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Related Experiment Videos

The predicted impact of coding single nucleotide polymorphisms database.

Matthew F Rudd1, Richard D Williams, Emily L Webb

  • 1Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom.

Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology
|November 15, 2005
PubMed
Summary

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This study catalogs nonsynonymous single nucleotide polymorphisms (nsSNPs) in cancer-related genes, predicting their functional impact. The findings aid in understanding inherited cancer susceptibility through sequence-based association studies.

Area of Science:

  • Genetics
  • Bioinformatics
  • Cancer Biology

Background:

  • Nonsynonymous single nucleotide polymorphisms (nsSNPs) can alter protein structure and function, potentially modifying inherited susceptibility to diseases.
  • Identifying functional nsSNPs in cancer-related genes is crucial for advancing sequence-based association studies in cancer research.

Purpose of the Study:

  • To classify and catalog the predicted functionality of nsSNPs within genes relevant to cancer biology.
  • To create a resource facilitating sequence-based association studies for inherited cancer susceptibility.

Main Methods:

  • Candidate cancer-related genes were identified using multiple databases (Gene Ontology, KEGG, etc.).
  • Validated nsSNPs (Build 123) were retrieved from NCBI dbSNP, filtered for minor allele frequency >0.01 in Caucasians.

Related Experiment Videos

  • Functional effects of nsSNPs were predicted using Grantham matrix, PolyPhen, and SIFT algorithms.

    • Main Results:

    • A total of 9,537 validated nsSNPs were initially retrieved.
    • This was refined to 3,666 nsSNPs linked to 7,080 candidate genes.
    • The study resulted in a curated pool of 3,009 fully annotated nsSNPs, accessible via the PICS database.

    Conclusions:

    • The PICS database provides a valuable resource for researchers studying the functional impact of coding SNPs in cancer genetics.
    • This ongoing project aims to continuously curate and release data on the putative functionality of coding SNPs.
    • The cataloged nsSNPs can aid in identifying genetic modifiers of inherited cancer susceptibility.