David Geffen School of Medicine at UCLA
Department of Human Genetics

Speaker Series - Spring Quarter 2016

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

Mon, Apr 04
Challenges in Genomic Medicine
Gail P. Jarvik, MD, PhD, Head, Division of Medical Genetics, The Arno G. Motulsky Endowed Chair in Medicine, Joint Professor of Medicine and Genome Sciences, University of Washington
Contact & Intro: Paivi Pajukanta, x 72011
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ABSTRACT: Challenges to the implementation of genomic medicine include incidental findings, cost effectiveness, and variant classification. The Clinical Sequencing Exploratory Research (CSER) Consortia has explored these and related issue in bringing the genome to the clinic. Dr. Jarvik will discuss the expected rate of actionable incidental findings, strategies to demonstrate cost-effectiveness in genomic tests, and work to make variant pathogenicity classification more consistent, based on research from the CSER program.

Mon, Apr 11
An Epigenomics Approach to Dissecting Genetic and Environmental Components of Asthma
Carole Ober, PhD, Blum-Riese Professor and Chair Department of Human Genetics, The University of Chicago
Contact & Intro: Rita Cantor (x 72440) and Karen Reue (x 45631)
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ABSTRACT: Asthma is a heterogeneous disease with both genetic and environmental risk factors. We are applying multiple omic approaches to studies of GEIs in cell culture models and in airway epithelial cells from asthmatic and non-asthmatic individuals to separate genetic from environmental effects on gene expression.

Mon, Apr 25
Assessing Human Genome Function In Vivo
Len A. Pennacchio, PhD, Senior Staff Scientist, Genomics Division & Deputy Director, Joint Genome Institute Lawrence Berkeley National Laboratory
Contact & Intro: Nelson Freimer, x 46427
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ABSTRACT: Dr. Pennacchio's research is focused on understanding human genome function through studies in vivo. A major theme over the past decade has been identifying and understanding distant-acting gene regulatory sequences and exploring their role in human disease.

Mon, May 02
Diagnostic Role of Exome Sequencing in Immune Deficiency Disorders and the Critical Assessment of Genome Interpretation
Steven E. Brenner, PhD, Professor, Department of Plant and Microbial Biology, University of California, Berkeley
Contact & Intro: Daniel Geschwind, x 46570
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ABSTRACT: The presentation will cover three projects in interpretation of human genomic variation. We have developed an analysis protocol whose distinctive features enabled solving clinical cases. Applied to exomes from newborn patients with undiagnosed primary immune disorders, it helped guide appropriate treatment, family genetic counseling, and avoidance of diagnostic odyssey.

Preliminary findings will be shared from NBSeq, a project that explores the feasibility of sequencing to augment or supersede mass spectrometry for public health newborn screening. The Critical Assessment of Genome Interpretation (CAGI, \'kā-jē), is a community experiment to objectively assess computational methods for predicting the phenotypic impacts of genomic variation. The fourth international CAGI concluded in March 2016 and new results will be presented.

Mon, May 09
LOCATION: Center for Health Sciences (CHS) Room 13-105
Cancer genes in Hispanics: Population-specific variants, founder effects and the prevalence of mutations in known genes
Luis Carvajal, PhD, Assistant Professor, Genome Center and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis
Contact & Intro: Daniel Geschwind (x 46570) and Nelson Freimer (x 46427)
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ABSTRACT: Hispanics populations have a complex demographic history that involve genetic admixture and in some cases, geographic isolation. This demographic history, along with population-specific environmental factors, has effects on the cancer epidemiology patterns in the region. In this talk, I will review key findings in Hispanic cancer genetics and epidemiology and will present unpublished studies on the extensive founders effects and high prevalence of mutations in highly penetrant cancer genes that could potentially led to paradigm changes in the way we carry out genetic testing. I will also present data suggesting that genetic admixture affects both cancer risk and patterns of somatic mutations in tumors from Hispanics and on recent genome-wide studies for colorectal cancer in the population.

Mon, May 16
Genome-wide mutation rates viewed through a seven-nucleotide window
Benjamin F. Voight, PhD, Assistant Professor, Department of Systems Pharmacology and Translational Therapeutics, Department of Genetics
Contact & Intro: Eleazar Eskin, x 51322
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ABSTRACT: The rate of single-nucleotide polymorphism varies substantially across the human genome and fundamentally influences evolution and incidence of genetic disease. Previous studies have only considered the immediately flanking nucleotides around a polymorphic site—the site’s trinucleotide sequence context—to study polymorphism levels across the genome. Moreover, the impact of larger sequence contexts has not been fully clarified, even though context substantially influences rates of polymorphism. I will describe a new statistical framework we apply to data from the 1000 Genomes Project to demonstrate that a heptanucleotide (seven nucleotide) context window explains a large fraction of variability in substitution probabilities in the human genome along. We identify new, mutation promoting sequence motifs as well as additional rate variation at sequence contexts known to be highly mutable (CpG sites). I will describe application of our model and computational tools we are developing to interpret human disease genetic studies of de novo mutational burden.

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