[PMID: 29973584] [Nature Communications]

Systematic discovery of germline cancer predisposition genes through the identification of somatic second hits

“a statistical method, ALFRED, that tests Knudson’s two-hit hypothesis to systematically identify CPGs (cancer predisposition genes) from cancer genome data.”


SEQC and Biscuit

[PMID: 29961579] [Cell]

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

“We profiled 45,000 immune cells from eight breast carcinomas, as well as matched normal breast tissue, blood, and lymph nodes, using single-cell RNA-seq. We developed a preprocessing pipeline, SEQC, and a Bayesian clustering and normalization method, Biscuit, to address computational challenges inherent to single-cell data. Despite significant similarity between normal and tumor tissue-resident immune cells, we observed continuous phenotypic expansions specific to the tumor microenvironment. “


[PMID: 29915429] [Nature Genetics]

Accurate genotyping across variant classes and lengths using variant graphs

“a new method (BayesTyper) that uses exact alignment of read k-mers to a graph representation of the reference and variants to efficiently perform unbiased, probabilistic genotyping across the variation spectrum.”  The BayesTyper genotyping process occurs in two stages: 1) Generation of variant candidates (using other tools); 2) Genotyping based on variant candidates (using BayesTyper). As indicated, BayesTyper does not find candidate variants on its own.