Continuing difficulties in interpreting CNV data: lessons from a genome-wide CNV association study of Australian HNPCC/lynch syndrome patients

Bente A Talseth-Palmer,Mark Mcevoy,Allan Spigelman,Elizabeth G Holliday,Amy L Masson,John Attia,Desma M Grice,Cliff Meldrum,Rodney J Scott,Tiffany-Jane Evans

doi:10.1186/1755-8794-6-10

Abstract

BackgroundHereditary non-polyposis colorectal cancer (HNPCC)/Lynch syndrome (LS) is a cancer syndrome characterised by early-onset epithelial cancers, especially colorectal cancer (CRC) and endometrial cancer. The aim of the current study was to use SNP-array technology to identify genomic aberrations which could contribute to the increased risk of cancer in HNPCC/LS patients.MethodsIndividuals diagnosed with HNPCC/LS (100) and healthy controls (384) were genotyped using the Illumina Human610-Quad SNP-arrays. Copy number variation (CNV) calling and association analyses were performed using Nexus software, with significant results validated using QuantiSNP. TaqMan Copy-Number assays were used for verification of CNVs showing significant association with HNPCC/LS identified by both software programs.ResultsWe detected copy number (CN) gains associated with HNPCC/LS status on chromosome 7q11.21 (28% cases and 0% controls, Nexus; p = 3.60E-20 and QuantiSNP; p < 1.00E-16) and 16p11.2 (46% in cases, while a CN loss was observed in 23% of controls, Nexus; p = 4.93E-21 and QuantiSNP; p = 5.00E-06) via in silico analyses. TaqMan Copy-Number assay was used for validation of CNVs showing significant association with HNPCC/LS. In addition, CNV burden (total CNV length, average CNV length and number of observed CNV events) was significantly greater in cases compared to controls.ConclusionA greater CNV burden was identified in HNPCC/LS cases compared to controls supporting the notion of higher genomic instability in these patients. One intergenic locus on chromosome 7q11.21 is possibly associated with HNPCC/LS and deserves further investigation. The results from this study highlight the complexities of fluorescent based CNV analyses. The inefficiency of both CNV detection methods to reproducibly detect observed CNVs demonstrates the need for sequence data to be considered alongside intensity data to avoid false positive results.

Highlights

Hereditary non-polyposis colorectal cancer (HNPCC)/Lynch syndrome (LS) is a cancer syndrome characterised by early-onset epithelial cancers, especially colorectal cancer (CRC) and endometrial cancer
We have identified one locus in an intergenic region on chromosome 7q11.21 possibly associated with disease risk in patients diagnosed with HNPCC/LS and observed a greater Copy number variation (CNV) burden in cases compared to controls
The results from this study highlight the complexities of fluorescent based CNV analyses

Summary

Introduction

Hereditary non-polyposis colorectal cancer (HNPCC)/Lynch syndrome (LS) is a cancer syndrome characterised by early-onset epithelial cancers, especially colorectal cancer (CRC) and endometrial cancer. The aim of the current study was to use SNP-array technology to identify genomic aberrations which could contribute to the increased risk of cancer in HNPCC/LS patients. Genetic variation explains a significant proportion of susceptibility to common disease [1,2,3,4,5]. The widespread distribution of CNVs across the genome suggests they can account for a proportion of population variation in common disease status. Chromosomal deletions have been found more prevalent than duplications in case–control studies [19,20] and interestingly, microRNAs (miRNAs) and miRNA-binding sites are concentrated in CNV regions [21]. It has been suggested that the development of a disease phenotype may not depend upon a single CNV but rather a combination of various CNVs and other genetic variations (e.g. single nucleotide polymorphisms (SNPs)) [14]. Studies of CNV burden have yielded inconclusive results [25]

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