Optical genome mapping, a promising alternative to gold standard cytogenetic approaches in a series of acute lymphoblastic leukemias

Abstract

Acute lymphoblastic leukemias (ALL) are characterized by a large number of cytogenetic abnormalities of clinical interest that require the use of several complementary techniques. Optical genome mapping (OGM) is based on analysis of ultra-high molecular weight DNA molecules that provides a high-resolution genome-wide analysis highlighting copy number and structural anomalies, including balanced translocations.We compared OGM to standard techniques (karyotyping, fluorescent in situ hybridization, single nucleotide polymorphism-array and reverse transcription multiplex ligation-dependent probe amplification) in 10 selected B or T-ALL. Eighty abnormalities were found using standard techniques of which 72 (90%) were correctly detected using OGM. Eight discrepancies were identified, while 12 additional anomalies were found by OGM. Among the discrepancies, four were detected in raw data but not retained because of filtering issues. However, four were truly missed, either because of a low variant allele frequency or because of a low coverage of some regions. Of the additional anomalies revealed by OGM, seven were confirmed by another technique, some of which are recurrent in ALL such as LMO2-TRA and MYC-TRB fusions. Despite false positive anomalies due to background noise and a case of inter-sample contamination secondarily identified, the OGM technology was relatively simple to use with little practice. Thus, OGM represents a promising alternative to cytogenetic techniques currently performed for ALL characterization. It enables a time and cost effective analysis allowing identification of complex cytogenetic events, including those currently inaccessible to standard techniques. K E Y W O R D S acute lymphoblastic leukemia, chromosome mapping, cytogenetics, optical genome mapping 1 | INTRODUCTION Acute lymphoblastic leukemias (ALLs) are neoplasms resulting from an early blockage of cells committed to B or T-lymphoid lineage.Although rare (1.7 cases/year/100000 inhabitants) in the general population, they are the most common cancer in children, with an incidence approximately three times higher than in adults. 1 ALLs are pathologies of great genetic diversity 2-4 which routinely require the

Optimizing the diagnostic workflow for acute lymphoblastic leukemia by optical genome mapping

“…16,18 Following this finding the OGM analytical soft- this study. 16,18 Moreover, Lestringant et al also reported cross-contamination between samples, a problem we did not encounter. 16 Besides potentially missing important alterations, OGM sometimes also provides false-positive results.…”

“…Discordances were seen in 3 cases where there was a gain or loss of an almost entire haploid/diploid set (changes in ploidy). In 2 cases with low hypodiploidy (12,16), the chromosomal gains were correctly identified by OGM but the results were incorrectly interpreted as hyperdiploid (Table 2). The OGM software allows you to manually plot the zygosity states of all the SVs (using filter set B, described in Supplementary Methods (Data S1) section, on the "De Novo Assembly" data), chromosome per chromosome.…”

The Clinical Utility of Optical Genome Mapping for the Assessment of Genomic Aberrations in Acute Lymphoblastic Leukemia

“…With the aim to test the feasibility of OGM in the genetic classification of pediatric ALL, we selected genetically well-characterized ALL samples, which were intensively analyzed by well-established technologies (SNP-array, RNA-Seq, FISH, karyotyping, MLPA) used within our routine diagnostic workflow. Recently, it was shown that OGM may have the potential to be a routine tool in malignant hematology [24]. We show here for the first time that OGM allowed the detection of all chromosomal stratification-relevant genomic markers in ALL, including translocations, aneuploidies, and copy number profiles including IKZF1 plus in a retrospective as well as in a prospective manner.…”

“…The detection resolution for SVs mainly depends on the label distribution (~15 labels/100 kb) and can be as low as some hundred bp due to the calculation of label distances. A limitation of OGM is the detection of whole arm translocations (Robertsonian translocations) and SVs located in telomeric regions due to the absence of labels in these regions Depending on the amount of data generated (up to 4000 Gb), detection of SVs with allele frequencies below 10% may be possible [24]. Similar to observations by Lestringant et al, we were not able to detect CRLF2/P2RY8 fusions in patients #2 and #5 because of subclonality (#2) and the repetitive nature of the PAR region at Xp22.33 [24].…”

“…A limitation of OGM is the detection of whole arm translocations (Robertsonian translocations) and SVs located in telomeric regions due to the absence of labels in these regions Depending on the amount of data generated (up to 4000 Gb), detection of SVs with allele frequencies below 10% may be possible [24]. Similar to observations by Lestringant et al, we were not able to detect CRLF2/P2RY8 fusions in patients #2 and #5 because of subclonality (#2) and the repetitive nature of the PAR region at Xp22.33 [24]. To integrate OGM into the routine diagnostic workflow and on a larger scale, further validation and optimization of the workflow (e.g., increasing computing capacity and automated sample preparation to reduce processing time) is required.…”