David Geffen School of Medicine at UCLA
Department of Human Genetics

Speaker Series - Spring Quarter 2017

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

Mon, Apr 03
An assessment of the population genetic evidence for selection across twenty brain related phenotypes
Barbara Stranger, PhD, Assistant Professor, Section of Genetic Medicine, Dept of Medicine, Institute for Genomics and Systems Biology, Center for Data Intensive Science, University of Chicago
Contact & Intro: Eleazar Eskin x 51322
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ABSTRACT: Inter-individual variation in neuropsychiatric traits is present across diverse human populations, has persisted through recorded history, and has been shown to have a genetic basis primarily accounted for by common single nucleotide polymorphisms. Motivated by recent observations that SNPs with high minor allele frequency (MAF) contribute disproportionately to some neuropsychiatric phenotypes, we tested the hypothesis that common susceptibility variants for neuropsychiatric phenotypes have experienced selection over the course of human history.

Mon, Apr 10
Analysis of Genome, Exposome and Phenome
Xihong Lin, PhD, Chair and Henry Pickering Walcott Professor of Biostatistics; Harvard T.H. Chan School of Public Health
Contact & Intro: Jessica Li
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ABSTRACT: This talk will discuss analysis of massive genome, exposome, and phenome data. Specific topics include rare variant analysis of whole-genome sequencing association studies; analysis of multiple phenotypes (pleiotropy), and integrative analysis of different types of genetic and genomic, environmental data using mediation analysis. Connection between mediation analysis and Mendelian Randomization will be discussed.

Mon, Apr 24
Epigenetic fine-mapping of cardiovascular disease loci
Christopher Brown, PhD, Assistant Professor, Department Genetics and Institute for Biomedical Informatics, University of Pennsylvania
Contact & Intro: Eleazar Eskin x 51322
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ABSTRACT: I will present our recent research that aims to characterize the mechanisms that underlie cardiovascular disease loci. To identify the specific variants and genes that affect CVD risk, we have deeply phenotyped liver biopsies and iPSC derived hepatocytes form more than 400 donors, collecting RNA-seq along with histone modification and transcription factor ChIP-seq data. We have used these data to identify thousands of genetic variants associated with allele-specific transcription factor binding, histone modification, gene expression, and splicing. Using a combination of massively parallel reporter assays, genome-edited stem cells, CRISPR interference, and in vivo mouse models, we establish rs2277862-CPNE1, rs10889356-ANGPTL3, rs10889356-DOCK7, and rs10872142-FRK as causal SNP-gene sets for CVD. These results demonstrate that a molecular trait mapping framework can rapidly identify causal genes and variants contributing to complex human traits and demonstrates that, at many GWAS loci, candidate genes have been falsely implicated based on proximity to the lead SNP.

Mon, May 01
Hood: Trailblazer of the Genomics Age
Luke Timmerman, Author
Contact & Intro: Same
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ABSTRACT: Leroy (Lee) Hood is best known for leading the team at Caltech in the 1980s that developed the first automated DNA sequencing instrument. It was the tool that paved the way for emerging fields of genomics, bioinformatics, and systems biology. In Luke Timmerman’s book, “Hood: Trailblazer of the Genomics Age,” he delves into Hood’s battles with university administrators, colleagues, and big companies that did not always share his high-tech vision for biology.

Luke Timmerman is a journalist and author. He is the founder of Timmerman Report, a biotech newsletter and the co-host of the Signal podcast for STAT. He will hold a 30-40 minute talk about the book and trends in biotechnology followed by Q&A for the rest of the hour.

Mon, May 15
How you can use 70,000 RNA-seq samples in your research
Jeffrey Leek, PhD, Associate Professor, Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
Contact & Intro: Eleazar Eskin x 51322
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ABSTRACT: There are hundreds of thousands of sequencing samples available through public archives. In this talk I'll discuss a long term collaboration focused on organizing, tidying, and labeling more than 70,000 human RNA-seq samples. I'll discuss some insights we've gained from analyzing all these data together and how you can you use the data we've processed to improve analyses in your group.

Mon, May 22
Hua Tang, PhD, Professor, Department of Genetics, Stanford University
Contact & Intro: Jessica Li x 68375
Mon, Jun 05
Noah Zaitlen, PhD, Assistant Professor, Department of Medicine in Human Genetics, University of California San Francisco
Contact & Intro: Eleazar Eskin x 51322
Mon, Jun 12
Causes and Consequences of Human Genomic Variation
Sohini Ramachandran, PhD, Manning Assistant Professor, Ecology and Evolutionary Biology, Brown University
Contact & Intro: Jazlyn Mooney
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ABSTRACT: Determining the genomic elements underlying adaptive evolution and diseases in a species is essential for connecting genetic variation to phenotypes and fitness, but current statistical methods overlook the confounding effect population histories have on the identification and localization of adaptive and disease-associated mutations. I'll discuss two methods developed in my laboratory that (i) model the complex interaction between various modes of selection and population histories; and (ii) accurately identify and localize mutations, genes, and pathways underlying adaptive traits and disease for further experimental validation. These methods can be extended and applied to existing and emerging genome-wide polymorphism and next-generation sequencing datasets for humans and a range of other organisms. Our goal is to yield new insight into the interaction between selection and dynamic population histories in generating human genetic diversity and the human phenotype.

Mon, Jun 26
LOCATION: Neuroscience Research Building (NRB) Auditorium, Room 132
Bradley Bernstein, MD, PhD, Department of Pathology, Massachusetts General Hospital, Harvard, Medical School and Broad Institute
Contact & Intro: Jason Ernst x 53658

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