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

Abstract

IntroductionThe 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.MethodsFor 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.ResultsBoth 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.DiscussionThe 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.

The impact of comparative genomic hybridization/single‐nucleotide polymorphism microarray in risk stratification of pediatric acute lymphoblastic leukemia

“…Novel molecular modalities with the ability to assess aneuploidies, CNA, and structural variations such as whole-genome sequencing and optical genome mapping have been investigated in ALL workup, and may be increasingly used in clinical laboratories in the future. 36,37 Furthermore, the costs of CGH/SNP microarray and G-banding karyotypes are currently equivalent at our institution; further cost-effectiveness analysis would be necessary to fully compare each modality.…”

Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia

“…This may be due to differences in how these subtypes were defined in the training sets. PAX5 alterations have been carefully curated in the Nordics, based on a combination of PCR and high-resolution genome-wide analyses 21 , 42 , 63 , 64 . For example, the PAX5 -driven aberration dic(9;20) was included as an obligatory risk-stratifying subgroup in the NOPHO-2008 protocol, and thus this aberration has been studied in detail 38 , 65 .…”

High‐throughput molecular assays for inclusion in personalised oncology trials – State‐of‐the‐art and beyond

“…In a recent Swedish study, WGS provided clinically relevant information in >90% of patients with paediatric solid tumours while adding new information in half of patients and contributed to the revision of the diagnosis in a few cases [37]. In most studies including haematological malignancies, an almost perfect match with the findings of standard‐of‐care assays has been reported while also providing new clinically important information in a proportion of patients [38, 39]. In sarcomas, which consist of around 100 entities [40], WGS significantly improves the diagnostic procedure and identifies treatment targets, and, as evidenced by the Dutch experience, the WGS workflow can be integrated in routine diagnostics [41].…”