Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia

Fatemah Rezayee; Jesper Eisfeldt; Aron Skaftason; Ingegerd Öfverholm; Shumaila Sayyab; Ann Christine Syvänen; Khurram Maqbool; Henrik Lilljebjörn; Bertil Johansson; Linda Olsson-Arvidsson; Christina Orsmark Pietras; Anna Staffas; Lars Palmqvist; Thoas Fioretos; Lucia Cavelier; Linda Fogelstrand; Jessica Nordlund; Valtteri Wirta; Richard Rosenquist; Gisela Barbany

doi:10.3389/fonc.2023.1217712

Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia

Front Oncol. 2023 Aug 14:13:1217712. doi: 10.3389/fonc.2023.1217712. eCollection 2023.

Authors

Fatemah Rezayee^{1

2}, Jesper Eisfeldt^{1

2}, Aron Skaftason^{1

3}, Ingegerd Öfverholm^{1

2}, Shumaila Sayyab^{4

5}, Ann Christine Syvänen^{4

5}, Khurram Maqbool⁶, Henrik Lilljebjörn⁷, Bertil Johansson^{7

8}, Linda Olsson-Arvidsson^{7

8}, Christina Orsmark Pietras⁷, Anna Staffas^{9

10}, Lars Palmqvist^{11

12}, Thoas Fioretos^{7

8

13}, Lucia Cavelier^{1

2}, Linda Fogelstrand^{11

12}, Jessica Nordlund^{4

5}, Valtteri Wirta^{14

15}, Richard Rosenquist^{1

2

15}, Gisela Barbany^{1

2}

Affiliations

¹ Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
² Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
³ Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
⁴ Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
⁵ Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
⁶ Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
⁷ Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.
⁸ Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden.
⁹ Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden.
¹⁰ Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
¹¹ Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden.
¹² Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
¹³ Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden.
¹⁴ Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
¹⁵ Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden.

Abstract

Introduction: The suitability of whole-genome sequencing (WGS) as the sole method to detect clinically relevant genomic aberrations in B-cell acute lymphoblastic leukemia (ALL) was investigated with the aim of replacing current diagnostic methods.

Methods: For this purpose, we assessed the analytical performance of 150 bp paired-end WGS (90x leukemia/30x germline). A set of 88 retrospective B-cell ALL samples were selected to represent established ALL subgroups as well as ALL lacking stratifying markers by standard-of-care (SoC), so-called B-other ALL.

Results: Both the analysis of paired leukemia/germline (L/N)(n=64) as well as leukemia-only (L-only)(n=88) detected all types of aberrations mandatory in the current ALLTogether trial protocol, i.e., aneuploidies, structural variants, and focal copy-number aberrations. Moreover, comparison to SoC revealed 100% concordance and that all patients had been assigned to the correct genetic subgroup using both approaches. Notably, WGS could allocate 35 out of 39 B-other ALL samples to one of the emerging genetic subgroups considered in the most recent classifications of ALL. We further investigated the impact of high (90x; n=58) vs low (30x; n=30) coverage on the diagnostic yield and observed an equally perfect concordance with SoC; low coverage detected all relevant lesions.

Discussion: The filtration of the WGS findings with a short list of genes recurrently rearranged in ALL was instrumental to extract the clinically relevant information efficiently. Nonetheless, the detection of DUX4 rearrangements required an additional customized analysis, due to multiple copies of this gene embedded in the highly repetitive D4Z4 region. We conclude that the diagnostic performance of WGS as the standalone method was remarkable and allowed detection of all clinically relevant genomic events in the diagnostic setting of B-cell ALL.

Keywords: B-cell acute lymphoblastic leukemia; class-defining genetic lesions; diagnostic validation; genomic aberrations; whole-genome sequencing.

Copyright © 2023 Rezayee, Eisfeldt, Skaftason, Öfverholm, Sayyab, Syvänen, Maqbool, Lilljebjörn, Johansson, Olsson-Arvidsson, Pietras, Staffas, Palmqvist, Fioretos, Cavelier, Fogelstrand, Nordlund, Wirta, Rosenquist and Barbany.

Grants and funding

This work was supported by the Science for Life Laboratory Swedish Genomes Program. The Swedish Genomes Program has been made available with support from the Knut and Alice Wallenberg Foundation. We also acknowledge the support from the Swedish Childhood Cancer Fund (Barncancerfonden) through grants TJ 2021-0082, PR2019-0072, and PR 2022-00.76, and the Swedish Research Council grant 2018-05661 under the frame of ERA PerMed.