Chip Stewart

SVelfie: A method for discovering cancer drivers based on enrichment of likely functional structural variants

SVelfie identifies cancer driver genes by analyzing enrichment of functional structural variants in cancer genomes.

Integrative Analysis of Checkpoint Blockade Response in Advanced Non-Small Cell Lung Cancer

This study identifies molecular and immune features associated with response to anti-PD-(L)1 therapy in NSCLC using a cohort of 393 patients.

Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma

The paper develops DNA- and RNA-based models combining immune and tumor features to predict outcomes of checkpoint inhibition in melanoma.

Genomic signatures of past and present chromosomal instability in the evolution of Barretts esophagus to esophageal adenocarcinoma

This study identifies genomic signatures of chromosomal instability in Barrett's esophagus progressing to esophageal adenocarcinoma, showing sloping copy-number variation as a precursor to complexity.

Genomic footprints of activated telomere maintenance mechanisms in cancer

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

Spatial Genome Organization as a Framework for Somatic Alterations in Human Cancer

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.

Calling Somatic SNVs and Indels with Mutect2

Mutect2 calls somatic SNVs and indels via local haplotype assembly, Bayesian genotyping and F-score-optimised filtering, with roughly one false call per 5 Mb in exome replicate-versus-replicate tests.

A comprehensive analysis of RNA sequences reveals macroscopic somatic clonal expansion across normal tissues

This study analyzes RNA-seq data from 6,700 normal tissues to identify somatic mutations and their association with age and tissue proliferation, finding tissue-specific cancer mutation hotspots.

Comprehensive analysis of tumour initiation, spatial and temporal progression under multiple lines of treatment

PhylogicNDT statistically reconstructs cancer driver timing, subclonal phylogenies, and population dynamics from single- or multi-timepoint sequencing, revealing subtype-specific trajectories and therapy resistance evolution across 498 lung adenocarcinomas.

Genome-wide detection of structural variants and indels by local assembly

SvABA detects structural variants and indels using genome-wide local assembly, showing improved sensitivity and specificity, especially for small variants and complex rearrangements in cancer genomes.

FireCloud, a scalable cloud-based platform for collaborative genome analysis: Strategies for reducing and controlling costs

Four levers for cheaper cloud genomics on FireCloud: size virtual disks dynamically, tune VM provisioning from monitoring data, buy preemptible machines, and parallelise tasks at the right width.

Selective and mechanistic sources of recurrent rearrangements across the cancer genome

The paper analyzes somatic rearrangements in cancer genomes using whole-genome sequencing data, identifying recurrent breakpoints and their genomic features.