Best practices for variant calling in clinical sequencing

DC Koboldt - Genome medicine, 2020 - Springer
Next-generation sequencing technologies have enabled a dramatic expansion of clinical
genetic testing both for inherited conditions and diseases such as cancer. Accurate variant …

Patient-derived explants (PDEs) as a powerful preclinical platform for anti-cancer drug and biomarker discovery

IR Powley, M Patel, G Miles, H Pringle… - British journal of …, 2020 - nature.com
Preclinical models that can accurately predict outcomes in the clinic are much sought after in
the field of cancer drug discovery and development. Existing models such as organoids and …

A deep-learning model for transforming the style of tissue images from cryosectioned to formalin-fixed and paraffin-embedded

KB Ozyoruk, S Can, B Darbaz, K Başak… - Nature Biomedical …, 2022 - nature.com
Histological artefacts in cryosectioned tissue can hinder rapid diagnostic assessments
during surgery. Formalin-fixed and paraffin-embedded (FFPE) tissue provides higher quality …

Tumor mutation burden as a biomarker in resected non–small-cell lung cancer

S Devarakonda, F Rotolo, MS Tsao, I Lanc… - Journal of Clinical …, 2018 - ascopubs.org
Purpose The survival benefit with adjuvant chemotherapy for patients with resected stage II-
III non–small-cell lung cancer (NSCLC) is modest. Efforts to develop prognostic or predictive …

A critical spotlight on the paradigms of FFPE-DNA sequencing

TA Steiert, G Parra, M Gut, N Arnold… - Nucleic Acids …, 2023 - academic.oup.com
In the late 19th century, formalin fixation with paraffin-embedding (FFPE) of tissues was
developed as a fixation and conservation method and is still used to this day in routine …

ERIC recommendations for TP53 mutation analysis in chronic lymphocytic leukemia—update on methodological approaches and results interpretation

J Malcikova, E Tausch, D Rossi, LA Sutton, T Soussi… - Leukemia, 2018 - nature.com
In chronic lymphocytic leukemia (CLL), TP53 gene defects, due to deletion of the 17p13
locus and/or mutation (s) within the TP53 gene, are associated with resistance to …

Best practices for bioinformatic characterization of neoantigens for clinical utility

MM Richters, H **a, KM Campbell, WE Gillanders… - Genome medicine, 2019 - Springer
Neoantigens are newly formed peptides created from somatic mutations that are capable of
inducing tumor-specific T cell recognition. Recently, researchers and clinicians have …

Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project

P Robbe, N Popitsch, SJL Knight, P Antoniou… - Genetics in …, 2018 - nature.com
Purpose Fresh-frozen (FF) tissue is the optimal source of DNA for whole-genome
sequencing (WGS) of cancer patients. However, it is not always available, limiting the …

Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients

M Menzel, S Ossowski, S Kral, P Metzger… - NPJ Precision …, 2023 - nature.com
A growing number of druggable targets and national initiatives for precision oncology
necessitate broad genomic profiling for many cancer patients. Whole exome sequencing …

[HTML][HTML] Next-generation sequencing in high-sensitive detection of mutations in tumors: challenges, advances, and applications

RR Singh - The Journal of Molecular Diagnostics, 2020 - Elsevier
Next-generation sequencing (NGS) technologies have come of age as preferred
technologies for screening of genomic variants of pathologic and therapeutic potential …