用了旧的CNV芯片还用旧的参考基因组

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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)

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