Chip-based genotyping by mass spectrometry

Tang, Kai; Fu, Dong-Jing; Julien, Dominique; Braun, Andreas; Cantor, Charles R.; Köster, Hubert

doi:10.1073/pnas.96.18.10016

Cited by 264 publications

(157 citation statements)

References 19 publications

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“…Genotyping was performed on a matrix-assisted laser desorption/ionization (MALDI)-TOF mass-spectrometer (MassArray system) employing the Spectrodesigner software (Sequenom, CA, USA) for primer selection and multiplexing, and the homogeneous mass-extension (hMe) process for producing primer extension products. 23 Genotyping was performed at the Genetics Research Centre GmbH, Munich, Germany. All primer sequences are available upon request.…”

Section: Snp Genotypingmentioning

confidence: 99%

Polymorphisms in the angiotensin-converting enzyme gene are associated with unipolar depression, ACE activity and hypercortisolism

et al. 2006

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Angiotensin-converting enzyme (ACE) is assumed to influence the activity of the hypothalamic-pituitary-adrenocortical (HPA) system, which shows hyperactivity in the majority of patients with major depression. The ACE gene, known to be associated with cardiovascular disorders, which in turn are accompanied with an increased susceptibility for depression, is therefore a promising candidate gene for affective disorders. We investigated the genetic association between 35 single-nucleotide polymorphisms (SNPs) and an insertion/deletion (I/D)-polymorphism in the ACE gene and the susceptibility for unipolar major depression together with the genetic association with ACE serum activity and functional parameters of the HPA system. Two independent case/control samples with a total of 843 unrelated unipolar depressed patients and 1479 healthy controls were investigated. A case/control sample was screened to detect genetic associations with unipolar major depression. In addition, a replication sample was used to confirm the detected associations and to further investigate functional consequences of the genetic variants associated with depression. In the screening sample, two SNPs within the ACE gene were significantly associated with unipolar major depression. The association with unipolar major depression of one SNP (rs4291) located in the promoter region of the ACE gene was confirmed in our replication sample. The T-allele of this SNP was associated with depression and depressed T-allele carriers showed higher ACE serum activity and HPA-axis hyperactivity. Variants of the ACE gene such as SNP rs4291 are suggested susceptibility factors for unipolar major depression. We could show that SNP rs4291 influences ACE activity and HPA-axis hyperactivity and might therefore represent a common pathophysiologic link for unipolar depression and cardiovascular disease.

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Section: Snp Genotypingmentioning

confidence: 99%

Polymorphisms in the angiotensin-converting enzyme gene are associated with unipolar depression, ACE activity and hypercortisolism

et al. 2006

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“…The genotypes collected for this study are available from the authors to the extent that is consistent with the informed consent provided by the study participants. We used matrix-associated laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) 29 with 5 ng of DNA per multiplex genotyping reaction to genotype most SNPs in this study. The PCR protocol is described elsewhere 25 .…”

Section: Bipolar Disorder In European Americansmentioning

confidence: 99%

Assessing the impact of population stratification on genetic association studies

et al. 2004

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Population stratification refers to differences in allele frequencies between cases and controls due to systematic differences in ancestry rather than association of genes with disease. It has been proposed that false positive associations due to stratification can be controlled by genotyping a few dozen unlinked genetic markers. To assess stratification empirically, we analyzed data from 11 case-control and casecohort association studies. We did not detect statistically significant evidence for stratification but did observe that assessments based on a few dozen markers lack power to rule out moderate levels of stratification that could cause false positive associations in studies designed to detect modest genetic risk factors. After increasing the number of markers and samples in a case-cohort study (the design most immune to stratification), we found that stratification was in fact present. Our results suggest that modest amounts of stratification can exist even in well designed studies.

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“…We performed genotype analysis of this Ϫ156 SNP on placental tissues, maternal blood cells, and plasma collected from eight fetomaternal pairs. SNP genotyping was performed on genomic DNA from the placental tissues and maternal blood cells using the standard primer extension (homogenous MassEXTEND) protocol on a MassARRAY Compact system (Sequenom, San Diego), which is a MALDI-TOF MS system (26).…”

mentioning

confidence: 99%

Detection of the placental epigenetic signature of the maspin gene in maternal plasma

Chim

Chiu

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

312

227

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The discovery of fetal DNA in the plasma of pregnant women has opened up new approaches for noninvasive prenatal diagnosis and monitoring. Up to now, the lack of a fetal DNA marker that can be universally detected in maternal plasma has limited the clinical application of this technology. We hypothesized that epigenetic differences between the placenta and maternal blood cells could be used for developing such a marker. By using bisulfite DNA sequencing, the methylation status of the maspin gene promoter in placental tissues and paired maternal blood cells from pregnant women was analyzed. The maspin gene promoter was found to be hypomethylated in placental tissues and densely methylated in maternal blood cells. Genotyping of a single nucleotide polymorphism within the unmethylated maspin sequences in maternal plasma demonstrated that these sequences were derived from the fetus. By using real-time quantitative methylation-specific PCR, unmethylated maspin sequences were detected in maternal plasma in all three trimesters of pregnancy and were cleared within 24 h after delivery. The maternal plasma concentration of unmethylated maspin sequences was elevated by a median of 5.7 times in preeclamptic pregnancies compared with nonpreeclamptic pregnancies. Hypomethylated maspin DNA is the first universal marker for fetal DNA in maternal plasma, thus allowing the measurement of fetal DNA concentrations in pregnancy-associated disorders, irrespective of fetal gender and genetic polymorphisms. Differential DNA methylation between the placenta and maternal blood cells may be exploited to develop further markers for noninvasive prenatal assessment.DNA methylation ͉ noninvasive prenatal diagnosis ͉ circulating nucleic acids

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Chip-based genotyping by mass spectrometry

Cited by 264 publications

References 19 publications

Polymorphisms in the angiotensin-converting enzyme gene are associated with unipolar depression, ACE activity and hypercortisolism

Polymorphisms in the angiotensin-converting enzyme gene are associated with unipolar depression, ACE activity and hypercortisolism

Assessing the impact of population stratification on genetic association studies

Detection of the placental epigenetic signature of the maspin gene in maternal plasma

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