NDLI: Mutation patterns in cancer genomes

Content Provider	PubMed Central
Author	Rubin, Alan F. Green, Phil
Abstract	Recent large-scale cancer sequencing studies have focused primarily on identifying cancer-associated genes, but as an important byproduct provide “passenger mutation” data that can potentially illuminate the mutational mechanisms at work in cancer cells. Here, we explore patterns of nucleotide substitution in several cancer types using published data. We first show that selection (negative or positive) has affected only a small fraction of mutations, allowing us to attribute observed trends to underlying mutational processes rather than selection. We then show that the increased CpG mutation frequency observed in some cancers primarily occurs outside of CpG islands and CpG island shores, thus rejecting the hypothesis that the increase is a byproduct of island or shore methylation followed by deamination. We observe an A→G vs. T→C mutational asymmetry in some cancers similar to one that has been observed in germline mutations in transcribed regions, suggesting that the mutation process may be influenced by gene expression. We also demonstrate that the relative frequency of mutations at dinucleotide “hotspots” can be used as a tool to detect likely technical artifacts in large-scale studies.
Related Links	http://dx.doi.org/10.1073/pnas.0912499106
Starting Page	21766
File Format	PDF
ISSN	10916490
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	51
Volume Number	106
Language	English
Publisher	National Academy of Sciences
Publisher Date	2009-12-22
Access Restriction	Open
Rights Holder	National Academy of Sciences
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Patterns of somatic mutation in human cancer genomes

Mutation rates in mammalian genomes

Patterns of nucleotide substitution in Drosophila and mammalian genomes

A long interspersed (LINE) DNA exhibiting polymorphic patterns in human genomes.

The somatic autosomal mutation matrix in cancer genomes

The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model.

Distinct Functional Patterns of Gene Promoter Hypomethylation and Hypermethylation in Cancer Genomes

Mutation and Selection on the Wobble Nucleotide in tRNA Anticodons in Marine Bivalve Mitochondrial Genomes

Optimization of Mutation Pressure in Relation to Properties of Protein-Coding Sequences in Bacterial Genomes

Mutation patterns in cancer genomes

Similar Documents

Patterns of somatic mutation in human cancer genomes

Mutation rates in mammalian genomes

Patterns of nucleotide substitution in Drosophila and mammalian genomes

A long interspersed (LINE) DNA exhibiting polymorphic patterns in human genomes.

The somatic autosomal mutation matrix in cancer genomes

The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model.

Distinct Functional Patterns of Gene Promoter Hypomethylation and Hypermethylation in Cancer Genomes

Mutation and Selection on the Wobble Nucleotide in tRNA Anticodons in Marine Bivalve Mitochondrial Genomes

Optimization of Mutation Pressure in Relation to Properties of Protein-Coding Sequences in Bacterial Genomes

Mutation patterns in cancer genomes