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Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs.

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.

Pubmed ID: 18776909


  • 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


Nature genetics

Publication Data

October 26, 2008

Associated Grants

  • Agency: NIGMS NIH HHS, Id: T32 GM008313
  • Agency: NIGMS NIH HHS, Id: T32 GM008313-17
  • Agency: NIGMS NIH HHS, Id: T32 GM008313-18
  • Agency: NHGRI NIH HHS, Id: T32 HG002295
  • Agency: NHGRI NIH HHS, Id: T32 HG002295-03
  • Agency: NHGRI NIH HHS, Id: T32 HG002295-04
  • Agency: NHLBI NIH HHS, Id: T32 HL007627

Mesh Terms

  • Algorithms
  • Chromosomes, Human
  • Chromosomes, Human, Pair 4
  • DNA
  • Female
  • Gene Dosage
  • Genome, Human
  • Genotype
  • Haplotypes
  • Humans
  • Male
  • Markov Chains
  • Models, Statistical
  • Oligonucleotide Array Sequence Analysis
  • Polymerase Chain Reaction
  • Polymorphism, Single Nucleotide
  • Software