泛癌症研究文献解读中的泛癌症拷贝数变异性探索
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2024-07-09 19:56:13
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关于SCNA
肿瘤的somatic的拷贝数变异,区别于肿瘤的somatic SNV,也非常重要,这里作者选取了11个癌症的近五千个样本,超过20万的CNA,平均每个样本是40个CNA,这里作者对SCNA进行分类:
- focal SCNAs that were shorter than the chromosome arm (median of 11 amplifications and 12 deletions per sample);
- arm-level SCNAs that were chromosome-arm length or longer (median of 3 amplifications and 5 deletions per sample);
- copy-neutral loss-of-heterozygosity (LOH) events in which one allele was deleted and the other was amplified coextensively (median of 1 per sample);
- whole-genome duplications (WGDs; in 37% of cancers).
肿瘤纯度和倍性的分布
很多软件都可以针对NGS数据计算肿瘤纯度和倍性,而且最新的TCGA pan-cancer计划,本来就会提供这些数据, https://gdc.cancer.gov/about-data/publications/panimmune
关于 Recurrent focal SCNAs
需要使用算法来得到显著的Recurrent focal SCNAs,比如GISTIC2算法
也有其它就,欢迎大家试用:RUBIC identifies driver genes by detecting recurrent DNA copy number breaks 有趣的是,发表到现在,引用才4个,Nat Commun. 2016 Jul
癌症特异性SCNAs
结论也平淡无奇,就是每个癌症内部都有SCNAs,是在泛癌分析结果里面没有的。
关于Chromothripsis
染色体破碎,Chromothripsis
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