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Multicenter Study
. 2024 Nov:211:114306.
doi: 10.1016/j.ejca.2024.114306. Epub 2024 Sep 8.

Benchmarking whole exome sequencing in the German network for personalized medicine

Michael Menzel  1 , Mihaela Martis-Thiele  2 , Hannah Goldschmid  3 , Alexander Ott  4 , Eva Romanovsky  3 , Janna Siemanowski-Hrach  5 , Lancelot Seillier  6 , Nadina Ortiz Brüchle  7 , Angela Maurer  8 , Kjong-Van Lehmann  9 , Matthias Begemann  10 , Miriam Elbracht  11 , Robert Meyer  12 , Sebastian Dintner  13 , Rainer Claus  14 , Jan P Meier-Kolthoff  15 , Eric Blanc  16 , Markus Möbs  17 , Maria Joosten  17 , Manuela Benary  18 , Patrick Basitta  19 , Florian Hölscher  19 , Verena Tischler  19 , Thomas Groß  20 , Oliver Kutz  21 , Rebecca Prause  20 , Doreen William  22 , Kai Horny  23 , Wolfgang Goering  24 , Sugirthan Sivalingam  25 , Arndt Borkhardt  26 , Cornelia Blank  25 , Stefanie V Junk  27 , Layal Yasin  27 , Evgeny A Moskalev  28 , Maria Giulia Carta  28 , Fulvia Ferrazzi  29 , Lars Tögel  28 , Steffen Wolter  30 , Eugen Adam  30 , Uta Matysiak  30 , Tessa Rosenthal  31 , Jürgen Dönitz  32 , Ulrich Lehmann  33 , Gunnar Schmidt  34 , Stephan Bartels  33 , Winfried Hofmann  34 , Steffen Hirsch  35 , Nicola Dikow  35 , Kirsten Göbel  36 , Rouzbeh Banan  36 , Stefan Hamelmann  36 , Annette Fink  3 , Markus Ball  37 , Olaf Neumann  3 , Jan Rehker  5 , Michael Kloth  38 , Justin Murtagh  38 , Nils Hartmann  38 , Phillip Jurmeister  39 , Andreas Mock  39 , Jörg Kumbrink  39 , Andreas Jung  39 , Eva-Maria Mayr  2 , Anne Jacob  2 , Marcel Trautmann  40 , Santina Kirmse  40 , Kim Falkenberg  40 , Christian Ruckert  41 , Daniela Hirsch  42 , Alexander Immel  43 , Wolfgang Dietmaier  42 , Tobias Haack  4 , Ralf Marienfeld  44 , Axel Fürstberger  44 , Jakob Niewöhner  44 , Uwe Gerstenmaier  44 , Timo Eberhardt  45 , Philipp A Greif  46 , Silke Appenzeller  47 , Katja Maurus  48 , Julia Doll  48 , Yvonne Jelting  49 , Danny Jonigk  50 , Bruno Märkl  13 , Dieter Beule  16 , David Horst  17 , Anna-Lena Wulf  19 , Daniela Aust  51 , Martin Werner  52 , Kirsten Reuter-Jessen  31 , Philipp Ströbel  31 , Bernd Auber  34 , Felix Sahm  53 , Sabine Merkelbach-Bruse  5 , Udo Siebolts  5 , Wilfried Roth  38 , Silke Lassmann  54 , Frederick Klauschen  55 , Nadine T Gaisa  56 , Wilko Weichert  2 , Matthias Evert  42 , Sorin Armeanu-Ebinger  4 , Stephan Ossowski  4 , Christopher Schroeder  4 , Christian P Schaaf  35 , Nisar Malek  57 , Peter Schirmacher  3 , Daniel Kazdal  37 , Nicole Pfarr  2 , Jan Budczies  3 , Albrecht Stenzinger  58
Affiliations
Free article
Multicenter Study

Benchmarking whole exome sequencing in the German network for personalized medicine

Michael Menzel et al. Eur J Cancer. 2024 Nov.
Free article

Abstract

Introduction: Whole Exome Sequencing (WES) has emerged as an efficient tool in clinical cancer diagnostics to broaden the scope from panel-based diagnostics to screening of all genes and enabling robust determination of complex biomarkers in a single analysis.

Methods: To assess concordance, six formalin-fixed paraffin-embedded (FFPE) tissue specimens and four commercial reference standards were analyzed by WES as matched tumor-normal DNA at 21 NGS centers in Germany, each employing local wet-lab and bioinformatics. Somatic and germline variants, copy-number alterations (CNAs), and complex biomarkers were investigated. Somatic variant calling was performed in 494 diagnostically relevant cancer genes. The raw data were collected and re-analyzed with a central bioinformatic pipeline to separate wet- and dry-lab variability.

Results: The mean positive percentage agreement (PPA) of somatic variant calling was 76 % while the positive predictive value (PPV) was 89 % in relation to a consensus list of variants found by at least five centers. Variant filtering was identified as the main cause for divergent variant calls. Adjusting filter criteria and re-analysis increased the PPA to 88 % for all and 97 % for the clinically relevant variants. CNA calls were concordant for 82 % of genomic regions. Homologous recombination deficiency (HRD), tumor mutational burden (TMB), and microsatellite instability (MSI) status were concordant for 94 %, 93 %, and 93 % of calls, respectively. Variability of CNAs and complex biomarkers did not decrease considerably after harmonization of the bioinformatic processing and was hence attributed mainly to wet-lab differences.

Conclusion: Continuous optimization of bioinformatic workflows and participating in round robin tests are recommended.

Keywords: Clinical exome; Molecular pathology; Multi-centric inter-laboratory test; Precision oncology; Whole exome sequencing.

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Conflict of interest statement

Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: MMT reports speaker and travel Expenses from Twist. JS reports speaker honoraria from DLS, Molecular Health, AstraZeneca and Biocartis, outside the submitted work. UL reports speaker fees from AstraZeneca, GSK, Novartis, Menarini, advisory board from AstraZeneca and Novartis. DH reports speaker honorary AstraZeneca, adboard BMS, WD speaker honoraries BMS & Novartis. SMB reports speaker honoraria, advisory board fees and research grants from AstraZeneca, Daiichi, Menarini, Novartis, Roche, BMS, Pfizer, Bayer, MSD, Merck, Amgen, Molecular Health, Targos, DLS, Janssen, GSK, QuIP, outside the submitted work. SL reports research grant from BMS, advisory board/speaker invitation from AstraZeneca, Eli Lilly, Roche and Takeda outside of this work. NTG reports research support from Janssen-Cilag and Advisory Boards from Janssen-Cilag, AstraZeneca, Daiichi-Sankyo and BMS outside the submitted work. WW reports research grants from Roche, MSD, BMS and AstraZeneca. Advisory board, lectures and speaker bureau fees from Roche, MSD, BMS, AstraZeneca, Pfizer, Merck, Lilly, Boehringer, Novartis, Takeda, Bayer, Janssen, Amgen, Astellas, Illumina, Eisai, Siemens, Agilent, ADC, GSK und Molecular Health. SO received reimbursement for travel expenses and payment for conference presentations from Illumina Inc. and Oxford Nanopore Technologies. CS reports research funding from BMS Stiftung Immunonkologie and institutional grants from Illumina outside the submitted work. CPS reports an investigator-initiated grant from Illumnia outside of the submitted work. PS reports grants from Inctye, BMS, Gilead, Falk, speakers bureau/advisory board from MSD, BMS, AstraZeneca, Incyte, Astellas, Janssen, Eisai, Amgen, Boehringer Ingelheim. DK reports personal fees for speaker honoraria from AstraZeneca, and Pfizer, personal fees for Advisory Board from Bristol-Myers Squibb, outside the submitted work. NP reports speaker fees from Novartis, Bayer, Roche, AstraZeneca, Illumina, BMS, MSD, PGDX/Labcorp, advisory board from Novartis, Lilly, Roche, Janssen, travel expenses from Novartis, AstraZeneca, Illumina, BMS, MSD, PGDX/Labcorp, Research grants from Illumina. JB reports grants from German Cancer Aid and consulting from MSD, outside the submitted work. AS reports participation in Advisory Board/Speaker’s Bureau for Astra Zeneca, AGCT, Bayer, Bristol-Myers Squibb, Eli Lilly, Illumina, Janssen, MSD, Novartis, Pfizer, Roche, Seattle Genetics, Takeda, and Thermo Fisher, grants from Bayer, Bristol-Myers Squibb, and Chugai, outside the submitted work. All other authors report no conflicts of interest.

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