ATME Affinity Group Seminars

Biostatistics Program

ATME Affinity Group Seminars

Analysis Tools and Methods for High-Throughput Genomic Data

When: 1:00 p.m. unless otherwise noted

: M4-A805/A817 unless otherwise noted

Sponsors: Chad He, Janet Stanford, Ruth Etzioni

Upcoming Seminars

April 25, 2019

1:00 - 2:00 pm

Andrea Burnett-Hartman, Kaiser Permanente Colorado

Collaborative Research with Integrated Health Systems: Challenges and Opportunities

Integrated health care systems provide the ideal setting for pragmatic research aimed at improving population-level health, and several research networks leverage these system’s electronic health records and defined populations. These include the Health Care Systems Research Network (HCSRN), Cancer Research Network (CRN), and Patient Outcomes Research to Advance Learning (PORTAL) network. This presentation will focus on some of the challenges of collaborative research in integrated health care systems and highlight opportunities for translational research, including large biobanks that are being developed to advance precision medicine research.


May 8, 2019

12:00 - 1:00 pm

Andrea Foulkes, Mount Holyoke College

Past Seminars

April 10, 2019

Lin Chen, University of Chicago

Integrative genomic association and mediation analysis

In this talk, I will discuss two related works. To provide a comprehensive mechanistic interpretation of how known trait-associated SNPs affect complex traits, we propose a method -- Primo -- for integrative analysis of GWAS summary statistics with multiple sets of omics QTL summary statistics from different cellular conditions or studies.  Primo examines SNPs’ association patterns to complex and omics traits, and in gene regions harboring known susceptibility loci, Primo performs conditional association analysis to account for linkage disequilibrium. Primo allows for unknown study heterogeneity and sample correlations. We show two applications using Primo to examine the molecular mechanisms of known susceptibility loci and to detect and interpret pleiotropic effects.

I will then introduce another work -- Cross-condition mediation analysis (CCmed) that borrows information across tissue types to detect robust and interpretable trans-associations mediated by cis-genes. The method establishes trans-associations by jointly testing for non-zero associations between SNPs and cis-gene expression levels and for non-zero conditional correlations between cis and trans-gene expression levels across conditions, allowing for partial mediation. We apply CCmed to data from 13 brain tissues in the Genotype-Tissue Expression project to detect cross-tissue trans-associations, as well as trans-associations of 108 known schizophrenia-associated SNPs. Additionally, we propose a new validation framework to establish the trait-associations of our detected trans-genes by recapitalizing on GWAS summary statistics from the Psychiatric Genomics Consortium.


January 23, 2019

*Joint Biostatistics & ATME Affinity Group Seminar*

Saonli Basu, University of Minnesota

“Estimating Variance Components in Longitudinal Family Studies with Applications to Genetic Heritability”

A longitudinal familial study with repeated measurements on relatives and can serve as a powerful resource to detect genetic association in the development of complex traits.   Modeling the covariance structure in a longitudinal family study is often quite challenging, as one needs to capture three distinct levels of dependencies. The dependency among family members at each time point, the dependency of outcomes in an individual across all time-points and modeling the outcome dependencies between two family members among different time points. Heritability measures the contribution of the additive genetic component in a trait variance.  In this talk, we investigate the challenges with joint genetic association testing and heritability estimation with longitudinal family data. We will focus on twin studies as this unique study design with MZs and DZs can separate additive genetic effects from shared environmental component and thus provides means for accurate heritability estimation. We develop a model that enables both heritability estimation and association testing with more flexible assumptions and is an extension of the traditional Falconer's approach. For our model, we propose a rapid two stage estimation procedure and a method of moments approach which can even be used to estimate variance components in a multivariate ACE model.  We compare our approach with existing approaches through extensive simulation studies and illustrate our approach on Minnesota twin studies.

December 10, 2018

Donghui Yan, University of Massachussetts Dartmouth

Randon Projection Forests

In this talk, I will introduce a new tool for data mining and inference — Random Projection Forests (rpForests). rpForests is an ensemble of random projection trees constructed recursively through a series of carefully chosen random projections. rpForests combines the power of ensemble methods and the flexibility of trees; it is simple to implement, highly scalable, and readily adapt to the geometry of the underlying data. The ensemble nature of rpForests makes it easy to run in parallel on multicore or clustered computers, with running time nearly inversely proportional to the number of cores or computers used in the computation. This complements previous development of unsupervised extension to Random Forests-Cluster Forests-which aims at clustering by random feature pursuits. One potential use of rpForests is to leverage the locality of data points captured by rpForests, which has the desired property that the probability of neighboring points being separated decays exponentially fast when the ensemble size increases. We discuss two applications along this line, fast k-nearest neighbor (kNN) search and deep representation learning in the scoring of tissue microarray images.

October 25, 2018

Teresa S. Kim, University of Washington

Neoadjuvant therapy induces a potent inflammatory and corresponding regulatory response within the sarcoma immune microenvironment

Soft tissue sarcoma is a prototype for many solid tumors, which are curable when localized, but prone to recurrence and metastasis, at which point survival is limited and more effective treatment strategies are essential. In the current project, we are utilizing multiple techniques of immunologic investigation, including multiplex immunohistochemistry (mIHC), and transcriptomic analysis with the NanoString platform, to define: (1) the immune response to sarcoma, (2) the effect of preoperative radiation and chemotherapy, and (3) the patterns of immune infiltration that predict treatment response and clinical outcome. We will discuss the benefits of each technique, our findings in sarcoma, and applicability to other solid tumors.