Genotyping of thrombotic risk factors by maldi-tof mass spectrometry

Humeny, Andreas; Bonk, Thomas; Berkholz, Alexander; Wildt, L.; Becker, Cord‐Michael

doi:10.1016/s0009-9120(01)00264-8

Cited by 27 publications

(20 citation statements)

References 15 publications

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“…the primer needs to be complementary to either one of the nonrepetitive sequences flanking the microsatellite. Depending on the flanking sequence of the microsatellites, reverse or forward extension primers were selected that yielded optimal melting temperatures, high specificity, and reduced formation of secondary structures [e.g., primer dimers, and loops (25,27,28 )]. On the other hand, in MALDI-TOF-MS analysis, signal intensities of oligonucleotides decrease parallel to increases in molecular mass (28 ).…”

Section: Discussionmentioning

confidence: 99%

“…Because of its high molecular resolution, excellent accuracy, reproducibility, and automation properties, this method offers the potential to replace other methods in molecular medicine (23)(24)(25)(26)(27)(28)(29). Although the feasibility of our semiquantitative approach has been demonstrated on HNPCC neoplasms and colorectal cancer cell lines, it may easily be adapted to MSI classification of cancers in other organs.…”

Section: Discussionmentioning

confidence: 99%

“…Methods commonly used for the detection of MSIs, including chromatography, electrophoresis, and DNA sequencing, are time-consuming and expensive and suffer from low sensitivity in the detection of quantitative differences. In this situation, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS)-based genotyping offers a promising technical alternative (23)(24)(25)(26)(27)(28)(29). Here we describe a novel method for enhanced genotyping of MSIs that affect mononucleotide repeats with prospects for high throughput by use of MALDI-TOF-MS for semiquantitative analysis.…”

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confidence: 99%

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Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry-based Detection of Microsatellite Instabilities in Coding DNA Sequences: A Novel Approach to Identify DNA-Mismatch Repair-deficient Cancer Cells

et al. 2003

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Background: Inherited defects in the DNA mismatch repair system lead to increased loss or gain of repeat units in microsatellites, commonly referred to as microsatellite instability (MSI). MSIs in coding regions of critical genes contribute to the pathogenesis of DNAmismatch repair-deficient cancers, particularly those associated with the hereditary nonpolyposis colorectal cancer syndrome (HNPCC). MSI typing is therefore increasingly used to guide the molecular diagnosis of HNPCC. Methods: We used matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to identify MSIs in mononucleotide repeats within the coding sequences of genes relevant to the pathogenesis of MSI؉ neoplastic lesions. After a primer extension reaction of PCR products encompassing the microsatellites, the molecular masses of the extension products were determined by MALDI-TOF-MS. Results: MSIs were detected by MALDI-TOF-MS in the GART, AC1, TGFBR2, MSH3, and MSH6 genes in neoplastic tissues and MSI؉ colorectal cancer cell lines but not in MSI؊ control tissues. The analysis of peakintegral ratios in a single spectrum of the peaks representing insertions or deletions compared with the full-

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry-based Detection of Microsatellite Instabilities in Coding DNA Sequences: A Novel Approach to Identify DNA-Mismatch Repair-deficient Cancer Cells

et al. 2003

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“…19,[22][23][24]32,34,35 Solid phase capturable ddNTPs in SBE have been developed using biotinylated ddNTPs to generate 3Ј-biotinylated extension DNA products, which then are purified by streptavidin-coated magnetic beads before analysis by MS. 27 This solid phase capturable-SBE method has been applied for simultaneous genotyping of 17 Y-chromosome SNPs, 36 detection of 30 point mutations in p53 in a single tube, 37 and for concurrent analysis of 40 SNPs of CYP2C9 and 50 SNPs of CYP2A13 genes. 38 However, the cost-effectiveness of this approach has not been evaluated.…”

Section: Discussionmentioning

confidence: 99%

“…21 MALDI-TOF MS in combination with multiplex minisequencing has proven to be a cost-effective and efficient procedure for high-throughput genotyping of a number of disease-causing genes or of single nucleotide polymorphisms (SNPs). 19,[22][23][24] Nevertheless, bottlenecks in multiplex genotyping using MALDI-TOF MS include optimization of highly multiplex-primer extension (PE) reactions 25 and the need to completely remove contaminating salt adducts that can compromise spectral quality and reduce accuracy of mass assignments. [25][26][27] For genotyping of HBB, there is the additional problem of the very close proximity and partial overlapping of the mutations to one another.…”

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confidence: 99%

Simple, Efficient, and Cost-Effective Multiplex Genotyping with Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry of Hemoglobin Beta Gene Mutations

Thongnoppakhun

Jiemsup

Yongkiettrakul

et al. 2009

The Journal of Molecular Diagnostics

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A number of common mutations in the hemoglobin ␤ (HBB) gene cause ␤-thalassemia, a monogenic disease with high prevalence in certain ethnic groups. As there are 30 HBB variants that cover more than 99.5% of HBB mutant alleles in the Thai population, an efficient and cost-effective screening method is required. Three panels of multiplex primer extensions, followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were developed. The first panel simultaneously detected 21 of the most common HBB mutations , while the second panel screened nine additional mutations , plus seven of the first panel for confirmation; the third panel was used to confirm three HBB mutations , yielding a 9-Da mass difference that could not be clearly distinguished by the previous two panels. The protocol was both standardized using 40 samples of known genotypes and subsequently validated in 162 blind samples with 27 different genotypes (including a normal control) , comprising heterozygous , compound heterozygous , and homozygous ␤-thalassemia. Results were in complete agreement with those from the genotyping results , conducted using three different methods overall. The method developed here permitted the detection of mutations missed using a single genotyping procedure. The procedure should serve as the method of choice for HBB genotyping due to its accuracy , sensitivity , and cost-effectiveness , and can be applied to studies of other gene variants that are potential disease biomarkers. (J Mol

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Analytic validity of genetic tests to identify factor V Leiden and prothrombin G20210A

et al. 2010

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The objective of this study is to systematically review methods for detecting Factor V Leiden or prothrombin G20210A. English-language literature from MEDLINE 1 , EMBASE 1 , The Cochrane Library, the Cumulative Index to Nursing and Allied Health Literature, PsycInfo , 2000-December 2008. Studies assessed methods for detection of these mutations in at least 10 human blood samples and reported concordance, discordance, or reproducibility. Two investigators abstracted data on the sample selection criteria, test operators, DNA extraction, experimental test, reference standard, commercial instruments, concordance rates, explanation of any discordance, and whether discordance resolved after repetition. We assessed strength of the evidence using the GRADE criteria. We reviewed 7,777 titles and included 66 articles. The majority of the reviewed studies used PCR-RFLP or AS-PCR as the reference standard. The studies demonstrated that commercially available and precommercial tests have high analytic validity with all having greater than 99% concordance with the reference standard. With a few exceptions, discordance resolved with repetition of the test, suggesting operator or administrative errors were responsible for the discordant results. In the quality assurance studies, greater than 98% of laboratories demonstrated high, even perfect, accuracy when asked to diagnose a sample with a known mutation. The majority of errors came from a limited number of laboratories. Although not all methods may be accurate, there is high-grade evidence that genetic tests for the detection of FVL and prothrombin G20210A have excellent analytic validity. There is high-grade evidence that most, but not all, clinical laboratories test for FVL and prothrombin G20210A accurately. Am. J. Hematol. 85:264-270, 2010. V

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Genotyping of thrombotic risk factors by maldi-tof mass spectrometry

Cited by 27 publications

References 15 publications

Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry-based Detection of Microsatellite Instabilities in Coding DNA Sequences: A Novel Approach to Identify DNA-Mismatch Repair-deficient Cancer Cells

Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry-based Detection of Microsatellite Instabilities in Coding DNA Sequences: A Novel Approach to Identify DNA-Mismatch Repair-deficient Cancer Cells

Simple, Efficient, and Cost-Effective Multiplex Genotyping with Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry of Hemoglobin Beta Gene Mutations

Analytic validity of genetic tests to identify factor V Leiden and prothrombin G20210A

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