David Geffen School of Medicine at UCLA
Department of Human Genetics

Speaker Series - Fall Quarter 2012

Mondays, 11am - 12pm, Gonda Building First Floor Conference Room, 1357

Mon, Oct 08
Genotype Imputation by Matrix Completion
Eric Chi, Ph.D., Post Doc, Department of Human Genetics, UCLA
Contact & Intro: Kate Wheeler, kwheeler@mednet.ucla.edu
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ABSTRACT: Most current genotype imputation methods are model-based and computationally intensive, taking days to impute one chromosome pair on 1000 individuals. We describe an efficient genotype imputation method based on matrix completion. Matrix completion aims to recover an entire matrix when only a small portion of its entries are actually observed. Making an appeal to Occam’s razor, it seeks the simplest matrix consistent with the observed entries. Often this statement formally translates to searching for a low rank matrix with a small squared error difference over the observed entries. Genotypes can be coded as 0, 1, or 2’s by counting reference alleles and entering the counts into a matrix whose rows are labeled by individuals and whose columns are labeled by SNPs. Despite matrix completion’s purely empirical nature, it seemed natural to us to investigate its application to a central problem in modern genetics research. Specifically, we apply a matrix completion strategy for the problems of imputation in a traditional GWAS and of genotype calling in low coverage sequencing. We consider simulated data based on haplotypes from HapMap and 1000 Genomes. Compared to the existing methods matrix completion as embodied in our program Mendel-Impute achieves similar accuracy while significantly reducing run times.

Mon, Nov 05
The Rasopathies: Distinct Disorders Related by Dysregulation of the RAS/MAPK signaling pathway
Karen Gripp, Karen W. Gripp, MD, FAAP, FACMG, Professor of Pediatrics, T. Jefferson College of Medicine, Philadelphia, PA; Chief, Division of Medical Genetics, A.I. DuPont Hospital for Children, Wilmington, DE
Contact & Intro: Julian Martinez, julian.martinez@mednet.ucla.edu
Tue, Nov 13
Note Time & Location Change: NRB Auditorium at 10am
Genomics Cannot be Done Alone, Working together for a better world
Huanming Yang, Ph.D., Professor & President BGI (Beijing Genomics Institute), China
Contact & Intro: Guoping Fan, x70439
Mon, Nov 26
From Morphogen to Transcriptional Mechanism: Shh Patterning of the Mammalian Central Nervous System
Andrew McMahon, Ph.D., Chair, Department of Stem Cell Biology and Regenerative Medicine, Keck Provost Professor, Director of the Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine at USC
Contact & Intro: Julian Martinez, julian.martinez@mednet.ucla.edu

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