Genotyping single-nucleotide polymorphisms by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry.
ABSTRACT In recent years matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI) has emerged as a very powerful method for genotyping single nucleotide polymorphisms. The accuracy, speed of data accumulation, and data structure are the major features of MALDI. Several SNP genotyping methods have been implemented with a high degree of automation and are being applied for large-scale association studies. Most methods for SNP genotyping using MALDI mass spectrometric detection and their potential application for high-throughput are reviewed here.
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ABSTRACT: SUMMARY The epidemiological study of human cryptosporidiosis requires the characterization of species and subtypes involved in human disease in large sample collections. Molecular genotyping is costly and time-consuming, making the implementation of low-cost, highly efficient technologies increasingly necessary. Here, we designed a protocol based on MALDI-TOF mass spectrometry for the high-throughput genotyping of a panel of 55 single nucleotide variants (SNVs) selected as markers for the identification of common gp60 subtypes of four Cryptosporidium species that infect humans. The method was applied to a panel of 608 human and 63 bovine isolates and the results were compared with control samples typed by Sanger sequencing. The method allowed the identification of species in 610 specimens (90·9%) and gp60 subtype in 605 (90·2%). It displayed excellent performance, with sensitivity and specificity values of 87·3 and 98·0%, respectively. Up to nine genotypes from four different Cryptosporidium species (C. hominis, C. parvum, C. meleagridis and C. felis) were detected in humans; the most common ones were C. hominis subtype Ib, and C. parvum IIa (61·3 and 28·3%, respectively). 96·5% of the bovine samples were typed as IIa. The method performs as well as the widely used Sanger sequencing and is more cost-effective and less time consuming.Parasitology 11/2013; · 2.36 Impact Factor
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ABSTRACT: The possibility to rapidly identify bacteria is required in many different fields. Due to rapid progress in the development of mass spectrometry devices during the last few years, identification by means of mass spectrometry has become a very powerful and usable tool. These methods offer fast analysis of biomarker ions, providing reliable information on bacteria characterization even at the sub-species level. Therefore, these approaches have been successfully established as routine methods, together with classical biochemical tests and genome sequencing. This review focuses on common biomarkers and on different mass spectrometry techniques which have been used for bacteria identification throughout the third millennium.International Journal of Mass Spectrometry 11/2013; 353(1):67-79. · 2.14 Impact Factor
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ABSTRACT: The Indian blood group antigens, In(a) and In(b), are clinically significant in transfusion medicine. However, antisera to type these antigens are difficult to obtain. The In(b) antigen is a high frequency antigen present in all populations, while the frequency of the antithetical In(a) ranges from 0.1% in Caucasians up to 11% in Middle Eastern groups. This antigen polymorphism is encoded by the single nucleotide polymorphism (SNP) 252G>C in CD44. The aim of this study was to establish and compare two genotyping methods to measure the frequency of the IN*A and IN*B alleles in a blood donor cohort.06/2014;