Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs.
paper
Cited
Public
- Authors
- Korn, Joshua M; Kuruvilla, Finny G; McCarroll, Steven A; Wysoker, Alec; Nemesh, James; Cawley, Simon; Hubbell, Earl; Veitch, Jim; Collins, Patrick J; Darvishi, Katayoon; Lee, Charles; Nizzari, Marcia M; Gabriel, Stacey B; Purcell, Shaun; Daly, Mark J; Altshuler, David
- Year
- 2008
- Journal
- Nature genetics
- PMID
- 18776909
- DOI
- 10.1038/ng.237
- PMCID
- PMC2756534
Accurate and complete measurement of single nucleotide (SNP) and copy number (CNV) variants, both common and rare, will be required to understand the role of genetic variation in disease. We present Birdsuite, a four-stage analytical framework instantiated in software for deriving integrated and mutually consistent copy number and SNP genotypes. The method sequentially assigns copy number across regions of common copy number polymorphisms (CNPs), calls genotypes of SNPs, identifies rare CNVs via a hidden Markov model (HMM), and generates an integrated sequence and copy number genotype at every locus (for example, including genotypes such as A-null, AAB and BBB in addition to AA, AB and BB calls). Such genotypes more accurately depict the underlying sequence of each individual, reducing the rate of apparent mendelian inconsistencies. The Birdsuite software is applied here to data from the Affymetrix SNP 6.0 array. Additionally, we describe a method, implemented in PLINK, to utilize these combined SNP and CNV genotypes for association testing with a phenotype.
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| Genome-wide analysis of loss of heterozygosity in breast infiltrating ductal carcinoma distant normal tissue highlights arm specific enrichment and expansion across tumor stages. | Ruan X et al. | β | 2014 | β |
| Genome-wide association studies identified novel loci for non-high-density lipoprotein cholesterol and its postprandial lipemic response. | An P et al. | β | 2014 | β |
| Genome-wide association study identified copy number variants important for appendicular lean mass. | Ran S et al. | β | 2014 | β |
| Genome-wide copy number variation study and gene expression analysis identify ABI3BP as a susceptibility gene for Kashin-Beck disease. | Zhang F et al. | β | 2014 | β |
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| Mapping of hepatic expression quantitative trait loci (eQTLs) in a Han Chinese population. | Wang X et al. | β | 2014 | β |
| Methylation at CPT1A locus is associated with lipoprotein subfraction profiles. | Frazier-Wood AC et al. | β | 2014 | β |
| New genetic biomarkers predicting azathioprine blood concentrations in combination therapy with 5-aminosalicylic acid. | Uchiyama K et al. | β | 2014 | β |
| Numerical analysis of intensity signals resulting from genotyping pooled DNA samples in beef cattle and broiler chicken. | Reverter A et al. | β | 2014 | β |
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| Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies. | Cowley GS et al. | β | 2014 | β |
| PRKCZ methylation is associated with sunlight exposure in a North American but not a Mediterranean population. | Aslibekyan S et al. | β | 2014 | β |
| Rare copy number variation in treatment-resistant major depressive disorder. | O'Dushlaine C et al. | β | 2014 | β |
| Set-based joint test of interaction between SNPs in the VEGF pathway and exogenous estrogen finds association with age-related macular degeneration. | Courtenay MD et al. | β | 2014 | β |
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| The challenges and importance of structural variation detection in livestock. | Bickhart DM et al. | β | 2014 | β |
| The phenotypic manifestations of rare CNVs in schizophrenia. | Merikangas AK et al. | β | 2014 | β |
| The population genomic landscape of human genetic structure, admixture history and local adaptation in Peninsular Malaysia. | Deng L et al. | β | 2014 | β |
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| VTET: a variable threshold exact test for identifying disease-associated copy number variations enriched in short genomic regions. | Shi J et al. | β | 2014 | β |
| A colorectal cancer genome-wide association study in a Spanish cohort identifies two variants associated with colorectal cancer risk at 1p33 and 8p12. | Fernandez-Rozadilla C et al. | β | 2013 | β |
| A common deletion in the APOBEC3 genes and breast cancer risk. | Long J et al. | β | 2013 | β |
| Advantage of using allele-specific copy numbers when testing for association in regions with common copy number variants. | Marenne G et al. | β | 2013 | β |
| A generalized Kruskal-Wallis test incorporating group uncertainty with application to genetic association studies. | Acar EF et al. | β | 2013 | β |
| A genome-wide investigation of copy number variation in patients with sporadic brain arteriovenous malformation. | Bendjilali N et al. | β | 2013 | β |
| A genome wide survey supports the involvement of large copy number variants in schizophrenia with and without intellectual disability. | Derks EM et al. | β | 2013 | β |
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| Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array. | Liu J et al. | β | 2013 | β |
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| Best practices and joint calling of the HumanExome BeadChip: the CHARGE Consortium. | Grove ML et al. | β | 2013 | β |
| BMPR1A mutations in early-onset colorectal cancer with mismatch repair proficiency. | Fernandez-Rozadilla C et al. | β | 2013 | β |
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| Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data. | Xu L et al. | β | 2013 | β |
| Comparison of genotyping using pooled DNA samples (allelotyping) and individual genotyping using the affymetrix genome-wide human SNP array 6.0. | Teumer A et al. | β | 2013 | β |
| Copy Number Studies in Noisy Samples. | Ginsbach P et al. | β | 2013 | β |
| Copy number variation on chromosome 10q26.3 for obesity identified by a genome-wide study. | Yang TL et al. | β | 2013 | β |
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| Detecting large copy number variants using exome genotyping arrays in a large Swedish schizophrenia sample. | Szatkiewicz JP et al. | β | 2013 | β |
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| EvoSNP-DB: A database of genetic diversity in East Asian populations. | Kim YU et al. | β | 2013 | β |
| Gene-environment interactions and obesity traits among postmenopausal African-American and Hispanic women in the Women's Health Initiative SHARe Study. | Velez Edwards DR et al. | β | 2013 | β |
| Genes and mutations causing retinitis pigmentosa. | Daiger SP et al. | β | 2013 | β |
| Genetic factors in nonsmokers with age-related macular degeneration revealed through genome-wide gene-environment interaction analysis. | Naj AC et al. | β | 2013 | β |
| Genetic variants associated with VLDL, LDL and HDL particle size differ with race/ethnicity. | Frazier-Wood AC et al. | β | 2013 | β |
| Genome Fusion Detection: a novel method to detect fusion genes from SNP-array data. | Thieme S et al. | β | 2013 | β |
| Genome scan study of prostate cancer in Arabs: identification of three genomic regions with multiple prostate cancer susceptibility loci in Tunisians. | Shan J et al. | β | 2013 | β |
| Genome-wide assessment of the association of rare and common copy number variations to testicular germ cell cancer. | EdsgΓ€rd D et al. | β | 2013 | β |
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| Genome-wide contribution of genotype by environment interaction to variation of diabetes-related traits. | Zheng JS et al. | β | 2013 | β |
| Genome-wide linkage analysis of congenital heart defects using MOD score analysis identifies two novel loci. | Flaquer A et al. | β | 2013 | β |
| Haplotype-based profiling of subtle allelic imbalance with SNP arrays. | Vattathil S et al. | β | 2013 | β |
| Human spermatogenic failure purges deleterious mutation load from the autosomes and both sex chromosomes, including the gene DMRT1. | Lopes AM et al. | β | 2013 | β |
| Identification of null alleles and deletions from SNP genotypes for an intercross between domestic and wild chickens. | Crooks L et al. | β | 2013 | β |
| Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. | Poultney CS et al. | β | 2013 | β |
| Linkage and association of successful aging to the 6q25 region in large Amish kindreds. | Edwards DR et al. | β | 2013 | β |
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| Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing. | Kirby A et al. | β | 2013 | β |
| Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations. | Robberecht C et al. | β | 2013 | β |
| Novel susceptibility variants at 10p12.31-12.2 for childhood acute lymphoblastic leukemia in ethnically diverse populations. | Xu H et al. | β | 2013 | β |
| Pan-cancer patterns of somatic copy number alteration. | Zack TI et al. | β | 2013 | β |
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| Pathogenic rare copy number variants in community-based schizophrenia suggest a potential role for clinical microarrays. | Costain G et al. | β | 2013 | β |
| Pharmacogenomics in colorectal cancer: a genome-wide association study to predict toxicity after 5-fluorouracil or FOLFOX administration. | Fernandez-Rozadilla C et al. | β | 2013 | β |
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| Rare genomic structural variants in complex disease: lessons from the replication of associations with obesity. | Walters RG et al. | β | 2013 | β |
| RNA-Seq optimization with eQTL gold standards. | Ellis SE et al. | β | 2013 | β |
| Schizophrenia two-hit hypothesis in velo-cardio facial syndrome. | Williams HJ et al. | β | 2013 | β |
| Sex-specific association of a common variant of the XG gene with autism spectrum disorders. | Chang SC et al. | β | 2013 | β |
| Susceptibility loci associated with specific and shared subtypes of lymphoid malignancies. | Vijai J et al. | β | 2013 | β |
| t(11;14)(q23;q32) involving IGH and DDX6 in nodal marginal zone lymphoma. | Stary S et al. | β | 2013 | β |
| The Role of Copy Number Variation in African Americans with Type 2 Diabetes-Associated End Stage Renal Disease. | Bailey JN et al. | β | 2013 | β |
| The role of SNP-loop diuretic interactions in hypertension across ethnic groups in HyperGEN. | de las Fuentes L et al. | β | 2013 | β |
| Unravelling the complexity of human olfactory receptor repertoire by copy number analysis across population using high resolution arrays. | Veerappa AM et al. | β | 2013 | β |
| Use of systems biology approaches to analysis of genome-wide association studies of myocardial infarction and blood cholesterol in the nurses' health study and health professionals' follow-up study. | Reilly D et al. | β | 2013 | β |
| Using population admixture to help complete maps of the human genome. | Genovese G et al. | β | 2013 | β |
| Whole-genome detection of disease-associated deletions or excess homozygosity in a case-control study of rheumatoid arthritis. | Wu CC et al. | β | 2013 | β |
| ZNF804A and cortical thickness in schizophrenia and bipolar disorder. | Bergmann O et al. | β | 2013 | β |
| Absolute quantification of somatic DNA alterations in human cancer. | Carter SL et al. | β | 2012 | β |
| A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer. | Ng KP et al. | β | 2012 | β |
| A discovery resource of rare copy number variations in individuals with autism spectrum disorder. | Prasad A et al. | β | 2012 | β |
| A genome-wide association study of inflammatory biomarker changes in response to fenofibrate treatment in the Genetics of Lipid Lowering Drug and Diet Network. | Aslibekyan S et al. | β | 2012 | β |
| Algorithm implementation for CNV discovery using Affymetrix and Illumina SNP array data. | Winchester L et al. | β | 2012 | β |
| An integrative segmentation method for detecting germline copy number variations in SNP arrays. | Shi J et al. | β | 2012 | β |
| ARID5B genetic polymorphisms contribute to racial disparities in the incidence and treatment outcome of childhood acute lymphoblastic leukemia. | Xu H et al. | β | 2012 | β |
| Association of 8q22.3 locus in Chinese Han with idiopathic premature ovarian failure (POF). | Qin Y et al. | β | 2012 | β |
| Calling amplified haplotypes in next generation tumor sequence data. | Dewal N et al. | β | 2012 | β |
| Clustering-Based Method for Developing a Genomic Copy Number Alteration Signature for Predicting the Metastatic Potential of Prostate Cancer. | Pearlman A et al. | β | 2012 | β |
| Contribution of global rare copy-number variants to the risk of sporadic congenital heart disease. | Soemedi R et al. | β | 2012 | β |
| Copy number variation in patients with cervical artery dissection. | Grond-Ginsbach C et al. | β | 2012 | β |
| Copy number variation in subjects with major depressive disorder who attempted suicide. | Perlis RH et al. | β | 2012 | β |
| Copy number variations associated with obesity-related traits in African Americans: a joint analysis between GENOA and HyperGEN. | Zhao W et al. | β | 2012 | β |
| Copy number variation signature to predict human ancestry. | Pronold M et al. | β | 2012 | β |
| Cutting-edge issues in primary biliary cirrhosis. | Folci M et al. | β | 2012 | β |
| De novo and inherited CNVs in MZ twin pairs selected for discordance and concordance on Attention Problems. | Ehli EA et al. | β | 2012 | β |
| Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. | Jun G et al. | β | 2012 | β |
| Detection and characterization of copy number variation in autism spectrum disorder. | Marshall CR et al. | β | 2012 | β |
| Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. | Fromer M et al. | β | 2012 | β |
| Discovery of variants unmasked by hemizygous deletions. | Hochstenbach R et al. | β | 2012 | β |
| Effect of Combining Multiple CNV Defining Algorithms on the Reliability of CNV Calls from SNP Genotyping Data. | Kim SY et al. | β | 2012 | β |
| Efficiency and power as a function of sequence coverage, SNP array density, and imputation. | Flannick J et al. | β | 2012 | β |
| Fast detection of de novo copy number variants from SNP arrays for case-parent trios. | Scharpf RB et al. | β | 2012 | β |
| Fatty Acid desaturase gene variants, cardiovascular risk factors, and myocardial infarction in the costa rica study. | Aslibekyan S et al. | β | 2012 | β |
| Finding genes and variants for lipid levels after genome-wide association analysis. | Willer CJ et al. | β | 2012 | β |
| Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. | Hou Y et al. | β | 2012 | β |
| FLNA genomic rearrangements cause periventricular nodular heterotopia. | Clapham KR et al. | β | 2012 | β |
| Gene-targeted analysis of copy number variants identifies 3 novel associations with coronary heart disease traits. | Costelloe SJ et al. | β | 2012 | β |
| Genetic variants and environmental factors associated with hormonal markers of ovarian reserve in Caucasian and African American women. | Schuh-Huerta SM et al. | β | 2012 | β |
| Genome-wide analysis of copy number variants in attention deficit hyperactivity disorder: the role of rare variants and duplications at 15q13.3. | Williams NM et al. | β | 2012 | β |
| Genome-wide association and linkage study in the Amish detects a novel candidate late-onset Alzheimer disease gene. | Cummings AC et al. | β | 2012 | β |
| Genome-wide association study identified CNP12587 region underlying height variation in Chinese females. | Zhang YP et al. | β | 2012 | β |
| Genome-wide association study identifies a maternal copy-number deletion in PSG11 enriched among preeclampsia patients. | Zhao L et al. | β | 2012 | β |
| Genome-wide association study identifies germline polymorphisms associated with relapse of childhood acute lymphoblastic leukemia. | Yang JJ et al. | β | 2012 | β |
| Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder. | Bergen SE et al. | β | 2012 | β |
| Genome-wide association study indicates variants associated with insulin signaling and inflammation mediate lipoprotein responses to fenofibrate. | Frazier-Wood AC et al. | β | 2012 | β |
| Genome-wide association study of copy number variants suggests LTBP1 and FGD4 are important for alcohol drinking. | Pei YF et al. | β | 2012 | β |
| Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13). | Hart AB et al. | β | 2012 | β |
| Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data. | Marenne G et al. | β | 2012 | β |
| Genome-wide copy number analysis uncovers a new HSCR gene: NRG3. | Tang CS et al. | β | 2012 | β |
| Genome-wide copy number variation association analyses for age at menarche. | Liu YZ et al. | β | 2012 | β |
| Genotype calling for the Affymetrix platform. | Schillert A et al. | β | 2012 | β |
| Genotype calling for the Illumina platform. | Teo YY | β | 2012 | β |
| Haplotypes with copy number and single nucleotide polymorphisms in CYP2A6 locus are associated with smoking quantity in a Japanese population. | Kumasaka N et al. | β | 2012 | β |
| Heritability and genome-wide association study to assess genetic differences between advanced age-related macular degeneration subtypes. | Sobrin L et al. | β | 2012 | β |
| Human gene copy number spectra analysis in congenital heart malformations. | Tomita-Mitchell A et al. | β | 2012 | β |
| Hybridization and amplification rate correction for affymetrix SNP arrays. | Wang Q et al. | β | 2012 | β |
| Hypothesis-driven candidate genes for schizophrenia compared to genome-wide association results. | Collins AL et al. | β | 2012 | β |
| Identification and validation of copy number variants using SNP genotyping arrays from a large clinical cohort. | Valsesia A et al. | β | 2012 | β |
| Identification of germline genomic copy number variation in familial pancreatic cancer. | Al-Sukhni W et al. | β | 2012 | β |
| Integrative analysis of single nucleotide polymorphisms and gene expression efficiently distinguishes samples from closely related ethnic populations. | Yang HC et al. | β | 2012 | β |
| Interpreting noncoding genetic variation in complex traits and human disease. | Ward LD et al. | β | 2012 | β |
| Meiotic errors followed by two parallel postzygotic trisomy rescue events are a frequent cause of constitutional segmental mosaicism. | Robberecht C et al. | β | 2012 | β |
| Mitochondrial mutations and polymorphisms in psychiatric disorders. | Sequeira A et al. | β | 2012 | β |
| Mutation discovery in regions of segmental cancer genome amplifications with CoNAn-SNV: a mixture model for next generation sequencing of tumors. | Crisan A et al. | β | 2012 | β |
| Phenotype-specific effect of chromosome 1q21.1 rearrangements and GJA5 duplications in 2436 congenital heart disease patients and 6760 controls. | Soemedi R et al. | β | 2012 | β |
| Rapid visualisation of microarray copy number data for the detection of structural variations linked to a disease phenotype. | Carr IM et al. | β | 2012 | β |
| Rare copy number variations in adults with tetralogy of Fallot implicate novel risk gene pathways. | Silversides CK et al. | β | 2012 | β |
| Rare genomic deletions and duplications and their role in neurodevelopmental disorders. | Glessner JT et al. | β | 2012 | β |
| Reliable single chip genotyping with semi-parametric log-concave mixtures. | Rippe RC et al. | β | 2012 | β |
| Replication analysis for severe diabetic retinopathy. | Grassi MA et al. | β | 2012 | β |
| The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes. | Cusanovich DA et al. | β | 2012 | β |
| The impact of errors in copy number variation detection algorithms on association results. | Wineinger NE et al. | β | 2012 | β |
| The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits. | Voight BF et al. | β | 2012 | β |
| Twins, tissue, and time: an assessment of SNPs and CNVs. | Scheet P et al. | β | 2012 | β |
| Ultraconserved elements in the human genome: association and transmission analyses of highly constrained single-nucleotide polymorphisms. | Chiang CW et al. | β | 2012 | β |
| zCall: a rare variant caller for array-based genotyping: genetics and population analysis. | Goldstein JI et al. | β | 2012 | β |
| A 32 kb critical region excluding Y402H in CFH mediates risk for age-related macular degeneration. | Sivakumaran TA et al. | β | 2011 | β |
| Accuracy of CNV Detection from GWAS Data. | Zhang D et al. | β | 2011 | β |
| A comparison of genomic copy number calls by Partek Genomics Suite, Genotyping Console and Birdsuite algorithms to quantitative PCR. | Grayson BL et al. | β | 2011 | β |
| A computational framework discovers new copy number variants with functional importance. | Banerjee S et al. | β | 2011 | β |
| A genome-wide association study of serum uric acid in African Americans. | Charles BA et al. | β | 2011 | β |
| A genome-wide association study reveals association between common variants in an intergenic region of 4q25 and high-grade myopia in the Chinese Han population. | Li Z et al. | β | 2011 | β |
| A genome-wide CNV association study on panic disorder in a Japanese population. | Kawamura Y et al. | β | 2011 | β |
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| A multilevel model to address batch effects in copy number estimation using SNP arrays. | Scharpf RB et al. | β | 2011 | β |
| A novel molecular signature identified by systems genetics approach predicts prognosis in oral squamous cell carcinoma. | Peng CH et al. | β | 2011 | β |
| A population-based study of copy number variants and regions of homozygosity in healthy Swedish individuals. | Teo SM et al. | β | 2011 | β |
| Approximate and exact tests of Hardy-Weinberg equilibrium using uncertain genotypes. | Shriner D | β | 2011 | β |
| A review of software for microarray genotyping. | Lamy P et al. | β | 2011 | β |
| Assessment of copy number variation using the Illumina Infinium 1M SNP-array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study. | Marenne G et al. | β | 2011 | β |
| Bayesian hierarchical mixture modeling to assign copy number from a targeted CNV array. | Cardin N et al. | β | 2011 | β |
| Characterization of autosomal copy-number variation in African Americans: the HyperGEN Study. | Wineinger NE et al. | β | 2011 | β |
| Clinical relevance of SKP2 alterations in metastatic melanoma. | Rose AE et al. | β | 2011 | β |
| cn.FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate. | Clevert DA et al. | β | 2011 | β |
| CNVassoc: Association analysis of CNV data using R. | Subirana I et al. | β | 2011 | β |
| Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration. | Yu Y et al. | β | 2011 | β |
| Common variants on 8p12 and 1q24.2 confer risk of schizophrenia. | Shi Y et al. | β | 2011 | β |
| Comparative analysis of copy number variation detection methods and database construction. | Koike A et al. | β | 2011 | β |
| Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips. | Ritchie ME et al. | β | 2011 | β |
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