community, to train expert individuals, and to develop specialized computational tools and
infrastructure that may be useful to other large-scale projects. As such, many secondary
analyses have allowed deep exploration of these data beyond the primary reports released
by TCGA Network. In 2018, TCGA published the Pan-Cancer Atlas, a number of coordinated papers reporting on the analysis of over 11,000 tumors from 33 cancer type
[44]. Data access website: https://portal.gdc.cancer.gov/.
2.7.2 International Cancer Genome Consortium (ICGC)
ICGC is a voluntary, international initiative launched in 2007 to coordinate the analysis of
tumor genomes from 25 primary untreated tumors from 50 cancer types from around the
world [45]. In 2019, its portal contained data aggregated from more than 20,000
contributors, including TCGA, and had information on about 77 million somatic mutations
[46]. ICGC has numerous initiatives, including PCAWG (reviewed below), The ICGC for
Medicine Initiative (ICGCmed), and ICGC for Accelerating Research in Genomic Oncology (ICGC-ARGO). Website: https://icgc.org/.
2.7.3 Pan-Cancer Analysis of Whole Genomes (PCAWG)
PCAWG is an initiative from ICGC that aims to study more than 2,600 cancer whole
genomes from 39 distinct tumor types, aiming to be a follow-up analysis to those
performed on coding sequences [47]. The PCAWG Network’s first publications, published
in 2020, focus on cataloging non-coding driver mutations, tumor evolutionary history,
identifying structural variation, mutational signatures analysis and inferring interactions
between somatic and germline variation [47]. ICGC has made data on somatic calls,
including SNPs, indels, structural and copy number variants, available for use by any
researcher. Website: https://dcc.icgc.org/pcawg.
2.7.4 Catalog of Somatic Mutations in Cancer (COSMIC)
COSMIC was launched in 2004 as a database of information on somatic mutations in
human cancer [48]. It has steadily grown over the years and in its latest release to this date
(in September 2019) it had information on every human gene, and on nearly nine million
coding mutations from more than 1.4 million samples [48]. Data in COSMIC is manually
curated by experts constantly reviewing the literature, as well as from systematic screens
released with these publications. It is widely used for exploring available information on
frequency and potential pathogenic consequences of somatic mutations. Website: https://
cancer.sanger.ac.uk/cosmic.
2 Opportunities and Perspectives of NGS Applications in Cancer Research
31
infrastructure that may be useful to other large-scale projects. As such, many secondary
analyses have allowed deep exploration of these data beyond the primary reports released
by TCGA Network. In 2018, TCGA published the Pan-Cancer Atlas, a number of coordinated papers reporting on the analysis of over 11,000 tumors from 33 cancer type
[44]. Data access website: https://portal.gdc.cancer.gov/.
2.7.2 International Cancer Genome Consortium (ICGC)
ICGC is a voluntary, international initiative launched in 2007 to coordinate the analysis of
tumor genomes from 25 primary untreated tumors from 50 cancer types from around the
world [45]. In 2019, its portal contained data aggregated from more than 20,000
contributors, including TCGA, and had information on about 77 million somatic mutations
[46]. ICGC has numerous initiatives, including PCAWG (reviewed below), The ICGC for
Medicine Initiative (ICGCmed), and ICGC for Accelerating Research in Genomic Oncology (ICGC-ARGO). Website: https://icgc.org/.
2.7.3 Pan-Cancer Analysis of Whole Genomes (PCAWG)
PCAWG is an initiative from ICGC that aims to study more than 2,600 cancer whole
genomes from 39 distinct tumor types, aiming to be a follow-up analysis to those
performed on coding sequences [47]. The PCAWG Network’s first publications, published
in 2020, focus on cataloging non-coding driver mutations, tumor evolutionary history,
identifying structural variation, mutational signatures analysis and inferring interactions
between somatic and germline variation [47]. ICGC has made data on somatic calls,
including SNPs, indels, structural and copy number variants, available for use by any
researcher. Website: https://dcc.icgc.org/pcawg.
2.7.4 Catalog of Somatic Mutations in Cancer (COSMIC)
COSMIC was launched in 2004 as a database of information on somatic mutations in
human cancer [48]. It has steadily grown over the years and in its latest release to this date
(in September 2019) it had information on every human gene, and on nearly nine million
coding mutations from more than 1.4 million samples [48]. Data in COSMIC is manually
curated by experts constantly reviewing the literature, as well as from systematic screens
released with these publications. It is widely used for exploring available information on
frequency and potential pathogenic consequences of somatic mutations. Website: https://
cancer.sanger.ac.uk/cosmic.
2 Opportunities and Perspectives of NGS Applications in Cancer Research
31