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Journal articles on the topic 'SNP Genotyping Arrays'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Wells, William. "SNP genotyping with arrays." Genome Biology 1 (2000): spotlight—20001019–01. http://dx.doi.org/10.1186/gb-spotlight-20001019-01.

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2

Yau, C., and C. C. Holmes. "CNV discovery using SNP genotyping arrays." Cytogenetic and Genome Research 123, no. 1-4 (2008): 307–12. http://dx.doi.org/10.1159/000184722.

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3

Lamy, Philippe, Claus L. Andersen, Friedrik P. Wikman, and Carsten Wiuf. "Genotyping and annotation of Affymetrix SNP arrays." Nucleic Acids Research 34, no. 14 (2006): e100-e100. http://dx.doi.org/10.1093/nar/gkl475.

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4

Bianchi, Davide, Lucio Brancadoro, and Gabriella De Lorenzis. "Genetic Diversity and Population Structure in a Vitis spp. Core Collection Investigated by SNP Markers." Diversity 12, no. 3 (2020): 103. http://dx.doi.org/10.3390/d12030103.

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Single nucleotide polymorphism (SNP) genotyping arrays are powerful tools to measure the level of genetic polymorphism within a population. The coming of next-generation sequencing technologies led to identifying thousands and millions of SNP loci useful in assessing the genetic diversity. The Vitis genotyping array, containing 18k SNP loci, has been developed and used to detect genetic diversity of Vitis vinifera germplasm. So far, this array was not validated on non-vinifera genotypes used as grapevine rootstocks. In this work, a core collection of 70 grapevine rootstocks, composed of indivi

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5

Ganal, Martin W., Andreas Polley, Eva-Maria Graner, et al. "Large SNP arrays for genotyping in crop plants." Journal of Biosciences 37, no. 5 (2012): 821–28. http://dx.doi.org/10.1007/s12038-012-9225-3.

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6

Shen, Richard, Jian-Bing Fan, Derek Campbell, et al. "High-throughput SNP genotyping on universal bead arrays." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 573, no. 1-2 (2005): 70–82. http://dx.doi.org/10.1016/j.mrfmmm.2004.07.022.

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7

Lapègue, S., E. Harrang, S. Heurtebise, et al. "Development of SNP-genotyping arrays in two shellfish species." Molecular Ecology Resources 14, no. 4 (2014): 820–30. http://dx.doi.org/10.1111/1755-0998.12230.

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8

Vogel, Ivan, Lishan Cai, Lea Jerman-Plesec, and Eva R. Hoffmann. "SureTypeSCR: R package for rapid quality control and genotyping of SNP arrays from single cells." F1000Research 10 (September 21, 2021): 953. http://dx.doi.org/10.12688/f1000research.53287.1.

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Genotyping of single cells using single nucleotide polymorphism arrays is a cost-effective technology that provides good coverage and precision, but requires whole genome amplification (WGA) due to the low amount of genetic material. Since WGA introduces noise, we recently developed SureTypeSC, an algorithm to minimize genotyping errors. Here, we present SureTypeSCR, an R package that integrates a state-of-the-art algorithm (SureTypeSC) for noise reduction in single cell genotyping and unites all common parts of genotyping workflow in a single tool. SureTypeSCR is built on top of the tidyverse

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9

Straub, T. M., M. D. Quinonez-Diaz, C. O. Valdez, D. R. Call, and D. P. Chandler. "Using DNA microarrays to detect multiple pathogen threats in water." Water Supply 4, no. 2 (2004): 107–14. http://dx.doi.org/10.2166/ws.2004.0035.

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We present four studies that illustrate the use of DNA microarrays for the detection and subsequent genotyping of waterborne pathogens. A genotyping array targeting four virulence factor genes in enterohemorrhagic Escherichia coli (EHEC) was tested. The arrays were clearly able to differentiate between E. coli O157:H7 genotypes and E. coli O91:H2. Non-pathogenic E. coli and non-target organisms were not detected on this array. In the second study, an hsp70 gene single nucleotide polymorphism (SNP) array for specific Cryptosporidium parvum detection was constructed to differentiate between prin

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10

Jankowska, Anna M., Bartlomiej P. Przychodzen, Lukasz P. Gondek, and Jaroslaw P. Maciejewski. "SNP Arrays Facilitate Genotyping of Non-Synonymous SNP in MDS To Identify Disease Susceptibility Loci." Blood 110, no. 11 (2007): 2421. http://dx.doi.org/10.1182/blood.v110.11.2421.2421.

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Abstract Myelodysplastic syndrome (MDS) is a clonal premalignant disease of hematopoietic stem cells characterized by cytopenias and predilection to acute myeloid leukemia (AML). While various exogenous factors (exemplified by chemotherapy-related MDS) constitute known risks for the development of MDS, it is possible that despite long latency, complex genetic traits contribute to MDS susceptibility. Such heritable factors include genes involving DNA repair, apoptosis, senescence, carcinogen catabolism and immune surveillance. Previously, disease association studies were mainly empiric and reli

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11

Vogel, Ivan, Robert C. Blanshard, and Eva R. Hoffmann. "SureTypeSC—a Random Forest and Gaussian mixture predictor of high confidence genotypes in single-cell data." Bioinformatics 35, no. 23 (2019): 5055–62. http://dx.doi.org/10.1093/bioinformatics/btz412.

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Abstract Motivation Accurate genotyping of DNA from a single cell is required for applications such as de novo mutation detection, linkage analysis and lineage tracing. However, achieving high precision genotyping in the single-cell environment is challenging due to the errors caused by whole-genome amplification. Two factors make genotyping from single cells using single nucleotide polymorphism (SNP) arrays challenging. The lack of a comprehensive single-cell dataset with a reference genotype and the absence of genotyping tools specifically designed to detect noise from the whole-genome ampli

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12

Tait, Rich, Ryan Ferretti, Barry Simpson, et al. "34 Present and future of genomic test reporting in the cattle industry." Journal of Animal Science 97, Supplement_2 (2019): 19–20. http://dx.doi.org/10.1093/jas/skz122.036.

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Abstract A series of custom low density (LD) SNP genotyping platforms have been created over the years. Recognized by the GeneSeek Genomic Profiler (GGP) nomenclature, these SNP arrays have increased in size as new versions were created, such as: GGP-LD-v1 (n = 8,762), GGP-LD-v2 (n = 20,057), GGP-LD-v3 (n = 26,151), GGP-LD-v4 (n = 30,108), and GGP Bovine 50K (n = 47,843), all of which contained a base of the Illumina Bovine LD array (n = 7,931) and then added SNPs to provide maximum information content (Shannon Entropy) and optimal genomic coverage into target populations without specific rest

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13

Hong, Huixiao, Lei Xu, Jie Liu, et al. "Technical Reproducibility of Genotyping SNP Arrays Used in Genome-Wide Association Studies." PLoS ONE 7, no. 9 (2012): e44483. http://dx.doi.org/10.1371/journal.pone.0044483.

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14

Huggins, Richard, Ling-Hui Li, You-Chin Lin, Alice L. Yu, and Hsin-Chou Yang. "Nonparametric estimation of LOH using Affymetrix SNP genotyping arrays for unpaired samples." Journal of Human Genetics 53, no. 11-12 (2008): 983–90. http://dx.doi.org/10.1007/s10038-008-0340-9.

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15

Sanada, Masashi, Yasuhito Nannya, Kumi Nakazaki, et al. "Genome-Wide Analysis of Copy Number Analysis of Myelodysplastic Syndromes Using High-Density SNP-Genotyping Microarrays." Blood 106, no. 11 (2005): 3420. http://dx.doi.org/10.1182/blood.v106.11.3420.3420.

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Abstract Myelodysplastic syndromes (MDS) are clonal disorders of hematopoietic progenitors characterized by impaired blood cell production due to ineffective hematopoiesis and high propensity to acute myeloid leukemias. One of the prominent features of MDS is the high frequency of unbalanced chromosomal abnormalities that result in genetic imbalances and copy number alterations. Although the chromosomal segments involved in these abnormalities are thought to contain relevant genes to the pathogenesis of MDS, conventional analyses including FISH have failed to identify critical regions small en

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16

Moser, Daniel W., Stephen P. Miller, Kelli J. Retallick, Duc Lu, and Larry A. Kuehn. "52 Genomic selection in the beef industry: Current achievements and future directions." Journal of Animal Science 97, Supplement_3 (2019): 54–55. http://dx.doi.org/10.1093/jas/skz258.110.

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Abstract In the past decade, genomic testing of beef cattle has evolved from applications in research to a routine practice for many beef cattle seedstock breeders. Testing for lethal genetic conditions or parentage was many breeders’ first experience with genomic testing. While the American Angus Association (AAA) began utilizing 384 SNP genotypes in genetic evaluations in 2009, the adoption of genotyping with higher density (~50,000 SNP) arrays by AAA in 2010 launched large-scale genotyping of Angus cattle for genetic evaluation. AAA transitioned from semi-annual to weekly genetic evaluation

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17

SINOQUET, CHRISTINE. "ITERATIVE TWO-PASS ALGORITHM FOR MISSING DATA IMPUTATION IN SNP ARRAYS." Journal of Bioinformatics and Computational Biology 07, no. 05 (2009): 833–52. http://dx.doi.org/10.1142/s0219720009004357.

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Though nowadays high-throughput genotyping techniques' quality improves, missing data still remains fairly common. Studies have shown that even a low percentage of missing SNPs is detrimental to the reliability of down-stream analyses such as SNP-disease association tests. This paper investigates the potentiality for improving the accuracy of an SNP inference method based on the algorithm formerly designed by Roberts and co-workers (NPUTE, 2007). This initial algorithm performs a single scan of an SNP array, inferring missing SNPs in the context of sliding windows. We have first designed a var

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18

Ballesta, Paulina, David Bush, Fabyano Fonseca Silva, and Freddy Mora. "Genomic Predictions Using Low-Density SNP Markers, Pedigree and GWAS Information: A Case Study with the Non-Model Species Eucalyptus cladocalyx." Plants 9, no. 1 (2020): 99. http://dx.doi.org/10.3390/plants9010099.

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High-throughput genotyping techniques have enabled large-scale genomic analysis to precisely predict complex traits in many plant species. However, not all species can be well represented in commercial SNP (single nucleotide polymorphism) arrays. In this study, a high-density SNP array (60 K) developed for commercial Eucalyptus was used to genotype a breeding population of Eucalyptus cladocalyx, yielding only ~3.9 K informative SNPs. Traditional Bayesian genomic models were investigated to predict flowering, stem quality and growth traits by considering the following effects: (i) polygenic bac

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19

Dong, K., Y. Pu, N. Yao, et al. "Copy number variation detection using SNP genotyping arrays in three Chinese pig breeds." Animal Genetics 46, no. 2 (2015): 101–9. http://dx.doi.org/10.1111/age.12247.

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20

Wu, X. ‐L, J. Xu, H. Li, et al. "Evaluation of genotyping concordance for commercial bovine SNP arrays using quality‐assurance samples." Animal Genetics 50, no. 4 (2019): 367–71. http://dx.doi.org/10.1111/age.12800.

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21

Smith, Edward M., Jack Littrell, and Michael Olivier. "Automated SNP Genotype Clustering Algorithm to Improve Data Completeness in High-Throughput SNP Genotyping Datasets from Custom Arrays." Genomics, Proteomics & Bioinformatics 5, no. 3-4 (2007): 256–59. http://dx.doi.org/10.1016/s1672-0229(08)60014-5.

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22

Li, Ming, Yalu Wen, and Wenjiang Fu. "A Single-Array-Based Method for Detecting Copy Number Variants Using Affymetrix High Density SNP Arrays and its Application to Breast Cancer." Cancer Informatics 13s4 (January 2014): CIN.S15203. http://dx.doi.org/10.4137/cin.s15203.

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Cumulative evidence has shown that structural variations, due to insertions, deletions, and inversions of DNA, may contribute considerably to the development of complex human diseases, such as breast cancer. High-throughput genotyping technologies, such as Affymetrix high density single-nucleotide polymorphism (SNP) arrays, have produced large amounts of genetic data for genome-wide SNP genotype calling and copy number estimation. Meanwhile, there is a great need for accurate and efficient statistical methods to detect copy number variants. In this article, we introduce a hidden-Markov-model (

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23

Klitø, Niels G. F., Qihua Tan, Mette Nyegaard, et al. "Arrayed Primer Extension in the “Array of Arrays” Format: A Rational Approach for Microarray-Based SNP Genotyping." Genetic Testing 11, no. 2 (2007): 160–66. http://dx.doi.org/10.1089/gte.2007.9998.

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24

Wang, Jiying, Jicai Jiang, Weixuan Fu, et al. "A genome-wide detection of copy number variations using SNP genotyping arrays in swine." BMC Genomics 13, no. 1 (2012): 273. http://dx.doi.org/10.1186/1471-2164-13-273.

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25

Muto, Satsuki, Go Yamamoto, Yasuhito Nannya, et al. "Molecular Allelo-Karyotyping of Adult T-Cell Leukemia Using High SNP Genotyping Microarrays." Blood 110, no. 11 (2007): 2385. http://dx.doi.org/10.1182/blood.v110.11.2385.2385.

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Abstract Adult T cell leukemia/lymphoma (ATL) is a mature T-cell neoplasm in adult that is caused by human T-cell leukemia virus type 1 (HTLV-1) and highly intractable to conventional therapeutics. Since there are 1.2 million HTLV-1 carriers in Japan and more than 50,000 carriers are expected to develop ATL from now on, it is of particular importance to understand the pathogenesis of ATL. The malignant processes of T-cell transformation in ATL are initiated by HTLV-1 infection in early childhood, and the HTLV-1 infected and immortalized T-cells are thought to accumulate a series of genetic hit

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26

Mitry, D., H. Campbell, D. G. Charteris, et al. "SNP mistyping in genotyping arrays-an important cause of spurious association in case-control studies." Genetic Epidemiology 35, no. 5 (2011): 423–26. http://dx.doi.org/10.1002/gepi.20559.

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27

Wang, Jiying, Haifei Wang, Jicai Jiang, et al. "Identification of Genome-Wide Copy Number Variations among Diverse Pig Breeds Using SNP Genotyping Arrays." PLoS ONE 8, no. 7 (2013): e68683. http://dx.doi.org/10.1371/journal.pone.0068683.

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28

Conlin, Laura K., Minjie Luo, Brooke Weckselblatt, et al. "34. Genome-wide mosaicism, chimerism, and contamination: Recognizing and interpreting genotyping patterns from SNP arrays." Cancer Genetics 226-227 (October 2018): 49. http://dx.doi.org/10.1016/j.cancergen.2018.04.095.

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29

Di Gerlando, Rosalia, Salvatore Mastrangelo, Maria Teresa Sardina, et al. "A Genome-Wide Detection of Copy Number Variations Using SNP Genotyping Arrays in Braque Français Type Pyrénées Dogs." Animals 9, no. 3 (2019): 77. http://dx.doi.org/10.3390/ani9030077.

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Copy number variants (CNVs) are an important source of genetic variation complementary to single nucleotide polymorphisms (SNPs). Only few studies have been conducted in dogs on CNVs derived from high-density SNP array data, and many canine breeds still remain uncharacterized, e.g., the Braque Français, type Pyrénées breed (BRA). Therefore, in an effort to more comprehensively investigate the canine genome for CNVs, we used a high-density SNP array (170 K) to discover CNVs in BRA. The CNV regions (CNVRs) were identified through the merging of two different CNVRs datasets, obtained separately f

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30

Chu, Y., C. C. Holbrook, T. G. Isleib, et al. "Phenotyping and genotyping parents of sixteen recombinant inbred peanut populations." Peanut Science 45, no. 1 (2018): 1–11. http://dx.doi.org/10.3146/ps17-17.1.

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ABSTRACT In peanut (Arachis hypogaea L.), most agronomically important traits such as yield, disease resistance, and pod and kernel characteristics are quantitatively inherited. Phenotypic selection of these traits in peanut breeding programs can be augmented by marker-assisted selection. However, reliable associations between unambiguous genetic markers and phenotypic traits have to be established by genetic mapping prior to early generation marker-assisted selection. Previously, a nested association mapping (NAM) population of 16 recombinant inbred line populations (RILs) consisting 4870 lin

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31

Huh, Jungwon, Lukasz Gondek, Christine O’Keefe, Karl S. Theil, and Jaroslaw P. Maciejewski. "Using Combined High Density SNP/CNV Arrays as a Clinical Karyotyping Tool in Myeloid Malignancies." Blood 112, no. 11 (2008): 1504. http://dx.doi.org/10.1182/blood.v112.11.1504.1504.

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Abstract We have evaluated various types of single nucleotide polymorphism arrays (SNP-A) as a karyotyping platform in over 600 cases of bone marrow failure and various myeloid disorders including MDS, MDS/MPD, and AML and in over 360 controls. We have shown that SNP-A not only reliably confirms chromosome gains and losses identified by metaphase cytogenetics (MC) but also allows for detection of previously cryptic chromosomal lesions. Moreover, through the ability of combining copy number measurement with genotyping, SNP-A also enables detection of copy-neutral loss of heterozygosity (LOH), a

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32

Valsesia, Armand, Brian J. Stevenson, Dawn Waterworth, et al. "Identification and validation of copy number variants using SNP genotyping arrays from a large clinical cohort." BMC Genomics 13, no. 1 (2012): 241. http://dx.doi.org/10.1186/1471-2164-13-241.

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33

Yu, Yongtao, Alexander S. Baras, Kanemitsu Shirasuna, Henry F. Frierson, and Christopher A. Moskaluk. "Concurrent loss of heterozygosity and copy number analysis in adenoid cystic carcinoma by SNP genotyping arrays." Laboratory Investigation 87, no. 5 (2007): 430–39. http://dx.doi.org/10.1038/labinvest.3700536.

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34

Zhou, Wei, Ranran Liu, Jingjing Zhang, et al. "A genome-wide detection of copy number variation using SNP genotyping arrays in Beijing-You chickens." Genetica 142, no. 5 (2014): 441–50. http://dx.doi.org/10.1007/s10709-014-9788-z.

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35

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 (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

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36

Wang, N., Y. Z. Xie, Y. Z. Li, S. N. Wu, H. S. Wei, and C. S. Wang. "Molecular mapping of a novel early leaf-senescence gene Els2 in common wheat by SNP genotyping arrays." Crop and Pasture Science 71, no. 4 (2020): 356. http://dx.doi.org/10.1071/cp19435.

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Early leaf senescence in wheat (Triticum aestivum L.) is one of the limiting factors for developing high yield potential. In this study, a stably inherited, early leaf-senescence mutant LF2099 was initially identified in an M2 population of the common wheat accession H261 after ethyl methanesulfonate (EMS) mutagenesis. Early leaf senescence was observed in the LF2099 mutant during the three-leaf-stage, and then the etiolated area of the wheat leaf increased gradually from the bottom to the top throughout development. Compared with H261, the chlorophyll (Chl a, Chl b) and carotenoid contents an

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37

Sellick, G. S. "Genomewide linkage searches for Mendelian disease loci can be efficiently conducted using high-density SNP genotyping arrays." Nucleic Acids Research 32, no. 20 (2004): e164-e164. http://dx.doi.org/10.1093/nar/gnh163.

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38

Shapero, M. H. "MARA: a novel approach for highly multiplexed locus-specific SNP genotyping using high-density DNA oligonucleotide arrays." Nucleic Acids Research 32, no. 22 (2004): e181-e181. http://dx.doi.org/10.1093/nar/gnh178.

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39

Maciejewski, Jaroslaw P., and Ghulam J. Mufti. "Whole genome scanning as a cytogenetic tool in hematologic malignancies." Blood 112, no. 4 (2008): 965–74. http://dx.doi.org/10.1182/blood-2008-02-130435.

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Abstract Over the years, methods of cytogenetic analysis evolved and became part of routine laboratory testing, providing valuable diagnostic and prognostic information in hematologic disorders. Karyotypic aberrations contribute to the understanding of the molecular pathogenesis of disease and thereby to rational application of therapeutic modalities. Most of the progress in this field stems from the application of metaphase cytogenetics (MC), but recently, novel molecular technologies have been introduced that complement MC and overcome many of the limitations of traditional cytogenetics, inc

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40

Poulain, Stephanie, Christophe Roumier, Meyling Cheok, et al. "Genome Wide SNP Analysis Reveals Frequent Cryptic Clonal Chromosomal Aberrations Including Uniparental Disomy (UPD) in Waldenstrom's Macroglobulinemia." Blood 114, no. 22 (2009): 3932. http://dx.doi.org/10.1182/blood.v114.22.3932.3932.

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Abstract Abstract 3932 Poster Board III-868 Background Waldenstrom's macroglobulinemia (WM) is a rare lymphoproliferative disorder characterized by bone marrow (BM) infiltration of lymphoplasmacytic cells that secrete monoclonal IgM antibody. Approximately 50% of patients (pts) with WM exhibit a normal karyotype using either conventional chromosome banding analysis (CBA) or FISH approach. However, CBA is a low resolution method and FISH only target previously described abnormalities. Comparative genomic hybridization (CGH) array delineated the minimal deleted region on 6q deletion, the most fr

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41

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 (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 re

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42

Kuroiwa, Tsukasa. "Poster 036: Analysis of Whole Genome Using Single Nucleotide Polymorphism (SNP) Genotyping Arrays in Tongue Squamous Cell Carcinoma." Journal of Oral and Maxillofacial Surgery 65, no. 9 (2007): 43.e20. http://dx.doi.org/10.1016/j.joms.2007.06.305.

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43

Jobs, M. "DASH-2: Flexible, Low-Cost, and High-Throughput SNP Genotyping by Dynamic Allele-Specific Hybridization on Membrane Arrays." Genome Research 13, no. 5 (2003): 916–24. http://dx.doi.org/10.1101/gr.801103.

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44

Wang, Ligang, Xin Liu, Longchao Zhang, et al. "Genome-Wide Copy Number Variations Inferred from SNP Genotyping Arrays Using a Large White and Minzhu Intercross Population." PLoS ONE 8, no. 10 (2013): e74879. http://dx.doi.org/10.1371/journal.pone.0074879.

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45

Perez-Enciso, Miguel. "229 DNA sequence assisted prediction: the uncomfortable truth." Journal of Animal Science 97, Supplement_3 (2019): 55. http://dx.doi.org/10.1093/jas/skz258.112.

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Abstract Using whole genome sequence for improving genomic prediction relative to that from high density SNP arrays has been well below expectations, despite some overoptimistic computer simulations. Why is this so? First, NGS data are massive, noisy and their computer bioinformatics analysis is expensive when applied to the scale needed in animal breeding. SNP calling is a tricky procedure that is especially sensitive to low depth sequencing. This makes it NGS data far more expensive than array genotyping. Second, rare variants are the most frequent class of variants. Population genetics theo

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46

Takita, Junko, Motohiro Kato, Fumihiko Nakamura, et al. "High-Resolution Analyses of Genetic and Epigenetic Aberrations in Infant Leukemia with MLL Rearrangement." Blood 110, no. 11 (2007): 4238. http://dx.doi.org/10.1182/blood.v110.11.4238.4238.

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Abstract MLL rearrangement-positive leukemia is one of the most aggressive types of leukemia. It is diagnosed predominantly in infants and typically shows a multilineage phenotype. Since current chemotherapy fails in more than 50% of infantile leukemia with MLL rearrangement, a better understanding of biological features of the disease is importantly in order to develop more specific and successful treatment strategies. Thus, to explore both genetic and epigenetic lesions associated with MLL rearrangement-positive infantile leukemia, we performed genome-wide analyses of copy number alterations

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47

Mohamedali, Azim, Joop Gäken, Natalie A. Twine, et al. "Prevalence and prognostic significance of allelic imbalance by single-nucleotide polymorphism analysis in low-risk myelodysplastic syndromes." Blood 110, no. 9 (2007): 3365–73. http://dx.doi.org/10.1182/blood-2007-03-079673.

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Abstract Low-risk myelodysplastic syndrome (MDS) with normal cytogenetics accounts for approximately 50% of MDS patients. There are no pathognomonic markers in these cases and the diagnosis rests on cytomorphologic abnormalities in bone marrow and/or peripheral blood. Affymetrix high-resolution single-nucleotide polymorphism (SNP) genotyping microarrays allow detection of cytogenetically cryptic genomic aberrations. We have studied 119 low-risk MDS patients (refractory anemia [RA] = 22; refractory cytopenia with multilineage dysplasia [RCMD] = 51; refractory anemia with ringed sideroblasts [RA

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48

Cluzeau, Thomas, Chimène Moreilhon, Nicolas Mounier, et al. "Total Genomic Loss Detected by High-Density Single Nucleotide Polymorphism Array Is Predictive of Azacitidine Response in Very Poor IPSS-Revised MDS or AML Patients." Blood 120, no. 21 (2012): 4936. http://dx.doi.org/10.1182/blood.v120.21.4936.4936.

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Abstract Abstract 4936 Background: Azacitidine (AZA) has changed the outcome of patients with myelodysplastic syndromes (MDS) or acute myeloid leukemia with multi-lineage dysplasia (AML-MLD) unfit for intensive chemotherapy. AZA is a hypomethylating agent providing about 50% of responses in MDS and AML with low blast count (Fenaux et al., Lancet Oncol 2009, JCO 2010). IPSS-R scoring was evaluated in MDS and AML with 20–29% of blasts untreated patients. Conventional cytogenetic have major prognostic interest in this score (Schanz et al., JCO 2012). To date, SNP array analysis are not included i

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Azam, Afifah Binti, and Elena Aisha Binti Azizan. "Brief Overview of a Decade of Genome-Wide Association Studies on Primary Hypertension." International Journal of Endocrinology 2018 (January 30, 2018): 1–14. http://dx.doi.org/10.1155/2018/7259704.

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Primary hypertension is widely believed to be a complex polygenic disorder with the manifestation influenced by the interactions of genomic and environmental factors making identification of susceptibility genes a major challenge. With major advancement in high-throughput genotyping technology, genome-wide association study (GWAS) has become a powerful tool for researchers studying genetically complex diseases. GWASs work through revealing links between DNA sequence variation and a disease or trait with biomedical importance. The human genome is a very long DNA sequence which consists of billi

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Stone, Brad, Scott Graves, Arnold Kas, et al. "Direct Genotyping of Coding Non-Synonymous SNPs for Identification of Novel Minor Histocompatibility Antigens." Blood 108, no. 11 (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 a

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