Single nucleotide polymorphisms as tools in human genetics

Gray, Ian C.

doi:10.1093/hmg/9.16.2403

Cited by 224 publications

(122 citation statements)

References 37 publications

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“…It may be useful to type several polymorphisms throughout the region of a candidate gene in order to construct haplotypes, which could be tested for association with the phenotype of interest. The increasing availability of mapped single nucle otide polymorphism markers (11)(12)(13)(14)(15) offers the opportunity for such an approach and presents methodological chal lenges (see the section on statistical issues).…”

Section: Definition and Grouping Of Genotypesmentioning

confidence: 99%

Reporting, Appraising, and Integrating Data on Genotype Prevalence and Gene-Disease Associations

Little¹,

Bradley²,

Bray³

et al. 2002

American Journal of Epidemiology

335

247

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Section: Definition and Grouping Of Genotypesmentioning

confidence: 99%

Reporting, Appraising, and Integrating Data on Genotype Prevalence and Gene-Disease Associations

Little¹,

Bradley²,

Bray³

et al. 2002

American Journal of Epidemiology

335

247

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“…It is widely accepted that SNPs represent the most abundant form of genetic variation between individuals. Indeed, SNPs can be considered to be powerful tools for the identification of genes involved in Mendelian, polygenic and multifactorial diseases (1). SNP analysis has been successfully used to understand the pathogenesis of several diseases.…”

mentioning

confidence: 99%

A cost-effective melting temperature assay for the detection of single-nucleotide polymorphism in the MBL2 gene of HIV-1-infected children

Arraes

Souza

Bruneska

et al. 2006

Braz J Med Biol Res

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We report a fast (less than 3 h) and cost-effective melting temperature assay method for the detection of single-nucleotide polymorphisms in the MBL2 gene. The protocol, which is based on the Corbett Rotor Gene real time PCR platform and SYBR Green I chemistry, yielded, in the cohorts studied, sensitive (100%) and specific (100%) PCR amplification without the use of costly fluorophore-labeled probes or post-PCR manipulation. At the end of the PCR, the dissociation protocol included a slow heating from 60º to 95ºC in 0.2ºC steps, with an 8-s interval between steps. Melting curve profiles were obtained using the dissociation software of the Rotor Gene-3000 apparatus. Samples were analyzed in duplicate and in different PCR runs to test the reproducibility of this technique. No supplementary data handling is required to determine the MBL2 genotype. MBL2 genotyping performed on a cohort of 164 HIV-1-positive Brazilian children and 150 healthy controls, matched for age and sex and ethnic origin, yielded reproducible results confirmed by direct sequencing of the amplicon performed in blind. The three MBL2 variants (Arg52Cys, Gly54Asp, Gly57Glu) were grouped together and called allele 0, while the combination of three wild-type alleles was called allele A. The frequency of the A/A homozygotes was significantly higher among healthy controls (0.68) than in HIV-infected children (0.55; P = 0.0234) and the frequency of MBL2 0/0 homozygotes was higher among HIV-1-infected children than healthy controls (P = 0.0296). The 0 allele was significantly more frequent among the 164 HIV-1-infected children (0.29) than among the 150 healthy controls (0.18; P = 0.0032). Our data confirm the association between the presence of the mutated MBL2 allele (allele 0) and HIV-1 infection in perinatally exposed children. Our results are in agreement with the literature data which indicate that the presence of the allele 0 confers a relative risk of 1.37 for HIV-1 infection through vertical transmission. Correspondence

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“…Potential candidates for these markers are single-nucleotide polymorphism (SNPs) that alter the sequence or the expression of a gene product (Lander and Schork, 1994;Cargill et al, 1999;Gray et al, 2000;Risch, 2000;Sunyaev et al, 2001). A large variety of SNPs have already been investigated for their association with breast cancer (Dunning et al, 2001;Nathanson and Weber, 2001).…”

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confidence: 99%

Association of NQO1 polymorphism with spontaneous breast cancer in two independent populations

Sarmanova

Souček

et al. 2004

Br J Cancer

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Eight different single-nucleotide polymorphisms (SNPs) in six different genes were investigated for possible association with breast cancer. We used a case -control study design in two Caucasian populations, one from Tyrol, Austria, and the other from Prague, Czech Republic. Two SNPs showed an association with breast cancer: R72P inTP53 and P187S in NQO1. Six SNPs, Q356R and P871L in BRCA1, N372H in BRCA2, C112R (E4) and R158C (E2) in ApoE and C825T in GNB3, did not show any sign of association. The P187S polymorphism in NQO1 was associated with breast cancer in both populations from Tyrol and Prague with a higher risk for carriers of the 187S allele. Combining the results of the two populations, we observed a highly significant difference (P ¼ 0.0004) of genotype and allele frequencies (odds ratio (OR) ¼ 1.46; 95% confidence interval (CI) 1.16 -1.85; P ¼ 0.001) and of the homozygote ratio (OR ¼ 3.8; 95% CI 1.73 -8.34; P ¼ 0.0001). Combining the two 'candidate' SNPs (P187S and R72P) revealed an increased risk for breast cancer of double heterozygotes (P187S/R72P) of the NQO1 and TP53 genes (OR ¼ 1.88; 95% CI 1.13 -3.15; P ¼ 0.011), suggesting a possible interaction of these two loci.

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Single nucleotide polymorphisms as tools in human genetics

Cited by 224 publications

References 37 publications

Reporting, Appraising, and Integrating Data on Genotype Prevalence and Gene-Disease Associations

Reporting, Appraising, and Integrating Data on Genotype Prevalence and Gene-Disease Associations

A cost-effective melting temperature assay for the detection of single-nucleotide polymorphism in the MBL2 gene of HIV-1-infected children

Association of NQO1 polymorphism with spontaneous breast cancer in two independent populations

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