全基因组癌症分析(PCAWG)文献精读

全基因组癌症分析（Pan-Cancer Analysis of Whole Genomes 缩写：PCAWG）项目旨在对38种不同肿瘤类型的2600多种原发癌及其配对正常组织进行了全基因组测序和综合分析。在PCAWG的主导下，来自全球700个科学家完成了对2658份癌症样本做了全基因组测序工作。

(PCAWG团队官方视频)

在2020年2月5日Nature杂志及其子刊上PCAWG项目组一共发表了22篇文章，涵盖了共计六个方面：

在检查癌症编码区的先前工作的基础上，PCAWG项目探索了编码区和非编码区中体细胞和种系变异的性质和后果，特别强调了顺式调控位点，非编码RNA和大规模结构变异。为了促进各种肿瘤类型之间的比较，所有肿瘤和匹配的正常基因组均经过统一的比对和变异检测算法，并且必须通过严格的质量控制测试。

可以使用右侧表中的链接下载表示单核苷酸变体，小插入缺失，结构变体和拷贝数变体的体细胞变体调用的VCF格式文件。

PCAWG项目组还提供了BAM文件，通过Cancer Genome Collaboratory https://cancercollaboratory.org/ 和Amazon Web Services访问和下载 https://dcc.icgc.org/icgc-in-the-cloud/aws 此外需要注意的是，和其他TGCA等的项目的数据一样，germline SNPs数据是controlled，需要通过dbGaP或者是ICGC数据委员会进行申请。

这里是22篇PCAWG项目文章列表

公众号后台回复“PCAWG”，获取本文提到的22篇文章下载链接。

1.Pan-cancer analysis of whole genomes. 5 FEB 2020, Nature

2.Patterns of somatic structural variation in human cancer genomes. 5 FEB 2020, Nature

3.The repertoire of mutational signatures in human cancer. 5 FEB 2020, Nature

4.The evolutionary history of 2,658 cancers. 5 FEB 2020, Nature

5.Genomic basis for RNA alterations in cancer. 5 FEB 2020, Nature

6.Analyses of non-coding somatic drivers in 2,658 cancer whole genomes 5 FEB 2020, Nature

7.Comprehensive molecular characterization of mitochondrial genomes in human cancers. 5 FEB 2020, Nature Genetics

8.Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. 5 FEB 2020, Nature Genetics

9.Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. 5 FEB 2020, Nature Genetics

10.The landscape of viral associations in human cancers. 5 FEB 2020, Nature Genetics

11.Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. 5 FEB 2020, Nature Genetics

12.Butler enables rapid cloud-based analysis of thousands of human genomes. 5 FEB 2020, Nature Biotechnology

13.Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. 5 FEB 2020, Communications Biology

14.Integrative pathway enrichment analysis of multivariate omics data. 5 FEB 2020, Nature Communications

15.Pathway and network analysis of more than 2500 whole cancer genomes. 5 FEB 2020, Nature Communications

16.A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. 5 FEB 2020, Nature Communications

17.High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

18.Genomic footprints of activated telomere maintenance mechanisms in cancer. 5 FEB 2020, Nature Communications

19.Combined burden and functional impact tests for cancer driver discovery using DriverPower. 5 FEB 2020, Nature Communications

20.Inferring structural variant cancer cell fraction. 5 FEB 2020, Nature Communications

21.Divergent mutational processes distinguish hypoxic and normoxic tumours. 5 FEB 2020, Nature Communications

22.Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. 5 FEB 2020, Nature Communications