Single nucleotide polymorphism analyses by MALDI-TOF MS

Tang, Kai; Opalsky, David; Abel, Ken; Boom, Dirk van den; Yip, Ping; Mistro, G. Del; Braun, Andreas; Cantor, Charles R.

doi:10.1016/s1387-3806(02)00980-6

Cited by 35 publications

(22 citation statements)

References 25 publications

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“…This method has been previously described in detail. 24 In brief, PCR primer pairs were designed to amplify the region around the SNP, along with extension primers using the Sequenom SpectroDESIGNERt software. The PCR primers (Metabion, Hamburg, Germany) were used to amplify 5 ng of genomic DNA in a multiplex reaction.…”

Section: Genotypingmentioning

confidence: 99%

Haplotype structure of TNFRSF5-TNFSF5 (CD40–CD40L) and association analysis in systemic lupus erythematosus

et al. 2005

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Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease that is caused by genetic and environmental factors. The tumour necrosis factor (TNF) superfamily of genes play a central role in immune regulation and have been proposed to be involved in the development of SLE. TNFRSF5 (CD40) falls on 20q11 -13, a region linked with SLE in three independent genome-wide studies. TNFSF5 (CD40L) falls on Xq26 and is the ligand for TNFRSF5. Seven single-nucleotide polymorphisms (SNPs) in CD40 and eight SNPs in CD40L were looked at for linkage disequilibrium (LD) and haplotype analysis in EuropeanCaucasians. Limited haplotype diversity was observed across CD40 and CD40L, and 497% of the diversity was captured. We also examined the association of SNPs and haplotypes in CD40 and CD40L with SLE in European-Caucasians. There was no evidence of association for CD40 or CD40L in 408 European-Caucasian families with SLE from UK. Haplotype tagging SNPs (htSNPs) are made known, which will facilitate analysis for susceptibility in other autoimmune diseases and risk for infectious disease.

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Section: Genotypingmentioning

confidence: 99%

Haplotype structure of TNFRSF5-TNFSF5 (CD40–CD40L) and association analysis in systemic lupus erythematosus

et al. 2005

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“…24,25 In brief, genotyping was performed by multiplexing SNP assays using the Sequenom s MassARRAYt genotyping system (Sequenom, Hamburg, Germany). Multiplex assays were designed for three to six SNPs per assay.…”

Section: Genotypingmentioning

confidence: 99%

Haplotype analysis of tumour necrosis factor receptor genes in 1p36: no evidence for association with systemic lupus erythematosus

et al. 2005

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Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with partially understood aetiology. The 1p36 region has been previously linked with SLE and harbours tumour necrosis factor receptor (TNFR) genes. Functional and genetic data implicate their gene products in SLE and other autoimmune diseases. In all, single-nucleotide polymorphisms (SNPs) across TNFRSF14 (HVEM), and 43 SNPs across the TNFRSF8 (CD30) and TNFRSF1B (CD120B) locus were investigated for linkage disequilibrium (LD) and haplotype analysis in European-Caucasians. Strong LD was observed across HVEM and CD120B, and little LD and recombination across CD30. We also examined the association of SNPs and haplotypes in HVEM, CD30 and CD120B with SLE in European-Caucasians. There was no evidence of association for these genes in 456 European-Caucasian families with SLE from UK. Haplotype tagging SNPs are made known across areas of strong LD, which will facilitate analysis for susceptibility in other diseases.

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“…M atrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) [1,2] could provide not only the molecular weight of large molecules, such as protein, DNA/ RNA, polysaccharides, polymer and so on [3][4][5][6][7][8], but also the structural information of molecules to identify the sequence by the post source decay (PSD) [9 -12] technique with high speed, accuracy, and sensitivity. Recently, MALDI-TOF-MS has also been developed to analyze small molecules [13] successfully by using the different matrix substances, such as desorption/ionization on porous silicon (DIOS) [14 -17], matrix with high molecular weight [18,19], surfactant suppressed matrix [20], inorganic materials [21][22][23][24][25], etc.…”

mentioning

confidence: 99%

Using oxidized carbon nanotubes as matrix for analysis of small molecules by MALDI-TOF MS

Pan

et al. 2005

J. Am. Soc. Mass Spectrom.

154

147

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Oxidized carbon nanotubes are tested as a matrix for analysis of small molecules by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS). Compared with nonoxidized carbon nanotubes, oxidized carbon nanotubes facilitate sample preparation because of their higher solubility in water. The matrix layer of oxidized carbon nanotubes is much more homogeneous and compact than that of nonoxidized carbon nanotubes. The efficiency of desorption/ionization for analytes and the reproducibility of peak intensities within and between sample spots are greatly enhanced on the surface of oxidized carbon nanotubes. The advantage of the oxidized carbon nanotubes in comparison with ␣-cyano-4-hydroxycinnamic acid (CCA) and carbon nanotubes is demonstrated by MALDI-TOF-MS analysis of an amino acid mixture. The matrix is successfully used for analysis of synthetic hydroxypropyl ␤-cyclodextrin, suggesting a great potential for monitoring reactions and for product quality control. Reliable quantitative analysis of jatrorrhizine and palmatine with a wide linear range (1-100 ng/mL) and good reproducibility of relative peak areas (RSD less than 10%) is achieved using this matrix. Concentrations of jatrorrhizine (8.65 mg/mL) and palmatine (10.4 mg/mL) in an extract of Coptis chinensis Franch are determined simultaneously using the matrix and a standard addition method. [27] developed a method for quantitative analysis of small molecules with desorption/ionization on porous silicon using electrospray deposition of analytes, and a quite good quantitative result with linear calibrations R 2 Ͼ 0.99 and values of RSD Ͻ 7% was achieved. It is believed that MALDI could be a powerful technique to provide both qualitative and quantitative determination of small compounds.Carbon nanotubes have been attracting wide interest [28,29] of scientists since they were initially discovered by Iijima et al. [30,31]. Recently, Carbon nanotubes have been developed as the matrix for MALDI-TOF-MS for analysis of small molecules [25], in which carbon nanotubes function both as the energy receptacle for laser radiation and as the energy transporter for desorption/ionization of analytes with the minimization of interference signals caused by matrix ion. The effectiveness of the method as matrix has been demonstrated by several compounds with low molecular weight. However, the low solubility of carbon nanotubes in water or organic solvent makes it hard to deposit carbon nanotubes onto the sample target and to form a homogeneous layer of matrix, leading to the relatively poor reproducibility and resolution of peaks for analytes.

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Single nucleotide polymorphism analyses by MALDI-TOF MS

Cited by 35 publications

References 25 publications

Haplotype structure of TNFRSF5-TNFSF5 (CD40–CD40L) and association analysis in systemic lupus erythematosus

Haplotype structure of TNFRSF5-TNFSF5 (CD40–CD40L) and association analysis in systemic lupus erythematosus

Haplotype analysis of tumour necrosis factor receptor genes in 1p36: no evidence for association with systemic lupus erythematosus

Using oxidized carbon nanotubes as matrix for analysis of small molecules by MALDI-TOF MS

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