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 am also an Affiliate Assistant Professor in the Department of Genome Sciences at the University of Washington.

I received my BSc in Microbiology & Immunology and Computer Science from the University of British Columbia (UBC) in 2008. In 2014, I completed a PhD in Bioinformatics from the Bioinformatics Training Program 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 Dr. 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 2 daughters, a 3-year-old and a 1-year-old. In my free time, my hobbies include playing volleyball and powerlifting. I am also a sports fan and follow tennis, hockey and basketball.

Papers

Distinctions between metastatic lower and upper tract urothelial carcinoma revealed through rapid autopsy

Detection of Circulating Tumor DNA in Patients With Leiomyosarcoma With Progressive Disease

Tumor fraction in cell-free DNA as a biomarker in prostate cancer

Genetic and transcriptional evolution alters cancer cell line drug response

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

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

Detection of Somatic Structural Variants Enables Quantification and Characterization of Circulating Tumor DNA in Children With Solid Tumors

Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

Genomic discovery and clonal tracking in multiple myeloma by cell-free DNA sequencing

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

The integrated genomic landscape of thymic epithelial tumors

Patient-derived xenografts undergo mouse-specific tumor evolution

Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma

Somatic super-enhancer duplications and hotspot mutations lead to oncogenic activation of the KLF5 transcription factor

Genetic interrogation of circulating multiple myeloma cells at single-cell resolution

Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting

The landscape of chromosomal aberrations in breast cancer mouse models reveals driver-specific routes to tumorigenesis

Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution

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

Distinguishing Somatic and Germline Copy Number Events in Cancer Patient DNA Hybridized to Whole-Genome SNP Genotyping Arrays

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

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

Projects

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

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

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

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

Posts

Maggie and Will join the lab for their MCB rotations.

Anna Hoge joins the lab.

Jonathan Reichel joins the lab.

Eliza Barkan joins the lab for her rotation.

Anna-Lisa Doebley joins the lab. Welcome, Anna-Lisa!

Welcome to the lab, Katharine Chen and Megan Chiang

Computational Biologist/Bioinformatics Analyst position available

Postdoc position available

Paper on structural alterations in prostate cancer published in Cell

New website for the (Gavin) Ha Lab