Large-scale genotyping of complex DNA.
paper
Cited
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- Authors
- Kennedy, Giulia C; Matsuzaki, Hajime; Dong, Shoulian; Liu, Wei-min; Huang, Jing; Liu, Guoying; Su, Xing; Cao, Manqiu; Chen, Wenwei; Zhang, Jane; Liu, Weiwei; Yang, Geoffrey; Di, Xiaojun; Ryder, Thomas; He, Zhijun; Surti, Urvashi; Phillips, Michael S; Boyce-Jacino, Michael T; Fodor, Stephen P A; Jones, Keith W
- Year
- 2003
- Journal
- Nature biotechnology
- PMID
- 12960966
- DOI
- 10.1038/nbt869
Genetic studies aimed at understanding the molecular basis of complex human phenotypes require the genotyping of many thousands of single-nucleotide polymorphisms (SNPs) across large numbers of individuals. Public efforts have so far identified over two million common human SNPs; however, the scoring of these SNPs is labor-intensive and requires a substantial amount of automation. Here we describe a simple but effective approach, termed whole-genome sampling analysis (WGSA), for genotyping thousands of SNPs simultaneously in a complex DNA sample without locus-specific primers or automation. Our method amplifies highly reproducible fractions of the genome across multiple DNA samples and calls genotypes at >99% accuracy. We rapidly genotyped 14,548 SNPs in three different human populations and identified a subset of them with significant allele frequency differences between groups. We also determined the ancestral allele for 8,386 SNPs by genotyping chimpanzee and gorilla DNA. WGSA is highly scaleable and enables the creation of ultrahigh density SNP maps for use in genetic studies.
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| AccuTyping: new algorithms for automated analysis of data from high-throughput genotyping with oligonucleotide microarrays. | Hu G et al. | — | 2006 | → |
| Acute lymphoblastic leukaemia: a model for the pharmacogenomics of cancer therapy. | Cheok MH et al. | — | 2006 | → |
| A genome-wide linkage search for bipolar disorder susceptibility loci in a large and complex pedigree from the eastern part of Cuba. | Marcheco-Teruel B et al. | — | 2006 | → |
| A genome-wide study of preferential amplification/hybridization in microarray-based pooled DNA experiments. | Yang HC et al. | — | 2006 | → |
| A genotype calling algorithm for affymetrix SNP arrays. | Rabbee N et al. | — | 2006 | → |
| Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan. | Ting JC et al. | — | 2006 | → |
| Application of oligonucleotide arrays to high-content genetic analysis. | Gibson NJ | — | 2006 | → |
| A role for mitotic recombination in leukemogenesis. | Young BD et al. | — | 2006 | → |
| Array-based comparative genomic hybridization and copy number variation in cancer research. | Cho EK et al. | — | 2006 | → |
| A whole genome long-range haplotype (WGLRH) test for detecting imprints of positive selection in human populations. | Zhang C et al. | — | 2006 | → |
| CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays. | Huang J et al. | — | 2006 | → |
| Comparisons of PCR-based genome amplification systems using CpG island microarrays. | Pike BL et al. | — | 2006 | → |
| Complex genomic alterations and gene expression in acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21. | Strefford JC et al. | — | 2006 | → |
| Current concepts in the molecular genetics of pediatric brain tumors: implications for emerging therapies. | Tamber MS et al. | — | 2006 | → |
| Deoxynucleotides can replace dideoxynucleotides in minisequencing by arrayed primer extension. | Tebbutt SJ et al. | — | 2006 | → |
| DNA microarray technology for target identification and validation. | Jayapal M et al. | — | 2006 | → |
| Dynamic variable selection in SNP genotype autocalling from APEX microarray data. | Podder M et al. | — | 2006 | → |
| Estimation of the number of genetic markers required for individual animal identification accounting for genotyping errors. | Weller JI et al. | — | 2006 | → |
| Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. | Komura D et al. | — | 2006 | → |
| Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array. | Hu N et al. | — | 2006 | → |
| Genomic and expression profiling identifies the B-cell associated tyrosine kinase Syk as a possible therapeutic target in mantle cell lymphoma. | Rinaldi A et al. | — | 2006 | → |
| Genomic approaches to lung cancer. | Thomas RK et al. | — | 2006 | → |
| Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription. | Swinburne IA et al. | — | 2006 | → |
| Genomic platforms for cancer research: potential diagnostic and prognostic applications in clinical oncology. | Jares P et al. | — | 2006 | → |
| Genotyping and annotation of Affymetrix SNP arrays. | Lamy P et al. | — | 2006 | → |
| Genotyping technologies for all. | Ragoussis J | — | 2006 | → |
| Highly parallel genomic assays. | Fan JB et al. | — | 2006 | → |
| High-throughput loss-of-heterozygosity study of chromosome 3p in lung cancer using single-nucleotide polymorphism markers. | Tai AL et al. | — | 2006 | → |
| Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays. | Beroukhim R et al. | — | 2006 | → |
| Large-scale characterization of public database SNPs causing non-synonymous changes in three ethnic groups. | Ireland J et al. | — | 2006 | → |
| Localization of breast cancer susceptibility loci by genome-wide SNP linkage disequilibrium mapping. | Ellis NA et al. | — | 2006 | → |
| Molecular karyotyping of human hepatocellular carcinoma using single-nucleotide polymorphism arrays. | Midorikawa Y et al. | — | 2006 | → |
| Nonsynonymous SNPs: validation characteristics, derived allele frequency patterns, and suggestive evidence for natural selection. | Fredman D et al. | — | 2006 | → |
| Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. | Friedman JM et al. | — | 2006 | → |
| Optimal genotype determination in highly multiplexed SNP data. | Moorhead M et al. | — | 2006 | → |
| Pharmacogenomics of acute leukemia. | Cheok MH et al. | — | 2006 | → |
| PQN and DQN: algorithms for expression microarrays. | Liu WM et al. | — | 2006 | → |
| Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. | Lockwood WW et al. | — | 2006 | → |
| Single nucleotide polymorphism array analysis to predict clinical outcome in neuroblastoma patients. | Hiyama E et al. | — | 2006 | → |
| SNP array-based homozygosity mapping reveals MCPH1 deletion in family with autosomal recessive mental retardation and mild microcephaly. | Garshasbi M et al. | — | 2006 | → |
| Strategies for the detection of copy number and other structural variants in the human genome. | Carson AR et al. | — | 2006 | → |
| Structural variation in the human genome. | Feuk L et al. | — | 2006 | → |
| Survey of microarray technologies suitable to elucidate transcriptional networks as exemplified by studying KRAB zinc finger gene families. | Koczan D et al. | — | 2006 | → |
| Technology Insight: querying the genome with microarrays--progress and hope for neurological disease. | Coppola G et al. | — | 2006 | → |
| The affymetrix GeneChip platform: an overview. | Dalma-Weiszhausz DD et al. | — | 2006 | → |
| The power of single-nucleotide polymorphisms for large-scale parentage inference. | Anderson EC et al. | — | 2006 | → |
| Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA. | Pettersson E et al. | — | 2006 | → |
| Using high-throughput SNP technologies to study cancer. | Engle LJ et al. | — | 2006 | → |
| Whole-genome genotyping. | Gunderson KL et al. | — | 2006 | → |
| A genome-wide linkage analysis of alcoholism on microsatellite and single-nucleotide polymorphism data, using alcohol dependence phenotypes and electroencephalogram measures. | Zhang C et al. | — | 2005 | → |
| A genome-wide scalable SNP genotyping assay using microarray technology. | Gunderson KL et al. | — | 2005 | → |
| A genotyping system capable of simultaneously analyzing >1000 single nucleotide polymorphisms in a haploid genome. | Wang HY et al. | — | 2005 | → |
| Allelic dosage analysis with genotyping microarrays. | Ishikawa S et al. | — | 2005 | → |
| ALOHOMORA: a tool for linkage analysis using 10K SNP array data. | Rüschendorf F et al. | — | 2005 | → |
| Alternative base calling method for resequencing microarrays. | Di X et al. | — | 2005 | → |
| Amplification and overexpression of prosaposin in prostate cancer. | Koochekpour S et al. | — | 2005 | → |
| Analysis of single nucleotide polymorphisms in the promoter region of interleukin-10 by denaturing high-performance liquid chromatography. | Guzowski D et al. | — | 2005 | → |
| An integrated microfluidic processor for single nucleotide polymorphism-based DNA computing. | Grover WH et al. | — | 2005 | → |
| Application of genomewide SNP arrays for detection of simulated susceptibility loci. | Kulle B et al. | — | 2005 | → |
| A rapid microarray based whole genome analysis for detection of uniparental disomy. | Altug-Teber O et al. | — | 2005 | → |
| A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. | Nannya Y et al. | — | 2005 | → |
| Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines. | Mund C et al. | — | 2005 | → |
| arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays. | Menten B et al. | — | 2005 | → |
| Association between large-scale genomic homozygosity without chromosomal loss and nonseminomatous germ cell tumor development. | Lu YJ et al. | — | 2005 | → |
| Candidate gene discovery in cardiovascular disease. | Winslow RL et al. | — | 2005 | → |
| Cardiovascular pharmacogenomics. | Johnson JA et al. | — | 2005 | → |
| Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data. | Leykin I et al. | — | 2005 | → |
| Comparing single-nucleotide polymorphism marker-based and microsatellite marker-based linkage analyses. | Ulgen A et al. | — | 2005 | → |
| Comparison of microsatellites, single-nucleotide polymorphisms (SNPs) and composite markers derived from SNPs in linkage analysis. | Xing C et al. | — | 2005 | → |
| Complementing the genome with an "exposome": the outstanding challenge of environmental exposure measurement in molecular epidemiology. | Wild CP | — | 2005 | → |
| Complex phenotypes and complex genetics: an introduction to genetic studies of complex traits. | Belmont JW et al. | — | 2005 | → |
| Conservation genomics: applying whole genome studies to species conservation efforts. | Ryder OA | — | 2005 | → |
| Description of the data from the Collaborative Study on the Genetics of Alcoholism (COGA) and single-nucleotide polymorphism genotyping for Genetic Analysis Workshop 14. | Edenberg HJ et al. | — | 2005 | → |
| Dynamic model based algorithms for screening and genotyping over 100 K SNPs on oligonucleotide microarrays. | Di X et al. | — | 2005 | → |
| Estimation of individual admixture: analytical and study design considerations. | Tang H et al. | — | 2005 | → |
| Estimation of the rate of SNP genotyping errors from DNA extracted from different tissues. | Montgomery GW et al. | — | 2005 | → |
| Evidence and implications for multiplicative interactions among loci predisposing to human common disease. | Jones HB et al. | — | 2005 | → |
| Genome-wide association study in esophageal cancer using GeneChip mapping 10K array. | Hu N et al. | — | 2005 | → |
| Genome-wide linkage analysis for alcohol dependence: a comparison between single-nucleotide polymorphism and microsatellite marker assays. | Ma Q et al. | — | 2005 | → |
| Genome-wide single nucleotide polymorphism analysis reveals frequent partial uniparental disomy due to somatic recombination in acute myeloid leukemias. | Raghavan M et al. | — | 2005 | → |
| Genome-wide single-nucleotide polymorphism arrays demonstrate high fidelity of multiple displacement-based whole-genome amplification. | Tzvetkov MV et al. | — | 2005 | → |
| Genomewide single nucleotide polymorphism microarray mapping in basal cell carcinomas unveils uniparental disomy as a key somatic event. | Teh MT et al. | — | 2005 | → |
| Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. | Brodsky AS et al. | — | 2005 | → |
| Genomic screening and replication using the same data set in family-based association testing. | Van Steen K et al. | — | 2005 | → |
| GERBIL: Genotype resolution and block identification using likelihood. | Kimmel G et al. | — | 2005 | → |
| Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. | Abecasis GR et al. | — | 2005 | → |
| High-resolution analysis of chromosomal imbalances using the Affymetrix 10K SNP genotyping chip. | Herr A et al. | — | 2005 | → |
| High-resolution identification of chromosomal abnormalities using oligonucleotide arrays containing 116,204 SNPs. | Slater HR et al. | — | 2005 | → |
| Inference and analysis of haplotypes from combined genotyping studies deposited in dbSNP. | Zaitlen NA et al. | — | 2005 | → |
| Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation. | Shriver MD et al. | — | 2005 | → |
| Linkage and association analyses of microsatellites and single-nucleotide polymorphisms in nuclear families. | Lin J et al. | — | 2005 | → |
| Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments. | Dahl F et al. | — | 2005 | → |
| Novel technology and the development of pharmacogenetics within the pharmaceutical industry. | Gibson N et al. | — | 2005 | → |
| PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays. | Brohede J et al. | — | 2005 | → |
| Rapid array-based genomic characterization of a subtle structural abnormality: a patient with psychosis and der(18)t(5;18)(p14.1;p11.23). | Drazinic CM et al. | — | 2005 | → |
| SimPed: a simulation program to generate haplotype and genotype data for pedigree structures. | Leal SM et al. | — | 2005 | → |
| Single-feature polymorphism discovery in the barley transcriptome. | Rostoks N et al. | — | 2005 | → |
| SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data. | Huentelman MJ et al. | — | 2005 | → |
| SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data. | Tebbutt SJ et al. | — | 2005 | → |
| SNP identification in unamplified human genomic DNA with gold nanoparticle probes. | Bao YP et al. | — | 2005 | → |
| SNP microarray analysis for genome-wide detection of crossover regions. | Wirtenberger M et al. | — | 2005 | → |
| The Autism Genome Project: goals and strategies. | Hu-Lince D et al. | — | 2005 | → |
| The future of microarray technology: networking the genome search. | D'Ambrosio C et al. | — | 2005 | → |
| The new cytogenetics: blurring the boundaries with molecular biology. | Speicher MR et al. | — | 2005 | → |
| Tools for genomics. | Southern E | — | 2005 | → |
| Toward genome-wide SNP genotyping. | Syvänen AC | — | 2005 | → |
| Whole genome SNP arrays using DNA derived from formalin-fixed, paraffin-embedded ovarian tumor tissue. | Thompson ER et al. | — | 2005 | → |
| A combined linkage-physical map of the human genome. | Kong X et al. | — | 2004 | → |
| A HOX gene mutation in a family with isolated congenital vertical talus and Charcot-Marie-Tooth disease. | Shrimpton AE et al. | — | 2004 | → |
| Algorithms for inferring haplotypes. | Niu T | — | 2004 | → |
| Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA. | Wong KK et al. | — | 2004 | → |
| An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. | Zhao X et al. | — | 2004 | → |
| Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. | Barrett MT et al. | — | 2004 | → |
| Decoding randomly ordered DNA arrays. | Gunderson KL et al. | — | 2004 | → |
| Detect and adjust for population stratification in population-based association study using genomic control markers: an application of Affymetrix Genechip Human Mapping 10K array. | Hao K et al. | — | 2004 | → |
| Detecting copy number changes in genomic DNA: MAPH and MLPA. | White SJ et al. | — | 2004 | → |
| Estimation of genotype error rate using samples with pedigree information--an application on the GeneChip Mapping 10K array. | Hao K et al. | — | 2004 | → |
| Exhaustive allelic transmission disequilibrium tests as a new approach to genome-wide association studies. | Lin S et al. | — | 2004 | → |
| Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification. | Paez JG et al. | — | 2004 | → |
| Genomewide linkage analysis of bipolar disorder by use of a high-density single-nucleotide-polymorphism (SNP) genotyping assay: a comparison with microsatellite marker assays and finding of significant linkage to chromosome 6q22. | Middleton FA et al. | — | 2004 | → |
| Genomics in sudden cardiac death. | Arking DE et al. | — | 2004 | → |
| Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. | Matsuzaki H et al. | — | 2004 | → |
| Global genetic analysis. | Elahi E et al. | — | 2004 | → |
| Guidelines for genotyping in genomewide linkage studies: single-nucleotide-polymorphism maps versus microsatellite maps. | Evans DM et al. | — | 2004 | → |
| High-resolution analysis of DNA copy number using oligonucleotide microarrays. | Bignell GR et al. | — | 2004 | → |
| High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines. | Jänne PA et al. | — | 2004 | → |
| How to track and assess genotyping errors in population genetics studies. | Bonin A et al. | — | 2004 | → |
| Human pharmacogenomics: the development of a science. | Kalow W | — | 2004 | → |
| Incorporating individual error rate into association test of unmatched case-control design. | Hao K et al. | — | 2004 | → |
| Mapping of sudden infant death with dysgenesis of the testes syndrome (SIDDT) by a SNP genome scan and identification of TSPYL loss of function. | Puffenberger EG et al. | — | 2004 | → |
| MARA: a novel approach for highly multiplexed locus-specific SNP genotyping using high-density DNA oligonucleotide arrays. | Shapero MH et al. | — | 2004 | → |
| Microarray genotyping resource to determine population stratification in genetic association studies of complex disease. | Tebbutt SJ et al. | — | 2004 | → |
| Missense mutations of ACTA1 cause dominant congenital myopathy with cores. | Kaindl AM et al. | — | 2004 | → |
| Mutations in RDH12 encoding a photoreceptor cell retinol dehydrogenase cause childhood-onset severe retinal dystrophy. | Janecke AR et al. | — | 2004 | → |
| Overexpression, amplification, and androgen regulation of TPD52 in prostate cancer. | Rubin MA et al. | — | 2004 | → |
| Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. | Matsuzaki H et al. | — | 2004 | → |
| Quantitative analysis of nucleic acids--the last few years of progress. | Ding C et al. | — | 2004 | → |
| Selective DNA amplification from complex genomes using universal double-sided adapters. | Callow MJ et al. | — | 2004 | → |
| Sequence-based linkage analysis. | Furman I et al. | — | 2004 | → |
| SNPs made routine. | Broman KW et al. | — | 2004 | → |
| Technology platforms for pharmacogenomic diagnostic assays. | Koch WH | — | 2004 | → |
| The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs. | Shriver MD et al. | — | 2004 | → |
| Whole genome DNA copy number changes identified by high density oligonucleotide arrays. | Huang J et al. | — | 2004 | → |
| Whole-genome scan, in a complex disease, using 11,245 single-nucleotide polymorphisms: comparison with microsatellites. | John S et al. | — | 2004 | → |
| Highly parallel SNP genotyping. | Fan JB et al. | — | 2003 | → |
| The power and promise of population genomics: from genotyping to genome typing. | Luikart G et al. | — | 2003 | → |