Evaluating Whole Genome Amplification via Multiply-Primed Rolling Circle Amplification for SNP Genotyping of Samples With Low DNA Yield

Silander, Kaisa; Komulainen, Kati; Ellonen, Pekka; Jussila, Minttu; Alanne, Mervi; Levander, Minna; Tainola, Päivi; Kuulasmaa, Kari; Salomaa, Veikko; Perola, Markus; Peltonen, Leena; Saarela, Janna

doi:10.1375/1832427054936664

Cited by 13 publications

(21 citation statements)

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“…In these analyses, one sample was found to be contaminated and was excluded. DNA samples with low DNA yield (<7.5 µg of genomic DNA) as measured by fluorescent label PicoGreen (Invitrogen, Carlsbad, CA, USA) were subjected to whole genome amplification before genotyping, followed by additional quality control checks [36]. A total of five samples were excluded due to biased whole genome amplification, and a further 4 samples were excluded due to extremely low quantities of DNA which was insufficient for whole genome amplification.…”

Section: Methodsmentioning

confidence: 99%

“…Approximately 5.5% of the genotypes were created with an in-house developed method of allele-specific primer extension on microarrays, as previously described [36]. Approximately 93.0% of the genotypes were produced with the MassARRAY System (Sequenom, San Diego, CA, USA), either with the homogeneous Mass Extension (hME) reaction or iPLEX reaction, using the protocols recommended by the manufacturer with these modifications: hME reactions were carried out with 5–7.5 ng of DNA and for the majority of the variants, the hME extension reaction was run using TERMIPol DNA polymerase (Solis Biodyne OÜ, Tartu, Estonia) [42] instead of ThermoSequenase (GE Healthcare Life Sciences, Chalfont St. Giles, UK).…”

Section: Methodsmentioning

confidence: 99%

“…Three of the variants were genotyped with other platforms: rs4340 was genotyped by a PCR assay followed by separation on 2% agarose gel with ethidium bromide staining and rs28665122 and rs3216183 were genotyped with TaqMan (Applied Biosystems, Foster City, CA) [30], [44]. For 100 samples where inadequate amount of genomic DNA was available, the DNA was amplified with GenomiPhi DNA amplification kit (GE Healthcare Life Sciences), as previously described [36].…”

Section: Methodsmentioning

confidence: 99%

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Gender Differences in Genetic Risk Profiles for Cardiovascular Disease

et al. 2008

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BackgroundCardiovascular disease (CVD) incidence, complications and burden differ markedly between women and men. Although there is variation in the distribution of lifestyle factors between the genders, they do not fully explain the differences in CVD incidence and suggest the existence of gender-specific genetic risk factors. We aimed to estimate whether the genetic risk profiles of coronary heart disease (CHD), ischemic stroke and the composite end-point of CVD differ between the genders.Methodology/Principal FindingsWe studied in two Finnish population cohorts, using the case-cohort design the association between common variation in 46 candidate genes and CHD, ischemic stroke, CVD, and CVD-related quantitative risk factors. We analyzed men and women jointly and also conducted genotype-gender interaction analysis. Several allelic variants conferred disease risk for men and women jointly, including rs1801020 in coagulation factor XII (HR = 1.31 (1.08–1.60) for CVD, uncorrected p = 0.006 multiplicative model). Variant rs11673407 in the fucosyltransferase 3 gene was strongly associated with waist/hip ratio (uncorrected p = 0.00005) in joint analysis. In interaction analysis we found statistical evidence of variant-gender interaction conferring risk of CHD and CVD: rs3742264 in the carboxypeptidase B2 gene, p(interaction) = 0.009 for CHD, and rs2774279 in the upstream stimulatory factor 1 gene, p(interaction) = 0.007 for CHD and CVD, showed strong association in women but not in men, while rs2069840 in interleukin 6 gene, p(interaction) = 0.004 for CVD, showed strong association in men but not in women (uncorrected p-values). Also, two variants in the selenoprotein S gene conferred risk for ischemic stroke in women, p(interaction) = 0.003 and 0.007. Importantly, we identified a larger number of gender-specific effects for women than for men.Conclusions/SignificanceA false discovery rate analysis suggests that we may expect half of the reported findings for combined gender analysis to be true positives, while at least third of the reported genotype-gender interaction results are true positives. The asymmetry in positive findings between the genders could imply that genetic risk loci for CVD are more readily detectable in women, while for men they are more confounded by environmental/lifestyle risk factors. The possible differences in genetic risk profiles between the genders should be addressed in more detail in genetic studies of CVD, and more focus on female CVD risk is also warranted in genome-wide association studies.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Gender Differences in Genetic Risk Profiles for Cardiovascular Disease

et al. 2008

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“…Genotyping was done with homogeneous mass extension using the MassARRAY System (Sequenom, San Diego, California) in multiplexes of two to six SNPs. The COMT variants were genotyped by microarray-based allele-specific primer extension method (12). Genotyping was performed in two phases.…”

Section: Methodsmentioning

confidence: 99%

Association of a Nonsynonymous Variant of DAOA with Visuospatial Ability in a Bipolar Family Sample

Soronen

Silander

Antila

et al. 2008

Biological Psychiatry

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BackgroundBipolar disorder and schizophrenia are hypothesized to share some genetic background.MethodsIn a two-phase study, we evaluated the effect of five promising candidate genes for psychotic disorders, DAOA, COMT, DTNBP1, NRG1, and AKT1, on bipolar spectrum disorder, psychotic disorder, and related cognitive endophenotypes in a Finnish family-based sample ascertained for bipolar disorder.ResultsIn initial screening of 362 individuals from 63 families, we found only marginal evidence for association with the diagnosis-based dichotomous classification. Those associations did not strengthen when we genotyped the complete sample of 723 individuals from 180 families. We observed a significant association of DAOA variants rs3916966 and rs2391191 with visuospatial ability (Quantitative Transmission Disequilibrium Test [QTDT]; p = 4 × 10−6 and 5 × 10−6, respectively) (n = 159) with the two variants in almost complete linkage disequilibrium. The COMT variant rs165599 also associated with visuospatial ability, and in our dataset, we saw an additive effect of DAOA and COMT variants on this neuropsychological trait.ConclusionsThe ancestral allele (Arg) of the nonsynonymous common DAOA variant rs2391191 (Arg30Lys) was found to predispose to impaired performance. The DAOA gene may play a role in predisposing individuals to a mixed phenotype of psychosis and mania and to impairments in related neuropsychological traits.

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“…The quantity of DNA was validated using PicoGreen (Invitrogen (Molecular Probes), Carlsbad, USA) Xuorescent label prior to aliquotting. Samples with low yield of DNA were ampliWed with GenomePhi [GE Healthcare (Amersham Biotech), Chalfont, St Giles, UK] whole genome ampliWcation kit as previously described (Silander et al 2005).…”

Section: Biochemical Measurementsmentioning

confidence: 99%

Variation in the selenoprotein S gene locus is associated with coronary heart disease and ischemic stroke in two independent Finnish cohorts

et al. 2007

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Selenoprotein S (SEPS1) is a novel candidate gene involved in the regulation of inflammatory response and protection from oxidative damage. This study explored the genetic variation in the SEPS1 locus for an association with CVD as well as with quantitative phenotypes related to obesity and inflammation. We used the case-cohort design and time-to-event analysis in two separate prospectively followed population-based cohorts FINRISK 92 and 97 (n = 999 and 1,223 individuals, respectively) to study the associations of five single nucleotide polymorphisms with the risk for coronary heart disease (CHD) and ischemic stroke events. We found a significant association with increased CHD risk in females carrying the minor allele of rs8025174 in the combined analysis of both cohorts [hazard ratio (HR) 2.95 (95% confidence interval: 1.37-6.39)]. Another variant, rs7178239, increased the risk for ischemic stroke significantly in females [HR: 3.35 (1.66-6.76)] and in joint analysis of both sexes and both cohorts [HR: 1.75 (1.17-2.64)]. These results indicate that variation in the SEPS1 locus may have an effect on CVD morbidity, especially in females. This observation should stimulate further investigations of the role of this gene and protein in the pathogenesis of CVD.

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Evaluating Whole Genome Amplification via Multiply-Primed Rolling Circle Amplification for SNP Genotyping of Samples With Low DNA Yield

Cited by 13 publications

References 14 publications

Gender Differences in Genetic Risk Profiles for Cardiovascular Disease

Gender Differences in Genetic Risk Profiles for Cardiovascular Disease

Association of a Nonsynonymous Variant of DAOA with Visuospatial Ability in a Bipolar Family Sample

Variation in the selenoprotein S gene locus is associated with coronary heart disease and ischemic stroke in two independent Finnish cohorts

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