Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations.

2.50
Hdl Handle:
http://hdl.handle.net/10146/64473
Title:
Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations.
Authors:
Savas, Sevtap; Schmidt, Steffen; Jarjanazi, Hamdi; Ozcelik, Hilmi
Abstract:
Although highly penetrant alleles of BRCA1 and BRCA2 have been shown to predispose to breast cancer, the majority of breast cancer cases are assumed to result from the presence of low-moderate penetrant alleles and environmental carcinogens. Non-synonymous single nucleotide polymorphisms (nsSNPs) are hypothesised to contribute to disease susceptibility and approximately 30 per cent of them are predicted to have a biological significance. In this study, we have applied a bioinformatics-based strategy to identify breast cancer-related nsSNPs from 981 carcinogenesis-related genes expressed in breast tissue. Our results revealed a total of 367 validated nsSNPs, 109 (29.7 per cent) of which are predicted to affect the protein function (functional nsSNPs), suggesting that these nsSNPs are likely to influence the development and homeostasis of breast tissue and hence contribute to breast cancer susceptibility. Sixty-seven of the functional nsSNPs presented as commonly occurring nsSNPs (minor allele frequencies > or =5 per cent), representing excellent candidates for breast cancer susceptibility. Additionally, a non-uniform distribution of the common functional nsSNPs among different human populations was observed: 15 nsSNPs were reported to be present in all populations analysed, whereas another set of 15 nsSNPs was specific to particular population(s). We propose that the nsSNPs analysed in this study constitute a unique resource of potential genetic factors for breast cancer susceptibility. Furthermore, the variations in functional nsSNP allele frequencies across major population backgrounds may point to the potential variability of the molecular basis of breast cancer predisposition and treatment response among different human populations.
Citation:
Hum. Genomics 2006, 2 (5):287-296
Journal:
Human genomics
Issue Date:
Mar-2006
URI:
http://hdl.handle.net/10146/64473
PubMed ID:
16595073
Additional Links:
http://henrystewart.metapress.com/app/home/contribution.asp?referrer=parent&backto=issue,4,9;journal,4,14;linkingpublicationresults,1:121141,1
Type:
Article
Language:
en
Description:
KEYWORDS CLASSIFICATION: biomarkers of individual susceptibility: validation;Breast Neoplasms;Canada;Carcinogenicity Tests;epidemiology;Female;genetics;Genes,Brca1;Genes,Brca2;Genes,Tumor Suppressor;Genetics,Population;Humans;Polymorphism,Single Nucleotide;Predictive Value of Tests;Research;Risk Factors;Variation (Genetics).
ISSN:
1479-7364
Appears in Collections:
Articles with annotation

Full metadata record

DC FieldValue Language
dc.contributor.authorSavas, Sevtap-
dc.contributor.authorSchmidt, Steffen-
dc.contributor.authorJarjanazi, Hamdi-
dc.contributor.authorOzcelik, Hilmi-
dc.date.accessioned2009-04-06T07:57:39Z-
dc.date.available2009-04-06T07:57:39Z-
dc.date.issued2006-03-
dc.identifier.citationHum. Genomics 2006, 2 (5):287-296en
dc.identifier.issn1479-7364-
dc.identifier.pmid16595073-
dc.identifier.urihttp://hdl.handle.net/10146/64473-
dc.descriptionKEYWORDS CLASSIFICATION: biomarkers of individual susceptibility: validation;Breast Neoplasms;Canada;Carcinogenicity Tests;epidemiology;Female;genetics;Genes,Brca1;Genes,Brca2;Genes,Tumor Suppressor;Genetics,Population;Humans;Polymorphism,Single Nucleotide;Predictive Value of Tests;Research;Risk Factors;Variation (Genetics).en
dc.description.abstractAlthough highly penetrant alleles of BRCA1 and BRCA2 have been shown to predispose to breast cancer, the majority of breast cancer cases are assumed to result from the presence of low-moderate penetrant alleles and environmental carcinogens. Non-synonymous single nucleotide polymorphisms (nsSNPs) are hypothesised to contribute to disease susceptibility and approximately 30 per cent of them are predicted to have a biological significance. In this study, we have applied a bioinformatics-based strategy to identify breast cancer-related nsSNPs from 981 carcinogenesis-related genes expressed in breast tissue. Our results revealed a total of 367 validated nsSNPs, 109 (29.7 per cent) of which are predicted to affect the protein function (functional nsSNPs), suggesting that these nsSNPs are likely to influence the development and homeostasis of breast tissue and hence contribute to breast cancer susceptibility. Sixty-seven of the functional nsSNPs presented as commonly occurring nsSNPs (minor allele frequencies > or =5 per cent), representing excellent candidates for breast cancer susceptibility. Additionally, a non-uniform distribution of the common functional nsSNPs among different human populations was observed: 15 nsSNPs were reported to be present in all populations analysed, whereas another set of 15 nsSNPs was specific to particular population(s). We propose that the nsSNPs analysed in this study constitute a unique resource of potential genetic factors for breast cancer susceptibility. Furthermore, the variations in functional nsSNP allele frequencies across major population backgrounds may point to the potential variability of the molecular basis of breast cancer predisposition and treatment response among different human populations.en
dc.language.isoenen
dc.relation.urlhttp://henrystewart.metapress.com/app/home/contribution.asp?referrer=parent&backto=issue,4,9;journal,4,14;linkingpublicationresults,1:121141,1en
dc.subjectBreast cancer predispositionen
dc.subjectnsSNPsen
dc.subjectBreast tissue expressionen
dc.subjectCarcinogenesis-related genesen
dc.subjectPolyPhenen
dc.subject.meshBreast Neoplasms-
dc.subject.meshCarcinogenicity Tests-
dc.subject.meshFemale-
dc.subject.meshGenes, BRCA1-
dc.subject.meshGenes, BRCA2-
dc.subject.meshGenes, Tumor Suppressor-
dc.subject.meshGenetic Variation-
dc.subject.meshGenetics, Population-
dc.subject.meshHumans-
dc.subject.meshPolymorphism, Single Nucleotide-
dc.subject.meshPredictive Value of Tests-
dc.subject.meshRisk Factors-
dc.titleFunctional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations.en
dc.typeArticleen
dc.identifier.journalHuman genomicsen

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