DNA Copy Number Variation and Loss of Heterozygosity in Relation to Recurrence of and Survival from Head and Neck Squamous Cell Carcinoma: a Review

Overview

Journal Head Neck

Specialties General Surgery
Oncology

Date 2008 Jul 22

PMID 18642290

Citations 23

Authors

Yu Chen

Chu Chen

Affiliations

Soon will be listed here.

Abstract

Genetic aberrations, such as DNA copy number variation (CNV) and loss of heterozygosity (LOH), have been implicated in head and neck squamous cell carcinoma (HNSCC) initiation and progression. This review examines CNV and LOH as predictors of HNSCC recurrence and mortality. We searched PubMed for relevant publications and compared and discussed results from the articles. Certain CNV and LOH events have consistently been associated with HNSCC recurrence and survival. The recent high-resolution single nucleotide polymorphism (SNP) arrays have the potential to identify many more genetic changes and concurrent genome-wide CNV, copy-neutral and/or allelic imbalance LOH in HNSCC that may bear on prognosis. Our review confirms that outcome in HNSCC can be predicted to a considerable extent by the presence of tumor cell genetic aberrations. It points out the limitations of some methodologies that were used in the past and discusses the advantages and challenges of using genome-wide SNP arrays.

Citing Articles

Multi omics analysis of mitophagy subtypes and integration of machine learning for predicting immunotherapy responses in head and neck squamous cell carcinoma.

Liu J, Li H, Dong Q, Liang Z Aging (Albany NY). 2024; 16(12):10579-10614.

PMID: 38913914 PMC: 11236326. DOI: 10.18632/aging.205964.

Genomic Immune Evasion: Diagnostic and Therapeutic Opportunities in Head and Neck Squamous Cell Carcinomas.

Kirtane K, St John M, Fuentes-Bayne H, Patel S, Mardiros A, Xu H J Clin Med. 2022; 11(24).

PMID: 36555876 PMC: 9781632. DOI: 10.3390/jcm11247259.

Formalin Fixation, Delay to Fixation, and Time in Fixative Adversely Impact Copy Number Variation Analysis by aCGH.

Li J, Greytak S, Guan P, Engel K, Goerlitz D, Islam M Biopreserv Biobank. 2022; 21(4):407-416.

PMID: 36169416 PMC: 10460690. DOI: 10.1089/bio.2022.0036.

Characterizing HDAC Pathway Copy Number Variation in Pan-Cancer.

Yang S, Xie S, Shi X, Su D, He B, Xu Y Pathol Oncol Res. 2022; 28:1610288.

PMID: 35769830 PMC: 9235358. DOI: 10.3389/pore.2022.1610288.

Multidimensional Mutational Profiling of the Indian HNSCC Sub-Population Provides IRAK1, a Novel Driver Gene and Potential Druggable Target.

Desai S, Rao K R, Jain A, Bawa P, Dutta P, Atre G Front Oncol. 2021; 11:723162.

PMID: 34796107 PMC: 8593415. DOI: 10.3389/fonc.2021.723162.

References

Lee D, Koch W, Yoo G, Lango M, Reed A, Califano J . Impact of chromosome 14q loss on survival in primary head and neck squamous cell carcinoma. Clin Cancer Res. 1997; 3(4):501-5. View

Scholnick S, Haughey B, Sunwoo J, El-Mofty S, Baty J, Piccirillo J . Chromosome 8 allelic loss and the outcome of patients with squamous cell carcinoma of the supraglottic larynx. J Natl Cancer Inst. 1996; 88(22):1676-82. DOI: 10.1093/jnci/88.22.1676. View

Liu W, Ewing C, Chang B, Li T, Sun J, Turner A . Multiple genomic alterations on 21q22 predict various TMPRSS2/ERG fusion transcripts in human prostate cancers. Genes Chromosomes Cancer. 2007; 46(11):972-80. DOI: 10.1002/gcc.20482. View

WEYMULLER E, Yueh B, Deleyiannis F, Kuntz A, Alsarraf R, Coltrera M . Quality of life in patients with head and neck cancer: lessons learned from 549 prospectively evaluated patients. Arch Otolaryngol Head Neck Surg. 2000; 126(3):329-35; discussion 335-6. DOI: 10.1001/archotol.126.3.329. View

Zhou X, C Mok S, Chen Z, Li Y, Wong D . Concurrent analysis of loss of heterozygosity (LOH) and copy number abnormality (CNA) for oral premalignancy progression using the Affymetrix 10K SNP mapping array. Hum Genet. 2004; 115(4):327-30. DOI: 10.1007/s00439-004-1163-1. View

Perez-Ordonez B, Beauchemin M, Jordan R . Molecular biology of squamous cell carcinoma of the head and neck. J Clin Pathol. 2006; 59(5):445-53. PMC: 1860277. DOI: 10.1136/jcp.2003.007641. View

Takebayashi S, Hickson A, Ogawa T, Jung K, Mineta H, Ueda Y . Loss of chromosome arm 18q with tumor progression in head and neck squamous cancer. Genes Chromosomes Cancer. 2004; 41(2):145-54. DOI: 10.1002/gcc.20066. View

Rodrigo J, Garcia L, Ramos S, Lazo P, Suarez C . EMS1 gene amplification correlates with poor prognosis in squamous cell carcinomas of the head and neck. Clin Cancer Res. 2000; 6(8):3177-82. View

Ashman J, Patmore H, Condon L, Cawkwell L, Stafford N, Greenman J . Prognostic value of genomic alterations in head and neck squamous cell carcinoma detected by comparative genomic hybridisation. Br J Cancer. 2003; 89(5):864-9. PMC: 2394495. DOI: 10.1038/sj.bjc.6601199. View

10.

Miyamoto R, Uzawa N, Nagaoka S, Hirata Y, Amagasa T . Prognostic significance of cyclin D1 amplification and overexpression in oral squamous cell carcinomas. Oral Oncol. 2003; 39(6):610-8. DOI: 10.1016/s1368-8375(03)00048-4. View

11.

Bignell G, Huang J, Greshock J, Watt S, Butler A, West S . High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res. 2004; 14(2):287-95. PMC: 327104. DOI: 10.1101/gr.2012304. View

12.

Bockmuhl U, Ishwad C, Ferrell R, Gollin S . Association of 8p23 deletions with poor survival in head and neck cancer. Otolaryngol Head Neck Surg. 2001; 124(4):451-5. DOI: 10.1067/mhn.2001.114794. View

13.

LaFramboise T, Weir B, Zhao X, Beroukhim R, Li C, Harrington D . Allele-specific amplification in cancer revealed by SNP array analysis. PLoS Comput Biol. 2005; 1(6):e65. PMC: 1289392. DOI: 10.1371/journal.pcbi.0010065. View

14.

Nogueira C, Dolan R, Gooey J, Byahatti S, Vaughan C, Fuleihan N . Inactivation of p53 and amplification of cyclin D1 correlate with clinical outcome in head and neck cancer. Laryngoscope. 1998; 108(3):345-50. DOI: 10.1097/00005537-199803000-00007. View

15.

Akervall J, Bockmuhl U, Petersen I, Yang K, Carey T, Kurnit D . The gene ratios c-MYC:cyclin-dependent kinase (CDK)N2A and CCND1:CDKN2A correlate with poor prognosis in squamous cell carcinoma of the head and neck. Clin Cancer Res. 2003; 9(5):1750-5. View

16.

Lazar A, Winter M, Nogueira C, Larson P, Finnemore E, Dolan R . Loss of heterozygosity at 11q23 in squamous cell carcinoma of the head and neck is associated with recurrent disease. Clin Cancer Res. 1998; 4(11):2787-93. View

17.

Reibel J . Prognosis of oral pre-malignant lesions: significance of clinical, histopathological, and molecular biological characteristics. Crit Rev Oral Biol Med. 2003; 14(1):47-62. DOI: 10.1177/154411130301400105. View

18.

Coleman W, Tsongalis G . The role of genomic instability in human carcinogenesis. Anticancer Res. 2000; 19(6A):4645-64. View

19.

Singh B, Stoffel A, Gogineni S, Poluri A, Pfister D, Shaha A . Amplification of the 3q26.3 locus is associated with progression to invasive cancer and is a negative prognostic factor in head and neck squamous cell carcinomas. Am J Pathol. 2002; 161(2):365-71. PMC: 1850746. DOI: 10.1016/S0002-9440(10)64191-0. View

20.

Bockmuhl U, Schluns K, Kuchler I, Petersen S, Petersen I . Genetic imbalances with impact on survival in head and neck cancer patients. Am J Pathol. 2000; 157(2):369-75. PMC: 1850146. DOI: 10.1016/S0002-9440(10)64549-X. View