Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumour tissue

We analysed a cohort of Lifepool IDC cases treated only with wide local excision for genome-wide copy number and loss of heterozygosity using Affymetrix OncoScan® MIP arrays. Cases included IDC (n=4).Benign cases were available for 2 cases. We have analysed copy number calling from the same samples using low-coverage whole genome sequencing in order to investigate the concordance between the two techniques. 4 cases of lifepool invasive ductal carcinoma (IDC) and 2 benign cases were microdissected from FFPE tissue and analysed by molecular inversion probe (MIP) copy number arrays. The data in this submission are CN values for the ~300,000 probes common to two batches performed.

本研究针对仅接受广泛局部切除术的Lifepool浸润性导管癌（invasive ductal carcinoma, IDC）病例队列，采用Affymetrix OncoScan®分子倒置探针（molecular inversion probe, MIP）阵列开展全基因组拷贝数与杂合性缺失分析。本队列共纳入4例IDC病例，其中2例配有匹配的良性对照样本。
为探究两种检测技术的一致性，我们采用低覆盖度全基因组测序（low-coverage whole genome sequencing）对同一样本进行拷贝数调用（copy number calling）分析。
我们从4例Lifepool浸润性导管癌病例与2例良性病例的福尔马林固定石蜡包埋（Formalin-Fixed Paraffin-Embedded, FFPE）组织中获取显微切割样本，并通过分子倒置探针拷贝数阵列完成分析。
本次提交的数据为两批实验共有的约30万个探针的拷贝数值。