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Open Access Highly Accessed Research article

Patterns and processes of somatic mutations in nine major cancers

Peilin Jia12, William Pao345 and Zhongming Zhao1245*

Author Affiliations

1 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA

2 Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA

3 Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA

4 Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA

5 Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA

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BMC Medical Genomics 2014, 7:11  doi:10.1186/1755-8794-7-11

Published: 19 February 2014

Additional files

Additional file 1: Text S1:

Additional description of NMF and the correlation between the K-signature and the expression of APOBEC family genes.

Format: DOCX Size: 34KB Download file

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Additional file 2: Table S1:

Comparison of NMF performance using r = 3:7 in each cancer.

Format: XLSX Size: 15KB Download file

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Additional file 3: Table S2:

Mutation burdens (C → T and C → G in the TCX context) versus expression changes of the APOBEC family genes.

Format: DOCX Size: 26KB Download file

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Additional file 4: Table S3:

Mutation burdens (C → T and C → G in the TCX context) versus expression changes of the APOBEC family genes in samples with ≤ 200 mutations per exome.

Format: DOCX Size: 25KB Download file

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Additional file 5: Figure S1:

APOBEC3B gene activity in TCGA cancers.

Format: DOCX Size: 913KB Download file

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Additional file 6: Figure S2:

Comparison of signatures obtained using all SNVs and those obtained excluding non-CpG island (CGI) C → T mutations.

Format: DOCX Size: 1MB Download file

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Additional file 7: Figure S3:

Mutation signature load in melanoma.

Format: DOCX Size: 638KB Download file

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Additional file 8: Figure S4:

The effect of the outlier sample in SQCC.

Format: DOCX Size: 744KB Download file

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