1
|
Chow S, Kis O, Mulder DT, Danesh A, Bruce J, Wang TT, Reece D, Bhalis N, Neri P, Sabatini PJ, Keats J, Trudel S, Pugh TJ. Myeloma immunoglobulin rearrangement and translocation detection through targeted capture sequencing. Life Sci Alliance 2023; 6:e202201543. [PMID: 36328595 PMCID: PMC9644417 DOI: 10.26508/lsa.202201543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
Multiple myeloma is a plasma cell neoplasm characterized by clonal immunoglobulin V(D)J signatures and oncogenic immunoglobulin gene translocations. Additional subclonal genomic changes are acquired with myeloma progression and therapeutic selection. PCR-based methods to detect V(D)J rearrangements can have biases introduced by highly multiplexed reactions and primers undermined by somatic hypermutation, and are not readily extended to include mutation detection. Here, we report a hybrid-capture approach (CapIG-seq) targeting the 3' and 5' ends of the V and J segments of all immunoglobulin loci that enable the efficient detection of V(D)J rearrangements. We also included baits for oncogenic translocations and mutation detection. We demonstrate complete concordance with matched whole-genome sequencing and/or PCR clonotyping of 24 cell lines and report the clonal sequences for 41 uncharacterized cell lines. We also demonstrate the application to patient specimens, including 29 bone marrow and 39 cell-free DNA samples. CapIG-seq shows concordance between bone marrow and cfDNA blood samples (both contemporaneous and follow-up) with regard to the somatic variant, V(D)J, and translocation detection. CapIG-seq is a novel, efficient approach to examining genomic alterations in myeloma.
Collapse
Affiliation(s)
- Signy Chow
- University Health Network, Toronto, Canada
- Sunnybrook Health Sciences Centre, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Olena Kis
- University Health Network, Toronto, Canada
| | | | | | - Jeff Bruce
- University Health Network, Toronto, Canada
| | - Ting Ting Wang
- University Health Network, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Donna Reece
- University Health Network, Toronto, Canada
- University of Toronto, Toronto, Canada
| | | | | | - Peter Jb Sabatini
- University Health Network, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Jonathan Keats
- Translational Genomics Research Institute, City of Hope, AZ, USA
| | - Suzanne Trudel
- University Health Network, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Trevor J Pugh
- University Health Network, Toronto, Canada
- University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| |
Collapse
|