Type

Journal Article

Authors

Michael Gill
Stephen V Faraone
Philip Asherson
Benjamin M Neale
Derek W Morris
Barbara Franke
Jessica Lasky-Su
Colm T O'Dushlaine
Elaine Kenny
Richard J L Anney

Subjects

Microbiology

Topics
alleles linkage disequilibrium homozygote genetic markers oligonucleotide array sequence analysis family studies genetics population child genome human random haplotypes genome wide association study genes society bias epidemiology genome wide association studies gwas computer simulation polymorphism single nucleotide algorithms humans chi square distribution gene dosage family cluster analysis genotype case control studies heterozygote implications parents procedures

Non-random error in genotype calling procedures: implications for family-based and case-control genome-wide association studies. (2008)

Abstract The considerable data-handling requirements for genome wide association studies (GWAS) prohibit individual calling of genotypes and create a reliance on sophisticated "genotype-calling algorithms." Despite their obvious utility, the current genotyping platforms and calling-algorithms used are not without their limitations. Specifically, some genotypes are not called due to the ambiguity of the data. Any bias in the missing data could create spurious results. Using data from the Genetic Analysis Information Network (GAIN) we observed that missing genotypes are not randomly distributed throughout the homozygous and heterozygous groups. Using simulation, we examined whether the level and type of missingness observed might influence deviation from the null-hypothesis under common case-control and family-based statistical approaches. Under a case-control model, where missingness is present in a case group but not the controls, we observed bias giving rise to genome-wide significant type-I error for missingness as low as 3%. The family-based association simulations show close to nominal type-I error at 4% genotype missingness. These findings have important implications to study design, quality-control procedures and reporting of findings in GWAS.
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Full list of authors on original publication

Michael Gill, Stephen V Faraone, Philip Asherson, Benjamin M Neale, Derek W Morris, Barbara Franke, Jessica Lasky-Su, Colm T O'Dushlaine, Elaine Kenny, Richard J L Anney

Experts in our system

1
Michael Gill
Trinity College Dublin
Total Publications: 260
 
2
P Asherson
University College Dublin
Total Publications: 9
 
3
Derek Morris
Trinity College Dublin
Total Publications: 150
 
4
Barbara Franke
Trinity College Dublin
Total Publications: 12
 
5
Colm T O'Dushlaine
Trinity College Dublin
Total Publications: 28
 
6
Elaine Kenny
Trinity College Dublin
Total Publications: 28
 
7
Richard Anney
Trinity College Dublin
Total Publications: 38