Assessing copy number aberrations and copy-neutral loss-of-heterozygosity across the genome as best practice: An evidence-based review from the Cancer Genomics Consortium (CGC) working group for chronic lymphocytic leukemia

Kathy Chun; Gail D Wenger; Alka Chaubey; D P Dash; Rashmi Kanagal-Shamanna; Sibel Kantarci; Ravindra Kolhe; Daniel L Van Dyke; Lu Wang; Daynna J Wolff; Patricia M Miron

doi:10.1016/j.cancergen.2018.07.004

Assessing copy number aberrations and copy-neutral loss-of-heterozygosity across the genome as best practice: An evidence-based review from the Cancer Genomics Consortium (CGC) working group for chronic lymphocytic leukemia

Cancer Genet. 2018 Dec:228-229:236-250. doi: 10.1016/j.cancergen.2018.07.004. Epub 2018 Oct 16.

Authors

Affiliations

¹ Genetics Program, North York General Hospital, Toronto, ON, Canada. Electronic address: [email protected].
² Cytogenetics Laboratory, Penrose St. Francis/Centura Health, Colorado Springs, CO, USA.
³ Greenwood Genetic Center, Greenwood, SC, USA.
⁴ Blood Center of Wisconsin, Milwaukee, WI, USA.
⁵ Department of Hematopathology and Molecular Diagnostics, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.
⁶ Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA.
⁷ Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, USA.
⁸ Genomics Laboratory, Mayo Clinic, Rochester, MN USA.
⁹ Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
¹⁰ Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA.
¹¹ Department of Pathology, UMassMemorial Medical Center, Worcester, MA, USA; Quest Diagnostics, Marlborough, MA, USA. Electronic address: [email protected].

PMID: 30554732
DOI: 10.1016/j.cancergen.2018.07.004

Abstract

The prognostic role of cytogenetic analysis is well-established in B-cell chronic lymphocytic leukemia (CLL). Approximately 80% of patients have a cytogenetic aberration. Interphase FISH panels have been the gold standard for cytogenetic evaluation, but conventional cytogenetics allows detection of additional abnormalities, including translocations, complex karyotypes and multiple clones. Whole genome copy number assessment, currently performed by chromosomal microarray analysis (CMA), is particularly relevant in CLL for the following reasons: (1) copy number alterations (CNAs) represent key events with biologic and prognostic significance; (2) DNA from fresh samples is generally available; and (3) the tumor burden tends to be relatively high in peripheral blood. CMA also identifies novel copy number variants and copy-neutral loss-of-heterozygosity (CN-LOH), and can refine deletion breakpoints. The Cancer Genomics Consortium (CGC) Working Group for CLL has performed an extensive literature review to describe the evidence-based clinical utility of CMA in CLL. We provide suggestions for the integration of CMA into clinical use and list recurrent copy number alterations, regions of CN-LOH and mutated genes to aid in interpretation.

Keywords: Chromosomal microarray analysis (CMA); Chronic lymphocytic leukemia (CLL); Copy number alterations (CNAs); Copy-neutral loss-of-heterozygosity (CN-LOH); Cytogenetics; Fluorescence in situ hybridization (FISH).

Publication types

Review

MeSH terms

DNA Copy Number Variations*
Evidence-Based Medicine*
Humans
Leukemia, Lymphocytic, Chronic, B-Cell / genetics*
Loss of Heterozygosity*