Gavin Ha

Principal investigator
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ghaobfuscate@fredhutch.org

I am an Assistant Member at the Fred Hutch in the Computational Biology Program and Public Health Sciences Division. I joined the faculty starting in July of 2018.

I received my BSc in Microbiology/Immunology and Computer Science from the University of British Columbia (UBC) in 2008. I completed a PhD in Bioinformatics in 2014, also at UBC, while working at the BC Cancer Agency under the supervision of Dr. Sohrab Shah and Dr. Sam Aparicio. In my doctoral work, I developed computational algorithms using Bayesian and machine learning approaches to analyze cancer genome data. I applied these methods to help uncover new insights into the aberrant genomes of ovarian and breast cancer. These contributions led to the Lloyd Skarsgard Graduate Research Excellence Award for most outstanding PhD research at the BC Cancer Agency.

I then joined the laboratory of Matthew Meyerson at the Dana-Farber Cancer Institute and the Broad Institue of MIT & Harvard as a postdoctoral fellow. Here, I worked on developing computational methods for analyzing long-range DNA sequencing technologies Using these approaches, we discovered novel non-coding alterations containing enhancers of the androgen receptor gene in metastatic prostate cancer. Furthermore, I was instrumental in establishing a scalable workflow to study genomes and exomes of cell-free DNA from liquid biopsies.

Outside of science, I enjoy spending time with my family. I have a 2 year old daughter and another baby girl on the way. In my free time, my hobbies include volleyball and powerlifting. I am also a sports fan and watch a lot of tennis, hockey and basketball.

Papers

Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing

Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

Projects

SV_10X_analysis - Structural variation analysis of 10X Genomics linked-read data

TitanCNA_10X_snakemake - Snakemake workflow for 10X Genomics WGS analysis using TitanCNA

TitanCNA - Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer

ichorCNA - Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

Posts

Postdoc position available

Paper on structural alterations in prostate cancer published in Cell

New website for the (Gavin) Ha Lab