Introduction

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.

Publications

  1. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs.
    Cite this
    Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, Cawley S, Hubbell E, Veitch J, Collins PJ, Darvishi K, Lee C, Nizzari MM, Gabriel SB, Purcell S, Daly MJ, Altshuler D, 2008-10-01 - Nature genetics

Credits

  1. Joshua M Korn
    Developer

    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge

  2. Finny G Kuruvilla
    Developer

  3. Steven A McCarroll
    Developer

  4. Alec Wysoker
    Developer

  5. James Nemesh
    Developer

  6. Simon Cawley
    Developer

  7. Earl Hubbell
    Developer

  8. Jim Veitch
    Developer

  9. Patrick J Collins
    Developer

  10. Katayoon Darvishi
    Developer

  11. Charles Lee
    Developer

  12. Marcia M Nizzari
    Developer

  13. Stacey B Gabriel
    Developer

  14. Shaun Purcell
    Developer

  15. Mark J Daly
    Developer

  16. David Altshuler
    Investigator

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Summary
AccessionBT000074
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByDavid Altshuler