Whole-genome genotyping.
paper
Cited
Public
Unavailable
- Authors
- Gunderson, Kevin L; Steemers, Frank J; Ren, Hongi; Ng, Pauline; Zhou, Lixin; Tsan, Chan; Chang, Weihua; Bullis, Dave; Musmacker, Joe; King, Christine; Lebruska, Lori L; Barker, David; Oliphant, Arnold; Kuhn, Kenneth M; Shen, Richard
- Year
- 2006
- Journal
- Methods in enzymology
- PMID
- 16938560
- DOI
- 10.1016/S0076-6879(06)10017-8
We have developed an array-based whole-genome genotyping (WGG) assay (Infinium) using our BeadChip platform that effectively enables unlimited multiplexing and unconstrained single nucleotide polymorphism (SNP) selection. A single tube whole-genome amplification reaction is used to amplify the genome, and loci of interest are captured by specific hybridization of amplified gDNA to 50-mer probe arrays. After target capture, SNPs are genotyped on the array by a primer extension reaction in the presence of hapten-labeled nucleotides. The resultant signal is amplified during staining and the array is read out on a high-resolution confocal scanner. We have employed our high-density BeadChips supporting up to 288,000 bead types to create an array that can query over 100,000 SNPs using the Infinium assay. In addition, we have developed an automated BeadChip processing platform using Tecan's GenePaint slide processing system. Hybridization, washing, array-based primer extension, and staining are performed directly in Tecan's capillary gap Te-Flow chambers. This automation process increases assay robustness and throughput greatly while enabling laboratory information management system control of sample tracking.
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| Gene-Based Elevated Triglycerides and Type 2 Diabetes Mellitus Risk in the Women's Genome Health Study. | Ahmad S et al. | — | 2019 | → |
| Genome-Wide Association Study Identifies Loci for Liver Enzyme Concentrations in Mexican Americans: The GUARDIAN Consortium. | Young KA et al. | — | 2019 | → |
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| Adiposity and Genetic Factors in Relation to Triglycerides and Triglyceride-Rich Lipoproteins in the Women's Genome Health Study. | Ahmad S et al. | — | 2018 | → |
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| The iPSYCH2012 case-cohort sample: new directions for unravelling genetic and environmental architectures of severe mental disorders. | Pedersen CB et al. | — | 2018 | → |
| Genome-Wide Associations Related to Hepatic Histology in Nonalcoholic Fatty Liver Disease in Hispanic Boys. | Wattacheril J et al. | — | 2017 | → |
| Polymorphisms in PDLIM5 gene are associated with alcohol dependence, type 2 diabetes, and hypertension. | Owusu D et al. | — | 2017 | → |
| Using Patterns of Genetic Association to Elucidate Shared Genetic Etiologies Across Psychiatric Disorders. | Cho SB et al. | — | 2017 | → |
| Variation in SWI/SNF Chromatin Remodeling Complex Proteins is Associated with Alcohol Dependence and Antisocial Behavior in Human Populations. | Mathies LD et al. | — | 2017 | → |
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| Quality control, imputation and analysis of genome-wide genotyping data from the Illumina HumanCoreExome microarray. | Coleman JR et al. | — | 2016 | → |
| Genetic mapping in grapevine using SNP microarray intensity values | Myles S et al. | — | 2015 | — |
| Genetic Variants Associated With Quantitative Glucose Homeostasis Traits Translate to Type 2 Diabetes in Mexican Americans: The GUARDIAN (Genetics Underlying Diabetes in Hispanics) Consortium. | Palmer ND et al. | — | 2015 | → |
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| Multiplexed genotyping of Bacillus anthracis by Luminex xMap suspension array. | Thierry S et al. | — | 2015 | → |
| Systems Genetics Reveals the Functional Context of PCOS Loci and Identifies Genetic and Molecular Mechanisms of Disease Heterogeneity. | Jones MR et al. | — | 2015 | → |
| Common genetic variations in the vitamin D pathway in relation to blood pressure. | Wang L et al. | — | 2014 | → |
| Expression of myeloperoxidase in acute myeloid leukemia blasts mirrors the distinct DNA methylation pattern involving the downregulation of DNA methyltransferase DNMT3B. | Itonaga H et al. | — | 2014 | → |
| A multiplex bead-based suspension array assay for interrogation of phylogenetically informative single nucleotide polymorphisms for Bacillus anthracis. | Thierry S et al. | — | 2013 | → |
| Common biological networks underlie genetic risk for alcoholism in African- and European-American populations. | Kos MZ et al. | — | 2013 | → |
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| Genome-wide association study in a Chinese population with diabetic retinopathy. | Sheu WH et al. | — | 2013 | → |
| Overview of DNA microarrays: types, applications, and their future. | Bumgarner R | — | 2013 | → |
| Systematic evaluation of validated type 2 diabetes and glycaemic trait loci for association with insulin clearance. | Goodarzi MO et al. | — | 2013 | → |
| Tomato breeding in the genomics era: insights from a SNP array. | Víquez-Zamora M et al. | — | 2013 | → |
| Trans-ethnic fine mapping identifies a novel independent locus at the 3' end of CDKAL1 and novel variants of several susceptibility loci for type 2 diabetes in a Han Chinese population. | Kuo JZ et al. | — | 2013 | → |
| A genome-wide association study identifies a potential novel gene locus for keratoconus, one of the commonest causes for corneal transplantation in developed countries. | Li X et al. | — | 2012 | → |
| Colorectal cancer linkage on chromosomes 4q21, 8q13, 12q24, and 15q22. | Cicek MS et al. | — | 2012 | → |
| Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma. | Wiggs JL et al. | — | 2012 | → |
| Identifying breast cancer risk loci by global differential allele-specific expression (DASE) analysis in mammary epithelial transcriptome. | Gao C et al. | — | 2012 | → |
| Large SNP arrays for genotyping in crop plants. | Ganal MW et al. | — | 2012 | → |
| Metabolic and cardiovascular genes in polycystic ovary syndrome: a candidate-wide association study (CWAS). | Jones MR et al. | — | 2012 | → |
| Replication of association of DENND1A and THADA variants with polycystic ovary syndrome in European cohorts. | Goodarzi MO et al. | — | 2012 | → |
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| Association of polymorphisms in the hepatocyte growth factor gene promoter with keratoconus. | Burdon KP et al. | — | 2011 | → |
| Buffy coat specimens remain viable as a DNA source for highly multiplexed genome-wide genetic tests after long term storage. | Mychaleckyj JC et al. | — | 2011 | → |
| Copy number variation in familial Parkinson disease. | Pankratz N et al. | — | 2011 | → |
| Discovery and replication of novel blood pressure genetic loci in the Women's Genome Health Study. | Ho JE et al. | — | 2011 | → |
| FTO and MC4R gene variants are associated with obesity in polycystic ovary syndrome. | Ewens KG et al. | — | 2011 | → |
| Genome-wide association study of theta band event-related oscillations identifies serotonin receptor gene HTR7 influencing risk of alcohol dependence. | Zlojutro M et al. | — | 2011 | → |
| Genomewide linkage study of modifiers of LRRK2-related Parkinson's disease. | Latourelle JC et al. | — | 2011 | → |
| High density DNA methylation array with single CpG site resolution. | Bibikova M et al. | — | 2011 | → |
| Replication of association of a novel insulin receptor gene polymorphism with polycystic ovary syndrome. | Goodarzi MO et al. | — | 2011 | → |
| SDM--a server for predicting effects of mutations on protein stability and malfunction. | Worth CL et al. | — | 2011 | → |
| SNPPicker: high quality tag SNP selection across multiple populations. | Sicotte H et al. | — | 2011 | → |
| Strategies for genotyping. | Crawford DC et al. | — | 2011 | → |
| Type 2 diabetes susceptibility single-nucleotide polymorphisms are not associated with polycystic ovary syndrome. | Ewens KG et al. | — | 2011 | → |
| Variants in ZNF365 isoform D are associated with Crohn's disease. | Haritunians T et al. | — | 2011 | → |
| A genome-wide association study of alcohol dependence. | Bierut LJ et al. | — | 2010 | → |
| A genome-wide association study on African-ancestry populations for asthma. | Mathias RA et al. | — | 2010 | → |
| Candidate loci for insulin sensitivity and disposition index from a genome-wide association analysis of Hispanic participants in the Insulin Resistance Atherosclerosis (IRAS) Family Study. | Palmer ND et al. | — | 2010 | → |
| Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease. | McGovern DP et al. | — | 2010 | → |
| Genetic predictors of medically refractory ulcerative colitis. | Haritunians T et al. | — | 2010 | → |
| Genome-wide association study of alcohol dependence implicates a region on chromosome 11. | Edenberg HJ et al. | — | 2010 | → |
| Genome-wide association study of bone mineral density in premenopausal European-American women and replication in African-American women. | Koller DL et al. | — | 2010 | → |
| Genome-wide association study of vitamin D concentrations in Hispanic Americans: the IRAS family study. | Engelman CD et al. | — | 2010 | → |
| High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes. | Fu Y et al. | — | 2010 | → |
| Maternal inheritance and mitochondrial DNA variants in familial Parkinson's disease. | Simon DK et al. | — | 2010 | → |
| Positional effects of polymorphisms in probe-target sequences on genoplot images of oligonucleotide microarrays. | Cui TL et al. | — | 2010 | → |
| A genome-wide association scan for acute insulin response to glucose in Hispanic-Americans: the Insulin Resistance Atherosclerosis Family Study (IRAS FS). | Rich SS et al. | — | 2009 | → |
| A high-throughput assay for rapid and simultaneous analysis of perfect markers for important quality and agronomic traits in rice using multiplexed MALDI-TOF mass spectrometry. | Masouleh AK et al. | — | 2009 | → |
| Genome-wide association study and follow-up analysis of adiposity traits in Hispanic Americans: the IRAS Family Study. | Norris JM et al. | — | 2009 | → |
| Genomewide association study for onset age in Parkinson disease. | Latourelle JC et al. | — | 2009 | → |
| Genomewide association study for susceptibility genes contributing to familial Parkinson disease. | Pankratz N et al. | — | 2009 | → |
| Integrating genomics, proteomics and bioinformatics in translational studies of molecular medicine. | Ostrowski J et al. | — | 2009 | → |
| Introduction to molecular combing: genomics, DNA replication, and cancer. | Herrick J et al. | — | 2009 | → |
| Molecular (SNP) analyses of overlapping hemizygous deletions of 10q25.3 to 10qter in four patients: evidence for HMX2 and HMX3 as candidate genes in hearing and vestibular function. | Miller ND et al. | — | 2009 | → |
| 3q29 interstitial microduplication: a new syndrome in a three-generation family. | Lisi EC et al. | — | 2008 | → |
| Application of machine learning algorithms to predict coronary artery calcification with a sibship-based design. | Sun YV et al. | — | 2008 | → |
| Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. | Hom G et al. | — | 2008 | → |
| FEM1A and FEM1B: novel candidate genes for polycystic ovary syndrome. | Goodarzi MO et al. | — | 2008 | → |
| Genotyping platforms for mass-throughput genotyping with SNPs, including human genome-wide scans. | Maresso K et al. | — | 2008 | → |
| Improvements to bead-based oligonucleotide ligation SNP genotyping assays. | Bruse S et al. | — | 2008 | → |
| Rationale, design, and methodology of the Women's Genome Health Study: a genome-wide association study of more than 25,000 initially healthy american women. | Ridker PM et al. | — | 2008 | → |
| Sequencing breakthroughs for genomic ecology and evolutionary biology. | Hudson ME | — | 2008 | → |
| The environmental genome project: reference polymorphisms for drug metabolism genes and genome-wide association studies. | Rieder MJ et al. | — | 2008 | → |
| A structural bioinformatics approach to the analysis of nonsynonymous single nucleotide polymorphisms (nsSNPs) and their relation to disease. | Worth CL et al. | — | 2007 | → |
| Indel arrays: an affordable alternative for genotyping. | Salathia N et al. | — | 2007 | → |
| Single nucleotide polymorphisms and linkage disequilibrium in sunflower. | Kolkman JM et al. | — | 2007 | → |
| The application of the HapMap to diabetic nephropathy and other causes of chronic renal failure. | Iyengar SK et al. | — | 2007 | → |
| Whole genome genotyping technologies on the BeadArray platform. | Steemers FJ et al. | — | 2007 | → |