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Activity Number: 408
Type: Contributed
Date/Time: Tuesday, August 5, 2014 : 2:00 PM to 3:50 PM
Sponsor: Section on Statistical Learning and Data Mining
Abstract #313039
Title: Genotype Calling in Trisomic Samples
Author(s): Yan Lin*+ and Soo Yeon Cheong and Eleanor Feingold
Companies: University of Pittsburgh and University of Pittsburgh and University of Pittsburgh
Keywords: genotype calling ; trisomy ; SNP ; Down syndrome
Abstract:

Genotypes calling methods for standard disomic genome are well established and software packages are available for various genotyping technologies. For individuals with chromosomal abnormalities (e.g. trisomic genome), however, standard genotype-calling software cannot be used. Previously, we developed both K-means based and parametric methods for trisomic genotype calling. Here we consider the problem of calling genotypes for a large sample of individuals with Down syndrome. We propose a method that first applies standard disomic genotype-calling algorithms and then adjusts the calls to handle the trisomy, and compare it to our previously-published methods that clusters the trisomic genotypes de novo. We also discuss the general practical approaches to call the genotypes for trisomic data.


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