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 Journal Article
| Authors: | Chun, K.; Wenger, G. D.; Chaubey, A.; Dash, D. P.; Kanagal-Shamanna, R.; Kantarci, S.; Kolhe, R.; Van Dyke, D. L.; Wang, L.; Wolff, D. J.; Miron, P. M. |
| Article Title: | 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 |
| 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. © 2018 |
| Keywords: | gene mutation; single nucleotide polymorphism; gene deletion; review; flow cytometry; evidence based medicine; mantle cell lymphoma; gene locus; cytogenetics; protein p53; risk assessment; carcinogenesis; blood; fluorescence in situ hybridization; dna; systematic review; microarray analysis; heterozygosity loss; chronic lymphatic leukemia; chromosome analysis; karyotype; myeloid differentiation factor 88; metaphase; trisomy 12; ribosome protein; notch1 receptor; b cell leukemia; fluorescence in situ hybridization (fish); copy number variation; exportin 1; early growth response factor 2; exportin 5; next generation sequencing; cancer prognosis; human; priority journal; chronic lymphocytic leukemia (cll); chromosomal microarray analysis (cma); copy number alterations (cnas); copy-neutral loss-of-heterozygosity (cn-loh) |
| Journal Title: | Cancer Genetics |
| Volume: | 228-229 |
| ISSN: | 2210-7762 |
| Publisher: | Elsevier Inc. |
| Date Published: | 2018-12-01 |
| Start Page: | 236 |
| End Page: | 250 |
| Language: | English |
| DOI: | 10.1016/j.cancergen.2018.07.004 |
| PROVIDER: | scopus |
| PUBMED: | 30554732 |
| DOI/URL: | |
| Notes: | Cancer Genet. -- Export Date: 2 January 2019 -- Review -- Source: Scopus C2 - 30554732 |
