Towards accurate and reliable resolution of structural variants for clinical diagnosis

Z Liu, R Roberts, TR Mercer, J Xu, FJ Sedlazeck… - Genome biology, 2022 - Springer
Structural variants (SVs) are a major source of human genetic diversity and have been
associated with different diseases and phenotypes. The detection of SVs is difficult, and a …

Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling

Y Yu, W Hou, Y Liu, H Wang, L Dong, Y Mai… - Nature …, 2024 - nature.com
Certified RNA reference materials are indispensable for assessing the reliability of RNA
sequencing to detect intrinsically small biological differences in clinical settings, such as …

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

W Jones, B Gong, N Novoradovskaya, D Li, R Kusko… - Genome biology, 2021 - Springer
Background Oncopanel genomic testing, which identifies important somatic variants, is
increasingly common in medical practice and especially in clinical trials. Currently, there is a …

2022 White Paper on Recent Issues in Bioanalysis: ICH M10 BMV Guideline & Global Harmonization; Hybrid Assays; Oligonucleotides & ADC; Non-Liquid & Rare …

M Szapacs, W Jian, D Spellman, J Cunliffe… - Bioanalysis, 2023 - Taylor & Francis
Abstract The 16th Workshop on Recent Issues in Bioanalysis (16th WRIB) took place in
Atlanta, GA, USA on September 26–30, 2022. Over 1000 professionals representing …

Concordance study of a 520-gene next-generation sequencing-based genomic profiling assay of tissue and plasma samples

M Wang, X Chen, Y Dai, D Wu, F Liu, Z Yang… - Molecular Diagnosis & …, 2022 - Springer
Introduction Next-generation sequencing (NGS) enables simultaneous detection of
actionable somatic variants and estimation of genomic signatures such as tumor mutational …

The Sequencing Quality Control 2 study: establishing community standards for sequencing in precision medicine

TR Mercer, J Xu, CE Mason, W Tong… - Genome Biology, 2021 - Springer
The MicroArray and Sequencing Quality Control (MAQC) consortium is a FDA-led,
community-wide effort to evaluate the use of genomic technologies in clinical applications …

Clinical validation of a single NGS targeted panel pipeline using the KAPA HyperChoice system for detection of germline, somatic and mitochondrial sequence and …

J Kerkhof, C Rastin, L Schenkel, H Lin… - Expert Review of …, 2023 - Taylor & Francis
Background Comprehensive molecular diagnostics are highly dependent on the technical
performance of next-generation sequencing (NGS) pipelines, which are assessed by data …

Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples

Y Zhang, TM Blomquist, R Kusko, D Stetson, Z Zhang… - Genome Biology, 2022 - Springer
Background Clinical laboratories routinely use formalin-fixed paraffin-embedded (FFPE)
tissue or cell block cytology samples in oncology panel sequencing to identify mutations that …

Assessments of tumor mutational burden estimation by targeted panel sequencing: A comprehensive simulation analysis

D Li, D Wang, DJ Johann Jr… - … Biology and Medicine, 2023 - journals.sagepub.com
Tumor mutational burden (TMB), when at a high level, is an emerging indicative factor of
sensitivity to immune checkpoint inhibitors. Previous studies have shown that the more …

Ultra-deep sequencing data from a liquid biopsy proficiency study demonstrating analytic validity

B Gong, IW Deveson, T Mercer, DJ Johann Jr, W Jones… - Scientific Data, 2022 - nature.com
Recently we reported the accuracy and reproducibility of circulating tumor DNA (ctDNA)
assays using a unique set of reference materials, associated analytical framework, and …