Gavin Ha

2014 PhD Graduate
Papers

ReMixT: clone-specific genomic structure estimation in cancer.

Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes.

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

Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.

Multifocal endometriotic lesions associated with cancer are clonal and carry a high mutation burden.

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

An RCOR1 loss-associated gene expression signature identifies a prognostically significant DLBCL subgroup.

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

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.

PyClone: statistical inference of clonal population structure in cancer.

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.

Mutation discovery in regions of segmental cancer genome amplifications with CoNAn-SNV: a mixture model for next generation sequencing of tumors.

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

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.

Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers.

Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities.

deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.

ARID1A mutations in endometriosis-associated ovarian carcinomas.

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.