Publications
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January 3, 2022
Assessing reproducibility of inherited variants detected with short-read whole genome sequencing
Background Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant…
Journal: Genome Biology
December 10, 2021
FDA-led consortium studies advance quality control of targeted next generation sequencing assays for precision oncology
Abstract: Cancer is the second leading cause of mortality worldwide despite tremendous advances in treatment. The promise of precision oncology depends on accurate characterization of tumor mutations and subsequent therapy selection….
Journal: Precision Cancer Medicine
November 17, 2021
Reporting guidelines for human microbiome research: the STORMS checklist
The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for…
Journal: Nature Medicine
November 3, 2021
Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA
Despite an increasing demand for precision medicine enabled by NGS measurement of actionable mutations in circulating tumor DNA (ctDNA) specimens, the ability to reliably measure and report low-frequency mutations using…
Journal: Cell Reports
October 4, 2021
Orchestrating and sharing large multimodal data for transparent and reproducible research
Reproducibility is essential to open science, as there is limited relevance for findings that can not be reproduced by independent research groups, regardless of its validity. It is therefore crucial…
Journal: Nature Communications
September 9, 2021
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics….
Journal: Nature Biotechnology
Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study…
Journal: Nature Biotechnology
June 3, 2021
Crowdsourced mapping of unexplored target space of kinase inhibitors
Despite decades of intensive search for compounds that modulate the activity of particular protein targets, a large proportion of the human kinome remains as yet undrugged. Effective approaches are therefore…
Journal: Nature Communications
April 27, 2021
A primer on applying AI synergistically with domain expertise to oncology
Abstract Background The concurrent growth of large-scale oncology data alongside the computational methods with which to analyze and model it has created a promising environment for revolutionizing cancer diagnosis, treatment,…
Journal: Biochimica et Biophysica Acta (BBA) - Reviews on Cancer
April 16, 2021
A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
Oncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having…
Journal: Genome Biology
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