High-resolution SNP microarray investigation of copy number variations on chromosome 18 in a control cohort

Chia, N. L., Bryce, M., Hickman, P. E., Potter, J. M., Glasgow, N., Koerbin, G., Danoy, P., Brown, M. A., & Cavanaugh, J. (2013) High-resolution SNP microarray investigation of copy number variations on chromosome 18 in a control cohort. Cytogenetic and Genome Research, 141(1), pp. 16-25.

View at publisher


Copy number variations (CNVs) as described in the healthy population are purported to contribute significantly to genetic heterogeneity. Recent studies have described CNVs using lymphoblastoid cell lines or by application of specifically developed algorithms to interrogate previously described data. However, the full extent of CNVs remains unclear. Using high-density SNP array, we have undertaken a comprehensive investigation of chromosome 18 for CNV discovery and characterisation of distribution and association with chromosome architecture. We identified 399 CNVs, of which loss represents 98%, 58% are less than 2.5 kb in size and 71% are intergenic. Intronic deletions account for the majority of copy number changes with gene involvement. Furthermore, one-third of CNVs do not have putative breakpoints within repetitive sequences. We conclude that replicative processes, mediated either by repetitive elements or microhomology, account for the majority of CNVs in the healthy population. Genomic instability involving the formation of a non-B structure is demonstrated in one region.

Impact and interest:

0 citations in Scopus
Search Google Scholar™

Citation counts are sourced monthly from Scopus and Web of Science® citation databases.

These databases contain citations from different subsets of available publications and different time periods and thus the citation count from each is usually different. Some works are not in either database and no count is displayed. Scopus includes citations from articles published in 1996 onwards, and Web of Science® generally from 1980 onwards.

Citations counts from the Google Scholar™ indexing service can be viewed at the linked Google Scholar™ search.

ID Code: 89293
Item Type: Journal Article
Refereed: Yes
Keywords: Chromosome 18, Microhomology, Sequence, SNP microarray, algorithm, Alu sequence, article, centromere, chromosome analysis, chromosome size, consensus sequence, controlled study, copy number variation, DNA microarray, gene frequency, genetic association, genomic instability, high density single nucleotide polymorphism microarray, human, human tissue, intron, long terminal repeat, priority journal, protein secondary structure, segmental duplication, short interspersed repeat, chromosome deletion, chromosome duplication, chromosome replication, cytoarchitecture, female, gene sequence, genome analysis, human cell, mass screening, microarray analysis, normal human, single nucleotide polymorphism, Algorithms, Chromosomes, Human, Pair 18, Cohort Studies, DNA Copy Number Variations, Genome, Human, Heterozygote, Homozygote, Humans, Introns, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Sequence Deletion
DOI: 10.1159/000350767
ISSN: 1424-8581
Divisions: Current > QUT Faculties and Divisions > Faculty of Health
Current > Institutes > Institute of Health and Biomedical Innovation
Copyright Owner: Copyright 2013 S. Karger AG
Deposited On: 20 Oct 2015 00:24
Last Modified: 18 Feb 2016 05:20

Export: EndNote | Dublin Core | BibTeX

Repository Staff Only: item control page