Leveraging off-target reads in panel sequencing for homologous recombination repair deficiency screening in tumor.

Journal

The Journal of molecular diagnostics : JMD
ISSN: 1943-7811
Titre abrégé: J Mol Diagn
Pays: United States
ID NLM: 100893612

Informations de publication

Date de publication:
22 Mar 2024
Historique:
received: 22 09 2023
revised: 24 01 2024
accepted: 14 02 2024
medline: 25 3 2024
pubmed: 25 3 2024
entrez: 24 3 2024
Statut: aheadofprint

Résumé

Targeted tumor only sequencing has become a standard practice in cancer diagnostics. This study aims to develop an approach for robust copy number variant (CNV) calling in tumor samples using only off-target region (OTR) reads. We also established a clinical use case for homologous recombination deficiency (HRD) score estimation (HRDest) using the sum of telomeric allelic imbalance (TAI) and large-scale state transitions (LST) scores without the need for loss of heterozygosity (LOH) information. We demonstrated a strong correlation between HRD score and the sum of TAI + LST in the TCGA cohort (rho = 0.99, p < 2.2x 10

Identifiants

DOI: 10.1016/j.jmoldx.2024.02.008 PMID: 38522840
pubmed: 38522840
pii: S1525-1578(24)00060-6
doi: 10.1016/j.jmoldx.2024.02.008
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Informations de copyright

Copyright © 2024. Published by Elsevier Inc.

Auteurs

Markus Ball (M)

Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.

Iordanis Ourailidis (I)

Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.

Klaus Kluck (K)

Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.

Michael Menzel (M)

Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.

Martina Kirchner (M)

Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.

Michael Allgäuer (M)

Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.

Timothy Kwang Yong Tay (TK)

Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Department of Anatomical Pathology, Department of Molecular Pathology, Singapore General Hospital, Singapore.

Fabian Schnecko (F)

Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.

Anna-Lena Volckmar (AL)

Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.

Hannah Goldschmid (H)

Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.

Olaf Neuman (O)

Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.

Stefan Fröhling (S)

Department of Translational Medical Oncology, National Center for Tumor Diseases, Heidelberg, Germany; German Cancer Consortium (DKTK), Germany.

Peter Schirmacher (P)

Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Center for Personalized Medicine Heidelberg (ZPM), Heidelberg, Germany.

Jan Budczies (J)

Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; German Cancer Consortium (DKTK), Germany; Center for Personalized Medicine Heidelberg (ZPM), Heidelberg, Germany; Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Germany.

Albrecht Stenzinger (A)

Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; German Cancer Consortium (DKTK), Germany; Center for Personalized Medicine Heidelberg (ZPM), Heidelberg, Germany; Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Germany. Electronic address: albrecht.stenzinger@med.uni-heidelberg.de.

Daniel Kazdal (D)

Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; German Cancer Consortium (DKTK), Germany; Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Germany. Electronic address: daniel.kazdal@med.uni-heidelberg.de.

Classifications MeSH