Document Type

Journal Article

Publication Date

2014

Journal

Nucleic Acids Research

DOI

10.1093/nar/gku772

Abstract

Identification of non-synonymous single nucleotide variations (nsSNVs) has exponentially increased due to advances in Next-Generation Sequencing technologies. The functional impacts of these variations have been difficult to ascertain because the corresponding knowledge about sequence functional sites is quite fragmented. It is clear that mapping of variations to sequence functional features can help us better understand the pathophysiological role of variations. In this study, we investigated the effect of nsSNVs on more than 17 common types of post-translational modification (PTM) sites, active sites and binding sites. Out of 1 705 285 distinct nsSNVs on 259 216 functional sites we identified 38 549 variations that significantly affect 10 major functional sites. Furthermore, we found distinct patterns of site disruptions due to germline and somatic nsSNVs. Pan-cancer analysis across 12 different cancer types led to the identification of 51 genes with 106 nsSNV affected functional sites found in 3 or more cancer types. 13 of the 51 genes overlap with previously identified Significantly Mutated Genes (Nature. 2013 Oct 17;502(7471)). 62 mutations in these 13 genes affecting functional sites such as DNA, ATP binding and various PTM sites occur across several cancers and can be prioritized for additional validation and investigations.

Comments

Reproduced with permission of Oxford Journals. Nucleic Acids Research.

Creative Commons License

Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 License.

Peer Reviewed

1

Open Access

1

SupplementaryData.docx (14 kB)
Supplementary Data

Sup_Tab_1_Datasets_summary_counts.xlsx (71 kB)
Datasets summary counts

Sup_Tab_2_Datasource_Based_Survey.xlsx (41 kB)
Datasource based survey

Sup_Tab_3_Pathway_and_GO_Overrepresenting_analysis.xlsx (52 kB)
Pathway and GO overrepresenting analysis

Sup_Tab_4_Cancer_type_based_analysis_of_nsSNV_affected_Functional_sties.xlsx (351 kB)
Cancer type based analysis of nsSNV affected functional sites

Sup_Tab_5_Conservation_Comparison.xlsx (38 kB)
Conservation comparison

Sup_Tab_6_DisVar_disease_mapping_to_nsSNV_affected_Functional_sites.xlsx (229 kB)
DisVar disease mapping to nsSNV affected functional sites

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