been collected from 2000 to 2009 from various locations in Manitoba, Canada were subjected to mixed model statistical analysis. The results of the mixed model analysis compared very favourably to the historical traditional approach, and proved to be superior in situations such as a specific year in the dataset (2007) when the designated check genotype performed anomalously poorly. These results indicated that as little as five trial sites in a single year provided sufficient data for reliable prediction of a new genotype’s yield performance, given a background dataset comprised of approximately 45 spring wheat genotypes tested over eight years. The wheat genotype yield data also was subjected to estimation of several different stability measures to investigate differences in yield stability between genotypes in the dataset. Results indicated relatively stable yield performance for most genotypes over a range of site-years (environments).
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Khushman, Moh’d, Girijesh Kumar Patel, Anu Singh Maharjan, Gwendolyn A. McMillin, Cindy Nelson, Peter Hosein, and Ajay P. Singh. "The prevalence and clinical relevance of 2R/2R TYMS genotype in patients with gastrointestinal malignancies treated with fluoropyrimidine-based chemotherapy regimens." Pharmacogenomics Journal 21, no. 3 (February 19, 2021): 308–17. http://dx.doi.org/10.1038/s41397-021-00210-2.
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Abstract Introduction The prevalence of 2R/2R TYMS genotype is variable but estimated to be around 20–30% in Caucasians. The clinical relevance of TYMS 2R/2R genotype in predicting severe fluoropyrimidine-related adverse events (FrAE) is controversial. Here, we explored the prevalence and clinical relevance of 2R/2R TYMS genotype. Methods Between 2011 and 2018, 126 patients were genotyped for TYMS. FrAEs were graded according to CTCAE version 5.0. Fisher’s exact test was used for statistical analysis. Results The prevalence of TYMS 2R/2R genotype was 24.6%. Among patients with TYMS genotypes (N = 71) that predict decreased TS expression, 2R/2R TYMS genotype was the most common TYMS genotype seen in female (57%) and African American (60%) patients. Among patients with genotypes that predict increased TS expression (N = 55), 12 patients had grade 3–4 FrAEs (22%), while among patients with genotypes that predict decreased TS expression (N = 71), 30 patients had grade 3–4 FrAEs (42%) (p = 0.0219). Compared to patients with genotypes predicting increased TS expression, 17 out of 31 patients (55%) with TYMS 2R/2R genotype had grade 3–4 FrAEs (p = 0.0039) and 15 out 40 patients (38%) with TYMS 2R/3RC and TYMS 3RC/3RC genotype had grade 3–4 FrAEs (p = 0.1108). Conclusion The prevalence of TYMS 2R/2R genotype was 24.6%, and it had a unique sex and ethnic distribution. Polymorphism in the promoter region of TYMS gene that predicts decreased TS expression due to 2R/2R variant was associated with grade 3–4 FrAEs. These data suggest that genotyping patients who are not DPD deficient for TYMS might identify patients at risk of severe FrAEs.
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GODFREY, A. J. R., G. R. WOOD, S. GANESALINGAM, M. A. NICHOLS, and C. G. QIAO. "Two-stage clustering in genotype-by-environment analyses with missing data." Journal of Agricultural Science 139, no. 1 (August 2002): 67–77. http://dx.doi.org/10.1017/s0021859602002125.
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Cluster analysis has been commonly used in genotype-by-environment (G×E) analyses, but current methods are inadequate when the data matrix is incomplete. This paper proposes a new method, referred to as two-stage clustering, which relies on a partitioning of squared Euclidean distance into two independent components, the G×E interaction and the genotype main effect. These components are used in the first and second stages of clustering respectively. Two-stage clustering forms the basis for imputing missing values in the G×E matrix, so that a more complete data array is available for other G×E analyses. Imputation for a given genotype uses information from genotypes with similar interaction profiles. This imputation method is shown to improve on an existing nearest cluster method that confounds the G×E interaction and the genotype main effect.
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Loparev, Vladimir N., Antonio Gonzalez, Marlene Deleon-Carnes, Graham Tipples, Helmut Fickenscher, Einar G. Torfason, and D. Scott Schmid. "Global Identification of Three Major Genotypes of Varicella-Zoster Virus: Longitudinal Clustering and Strategies for Genotyping." Journal of Virology 78, no. 15 (August 1, 2004): 8349–58. http://dx.doi.org/10.1128/jvi.78.15.8349-8358.2004.
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ABSTRACT By analysis of a single, variable, and short DNA sequence of 447 bp located within open reading frame 22 (ORF22), we discriminated three major varicella-zoster virus (VZV) genotypes. VZV isolates from all six inhabited continents that showed nearly complete homology to ORF22 of the European reference strain Dumas were assigned to the European (E) genotype. All Japanese isolates, defined as the Japanese (J) genotype, were identical in the respective genomic region and proved the most divergent from the E strains, carrying four distinct variations. The remaining isolates carried a combination of E- and J-specific variations in the target sequence and thus were collectively termed the mosaic (M) genotype. Three hundred twenty-six isolates collected in 27 countries were genotyped. A distinctive longitudinal distribution of VZV genotypes supports this approach. Among 111 isolates collected from European patients, 96.4% were genotype E. Consistent with this observation, approximately 80% of the VZV strains from the United States were also genotype E. Similarly, genotype E viruses were dominant in the Asian part of Russia and in eastern Australia. M genotype viruses were strongly dominant in tropical regions of Africa, Indochina, and Central America, and they were common in western Australia. However, genotype M viruses were also identified as a minority in several countries worldwide. Two major intertypic variations of genotype M strains were identified, suggesting that the M genotype can be further differentiated into subgenotypes. These data highlight the direction for future VZV genotyping efforts. This approach provides the first simple genotyping method for VZV strains in clinical samples.
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Hu, Yu-Wen, Evan Balaskas, Milena Furione, Pei-Hua Yen, Garry Kessler, Vito Scalia, Linda Chui, and Graham Sher. "Comparison and Application of a Novel Genotyping Method, Semiautomated Primer-Specific and Mispair Extension Analysis, and Four Other Genotyping Assays for Detection of Hepatitis C Virus Mixed-Genotype Infections." Journal of Clinical Microbiology 38, no. 8 (2000): 2807–13. http://dx.doi.org/10.1128/jcm.38.8.2807-2813.2000.
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To date the true prevalence of hepatitis C virus (HCV) mixed-genotype infections has not been established mainly because currently available methods are not suitable for the detection of mixed genotypes in a viral population. A novel semiautomated genotyping method, primer-specific and mispair extension analysis (S-PSMEA), which is more reliable than other genotyping assays was developed for detection of HCV mixed-genotype infections. A genotype present at levels as low as 0.8% in a defined mix of HCV genotypes was detected, showing a 20-fold increase in sensitivity over that of direct DNA sequencing. A total of 434 HCV isolates were genotyped and analyzed for a comparative study of the accuracy between S-PSMEA and four current genotyping methods. The results showed that viruses in approximately 40% of the samples from this group determined to be infected with mixed genotypes by S-PSMEA were undetected by direct DNA sequencing due to its low sensitivity. Type-specific PCR, line probe assay, and restriction fragment length polymorphism analysis performed poorly, being able to identify only 38.5, 16.1, and 15.4% of mixed-genotype infections, respectively, that were detected by direct DNA sequencing. The prevalence of mixed-genotype infections detected by S-PSMEA was 7.9% (12 of 152 donors) among HCV-infected blood donors, 14.3% (15 of 105) among patients with chronic hepatitis C, and 17.1% (6 of 36) among thalassemia patients who had received multiple transfusions. The data lead us to conclude that HCV mixed-genotype infections are more common than previously estimated and that S-PSMEA may be the method of choice when detection of genotypes present at low levels in mixed-genotype infections is required due to its higher level of sensitivity.
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Aust, D., C. Kohne, E. Goekkurt, J. De Greve, J. Hartmann, E. Van Cutsem, M. Debois, U. Bethe, M. P. Lutz, and J. Stoehlmacher. "Preliminary pharmacogenetic evaluation of toxicity data in the prospective multicentre EORTC trial 40015 in metastatic colorectal cancer (CRC)." Journal of Clinical Oncology 24, no. 18_suppl (June 20, 2006): 3072. http://dx.doi.org/10.1200/jco.2006.24.18_suppl.3072.
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3072 Background: EORTC phase III study 40015 was initiated in 2003 to compare capecitabine (C) + irinotecan (CPT-11) vs 5FU/LV/irinotecan ± celecoxib in 1st line treatment of mCRC. The study was suspended after enrollment of 85 pts due to 8 fatal events not related to disease progression, 4 of which included thrombo-embolic events. Purpose: To test whether genetic polymorphisms involved in metabolism of the drugs are related to the increased toxicity observed in the study. Methods: 71 pts signed informed consent for genetic analyses and material was available for 58 pts. DNA was extracted from normal colonic mucosa or peripheral leukocytes. Polymorphisms were determined using PCR-based RFLP and direct sequencing. Genotypes known to be associated with increased toxicity (diarrhea, mucositis, leucopenia) were classified as unfavorable. Results: Unfavorable genotypes were distributed equally between C+CPT-11 and LV/5FU+CPT-11 arms. Baseline characteristics and treatment duration were similar in the pts with or without unfavorable genotypes. Unfavorable genotypes of thymidylate synthase (TS-5; TS-3) and UDP-glucuronosyltransferase 1A1 (UGT1A1) were associated with increased grade 3/4 toxicity. 18/35 (51%) pts with unfavorable UGT1A1 genotype experienced toxicity grade 3/4 compared to 3/23 (13%) pts with favorable genotype. 16/36 pts (44%) with unfavorable TS-5 genotype showed toxicity grade 3/4 compared to 5/22 (23%) pts with favorable genotype. Toxicity grade 3/4 was observed in 18/41 (44%) pts with unfavorable TS-3 genotype and 3/17 (18%) pts with favorable genotype. Increasing grade 3/4 toxicity rates were observed in the pts expressing 0/1 (2/16 [13%]), 2 (7/24 [29%]) or 3 (12/16 [75%]) unfavorable genotype(s) (p=0.0001). Among the 4 pts who died of a thrombo-embolic event, only one has been analysed at this stage and showed a Factor (V) Leiden mutation linked to 10-fold increased risk for thrombo-embolic events. Analyses are ongoing and complete data will be available for presentation. Conclusion: Our data suggest an association between polymorphisms of TS and UGT1A1 and toxicity. No differences of pharmacogenetic patterns were observed that could explain the increased rate of fatal events in the C/CPT-11 arm. [Table: see text]
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Paraboni, Marisa Lúcia Romani, Marina Dallagasperina Sbeghen, Fernando Herz Wolff, and Leila Beltrami Moreira. "Risk Factors for Infection with Different Hepatitis C Virus Genotypes in Southern Brazil." Scientific World Journal 2012 (2012): 1–6. http://dx.doi.org/10.1100/2012/946954.
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Objectives. To investigate the proportion of different genotypes in countryside microregions in southern Brazil, and their association with risk factors.Methods. Cross-sectional study including a convenience sample of patients who tested positive for HCV-RNA and were referred to a regional health center for genotyping, from December 2003 to January 2008. Data were obtained through the National Disease Surveillance Data System, from laboratory registers and from patient charts. Identification of genotypes was carried out using the Restriction Fragment Length Polymorphism “in house” technique. Independent associations with genotypes were evaluated in multinomial logistic regression and prevalence rates of genotypes were estimated with modified Poisson regression.Results. The sample consisted of 441 individuals, years old, 56.5% men. Genotype 1 was observed in 41.5% (95% CI 37.9–48.1) of patients, genotype 2 in 19.3% (95% CI 15.0–23.6), and genotype 3 in 39.2% (95% CI 35.6–43.0). HCV genotype was significantly associated with gender and age. Dental procedures were associated with higher proportion of genotype 2 independently of age, education, and patient treatment center.Conclusions. The hepatitis C virus genotype 1 was the most frequent. Genotype 2 was associated with female gender, age, and dental procedure exposition.
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Waqar, Muhammad, Habib Ur Rehman, Muhammad Wasim, Asad Ullah Khan, Tauseef Ahmad, Noor Ul Akbar, Mubarak Zeb, et al. "Molecular detection of the Hepatitis C virus genotypes circulating among both sexes of Khyber Pakhtunkhwa, Pakistan." Asian Journal of Medical Sciences 5, no. 3 (February 26, 2014): 72–76. http://dx.doi.org/10.3126/ajms.v5i3.9449.
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Background: Hepatitis C Virus (HCV) is the major cause of viral hepatitis. A few studies revealed that HCV genotypes; 3a, 3b, 1a and 1b are the most common genotypes found in the general population of Khyber Pakhtunkhwa. Aims and Objective: The current is designed to find out the prevalence of HCV genotypes among both sexes of Khyber Pakhtunkhwa. Study Methods: The present study was carried out in various area of Khyber Pakhtunkhwa during the period of July, 2012 to July, 2013. All the HCV positive samples were genotyped. The statistical analysis of the data was done by using Statistix 9.0 software. Result: The results showed that the male, 53.1% (n=340) were more infected as to female, 46.8% (n=300). The overall result shows that in male patients; the high number of cases (216) was reported of 3a whereas the lowest cases (8) were reported of 1b. The mixed genotype is recorded in 8 patients. In female patients; the 3a is detected in 170 patients whereas the lowest cases of genotype (3b) are reported in 5 patients. In female patients; the mixed genotype is reported in 11 patients. Conclusion: From the present study, it was concluded that the male were more infected as compare to female and the genotype 3a was the most common genotype in both sexes. Asian Journal of Medical Science, Volume-5(3) 2014: 72-76 http://dx.doi.org/10.3126/ajms.v5i3.9449
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Li, Yun, Cristen J. Willer, Jun Ding, Paul Scheet, and Gonçalo R. Abecasis. "MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes." Genetic Epidemiology 34, no. 8 (November 5, 2010): 816–34. http://dx.doi.org/10.1002/gepi.20533.
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Pritchard, Jonathan K., Matthew Stephens, and Peter Donnelly. "Inference of Population Structure Using Multilocus Genotype Data." Genetics 155, no. 2 (June 1, 2000): 945–59. http://dx.doi.org/10.1093/genetics/155.2.945.
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Abstract We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
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Chien, Jason W., Xinyi Cindy Zhang, Wenhong Fan, Hongwei Wang, Lue Ping Zhao, Paul J. Martin, Barry E. Storer, Michael Boeckh, Edus H. Warren, and John A. Hansen. "Evaluation of published single nucleotide polymorphisms associated with acute GVHD." Blood 119, no. 22 (May 31, 2012): 5311–19. http://dx.doi.org/10.1182/blood-2011-09-371153.
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Candidate genetic associations with acute GVHD (aGVHD) were evaluated with the use of genotyped and imputed single-nucleotide polymorphism data from genome-wide scans of 1298 allogeneic hematopoietic cell transplantation (HCT) donors and recipients. Of 40 previously reported candidate SNPs, 6 were successfully genotyped, and 10 were imputed and passed criteria for analysis. Patient and donor genotypes were assessed for association with grades IIb-IV and III-IV aGVHD, stratified by donor type, in univariate and multivariate allelic, recessive and dominant models. Use of imputed genotypes to replicate previous IL10 associations was validated. Similar to previous publications, the IL6 donor genotype for rs1800795 was associated with a 20%-50% increased risk for grade IIb-IV aGVHD after unrelated HCT in the allelic (adjusted P = .011) and recessive (adjusted P = .0013) models. The donor genotype was associated with a 60% increase in risk for grade III-IV aGVHD after related HCT (adjusted P = .028). Other associations were found for IL2, CTLA4, HPSE, and MTHFR but were inconsistent with original publications. These results illustrate the advantages of using imputed single-nucleotide polymorphism data in genetic analyses and demonstrate the importance of validation in genetic association studies.
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Li, Ruowang, Rui Duan, Rachel L. Kember, Daniel J. Rader, Scott M. Damrauer, Jason H. Moore, and Yong Chen. "A regression framework to uncover pleiotropy in large-scale electronic health record data." Journal of the American Medical Informatics Association 26, no. 10 (July 27, 2019): 1083–90. http://dx.doi.org/10.1093/jamia/ocz084.
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Abstract Objective Pleiotropy, where 1 genetic locus affects multiple phenotypes, can offer significant insights in understanding the complex genotype–phenotype relationship. Although individual genotype–phenotype associations have been thoroughly explored, seemingly unrelated phenotypes can be connected genetically through common pleiotropic loci or genes. However, current analyses of pleiotropy have been challenged by both methodologic limitations and a lack of available suitable data sources. Materials and Methods In this study, we propose to utilize a new regression framework, reduced rank regression, to simultaneously analyze multiple phenotypes and genotypes to detect pleiotropic effects. We used a large-scale biobank linked electronic health record data from the Penn Medicine BioBank to select 5 cardiovascular diseases (hypertension, cardiac dysrhythmias, ischemic heart disease, congestive heart failure, and heart valve disorders) and 5 mental disorders (mood disorders; anxiety, phobic and dissociative disorders; alcohol-related disorders; neurological disorders; and delirium dementia) to validate our framework. Results Compared with existing methods, reduced rank regression showed a higher power to distinguish known associated single-nucleotide polymorphisms from random single-nucleotide polymorphisms. In addition, genome-wide gene-based investigation of pleiotropy showed that reduced rank regression was able to identify candidate genetic variants with novel pleiotropic effects compared to existing methods. Conclusion The proposed regression framework offers a new approach to account for the phenotype and genotype correlations when identifying pleiotropic effects. By jointly modeling multiple phenotypes and genotypes together, the method has the potential to distinguish confounding from causal genotype and phenotype associations.
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Pranckeviciene, Erinija, Valentina Gineviciene, Audrone Jakaitiene, Laimonas Januska, and Algirdas Utkus. "Total Genotype Score Modelling of Polygenic Endurance-Power Profiles in Lithuanian Elite Athletes." Genes 12, no. 7 (July 13, 2021): 1067. http://dx.doi.org/10.3390/genes12071067.
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Total genotype score (TGS) reflects additive effect of genotypes on predicting a complex trait such as athletic performance. Scores assigned to genotypes in the TGS should represent an extent of the genotype’s predisposition to the trait. Then, combination of genotypes highly ranks those individuals, who have a trait expressed. Usually, the genotypes are scored by the evidence of a genotype–phenotype relationship published in scientific studies. The scores can be revised computationally using genotype data of athletes, if available. From the available genotype data of 180 Lithuanian elite athletes we created an endurance-mixed-power performance TGS profile based on known ACE rs1799752, ACTN3 rs1815739, and AMPD1 rs17602729, and an emerging MB rs7293 gene markers. We analysed an ability of this TGS profile to stratify athletes according to the sport category that they practice. Logistic regression classifiers were trained to compute the genotype scores that represented the endurance versus power traits in the group of analysed athletes more accurately. We observed differences in TGS distributions in female and male group of athletes. The genotypes with possibly different effects on the athletic performance traits in females and males were described. Our data-driven analysis and TGS modelling tools are freely available to practitioners.
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Manuc, Mircea, Carmen M. Preda, Corneliu P. Popescu, Cristian Baicuș, Theodor Voiosu, Corina S. Pop, Liana Gheorghe, et al. "New Epidemiologic Data Regarding Hepatitis C Virus Infection in Romania." Journal of Gastrointestinal and Liver Diseases 26, no. 4 (December 1, 2017): 381–86. http://dx.doi.org/10.15403/jgld.2014.1121.264.cvr.
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Background & Aims: Literature data suggest that HCV genotype-1b is present in 93-99% of the Romanian patients infected with hepatitis C virus (HCV). We present the genotyping tests recently performed on patients with HCV and advanced fibrosis eligible for the Direct-Acting Antiviral (DAA) therapy, as well as the prevalence of these cases across Romania.Methods: The genotyping method was performed on 7,421 HCV patients with advanced fibrosis. The detection method was automatic real time PCR platform M2000 (Abbott). Every subject was introduced into a database including age, sex, county and address.Results: Genotype 1b was almost exclusively present: 7,392/7,421 (99.6%). Genotype 1b patients were 19.6% from Bucharest, 49% were males, with a median age of 60 years. Genotype non-1b was encountered in 29/7,421 subjects (0.4%), 62% were males, 69% from Bucharest and the median age was 52 years. Most of the subjects (75%) were in the 6th and 7th age decade. The prevalence of these cases varied significantly across Romanian counties: the highest was in Bucharest (61.3/105), Bihor (47/105), Iasi (46/105) and Constanța (43/105), and the lowest in Ilfov (2.8/105), Harghita (3.7/105), Covasna (5.4/105) and Maramureș (8.8/105) (p<0.001).Conclusions: Genotype 1b is encountered in 99.6% of patients with chronic hepatitis C and advanced fibrosis from Romania. The presence of genotypes non-1b is more common in Bucharest, in males and at a younger age. There are significant differences regarding the distribution of these cases across Romania: the highest rates are in Bucharest, Bihor, Iasi and Constanta.Abbreviations: BMI: body mass index; DAA: direct-acting antiviral agent; GT: genotype; HBV: hepatitis B virus; HCC: hepatocellular carcinoma; HCV: hepatitis C virus; IDU: intravenous drug users; MELD: model for end stage liver disease; NASH: non-alcoholic steatohepatitis; SVR; sustained virologic response.
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Zhang, Shuanglin, and Hongyu Zhao. "Linkage disequilibrium mapping with genotype data." Genetic Epidemiology 22, no. 1 (December 7, 2001): 66–77. http://dx.doi.org/10.1002/gepi.1044.
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Chen, Junjie, and Xinghua Shi. "Sparse Convolutional Denoising Autoencoders for Genotype Imputation." Genes 10, no. 9 (August 28, 2019): 652. http://dx.doi.org/10.3390/genes10090652.
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Genotype imputation, where missing genotypes can be computationally imputed, is an essential tool in genomic analysis ranging from genome wide associations to phenotype prediction. Traditional genotype imputation methods are typically based on haplotype-clustering algorithms, hidden Markov models (HMMs), and statistical inference. Deep learning-based methods have been recently reported to suitably address the missing data problems in various fields. To explore the performance of deep learning for genotype imputation, in this study, we propose a deep model called a sparse convolutional denoising autoencoder (SCDA) to impute missing genotypes. We constructed the SCDA model using a convolutional layer that can extract various correlation or linkage patterns in the genotype data and applying a sparse weight matrix resulted from the L1 regularization to handle high dimensional data. We comprehensively evaluated the performance of the SCDA model in different scenarios for genotype imputation on the yeast and human genotype data, respectively. Our results showed that SCDA has strong robustness and significantly outperforms popular reference-free imputation methods. This study thus points to another novel application of deep learning models for missing data imputation in genomic studies.
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Podrechneva, I. Y., P. O. Shchegolev, S. G. Belokurov, and I. A. Kofiadi. "COMPARATIVE ASSESSMENT OF KOSTROMA AND YAROSLAVL CATTLE BREEDS BY THE BETA-CASEIN GENE." Scientific Life 15, no. 9 (September 30, 2020): 1278–84. http://dx.doi.org/10.35679/1991-9476-2020-15-9-1278-1284.
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Abstract. The article presents the results of a comparative assessment of the frequency of alleles and genotypes for the gene of beta-casein (β-CN) in cattle of the Kostroma and Yaroslavl breeds. The data on 137 bulls-producers of comparable and related breeds, presented on the official sites of “OOO Head Center for the Reproduction of Farm Animals” and the breeding farm “OOO Yaroslavskoe”, have been analyzed. The blood of cows from the Kostroma and Yaroslavl breeds in the breeding farms of the Kostroma region served as the object of DNA research. A total of 80 animals were genotyped. Evaluation of the distribution of the desired genotype β-CNА2/А2 in stud bulls showed that two breeds are in the lead – the Schwyz and the Kostroma breed, with the frequency of occurrence – 0.9090 and 0.6250, respectively. Moreover, in the Kostroma breed, there are no bulls carriers of the homozygous β-CNА1/А1 genotype. If we take into account the frequency of distribution of the β-CNА2 allele in bulls of the analyzed breeds, then it is higher – in the Schwyz breed – 0.9091, Kostroma – 0.8125 and Holstein – 0.6776. In bulls of the Yaroslavl breed there is 0.2083 frequency of the β-CNА2/А2 genotype and 0.4167 frequency of the β-CNА2 allele. A comparative assessment of the polymorphism data of the beta-casein locus in cows of the Yaroslavl and Kostroma breeds showed that in the Yaroslavl breed there were least of all animals with the β-CNА2/А2 genotype – 0.0333 and more – with the β-CNА1/А1 genotype – 0.6667. In the Kostroma breed, the genetic situation is completely different. So cows with genotypes β-CNА2/А2 – 0.5490, and with genotype β-CNА1/А1 – 0.0785. However, it is necessary to take into account the main indicators of cattle productivity in order to consider the beta-casein genotype as an additional selection trait. It is not possible to study the milk productivity of Yaroslavl breed cows with different genotypes, since only one cow with the CNА2/А2 genotype has been identified. However, cows of the Kostroma breed homozygous for the CNА2 allele, for the third and older lactations, had a milk yield of 1534 kg higher than cows homozygous for the CNА1 allele. Consequently, the beta-casein genotype can be considered an additional promising breeding trait.
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Delic, Dragan, Zorica Nesic, Milica Prostran, Ivan Boricic, Nada Tomanovic, Milisav Cutovic, Ljubisa Dokic, Jasmina Simonovic, and Neda Svirtlih. "Histopathology of chronic hepatitis C in relation to virus genotype." Vojnosanitetski pregled 63, no. 9 (2006): 819–25. http://dx.doi.org/10.2298/vsp0609819d.
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Background/aim: The natural history of hepatitis C virus (HCV) infection is variable and the factors determining the course of the illness are unclear. There are geographical variations in the distribution of different HCV genotypes, and some of them are related to the specific infection routes. Regarding our country, the dominant genotype is genotype 1b. It is unclear and still remains a question whether the distinct histopathological manifestations are related to the particular genotypes of HCV. Thus, the aim of this study was to determine whether the distinct histopathological manifestations of HCV infection might be in relation to the individual virus genotype. Methods. In this study we examined 126 patients with chronic HCV infection regarding the histopathological features, demographic data, and virus genotype. The observed groups of patients were predominantly infected with HCV genotypes 1b and 3a. Results. In this study we found that the patients infected with HCV genotype 1b had more frequently moderate or severe necroinflammatory activity of the disease, significantly higher grading score as compared with other genotypes (p < 0.0001). A higher degree of fibrosis was, also, more common in the patients infected with genotype 1b of HCV as compared with other genotypes (p < 0.05). There were no significant correlations between the necroinflammatory activity of the disease and the stage of fibrosis in 1b, 4 and mixed genotypes. Conclusion. The present data support the hypothesis that distinct genotypes of HCV are associated with the particular histopathological manifestation of the disease.
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Scutt, Greg, Andrew Overall, Railton Scott, Bhavik Patel, Lamia Hachoumi, Mark Yeoman, and Juliet Wright. "Does the 5-HT1A rs6295 polymorphism influence the safety and efficacy of citalopram therapy in the oldest old?" Therapeutic Advances in Drug Safety 9, no. 7 (April 23, 2018): 355–66. http://dx.doi.org/10.1177/2042098618770620.
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Major depressive disorder (MDD) in older people is a relatively common, yet hard to treat problem. In this study, we aimed to establish if a single nucleotide polymorphism in the 5-HT1A receptor gene (rs6295) determines antidepressant response in patients aged > 80 years (the oldest old) with MDD. Nineteen patients aged at least 80 years with a new diagnosis of MDD were monitored for response to citalopram 20 mg daily over 4 weeks and genotyped for the rs6295 allele. Both a frequentist and Bayesian analysis was performed on the data. Bayesian analysis answered the clinically relevant question: ‘What is the probability that an older patient would enter remission after commencing selective serotonin reuptake inhibitor (SSRI) treatment, conditional on their rs6295 genotype?’ Individuals with a CC (cytosine–cytosine) genotype showed a significant improvement in their Geriatric Depression Score ( p = 0.020) and cognition ( p = 0.035) compared with other genotypes. From a Bayesian perspective, we updated reports of antidepressant efficacy in older people with our data and calculated that the 4-week relative risk of entering remission, given a CC genotype, is 1.9 [95% highest-density interval (HDI) 0.7–3.5], compared with 0.52 (95% HDI 0.1–1.0) for the CG (cytosine–guanine) genotype. The sample size of n = 19 is too small to draw any firm conclusions, however, the data suggest a trend indicative of a relationship between the rs6295 genotype and response to citalopram in older patients, which requires further investigation.
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WEI, D. H., H. Z. LIU, A. M. HUANG, X. L. LIU, and J. F. LIU. "A new trend of genotype distribution of hepatitis B virus infection in southeast China (Fujian), 2006–2013." Epidemiology and Infection 143, no. 13 (February 4, 2015): 2822–26. http://dx.doi.org/10.1017/s0950268815000059.
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SUMMARYHBV genotypes have specific geographical distributions and can serve as epidemiological markers. Accumulated data have shown that the major HBV genotypes in China are B and C. Here, the HBV genotypes were examined from 6817 blood samples, which were collected from patients with chronic HBV infection in Fujian Province during 2006–2013; genotype B was identified in 3384 patients (49·6%), while genotype C was identified in 3430 patients (50·3%). The percentage of patients infected with genotype C gradually increased with age from 39·5% (patients aged <20 years) to 63·9% (patients aged >50 years), reaching a peak of 67·3% in the 45–50 years age group. These results clearly demonstrate that the genotype distribution of HBV in Fujian Province has significantly changed in recent years with almost equal numbers of genotype B and genotype C infections existing in the entire patient population, while higher incidence of genotype C infection exists in older patients, but genotype B is no longer dominant in the Fujian area as previously reported.
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Deelen, Patrick, Marc Bonder, K. van der Velde, Harm-Jan Westra, Erwin Winder, Dennis Hendriksen, Lude Franke, and Morris A. Swertz. "Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration." BMC Research Notes 7, no. 1 (2014): 901. http://dx.doi.org/10.1186/1756-0500-7-901.
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Hageman, J. A., M. Malosetti, and F. A. van Eeuwijk. "Two-mode clustering of genotype by trait and genotype by environment data." Euphytica 183, no. 3 (August 18, 2010): 349–59. http://dx.doi.org/10.1007/s10681-010-0236-6.
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Hsiao, Fone-Ching, Yuh-Feng Lin, Po-Shiuan Hsieh, Nain-Feng Chu, Yii-Der Ida Chen, Yi-Shing Shieh, Chang-Hsun Hsieh, Chien-Hsing Lee, Ting-I. Lee, and Yi-Jen Hung. "Effect ofGAS6andAXLGene Polymorphisms on Adiposity, Systemic Inflammation, and Insulin Resistance in Adolescents." International Journal of Endocrinology 2014 (2014): 1–9. http://dx.doi.org/10.1155/2014/674069.
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The present study was designed to explore the effects ofGAS6andAXLgene polymorphisms on adiposity, systemic inflammation, and insulin resistance in adolescents. After multistage sampling from the data of the Taipei Children Heart Study-III, we collected 358 boys and 369 girls with an average age of 13.3 years. We genotyped the adolescents’GAS6rs8191973,GAS6rs8191974,AXLrs4802113, andAXLrs2304232 polymorphisms. Significantly higher body mass index (BMI), waist circumference (WC), and hsCRP levels were found in boys with the GG genotype ofGAS6rs8191974 than A allele carriers; higher IL-6 and insulin levels and increased HOMA-IR were found in boys with the GG genotype ofAXLrs2304232 than the A allele carriers. There was a significant difference in hsCRP levels of boys with the TT, TC, and CC genotypes ofAXLrs4802113. Boys with both the GG genotype ofGAS6rs8191973 and the GG genotype ofGAS6rs8191974 exhibited higher BMI, WC, IL-6, and hsCRP levels than the boys carrying both the C allele of theGAS6rs8191973 and the A allele of theGAS6rs8191974. In conclusion,GAS6andAXLpolymorphisms are associated with adiposity, systemic inflammation, and insulin resistance in adolescents, especially in boys.
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Mohammadi, Reza, and Ahmed Amri. "Analysis of genotype × environment interaction in rain-fed durum wheat of Iran using GGE-biplot and non-parametric methods." Canadian Journal of Plant Science 92, no. 4 (July 2012): 757–70. http://dx.doi.org/10.4141/cjps2011-133.
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Mohammadi, R. and Amri, A. 2012. Analysis of genotype × environment interaction in rain-fed durum wheat of Iran using GGE-biplot and non-parametric methods. Can. J. Plant Sci. 92: 757–770. Multi-environment trials (MET) are conducted annually throughout the world in order to use the information contained in MET data for genotype evaluation and mega-environment identification. In this study, grain yield data of 13 durum and one bread wheat genotypes grown in 16 diversified environments (differing in winter temperatures and water regimes) were used to analyze genotype by environment (GE) interactions in rain-fed durum MET data in Iran. The main objectives were (i) to investigate the possibility of dividing the test locations representative for rain-fed durum production in Iran into mega-environments using the genotype main effect plus GE interaction (GGE) biplot model and (ii) to compare the effectiveness of the GGE-biplot and several non-parametric stability measures (NPSM), which are not well-documented, for evaluating the stability performance of genotypes tested and the possibility of recommending the best genotype(s) for commercial release in the rain-fed areas of Iran. The results indicate that the grain yield of different genotypes was significantly influenced by environmental effect. The greater GE interaction relative to genotype effect suggested significant environmental groups with different top-yielding genotypes. Warm environments differed from cold environments in the ranking of genotypes, while moderate environments were highly divergent and correlated with both cold and warm environments. Cold and warm environments were better than moderate environments in both discriminating and representativeness, suggesting the efficiency and accuracy of genotype selection would be greatly enhanced in such environments. According to the NPSM, genotypes tend to be classified into groups related to the static and dynamic concepts of stability. Both the GGE-biplot and NPSM methods were found to be useful, and generally gave similar results in identifying high-yielding and stable genotypes. In contrast to NPSM, the GGE-biplot analysis would serve as a better platform to analyze MET data, because it always explicitly indicates the average yield and stability of the genotypes and the discriminating ability and representativeness of the test environments.
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Kamenicky, Peter, Christine Dos Santos, Consuelo Espinosa, Sylvie Salenave, Françoise Galland, Yves Le Bouc, Patrick Maison, Pierre Bougnères, and Philippe Chanson. "D3 GH receptor polymorphism is not associated with IGF1 levels in untreated acromegaly." European Journal of Endocrinology 161, no. 2 (August 2009): 231–35. http://dx.doi.org/10.1530/eje-09-0053.
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ContextA discrepancy between serum GH and IGF1 concentrations is frequent in patients with acromegaly. Here, we examined whether the exon 3-deleted (d3) GH receptor (GHR) variant, which has been linked to increased responsiveness to GH treatment in short children, influences the GH/IGF1 relationship in patients with acromegaly.ObjectiveTo study the possible influence of the GHR genotype on the GH/IGF1 relationship in untreated acromegalic patients.DesignGHR genotype analysis with retrospective clinical and biochemical data collection performed in a single third-reference medical center.Patients and methodsClinical data were obtained from the medical records of 105 acromegalic patients who had GH and IGF1 assays in the same laboratory and who were genotyped for the full-length (fl) or d3-GHR alleles.ResultsThe distribution of GHR genotypes was 51% fl/fl, 30% fl/d3, and 19% d3/d3. Patients with d3/d3 genotype were younger than the patients in the other two groups (P<0.05). Baseline GH and IGF1 concentrations did not differ among the three groups. The linear correlation between GH and IGF1 concentrations was similar in the three genotypic groups.ConclusionsThe exon 3 GHR genotype does not affect the GH/IGF1 relationship in untreated acromegalic patients with high circulating GH and IGF1 levels.
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RAKSHIT, S., K. N. GANAPATHY, S. S. GOMASHE, A. DHANDAPANI, M. SWAPNA, S. P. MEHTRE, S. R. GADAKH, et al. "Analysis of Indian post-rainy sorghum multi-location trial data reveals complexity of genotype × environment interaction." Journal of Agricultural Science 155, no. 1 (March 28, 2016): 44–59. http://dx.doi.org/10.1017/s0021859616000137.
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SUMMARYSorghum [Sorghum bicolor (L.) Moench] grown in India is of two adaptive types: rainy and post-rainy. The post-rainy sorghum is predominantly consumed by humans. While releasing new cultivars through multi-location testing, major emphasis is given to the superiority of new cultivars over existing cultivars, with very little emphasis on the genotype × environment interaction (GEI). To understand the complexity of GEI in post-rainy sorghum testing location trials, the multi-location evaluation data of two post-rainy seasons (2009/10 and 2010/11) under the All India Coordinated Sorghum Improvement Project were analysed. In both years, location explained the highest proportion of total sum of squares followed by the GEI effect and main effect of genotype. Additive main effects and multiplicative interaction (AMMI), stability values (ASV) and genotype + genotype × environment interaction (GGE) instability values recorded high correlation resulting in identification of the best performing cultivars. However, the rank correlations were lower, though still significant. A mixture of crossover and non-crossover GEI was a common occurrence in both years. ‘Which-won-where’ analysis suggested the existence of four possible mega-environments (ME) among post-rainy testing locations, with a few non-informative locations within ME. Mega-environments are characterized by soil type, rainfall pattern and moisture conservation practices. The present study indicated the possibility of reducing the number of test locations by eliminating non-representative highly correlated locations and suggested the need to breed for location-specific genotypes rather than genotypes with wider adaptability.
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Wijesena, Hiruni R., Gary A. Rohrer, Dan J. Nonneman, Brittney N. Keel, Jessica L. Petersen, Stephen D. Kachman, and Daniel C. Ciobanu. "Evaluation of genotype quality parameters for SowPro90, a new genotyping array for swine1." Journal of Animal Science 97, no. 8 (May 31, 2019): 3262–73. http://dx.doi.org/10.1093/jas/skz185.
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Abstract Understanding early predictors of sow fertility has the potential to improve genomic predictions. A custom SNP array (SowPro90 produced by Affymetrix) was developed to include genetic variants overlapping quantitative trait loci for age at puberty, one of the earliest indicators of sow fertility, as well as variants related to innate and adaptive immunity. The polymorphisms included in the custom genotyping array were identified using multiple genomic approaches including deep genomic and transcriptomic sequencing and genome-wide associations. Animals from research and commercial populations (n = 2,586) were genotyped for 103,476 SNPs included in SowPro90. To assess the quality of data generated, genotype concordance was evaluated between the SowPro90 and Porcine SNP60 BeadArray using a subset of common SNP (n = 44,708) and animals (n = 277). The mean genotype concordance rate per SNP was 98.4%. Differences in distribution of data quality were observed between the platforms indicating the need for platform specific thresholds for quality parameters. The optimal thresholds for SowPro90 (≥97% SNP and ≥93% sample call rate) were obtained by analyzing the data quality distribution and genotype concordance per SNP across platforms. At ≥97% SNP call rate, there were 42,151 SNPs (94.3%) retained with a mean genotype concordance of 98.6% across platforms. Similarly, ≥94% SNPs and ≥85% sample call rates were established as thresholds for Porcine SNP60 BeadArray. At ≥94% SNPs call rate, there were 41,043 SNPs (91.8%) retained with a mean genotype concordance of 98.6% across platforms. Final evaluation of SowPro90 array content (n = 103,476) at ≥97% SNPs and ≥93% sample call rates allowed retention of 89,040 SNPs (86%) for downstream analysis. The findings and strategy for quality control could be helpful in identifying consistent, high-quality genotypes for genomic evaluations, especially when integrating genotype data from different platforms.
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van Eeuwijk, Fred A., Marcos Malosetti, Xinyou Yin, Paul C. Struik, and Piet Stam. "Statistical models for genotype by environment data: from conventional ANOVA models to eco-physiological QTL models." Australian Journal of Agricultural Research 56, no. 9 (2005): 883. http://dx.doi.org/10.1071/ar05153.
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To study the performance of genotypes under different growing conditions, plant breeders evaluate their germplasm in multi-environment trials. These trials produce genotype × environment data. We present statistical models for the analysis of such data that differ in the extent to which additional genetic, physiological, and environmental information is incorporated into the model formulation. The simplest model in our exposition is the additive 2-way analysis of variance model, without genotype × environment interaction, and with parameters whose interpretation depends strongly on the set of included genotypes and environments. The most complicated model is a synthesis of a multiple quantitative trait locus (QTL) model and an eco-physiological model to describe a collection of genotypic response curves. Between those extremes, we discuss linear-bilinear models, whose parameters can only indirectly be related to genetic and physiological information, and factorial regression models that allow direct incorporation of explicit genetic, physiological, and environmental covariables on the levels of the genotypic and environmental factors. Factorial regression models are also very suitable for the modelling of QTL main effects and QTL × environment interaction. Our conclusion is that statistical and physiological models can be fruitfully combined for the study of genotype × environment interaction.
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Kusmana, NFN, Yenni Kusandriani, and Diny Djuariah. "Uji Daya Hasil Tujuh Genotipe Cabai Rawit pada Ekosistem Dataran Tinggi Pangalengan, Jawa Barat." Jurnal Hortikultura 27, no. 2 (February 19, 2018): 147. http://dx.doi.org/10.21082/jhort.v27n2.2017.p147-154.
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<p>Cabai rawit merupakan salah satu sayuran utama petani di dataran tinggi, karena memiliki nilai ekonomi tinggi dan dapat dengan mudah ditanam secara tumpang gilir dengan komoditas sayuran lainnya. Tujuan pengujian adalah mengetahui daya hasil genotipe-genotipe harapan cabai rawit pada agroekosistem dataran tinggi di Pangalengan. Pengujian menggunakan rancangan kelompok lengkap teracak, dengan empat ulangan. Bahan pengujian terdiri dari empat genotipe harapan cabai rawit yang merupakan koleksi plasma nutfah Balai Penelitian Tanaman Sayuran, yaitu CRM 01, CRM 02, CRM 03, dan CRM 04 serta tiga varietas pembanding, yaitu Hot Seed, Patra, dan Bara. Pengujian dilakukan di Desa Gunung Cupu, Kecamatan Pangalengan, Kabupaten Bandung, 1.500 m dpl. Waktu pengujian bulan Maret sampai dengan Desember 2014. Data yang diamati meliputi data morfologi tanaman dan produktivitas hasil. Hasil pengujian menunjukkan bahwa terdapat perbedaan karakter fenotipik antartujuh genotipe yang diuji. Genotipe CRM 03 menampilkan potensi hasil yang tertinggi (9,64 ton/ha), dengan karakter buah muda berwarna putih dan buah tua berwarna merah oranye. Genotipe CRM 03 dan genotipe Bara sangat cocok ditanam di dataran tinggi Pangalengan karena memiliki potensi hasil yang tinggi, yaitu CRM 03 mencapai 9,64 ton/ha sementara varietas pembanding Bara 8,76 ton/ha. Genotipe CRM 03 diharapkan akan menjadi varietas unggul baru cabai rawit yang mempunyai produktivitas tinggi dan cocok ditanam di Pangalengan dan akan mendongkrak produktivitas cabai rawit di Pangalengan dan daerah lainnya yang mempunyai agroekologi mirip dengan dataran tinggi Pangalengan.</p><p>Chili (Capsicum sp.) is the main vegetable for farmers in the highland because it has high economic value and can be grown intercrop with others vegetables. The objective of the research was to test advanced genotypes of chili on yield under ecosystem highland of Pangalengan. The experimental design was randomized complete block design with four replications. Four genotypes of chili that were CRM01, CRM 02, CRM 03, and CRM 04 derived from advanced genotype from Indonesian Vegetables Research Institute and three varieties as comparison (Hot seed, Patra, and Bara) were used for treatments. The trial was conducted at Pangalengan, Bandung District, West Java Province, 1.500 m above sea level. The experiment was conducted since March until December 2014. Data observed was plant morphology and yield productivity. The result showed that was different phenotypic among the seven genotypes tested. CRM 03 Genotype was showed highest yielding (9.64 ton/ha), which has fruit character white and red orange for young and mature fruit. CRM 03 genotypes as well as variety of Bara was suitable to be grown in highland of Pangalengan due to high yielding. Yield obtained from CRM 03 was 9.64 ton/ha, whereas, Bara was 8.76 ton/ha. CRM 03 genotype hopefully can be released as a new variety with high yielding and adapted for Pangalengan and others locations similar to Pangalengan.</p>
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Farshadfar, E. "Simultaneous selection of yield and yield stability in chickpea genotypes using the GGE biplot technique." Acta Agronomica Hungarica 61, no. 3 (September 1, 2013): 185–94. http://dx.doi.org/10.1556/aagr.61.2013.3.2.
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GGE biplot analysis is an effective method, based on principal component analysis (PCA), to fully explore multi-environment trials (METs). It allows visual examination of the relationships among the test environments, genotypes and the genotype-by-environment interactions (G×E interaction). The objective of this study was to explore the effect of genotype (G) and the genotype × environment interaction (GEI) on the grain yield of 20 chickpea genotypes under two different rainfed and irrigated environments for 4 consecutive growing seasons (2008–2011). The yield data were analysed using the GGE biplot method. The first mega-environment contained environments E1, E3, E4 and E6, with genotype G17 (X96TH41K4) being the winner; the second mega-environment contained environments E5, E7 and E8, with genotype G12 (X96TH46) being the winner. The E2 environment made up another mega-environment, with G19 (FLIP-82-115) the winner. The mean performance and stability of the genotypes indicated that genotypes G4, G16 and G20 were highly stable with high grain yield.
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Veloso, Carlos Eduardo, Luciana Negrão Frota de Almeida, and Márcio Bittar Nehemy. "CFH Y402H polymorphism and response to intravitreal Ranibizumab in brazilian patients with neovascular age-related macular degeneration." Revista do Colégio Brasileiro de Cirurgiões 41, no. 6 (December 2014): 386–92. http://dx.doi.org/10.1590/0100-69912014006002.
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Objective: To investigate the association between CFH gene polymorphism and response to ranibizumab in Brazilian patients with neovascular age-related macular degeneration (AMD).Methods: 95 patients were genotyped for the CFH rs1061170 (Y402H) single nucleotide polymorphism. Patients with neovascular AMD initially received intravitreal ranibizumab injections for three months and were retreated as needed. Visual acuity (VA) and central retinal thickness (CRT) were measured before treatment and at 1, 3, 6, and 12 months post-treatment.Results: For patients with the TT and TC genotypes, paired comparisons of VA showed a statistically significant improvement when the data obtained at all visits were compared with baseline. Patients homozygous for the risk genotype (CC) did not show a statistically significant improvement when VA obtained at visits 1, 3, 6 and 12 were compared with baseline. For all genotypes, paired comparisons of CRT showed a statistically significant improvement when the data obtained at visits 1, 3, 6 and 12 were compared with baseline.Conclusion: Patients with the CC genotype showed poorer long-term functional response to intravitreal ranibizumab.
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Tseng, Li-Hui, Ming-Tseh Lin, Barry Storer, Paul J. Martin, Bryan Grogan, Pei-Jer Chen, Lue Ping Zhao, and John A. Hansen. "Association of IL-10 and IL-10 Receptor Gene Polymorphisms and Graft-Versus-Host Disease Following Hematopoietic Cell Transplantation." Blood 104, no. 11 (November 16, 2004): 421. http://dx.doi.org/10.1182/blood.v104.11.421.421.
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Abstract Polymorphisms in cytokine genes can influence immune responses and may affect the outcome of hematopoietic cell transplantation (HCT). We have shown that the IL-10/-592*A allele of the recipient is a marker for less severe acute graft-versus-host disease (GVHD) and a lower risk of non-relapse mortality (NRM) after HCT from an HLA-identical sibling (N Engl J Med, 2003). To further test the hypothesis that IL-10 pathway is important in the intensity of acute GVHD, we undertook a study of variation in the IL-10 receptor β gene. A single nucleotide polymorphism (A/G) at cDNA position 238 of the IL-10 receptor β gene (IL-10RB/1304) was genotyped in 953 HCT recipients and their HLA-identical sibling donors. IL-10/-592 and IL-10RB alleles and genotypes were tested for association with GVHD by multivariable analysis. The IL-10/-592*A allele of the recipient and IL-10RB/238*G allele of the donor were significantly associated with a lower risk of acute grades III-IV GVHD (trend p value 0.0008 and 0.02, respectively). None of the 16 cases with a patient IL-10 A/A genotype and donor IL-10RB G/G genotype developed grades III-IV acute GVHD (HR = 0.0 and p value = 0.007), compared to pairs with a patient IL-10 C/C genotype and donor IL-10RB A/A genotype. The hazard ratios were 0.4–0.6 among pairs with a patient IL-10 A/A genotype and donor IL-10RB A/G or A/A genotype and among pairs with a patient IL-10 A/C genotype and donor IL-10RB G/G or A/G genotype. The effect of donor IL-10RB genotype on GVHD was observed only among pairs with a patient IL-10 A/C or A/A genotype (trend p value = 0.005 and 0.06 respectively), but not among pairs with a patient IL-10 C/C genotype (trend p value = 0.82). These data suggest an interaction in the effect of the patient IL-10/-592 and donor IL-10RB/1304 genotypes on GVHD, further supporting the hypothesis that the IL-10 pathway plays an important role in controlling the severity of acute GVHD.
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Thibeault, Diane, Christiane Bousquet, Rock Gingras, Lisette Lagacé, Roger Maurice, Peter W. White, and Daniel Lamarre. "Sensitivity of NS3 Serine Proteases from Hepatitis C Virus Genotypes 2 and 3 to the Inhibitor BILN 2061." Journal of Virology 78, no. 14 (July 15, 2004): 7352–59. http://dx.doi.org/10.1128/jvi.78.14.7352-7359.2004.
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ABSTRACT Hepatitis C virus (HCV) displays a high degree of genetic variability. Six genotypes and more than 50 subtypes have been identified to date. In this report, kinetic profiles were determined for NS3 proteases of genotypes 1a, 1b, 2ac, 2b, and 3a, revealing no major differences in activity. In vitro sensitivity studies with BILN 2061 showed a decrease in affinity for proteases of genotypes 2 and 3 (Ki , 80 to 90 nM) compared to genotype 1 enzymes (Ki , 1.5 nM). To understand the reduced sensitivity of genotypes 2 and 3 to BILN 2061, active-site residues in the proximity of the inhibitor binding site were replaced in the genotype-1b enzyme with the corresponding genotype-2b or -3a residues. The replacement of five residues at positions 78, 79, 80, 122, and 132 accounted for most of the reduced sensitivity of genotype 2b, while replacement of residue 168 alone could account for the reduced sensitivity of genotype 3a. BILN 2061 remains a potent inhibitor of these non-genotype-1 NS3-NS4A proteins, with Ki values below 100 nM. This in vitro potency, in conjunction with the good pharmacokinetic data reported for humans, suggests that there is potential for BILN 2061 as an antiviral agent for individuals infected with non-genotype-1 HCV.
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Shaw, Gary M., Cathy R. Wasserman, Jeffrey C. Murray, and Edward J. Lammer. "Infant TGF-Alpha Genotype, Orofacial Clefts, and Maternal Periconceptional Multivitamin Use." Cleft Palate-Craniofacial Journal 35, no. 4 (July 1998): 366–70. http://dx.doi.org/10.1597/1545-1569_1998_035_0366_itagoc_2.3.co_2.
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Objective We previously demonstrated a strong association between periconceptional maternal cigarette smoking, infant transforming growth factor–alpha (TGFa) genotype, and risk of orofacial clefts. Because serum folate may be decreased by cigarette smoking and because maternal periconceptional use of multivitamins containing folic acid has been associated with a reduced risk of clefting, we explored whether a potential relation existed between infant TGFa genotype, maternal multivitamin use, and risk of orofacial cleft phenotypes. Design Data were derived from a population-based case–control study of fetuses and live-born infants among a cohort of 1987 to 1989 California births (n = 548,844). Information concerning periconceptional multivitamin use was obtained via telephone interviews with mothers of 731 (84.7% of eligible) orofacial cleft case infants, and of 734 (78.2%) nonmalformed control infants. DNA was obtained from newborn screening bloodspots and genotyped for the Taq1 polymorphism of TGFa. Among infants of interviewed mothers, genotypes were available for 571 (78.1%) case infants and 640 (87.2%) control infants. Setting The study encompassed all hospitals in selected California counties. Main Outcome Measure The main outcome measures were the risks of specific cleft phenotypes among infants with uncommon TGFa genotypes and whose mothers did not use multivitamins periconceptionally. Results Compared with infants homozygous for the common TGFa genotype and whose mothers used multivitamins, increased clefting risks were observed for infants with the A2 genotype (homozygous or heterozygous) and whose mothers did not use multivitamins. Risk estimates were 3.0 (1.4–6.6 [95% confidence interval]) for isolated cleft lip with or without cleft palate (CLP), 2.4 (0.69–11.6) for multiple CLP, 2.6 (0.97–7.7) for isolated cleft palate (CP), 4.2 (1.3–16.2) for multiple CP, and 8.1 (2.6–27.7) for “known-syndrome” clefts. Clefting risks for infants with the A2 genotype and whose mothers used multivitamins were substantially smaller, as were the risks for infants with the A1 genotype whose mothers did not use multivitamins. Conclusion These data provide preliminary evidence for a gene–nutrient interaction in risk of clefting.
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Santos, Ana Paula de Torres, José Eduardo Levi, Marcílio Figueiredo Lemos, Samira Julien Calux, Isabel Takano Oba, and Regina Célia Moreira. "Identification of hepatitis B virus genotypes in the state of São Paulo." Revista da Associação Médica Brasileira 60, no. 5 (October 2014): 424–27. http://dx.doi.org/10.1590/1806-9282.60.05.009.
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Objective: the aim of this study was to identify HBV genotypes in serum samples from patients from the state of São Paulo, received by the viral hepatitis laboratory, at the Virology Centre of Instituto Adolfo Lutz, from various municipalities. Methods: a total of 94 serum samples were randomly analyzed. Genotyping was performed using nested PCR for amplification of S and Pol regions from viral genome. Genotypes were identified comparing the sequences obtained with the sequences deposited in GenBank. Results: we were able to determine the genotype of 91 (97%) samples, as follows: genotype A (55.3%), D (32%), F (5.3%), C (3.2%) and G (1%). There are few data on the epidemiology of genotype G. This genotype has been detected in restricted areas around the world. Frequently, the genotype G infection occurs in HIV-positive male patients. In our case, the sample identified as G was also positive for HIV but in a female patient, which is an uncommon finding in the scientific literature. Conclusion: in this work, we identified the most frequent genotypes in São Paulo as well as the genotype G, rare among the genotypes found in our environment.
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Paudel, Damodar, Myo Nein Aung, Pattaratida Sa-nguanmo, Sushma Suvedi, Anuj Patel, Dipendra Sharma, and Yong Poovorawan. "Diversity of Hepatitis B genotypes in Nepal and updated Phylogenetic Tree: a Pilot Survey in 2012." Journal of Nepal Medical Association 52, no. 196 (December 31, 2014): 986–91. http://dx.doi.org/10.31729/jnma.2799.
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Introduction: Hepatitis B virus is a current global health problem. HBV genotypes influence the treatment and long term outcome of HBV infected patients. Moreover, HBV genotypes differ in various region of the world. Such data was reported haphazardly but yet to be comprehensive for Nepal. This study attempted to find out the diverse hepatitis B genotypes in Nepal.
Methods: A convenient serum sample of 58 HBsAg positive patients from different parts of the country mainly from Nepalgunj, Palpa and Kathmandu were screened for hepatitis B genotype. Sequencing was done and Phylogenetic tree was created.
Results: Among 58 samples, 23 were genotype D, 17were genotype A and B wereC/D recombinant. Phylogenetic trees were created by distance-matrix and neighbor-joining analyses after bootstrapping to 1000 replicates.Discussion: HBV genotypes A and D are the most common genotype in Nepal. Horizontal transmission is common in these genotypes. C/D recombinant genotype may be transmitted from Tibetan people living in Kathmandu. Prophylactic major controlling, horizontal and cross border transmission could be effective.
Conclusions: Three major genotypes of HBV in Nepal were found to be A, C and D. Despite being a low prevalence area, Nepal has a diversity of hepatitis B genotypes.
Keywords: genotypes; HBV; nepal.
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Hemsley, Claudia M., Angela Essex-Lopresti, Isobel H. Norville, and Richard W. Titball. "Correlating Genotyping Data of Coxiella burnetii with Genomic Groups." Pathogens 10, no. 5 (May 14, 2021): 604. http://dx.doi.org/10.3390/pathogens10050604.
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Coxiella burnetii is a zoonotic pathogen that resides in wild and domesticated animals across the globe and causes a febrile illness, Q fever, in humans. Several distinct genetic lineages or genomic groups have been shown to exist, with evidence for different virulence potential of these lineages. Multispacer Sequence Typing (MST) and Multiple-Locus Variable number tandem repeat Analysis (MLVA) are being used to genotype strains. However, it is unclear how these typing schemes correlate with each other or with the classification into different genomic groups. Here, we created extensive databases for published MLVA and MST genotypes of C. burnetii and analysed the associated metadata, revealing associations between animal host and human disease type. We established a new classification scheme that assigns both MST and MLVA genotypes to a genomic group and which revealed additional sub-lineages in two genomic groups. Finally, we report a novel, rapid genomotyping method for assigning an isolate into a genomic group based on the Cox51 spacer sequence. We conclude that by pooling and streamlining existing datasets, associations between genotype and clinical outcome or host source were identified, which in combination with our novel genomotyping method, should enable an estimation of the disease potential of new C. burnetii isolates.
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Yang, Wenqian, Yanbo Yang, Cecheng Zhao, Kun Yang, Dongyang Wang, Jiajun Yang, Xiaohui Niu, and Jing Gong. "Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation." Nucleic Acids Research 48, no. D1 (October 4, 2019): D659—D667. http://dx.doi.org/10.1093/nar/gkz854.
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Abstract Animal-ImputeDB (http://gong_lab.hzau.edu.cn/Animal_ImputeDB/) is a public database with genomic reference panels of 13 animal species for online genotype imputation, genetic variant search, and free download. Genotype imputation is a process of estimating missing genotypes in terms of the haplotypes and genotypes in a reference panel. It can effectively increase the density of single nucleotide polymorphisms (SNPs) and thus can be widely used in large-scale genome-wide association studies (GWASs) using relatively inexpensive and low-density SNP arrays. However, most animals except humans lack high-quality reference panels, which greatly limits the application of genotype imputation in animals. To overcome this limitation, we developed Animal-ImputeDB, which is dedicated to collecting genotype data and whole-genome resequencing data of nonhuman animals from various studies and databases. A computational pipeline was developed to process different types of raw data to construct reference panels. Finally, 13 high-quality reference panels including ∼400 million SNPs from 2265 samples were constructed. In Animal-ImputeDB, an easy-to-use online tool consisting of two popular imputation tools was designed for the purpose of genotype imputation. Collectively, Animal-ImputeDB serves as an important resource for animal genotype imputation and will greatly facilitate research on animal genomic selection and genetic improvement.
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Gao, Yingjie, Zhiquan Yang, Wenqian Yang, Yanbo Yang, Jing Gong, Qing-Yong Yang, and Xiaohui Niu. "Plant-ImputeDB: an integrated multiple plant reference panel database for genotype imputation." Nucleic Acids Research 49, no. D1 (November 2, 2020): D1480—D1488. http://dx.doi.org/10.1093/nar/gkaa953.
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Abstract Genotype imputation is a process that estimates missing genotypes in terms of the haplotypes and genotypes in a reference panel. It can effectively increase the density of single nucleotide polymorphisms (SNPs), boost the power to identify genetic association and promote the combination of genetic studies. However, there has been a lack of high-quality reference panels for most plants, which greatly hinders the application of genotype imputation. Here, we developed Plant-ImputeDB (http://gong_lab.hzau.edu.cn/Plant_imputeDB/), a comprehensive database with reference panels of 12 plant species for online genotype imputation, SNP and block search and free download. By integrating genotype data and whole-genome resequencing data of plants from various studies and databases, the current Plant-ImputeDB provides high-quality reference panels of 12 plant species, including ∼69.9 million SNPs from 34 244 samples. It also provides an easy-to-use online tool with the option of two popular tools specifically designed for genotype imputation. In addition, Plant-ImputeDB accepts submissions of different types of genomic variations, and provides free and open access to all publicly available data in support of related research worldwide. In general, Plant-ImputeDB may serve as an important resource for plant genotype imputation and greatly facilitate the research on plant genetic research.