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Chronic Lymphocytic Leukemia IGHV Somatic Hypermutation Detection by Targeted Capture Next-Generation Sequencing.
Grants, Jennifer M; May, Christina; Bridgers, Josh; Huang, Shujun; Gillis, Sierra; Meissner, Barbara; Boyle, Merrill; Ben-Neriah, Susana; Hung, Stacy; Duns, Gerben; Hilton, Laura; Gerrie, Alina S; Marra, Marco; Kridel, Robert; Sabatini, Peter J B; Steidl, Christian; Scott, David W; Karsan, Aly.
Afiliación
  • Grants JM; Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
  • May C; Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
  • Bridgers J; Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
  • Huang S; Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
  • Gillis S; Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
  • Meissner B; Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada.
  • Boyle M; Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada.
  • Ben-Neriah S; Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada.
  • Hung S; Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada.
  • Duns G; Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada.
  • Hilton L; Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada.
  • Gerrie AS; Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada.
  • Marra M; Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
  • Kridel R; Princess Margaret Cancer Centre, Toronto, ON, Canada.
  • Sabatini PJB; Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
  • Steidl C; Princess Margaret Cancer Centre, Toronto, ON, Canada.
  • Scott DW; Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.
  • Karsan A; Centre for Lymphoid Cancer, BC Cancer Centre, Vancouver, BC, Canada.
Clin Chem ; 70(1): 273-284, 2024 01 04.
Article en En | MEDLINE | ID: mdl-38175592
ABSTRACT

BACKGROUND:

Somatic hypermutation (SHM) status of the immunoglobulin heavy variable (IGHV) gene plays a crucial role in determining the prognosis and treatment of patients with chronic lymphocytic leukemia (CLL). A common approach for determining SHM status is multiplex polymerase chain reaction and Sanger sequencing of the immunoglobin heavy locus; however, this technique is low throughput, is vulnerable to failure, and does not allow multiplexing with other diagnostic assays.

METHODS:

Here we designed and validated a DNA targeted capture approach to detect immunoglobulin heavy variable somatic hypermutation (IGHV SHM) status as a submodule of a larger next-generation sequencing (NGS) panel that also includes probes for ATM, BIRC3, CHD2, KLHL6, MYD88, NOTCH1, NOTCH2, POT1, SF3B1, TP53, and XPO1. The assay takes as input FASTQ files and outputs a report containing IGHV SHM status and V allele usage following European Research Initiative on CLL guidelines.

RESULTS:

We validated the approach on 35 CLL patient samples, 34 of which were characterized using Sanger sequencing. The NGS panel identified the IGHV SHM status of 34 of 35 CLL patients. We showed 100% sensitivity and specificity among the 33 CLL samples with both NGS and Sanger sequencing calls. Furthermore, we demonstrated that this panel can be combined with additional targeted capture panels to detect prognostically important CLL single nucleotide variants, insertions/deletions, and copy number variants (TP53 copy number loss).

CONCLUSIONS:

A targeted capture approach to IGHV SHM detection can be integrated into broader sequencing panels, allowing broad CLL prognostication in a single molecular assay.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Leucemia Linfocítica Crónica de Células B / Hipermutación Somática de Inmunoglobulina Tipo de estudio: Diagnostic_studies / Guideline / Prognostic_studies Límite: Humans Idioma: En Revista: Clin Chem Asunto de la revista: QUIMICA CLINICA Año: 2024 Tipo del documento: Article País de afiliación: Canadá

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Leucemia Linfocítica Crónica de Células B / Hipermutación Somática de Inmunoglobulina Tipo de estudio: Diagnostic_studies / Guideline / Prognostic_studies Límite: Humans Idioma: En Revista: Clin Chem Asunto de la revista: QUIMICA CLINICA Año: 2024 Tipo del documento: Article País de afiliación: Canadá