Assessment of multiple displacement amplification for polymorphism discovery and haplotype determination at a highly polymorphic locus,MC1R

Murthy, Kenton K.; Mahboubi, Vafa; Santiago, Alicia; Barragan, Mandy T.; Knöll, Ralph; Schultheiss, Heinz‐Peter; O’Connor, Daniel T.; Schork, Nicholas J.; Rana, Brinda K.

doi:10.1002/humu.20199

Cited by 28 publications

(17 citation statements)

References 22 publications

(24 reference statements)

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“…Moreover, even small amounts of genotype misclassification can substantially attenuate the parameter estimate for gene-environment interactions (24). The cumulative effect of allele-calling errors may lead to misrepresentation of haplotypes (25), particularly at loci with multiple polymorphic sites (26). Some genotyping error is inevitable due to instability of genotyping reagents, operator error, and chance.…”

Section: Discussionmentioning

confidence: 99%

Whole-Genome Amplification of Oral Rinse Self-Collected DNA in a Population-Based Case-Control Study of Breast Cancer

Liang¹,

Trentham‐Dietz²,

Titus-Ernstoff³

et al. 2007

Cancer Epidemiology, Biomarkers &Amp; Prevention

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The availability of large amounts of genomic DNA (gDNA) is the limiting factor for many of the molecular biology assays in genetic epidemiologic studies. Whole-genome amplification using multiple displacement amplification is used to amplify a representative sample of gDNA from small amounts of gDNA to optimize gDNA yield. We collected oral rinse DNA samples through the mail from 3,377 women enrolled in a population-based U.S. breast cancer case-control study and did whole-genome amplification by multiple displacement amplification. Genotyping was done for 66 single nucleotide polymorphisms (SNP) in 18 candidate susceptibility genes using amplified DNA with genomic replicates included for quality control. The concordance rates (percentages of agreement) in 95 quality control replicates of gDNA and amplified DNA for 66 SNPs ranged from 88% to 100% (median, 97%). The average allelic error rate was 0.9%. However, in further analyses based on the full control series (n = 1,492), >60% of the SNPs failed tests for Hardy-Weinberg equilibrium (P < 0.05), with evidence of heterozygote loss in the great majority. Even eliminating the 9% of samples with lower quality or input DNA, tests for Hardy-Weinberg equilibrium indicated persistent allele bias in nearly a third of the SNPs. Whole-genome amplification may introduce substantial allele amplification bias in gDNA collected using a common protocol in population-based epidemiologic studies. (Cancer Epidemiol Biomarkers Prev 2007;16(8):1610-4)

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Section: Discussionmentioning

confidence: 99%

Whole-Genome Amplification of Oral Rinse Self-Collected DNA in a Population-Based Case-Control Study of Breast Cancer

Liang¹,

Trentham‐Dietz²,

Titus-Ernstoff³

et al. 2007

Cancer Epidemiology, Biomarkers &Amp; Prevention

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“…Amplification of genomic DNA was carried out on 5-ng samples and 2 H 2 O-negative controls using GenomiPhi DNA Amplification kit (Amersham Biosciences) according to the recommended protocol. 10 …”

Section: Subjects and Dna Samplesmentioning

confidence: 99%

Polymorphisms and Haplotypes of the Regulator of G Protein Signaling-2 Gene in Normotensives and Hypertensives

et al. 2006

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Abstract-Regulator of G protein signaling (RGS) proteins stimulate the GTPase activity of G ␣ subunits of heterotrimeric G proteins, thereby negatively regulating G protein-coupled receptor signaling. RGS2, which preferentially alters G ␣q -mediated signaling, may be important for cardiovascular health, because knockout of RGS2 in mice is associated with altered smooth muscle relaxation and hypertension. In this study, we determined genetic variation in the human RGS2 gene by sequencing DNA in normotensive and hypertensive populations of whites (nϭ128) and blacks (nϭ122). We identified 14 single nucleotide polymorphisms and 2 two-base insertion/deletions (in/del; 1891 to 1892 TC and 2138 to 2139 AA). Although most of the genetic variants were found at low allelic frequency, in particular in coding regions, the 1891 to 1892 TC and 2138 to 2139 AA intronic in/del were in linkage disequilibrium and were associated with hypertension in blacks (PϽ0.05). We defined several haplotypes for the RGS2 gene, certain of which showed striking differences between whites and blacks. Additionally, 2 haplotypes had significantly different frequencies between hypertensive and normotensive black groups (PϽ0.05). We conclude that RGS2 is genetically conserved within coding regions but that the intronic in/del define ethnicity-specific haplotypes. Moreover, certain RGS2 variants that occur at greater frequency in hypertensive blacks may serve as ethnicity-specific genetic variants for this disease.

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“…Furthermore the gene sequences were almost identical confirming the genome coverage of the MDA technique. The MDA-synthesized template has been used for a diverse set of downstream applications such as allele amplification, single nucleotide polymorphism (SNP) analysis (Dean et al, 2002), restriction fragment length polymorphisms (RFLP) analysis (Gadkar and Rilling, 2005b), polymorphism discovery, single sperm typing, chromosome translocation, and gene mutation analysis (Jiang et al, 2005;Luthra and Medeiros, 2004;Murthy et al, 2005). Future research in these fields on P. striiformis f. sp.…”

Section: Discussionmentioning

confidence: 99%

Whole genome amplification of the rust Puccinia striiformis f. sp. tritici from single spores

Wang

Zhu

Zhang

et al. 2009

Journal of Microbiological Methods

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Rust fungi are obligate parasites and cannot be routinely cultured to obtain sufficient biomass for DNA extractions. Multiple displacement amplification (MDA) was demonstrated in this study for whole genome amplification from single spores of the rust fungus, Puccinia striiformis. The genomic DNA coverage and fidelity of this method was evaluated by PCR amplification and sequencing of two genetic markers: portions of the multi-copy nuclear ribosomal DNA internal transcribed spacer region (ITS) and the single copy β-tubulin gene from two geographical diverse isolates. Our results show that MDA is a valuable tool for whole genome amplification from single spores, and we propose that MDA-amplified DNA can be used for molecular genetic analysis of the wheat yellow rust fungus.

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Assessment of multiple displacement amplification for polymorphism discovery and haplotype determination at a highly polymorphic locus,MC1R

Cited by 28 publications

References 22 publications

Whole-Genome Amplification of Oral Rinse Self-Collected DNA in a Population-Based Case-Control Study of Breast Cancer

Whole-Genome Amplification of Oral Rinse Self-Collected DNA in a Population-Based Case-Control Study of Breast Cancer

Polymorphisms and Haplotypes of the Regulator of G Protein Signaling-2 Gene in Normotensives and Hypertensives

Whole genome amplification of the rust Puccinia striiformis f. sp. tritici from single spores

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