Andrew D. Cherniack

TangentXY improves copy-number estimation for sex chromosomes, revealing associations between chrX and chrY copy-number alterations and cancer features.

This study analyzes genomic alterations in a large IBC cohort, finding high TP53 mutation frequency and NOTCH pathway enrichment, but no major genomic differences compared to non-IBC cases.

This paper introduces two methods to detect recurrent genomic rearrangements in cancer genomes and identifies 80 simple and 29 complex rearrangements across 2,500 cancers.

The paper identifies ancestry-specific germline variants in cancer predisposition genes and their somatic effects across diverse populations.

The paper introduces Tangent and Pseudo-Tangent pipelines for copy-number inference from cancer genome data, improving noise reduction and accuracy in SNP array and WES analyses.

This study characterizes genomic, transcriptomic, and epigenomic artifacts in FFPE tissues and provides best practices to mitigate their impact on molecular analysis.