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White BS, Lanc I, O'Neal J, Gupta H, Fulton RS, Schmidt H, Fronick C, Belter EA, Fiala M, King J, Ahmann GJ, DeRome M, Mardis ER, Vij R, DiPersio JF, Levy J, Auclair D, Tomasson MH. A multiple myeloma-specific capture sequencing platform discovers novel translocations and frequent, risk-associated point mutations in IGLL5. Blood Cancer J 2018; 8:35. [PMID: 29563506 PMCID: PMC5862875 DOI: 10.1038/s41408-018-0062-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 12/10/2017] [Accepted: 12/18/2017] [Indexed: 12/28/2022] Open
Abstract
Multiple myeloma (MM) is a disease of copy number variants (CNVs), chromosomal translocations, and single-nucleotide variants (SNVs). To enable integrative studies across these diverse mutation types, we developed a capture-based sequencing platform to detect their occurrence in 465 genes altered in MM and used it to sequence 95 primary tumor-normal pairs to a mean depth of 104×. We detected cases of hyperdiploidy (23%), deletions of 1p (8%), 6q (21%), 8p (17%), 14q (16%), 16q (22%), and 17p (4%), and amplification of 1q (19%). We also detected IGH and MYC translocations near expected frequencies and non-silent SNVs in NRAS (24%), KRAS (21%), FAM46C (17%), TP53 (9%), DIS3 (9%), and BRAF (3%). We discovered frequent mutations in IGLL5 (18%) that were mutually exclusive of RAS mutations and associated with increased risk of disease progression (p = 0.03), suggesting that IGLL5 may be a stratifying biomarker. We identified novel IGLL5/IGH translocations in two samples. We subjected 15 of the pairs to ultra-deep sequencing (1259×) and found that although depth correlated with number of mutations detected (p = 0.001), depth past ~300× added little. The platform provides cost-effective genomic analysis for research and may be useful in individualizing treatment decisions in clinical settings.
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Affiliation(s)
- Brian S White
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA.,Sage Bionetworks, Seattle, WA, 91809, USA
| | - Irena Lanc
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA
| | - Julie O'Neal
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA
| | - Harshath Gupta
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Heather Schmidt
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Catrina Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Edward A Belter
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Mark Fiala
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA
| | - Justin King
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA
| | - Greg J Ahmann
- Division of Hematology-Oncology, Mayo Clinic, Rochester, 55905, MN, USA
| | - Mary DeRome
- Multiple Myeloma Research Foundation, Norwalk, CT, 06851, USA
| | - Elaine R Mardis
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA.,Genomics Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Ravi Vij
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA
| | - John F DiPersio
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA
| | - Joan Levy
- Multiple Myeloma Research Foundation, Norwalk, CT, 06851, USA.,Chordoma Foundation, Durham, NC, 27702, USA
| | - Daniel Auclair
- Multiple Myeloma Research Foundation, Norwalk, CT, 06851, USA
| | - Michael H Tomasson
- Department of Medicine, Washington University School of Medicine, St. Louis, 63110, MO, USA. .,Division of Hematology, Oncology and Bone Marrow Transplantation, 5204 MERF, University of Iowa, Iowa City, IA, 52242, USA.
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