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
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
Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
Background Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence…
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
March 15, 2018
Integrity, standards, and QC-related issues with big-data in pre-clinical drug discovery
The tremendous expansion of data analytics and public and private big datasets presents an important opportunity for pre-clinical drug discovery and development. In the field of life sciences, the growth…
Journal: Biochemical Pharmacology
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