家族性乳腺癌中目标连锁分析鉴定区域的深度测序：方法、分析流程和故障排除。
Deep sequencing of target linkage assay-identified regions in familial breast cancer: methods, analysis pipeline and troubleshooting.
机构信息
Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
出版信息
PLoS One. 2010 Apr 2;5(4):e9976. doi: 10.1371/journal.pone.0009976.
BACKGROUND
The classical candidate-gene approach has failed to identify novel breast cancer susceptibility genes. Nowadays, massive parallel sequencing technology allows the development of studies unaffordable a few years ago. However, analysis protocols are not yet sufficiently developed to extract all information from the huge amount of data obtained.
METHODOLOGY/PRINCIPAL FINDINGS: In this study, we performed high throughput sequencing in two regions located on chromosomes 3 and 6, recently identified by linkage studies by our group as candidate regions for harbouring breast cancer susceptibility genes. In order to enrich for the coding regions of all described genes located in both candidate regions, a hybrid-selection method on tiling microarrays was performed.
CONCLUSIONS/SIGNIFICANCE: We developed an analysis pipeline based on SOAP aligner to identify candidate variants with a high real positive confirmation rate (0.89), with which we identified eight variants considered candidates for functional studies. The results suggest that the present strategy might be a valid second step for identifying high penetrance genes.
背景
经典的候选基因方法未能鉴定出新型乳腺癌易感基因。如今，大规模平行测序技术使得几年前无法进行的研究成为可能。然而，分析方案尚未充分发展，无法从获得的大量数据中提取所有信息。
方法/主要发现：在这项研究中，我们对两个位于染色体 3 和 6 上的区域进行了高通量测序，这两个区域是我们小组最近通过连锁研究确定的候选区域，可能含有乳腺癌易感基因。为了富集位于两个候选区域的所有已描述基因的编码区，在平铺微阵列上进行了混合选择方法。
结论/意义：我们开发了一种基于 SOAP aligner 的分析管道，以识别具有高真实阳性确认率（0.89）的候选变体，我们用该方法鉴定了 8 个被认为是功能研究候选的变体。结果表明，目前的策略可能是识别高外显率基因的有效第二步。
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