用了旧的CNV芯片还用旧的参考基因组

文章发表在 Breast Cancer Res. 2017; 19: 30.

Published online 2017 Mar 16. doi: 10.1186/s13058-017-0825-6

样本量并不少： case-control study of breast cancer diagnosed before age 40 years (200 cases, 293 controls)

可惜使用的芯片及技术手段比较旧了： Genome-wide scanning for CNVs was performed using the Human610-Quad BeadChip and fine-mapping was conducted using PennCNV.

既然是illumina的芯片，那么直接使用官网提供的 GenomeStudio 软件就可以分析得到：

• genomic location
• ignal intensity (Norm R)
• allele frequency (Norm theta)
• log R ratios (LRRs)
• B allele frequencies (BAF)

有了每个样本的芯片数据的分析结果，就可以使用 PennCNV 做下游分析，质量控制步骤必不可少，最后的分析结果在; CNV data used in the study are shown in Additional file 2: Table S1.

Additional file 2: Table S1.(819K, xlsx)

虽然是基于HG18参考基因组的，这些信息也可以用来绘图及可视化

Sample ID	Chromosome	Start	Stop	StartSNP	StopSNP	Number of Probes	Size	Copy number call	Case / control
Control 1	chr3	53003023	53013826	rs2246556	rs2581795	6	10804	0	Control
Control 1	chr3	164004033	164101579	rs13098441	rs2058827	8	97547	0	Control
Control 1	chr6	32563460	32589485	cnvi0006546	cnvi0006576	24	26026	0	Control
Control 1	chr7	93165330	93168493	rs10274663	rs10243929	6	3164	0	Control
Control 1	chr10	66980652	66983043	rs16921552	cnvi0004635	5	2392	0	Control
Control 1	chr2	40270516	40279466	rs10490207	rs385561	8	8951	1	Control
Control 1	chr3	176564661	176570084	rs9833334	cnvi0011722	6	5424	1	Control
Control 1	chr4	69125902	69163188	cnvi0023541	rs4860978	19	37287	1	Control
Control 1	chr4	87195437	87198951	rs1898249	rs3775183	6	3515	1	Control
Control 1	chr5	113188389	113197319	rs1482358	rs1482350	7	8931	1	Control
Control 1	chr10	81478475	81492542	cnvi0016261	cnvi0020124	11	14068	1	Control
Control 1	chr3	120211804	120284544	rs1369582	rs16829334	17	72741	3	Control
Control 1	chr5	175492445	175561995	rs7443800	rs11957952	15	69551	3	Control
Control 1	chr6	241257	306547	rs1111362	rs7744405	12	65291	3	Control
Control 1	chr8	39356825	39457081	rs6998199	rs10104634	12	100257	3	Control
Control 1	chr9	17573310	17615002	rs1028594	rs2208494	23	41693	3	Control
Control 1	chr11	4253369	4323772	rs390285	rs4910951	6	70404	3	Control
Control 1	chr11	55147807	55209499	cnvi0020178	rs2102269	24	61693	3	Control
Control 1	chr15	22134751	22288804	rs11854134	rs7497695	20	154054	3	Control
Control 1	chr16	32470193	32482392	cnvi0022822	cnvi0020622	23	12200	3	Control
Control 2	chr4	115398433	115401739	rs7686222	rs4279283	6	3307	0	Control
Control 2	chr6	32563460	32589485	cnvi0006546	cnvi0006576	24	26026	0	Control
Control 2	chr6	79029649	79090197	rs818248	rs7773124	31	60549	0	Control
Control 2	chr2	24451783	24459556	rs7577964	rs2339980	5	7774	1	Control
Control 2	chr2	180123158	180129913	rs4530328	rs16866773	6	6756	1	Control
Control 2	chr6	32746293	32756221	rs9274759	rs28746896	8	9929	1	Control
Control 2	chr6	67075448	67101257	rs9453702	rs1708553	12	25810	1	Control
Control 2	chr7	141969085	142005626	rs6947359	rs7789642	26	36542	1	Control
Control 2	chr8	7242915	7366447	cnvi0015634	rs2737967	11	123533	1	Control

可以看到，分析的拷贝数变异区域片段都不大。

发现作者给出的最后整合分析结果在：

CNV data for cases and controls. Chromosome coordinates given according to Hg18. (XLSX 819 kb)Additional file 3: Table S2.(19K, docx)