KEY TAKEAWAYS
- The study aimed to investigate the efficacy of a targeted capture approach for determining SHM status in the IGHV gene in patients with CLL.
- Researchers noticed that a targeted capture approach enables broad CLL prognostication via IGHV SHM integration in a single assay.
The somatic hypermutation (SHM) status of the immunoglobulin heavy variable (IGHV) gene is pivotal for assessing the prognosis and guiding treatment decisions in patients with chronic lymphocytic leukemia (CLL). However, the conventional method for determining SHM status, involving multiplex polymerase chain reaction (PCR) and Sanger sequencing of the immunoglobulin heavy locus, suffers from limitations such as low throughput, susceptibility to failure, and lack of compatibility with multiplexing other diagnostic assays.
Jennifer M Grants and the team aimed to address these challenges by exploring an alternative approach for assessing SHM status in patients with CLL.
They conducted an inclusive analysis wherein a DNA-targeted capture approach was devised and validated to detect SHM status in the IGHV gene. This method was integrated as a submodule within a larger next-generation sequencing (NGS) panel comprising probes for various genes associated with CLL prognosis and treatment, including ATM, BIRC3, CHD2, KLHL6, MYD88, NOTCH1, NOTCH2, POT1, SF3B1, TP53, and XPO1. Inputting FASTQ files, the assay yields a comprehensive report consistent with the European Research Initiative on CLL guidelines, detailing IGHV SHM status and V allele usage.
The approach was validated on 35 CLL patient samples, 34 of which had been characterized via Sanger sequencing. Using the NGS panel, IGHV SHM status was successfully identified in 34 out of 35 patients with CLL. Sensitivity and specificity were demonstrated to be 100% among the 33 CLL samples with both NGS and Sanger sequencing calls. Additionally, it was shown that this panel could be integrated with other targeted capture panels to detect prognostically relevant CLL single nucleotide variants, insertions/deletions, and copy number variants, particularly TP53 copy number loss.
The study concluded that a targeted capture approach for detecting IGHV SHM can seamlessly integrate into broader sequencing panels, thereby enabling comprehensive prognostication of CLL within a single molecular assay.
The study was sponsored by a Large Scale Applied Research Project funded by Genome Canada, Genome British Columbia, Canadian Institutes of Health Research, the British Columbia Cancer Foundation, and the Provincial Health Services Authority.
Source: https://pubmed.ncbi.nlm.nih.gov/38175592/
Grants JM, May C, Bridgers J, et al. (2024). “Chronic Lymphocytic Leukemia IGHV Somatic Hypermutation Detection by Targeted Capture Next-Generation Sequencing.” Clin Chem. 2024 Jan 4;70(1):273-284. doi: 10.1093/clinchem/hvad147. PMID: 38175592.
