A multi-modal molecular characterization of the Philadelphia translocation featuring long read sequencing

Abstract

Objective: Clinically significant structural variation (SV), notably chromosomal translocation, results in the formation of fusion genes that drive leukaemogenesis. Detection of SVs is vital in clinical diagnosis, prognosis and therapy of haematological malignancies. Current methods for SV identification are low in sensitivity for cryptic cases and time-consuming for complex cases. This study investigated the feasibility of long read sequencing as an approach for SV detection and precise breakpoint characterization.

Methods: Six archival samples, including 4 bone marrow blood samples (F/66 B-ALL, F/25 B-ALL, M/53 CML, F/34 B-ALL) and 1 cytogenetic cell pellet each in cell culture medium (M/52 CML) or Carnoy's fixative (M/44 CML) with known and previously characterized BCR::ABL1 fusion transcript were selected for study. The genomic DNA was extracted from each case for further breakpoint characterization by long read sequencing (MinION R9.4.1 flow cell, Oxford Nanopore Technologies, UK).

Results: All the genomic breakpoints were concordant with the RNA fusion transcript breakpoints. Three typical (e1a2, e13a2, and e14a2) and 3 variant (e23a2Ins52, e8a2, and e13a2ins74) BCR breakpoints were identified.

Conclusion: Using the Ph translocation as an example, long read sequencing is a promising alternative method to detect SV, revolutionizing detection of chromosomal translocation to a higher precision. A more comprehensive spectrum of SV can be resolved along with cytogenetic results, enabling precise diagnosis and personalized monitoring of haematological malignancies.

Keywords: BCR::ABL1; Chromosomal translocation; Chronic myeloid leukaemia; Long read sequencing; Philadelphia translocation; Structural variation.