American Statistical Association
New York City
Metropolitan Area Chapter

Mailman School of Public Health
Columbia University
Department of Biostatistics Colloquium



IMPUTATION OF MISSING GENETIC DATA - FROM RAW TO PHASED

by

Professor Zhaoxia Yu
Department of Statistics
University of California, Irvine


Abstract

Genome-wide association studies with single nucleotide polymorphisms (SNPs) show great promise to identify genetic determinants of complex human traits. In practice, two steps are required before conducting statistical analysis: genotype calling and imputation of missing genotypes, which are traditionally considered as two separated problems. In the genotype calling step, although different clustering / classification strategies have been applied, when the allele signal of a marker is not perfectly separated, missing values are generated. The missing genotypes are then imputed based on the called genotypes and linkage disequilibrium (LD) structure among multiple markers. In this talk, Professor Yu will show how signal intensities can be used to improve the imputation of missing genotype data. A new method that simultaneously considers signal intensities and the underlying non-random association structure among SNPs will be introduced. By incorporating signal information, missing genotype data can be imputed more accurately. In addition, the new method achieves better estimation of haplotype frequencies than traditional methods that only use called genotypes.


Date: Thursday, October 23, 2008
Time: 4:00 - 5:00 P.M.
Location: Mailman School of Public Health
Department of Biostatistics
722 West 168th Street
Judith Jansen Conference Room
4th Floor - Room 425
New York, New York

RESERVATIONS ARE NOT REQUIRED

Refreshments will be served at 3:30 P.M. in the
Biostatistics Conference Room (R627).


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