[PMID: 29860484] [Nucleic Acids Research]

VarAFT: a variant annotation and filtration system for human next generation sequencing data

“VarAFT is a multiplatform freely available software that allows the simultaneous annotation, filtration, and breadth and depth of coverage analysis of WES, WGS and targeted sequencing experiments from any sequencing platform. Its graphical user interface, various modules and unique features, such as pathogenicity predictions from UMD-Predictor and HSF, allow untrained users to rapidly highlight disease-causing mutations in multiple genetic scenarios.”


Subclonal Architectures from Bulk Seq

[PMID: 29808029] [Nature Genetics]

Quantification of subclonal selection in cancer from bulk sequencing data

“Here we build upon theoretical population-genetics models of asexual evolution and Bayesian statistical inference on genetic data to measure cancer evolution in human tumors.”

Heritability from EHR

[PMID: 29779949] [Cell]

Disease Heritability Inferred from Familial Relationships Reported in Medical Records

“We mined emergency contact data at three academic medical centers and identified 7.4 million familial relationships while maintaining patient privacy. Identified relationships were consistent with genetically derived relatedness. We used EHR data to compute heritability estimates for 500 disease phenotypes. Overall, estimates were consistent with the literature and between sites. Inconsistencies were indicative of limitations and opportunities unique to EHR research.”

Multi-region Omics in Ovarian Cancer

[PMID: 29754820] [Cell]

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer

“Through multi-region study of 212 samples from 38 patients with whole-genome sequencing, immunohistochemistry, histologic image analysis, gene expression profiling, and T and B cell receptor sequencing, we identified three immunologic subtypes across samples and extensive within-patient diversity. “