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首页> 外文期刊>BMC Medical Genomics >Continuing difficulties in interpreting CNV data: lessons from a genome-wide CNV association study of Australian HNPCC/lynch syndrome patients
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Continuing difficulties in interpreting CNV data: lessons from a genome-wide CNV association study of Australian HNPCC/lynch syndrome patients

机译：解释CNV数据的持续困难：澳大利亚HNPCC /淋巴综合征患者全基因组CNV关联研究的经验教训

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Background 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. Methods Individuals 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. Results We 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 Conclusion A 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.
机译：背景技术遗传性非息肉性大肠直肠癌（HNPCC）/林奇综合征（LS）是一种以早期发作的上皮癌，尤其是大肠癌（CRC）和子宫内膜癌为特征的癌症综合征。本研究的目的是使用SNP阵列技术鉴定可能导致HNPCC / LS患者患癌风险增加的基因组畸变。方法使用Illumina Human610-Quad SNP阵列对诊断为HNPCC / LS（100）和健康对照（384）的个体进行基因分型。使用Nexus软件进行了拷贝数变异（CNV）呼叫和关联分析，使用QuantiSNP验证了重要结果。 TaqMan拷贝数测定法用于验证显示与两个软件程序都鉴定出的HNPCC / LS有显着关联的CNV。结果我们在染色体7q11.21上检测到与HNPCC / LS状态相关的拷贝数（CN）增益（28％的病例和0％的对照，Nexus; p =？3.60E-20和QuantiSNP; p结论）结论与对照组相比，HNPCC / LS病例支持更高的基因组不稳定性概念，HNPCC / LS可能与染色体7q11.21上的一个基因间位点有关，值得进一步研究，该研究结果突出了基于荧光的CNV的复杂性。两种CNV检测方法都无法有效地重复检测观察到的CNV，这表明需要将序列数据与强度数据一起考虑以避免假阳性结果。

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