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
April 30, 2021
Human transthyretin binding affinity of halogenated thiophenols and halogenated phenols: An in vitro and in silico study
Introduction: Daratumumab (DARA) is a human IgG1κ monoclonal antibody that binds with high affinity to a unique epitope on CD38. DARA monotherapy has shown promising activity in relapsed and/or refractory…
Journal: Chemosphere
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
April 12, 2021
Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of…
Journal: Nature Biotechnology
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