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Comprehensive genomic characterization of head and neck squamous cell carcinomas

The Cancer Genome Atlas Network·2015·Nature
DOI 10.1038/nature14129PMC PMC4311405
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Figure 1 DNA copy number alterations. a, Copy number alterations by anatomic site and HPV status for squamous cancers. Lung squamous cell carcinoma (LUSC, n = 358) and cervical squamous cell carcinoma (CESC, n = 114). b, Unsupervised analysis of copy number alteration of HNSCC (n = 279) with associated characteristics. The rectangle indicates chromosome 7 amplifications in the purple cluster. NA, not available. PowerPoint slide
Figure 1 DNA copy number alterations. a, Copy number alterations by anatomic site and HPV status for squamous cancers. Lung squamous cell carcinoma (LUSC, n = 358) and cervical squamous cell carcinoma (CESC, n = 114). b, Unsupervised analysis of copy number alteration of HNSCC (n = 279) with associated characteristics. The rectangle indicates chromosome 7 amplifications in the purple cluster. NA, not available. PowerPoint slideCC BY-NC-SA · PubMed Central
Figure 2 Significantly mutated genes in HNSCC. Genes (rows) with significantly mutated genes (identified using the MutSigCV algorithim; q < 0.1) ordered by q value; additional genes with trends towards significance are also shown. Samples (columns, n = 279) are arranged to emphasize mutual exclusivity among mutations. Left, mutation percentage in TCGA. Right, mutation percentage in COSMIC (‘upper aerodigestive tract’ tissue). Top, overall number of mutations per megabase. Colour coding indicates mutation type. PowerPoint slide
Figure 2 Significantly mutated genes in HNSCC. Genes (rows) with significantly mutated genes (identified using the MutSigCV algorithim; q < 0.1) ordered by q value; additional genes with trends towards significance are also shown. Samples (columns, n = 279) are arranged to emphasize mutual exclusivity among mutations. Left, mutation percentage in TCGA. Right, mutation percentage in COSMIC (‘upper aerodigestive tract’ tissue). Top, overall number of mutations per megabase. Colour coding indicates mutation type. PowerPoint slideCC BY-NC-SA · PubMed Central
Figure 3 Candidate therapeutic targets and driver oncogenic events. Alteration events for key genes are displayed by sample (n = 279). TSG, tumour suppressor gene. PowerPoint slide
Figure 3 Candidate therapeutic targets and driver oncogenic events. Alteration events for key genes are displayed by sample (n = 279). TSG, tumour suppressor gene. PowerPoint slideCC BY-NC-SA · PubMed Central
Figure 4 Integrated analysis of genomic alterations. a, b, Samples (n = 279) are displayed in columns and grouped by gene expression (a) or methylation (b) subtype (sub.). Unadjusted two-sided Fisher’s exact test P values assess the association of each genomic alteration. Methylation probe location of CpG islands, shores and shelves are shown on the left of b. Annotation shows HPV status and subtype (16, 33 and 35). CN, copy number. PowerPoint slide
Figure 4 Integrated analysis of genomic alterations. a, b, Samples (n = 279) are displayed in columns and grouped by gene expression (a) or methylation (b) subtype (sub.). Unadjusted two-sided Fisher’s exact test P values assess the association of each genomic alteration. Methylation probe location of CpG islands, shores and shelves are shown on the left of b. Annotation shows HPV status and subtype (16, 33 and 35). CN, copy number. PowerPoint slideCC BY-NC-SA · PubMed Central
Figure 5 Deregulation of signalling pathways and transcription factors. Key affected pathways, components and inferred functions, are summarized in the main text and Supplementary Information section 7 for n = 279 samples. The frequency (%) of genetic alterations for HPV(−) and HPV(+) tumours are shown separately within sub-panels and highlighted. Also see Supplementary Fig. 7.15. Pathway alterations include homozygous deletions, focal amplifications and somatic mutations. Activated and inactivated pathways/genes, and activating or inhibitory symbols are based on predicted effects of genome alterations and/or pathway functions. PowerPoint slide
Figure 5 Deregulation of signalling pathways and transcription factors. Key affected pathways, components and inferred functions, are summarized in the main text and Supplementary Information section 7 for n = 279 samples. The frequency (%) of genetic alterations for HPV(−) and HPV(+) tumours are shown separately within sub-panels and highlighted. Also see Supplementary Fig. 7.15. Pathway alterations include homozygous deletions, focal amplifications and somatic mutations. Activated and inactivated pathways/genes, and activating or inhibitory symbols are based on predicted effects of genome alterations and/or pathway functions. PowerPoint slideCC BY-NC-SA · PubMed Central

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Metadata

Authors
The Cancer Genome Atlas Network
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2015-01-28
Volume
517
Issue
7536
Pages
576-582
ISSN
  • 0028-0836
  • 1476-4687
DOI
10.1038/nature14129
PMC
PMC4311405
Cited by
3,877
References
2
Language
en
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