Snp genotyping starts with a multiplex pcr amplification of the genomic. Gabriel s, ziaugra l, tabbaa d 2009 snp genotyping using the sequenom massarray iplex platform. In summary, the sequenom massarray iplex platform provides a costeffective, high throughput means of snp characterisation and has provided a signi. Snp genotyping with iplex reagents and the massarray system. Matrixassisted laser desorption ionizationtime of flight. Massarray snp genotyping has a very good application prospect in the. Highthroughput detection of fusion genes in cancer using the sequenom massarray platform. It utilizes a single extension primer to generate allelespecific products for all pcr sites ensuring a. In this study, we investigated the use of iplex massarray technology for methicillinresistant staphylococcus aureus mrsa. Some of the many advantages of using this technique are. With different detection and software modules, the massarray iplex gold technology can realize the research or application of snp genotyping, gene expression research, copy number variation, gene methylation analysis, pathogen typing and prenatal diagnosis on one platform. Sequenom presents here a newly developed genotyping assay termed iplex for use with the.
Comparison of a multiplexed massarray system with realtime. A snp typing assay developed for human identification and sample. Increased pl exing efficiency and flexibility for massarray system through single base primer extension with mass modified terminators 1 november 10, 2006 doc. This highthroughput approach allows rapid and costeffective testing for a large number of different mutations simultaneously. Snp genotyping using sequenom massarray 7k platform. Correct identification and traceability of barley varieties is a prominent issue for quality assurance throughout the entire barley production supply chain in australia and worldwide. Our mission is to improve individual patient care through the integration of innovative molecular diagnostic technology, manufacturing genetic tests for over 200 different types of health concerns. Snp genotyping using the sequenom massarray system iplex gold sequenom, san diego, ca, usa sequenom, san diego, ca, usa was performed according to the manufacturers recommendations sequenom, san diego, ca, usa. Snp genotyping on the massarray system combines the robust multiplexed primer. Massarray snp genotyping can carry out multiple snp typing in one reaction.
Genomic dnas are submitted to iplex gold reaction and the product are transferred to chip wells by a robot. This technique is accurate and has a price advantage when analyzing dozens or hundreds of snps. Recent highthroughput techniques, such as illumina goldengate and sequenom iplex massarray, have made it possible to accurately estimate the relative abundances of different alleles even when the ploidy of the population is unknown. The iplex workflow begins by using assay design suite ads software to design the pcr and iplex extension primers for each snp or somatic mutation of interest from dbsnp rs numbers or dbsnp data in fasta format figure 2. Snp genotyping using the sequenom massarray iplex platform. Accurate genotyping is essential for building genetic maps and performing genome assembly of polyploid species. The first step in this process is to perform pcr to amplify the region surrounding the snp. Application note iplex chemistry single nucleotide. Postmortem cyp2d6 genotyping and copy number determinations. All snp genotyping methods combine two distinct steps one to discriminate between alternative alleles at the snp locus and one to report the nature of the allele by generating a signal that can be detected, in an automated fashion if possible. Single nucleotide polymorphism detection with the massarray system from agena 16 october, 2017 by labclinics 0 since its introduction in 2000, the massarray system previously named sequenom has been widely adopted for a variety of genomic applications.
A single nucleotide polymorphism snp genotyping panel has been designed to require amplification of shorter targets, and provide greater than 1. Sequenom massarray iplex gold iplex gold is a leading technology for snp genotyping. Sequenom taqman and iplex gold, for instance, require an initial amplification step. The aims of this study were to adapt the 14 snp method to the sequenom massarray iplex platform 6 and then apply it to isolates referred for amr testing in the state of queensland over a 6 month period. All snp genotyping methods combine two distinct steps one to discriminate between alternative alleles at the snp locus and one to report the nature of the allele by generating a signal that can be detected, in an automated fashion if possible there are three general allele discrimination methods. Massarray platform with the iplex gold genotyping assay. In this study, we investigated the use of iplex massarray technology for methicillinresistant staphylococcus aureus. Highthroughput molecular typing of microbes using the. However, smallerscale genotyping platforms capable of efficiently genotyping tens to hundreds of snps are still crucial for many aspects of this work, including replication of associations. The iplex panel includes three independent multiplexed pcr assays that amplify 17, 16 and 10 of the total 35 variants, respectively.
We utilize the massarray iplex platform by sequenom for highthroughput snp analysis. Highthroughput detection of fusion genes in cancer using the. As a specific color or both colors light up during amplification, the genotype at the particular snp can be easily determined. The massarray system includes the massarray analyzer mass spectrometer and integrated data analysis software. All of the files are pdf format, so you should be able to drag each link to your desktop or directory and open it there with your pdf viewer of choice.
The assay consists of an initial locusspecific pcr reaction, followed by single base extension using massmodified dideoxynucleotide terminators of an oligonucleotide primer which anneals immediately upstream of the. Evaluation of the iplex sample id plus panel designed for the. The primer sequences used for genotyping are listed in table 4. For the snps we examined, 74% had call frequencies of 95% or higher qc criteria commonly used in. A custom twomultiplexed genotyping assay was designed and optimized for a panel of 40 snps using the assay design suite 1. Single nucleotide polymorphism detection with the iplex assay. Genotyping of cyp2d6 polymorphisms by malditof mass.
Sequenoms massarray platform has been used for the genotyping. An overview of snp genotyping technologies cd genomics. A different approach is used by sequenom s iplex snp genotyping method, which uses a massarray mass spectrometer. Dna preparation for sequenom malditof based human snp. Institute of genetic medicine, newcastle university, international centre for life, newcastle upon tyne, uk, ne1 4ep. The massarray system is widely used for fine mapping and validation of gwas studies linkage studies, as well as routine genetic testing of snp panels of interest. Technical principle and methods applied in snp genotyping.
Analysis of genetic and epigenetic variation using massarray compact from sequenom. We conducted a study to assess the utility of the multiplex sequenom massarray system sequenom inc. For those who are interested in using the sequenom massarray system for genotyping, we have provided several of the manuals and the software documentation. Malditof msbased snp genotyping assay using the iplex gold. Multiplex snp genotyping by malditof mass spectrometry. Snp genotyping was done with a sequenom massarray rs using the standard protocol recommended by the manufacturer 25. The genotypes of the 10 tag snps were analysed by massarray platform sequenom, san diego, california, usa and iplex gold genotyping. Request pdf snp genotyping using the sequenom massarray iplex platform the method for snp genotyping described in this unit is based on the. Abstract the method for snp genotyping described in this unit is based on the commercially available sequenom massarray platform. The assay consists of an initial locusspecific pcr reaction, followed by single base extension using massmodified dideoxynucleotide terminators of an oligonucleotide primer which anneals immediately upstream of the polymorphic site of interest.
Published studies using the massarray system visit. Of the 45 loci screened, 33 were informative and successfully used to generate. We provide genotyping service from monday to friday. Mdr1 single nucleotide polymorphism c3435t in normal colorectal tissue and colorectal carcinomas. Massarray provides accurate clopidogrel related genotyping with. Snp genotyping was performed using the agena massarray assay agena, san diego, ca, usa based on the standard manufacturer. Snp genotyping is easy with massarray of agena labclinics. All genotyping was performed with the massarray iplex platform sequenom inc, san diego, california, usa. The sequenom massarray iplex platform this technology uses silicon chips and dna amplification products for accurate genotyping by mass spectrometry. San deigo, california using the iplex biochemistry on massarray system 23. High quality data based on direct allelespecific mass. Screening of genetic alterations related to nonsyndromic. More recently, mrsa genotyping based on a set of informative. The sequenom brisbane, australia massarray iplex snp typing platform uses.
Another significant advantage of using the iplex gold assay for snp genotyping is the ability to obtain highly precise, quantitative results. Also, please contact us if you are interested in snp analysis using massarray discovery apart from iplex applications. The oil palm snp assay design and genotyping were performed by a service provider, agena bioscience, inc. May 29, 2019 dna preparation for sequenom malditof based human snp genotyping using the prepgem universal storage card blood harsh jayesh sheth. The iplex gold technology based on the massarray platform can design pcr reactions and genotype detection up to 40. Quantitative snp genotyping of polyploids with massarray and. Sequenom 5 to 10 snp genotyping overview project rationale genotyping strategiestechnical leaps data managementquality control overview of snp genotyping debbie nickerson department of genome sciences university of washington. Association of tolllike receptor 10 polymorphisms with. Genotyping of single nucleotide polymorphisms in dna.
Massarray assay design software was used to design the primers of all examined snps. Stacey gabriel,1 liuda ziaugra,1 and diana tabbaa1. Research to understand the genetic basis of disease, particularly complex disease, regularly involves single nucleotide polymorphism snp genotyping. The snp genotyping method was based on malditof analysis performed on a mass spectrometer platform from sequenom inc. Biomarker validation routine genetic testing somatic mutation profiling snp genotyping with iplex reagents and the massarray system. In the present study, we investigated the potential use of a novel snp genotyping technology based on the commercially available sequenom s massarra y platform for the simultaneous analysis of the 16 snps that we previously selected for the identification of mtbc species and lineages by the snapshot approach 6. Quantitative snp genotyping of polyploids with massarray. Snp genotyping using sequenom massarray 7k platform request pdf. The massarray platform supports genotyping, cnv, qge, and methylation applications.
Our study demonstrates that sequenom massarray technology can be used to genotype snps with a multiplex approach using a small volume of serum dna. Comparison of a multiplexed massarray system with real. Get competitive quotes from sequenom snp genotyping facility on science exchange, the worlds leading online science marketplace. Increased pl exing efficiency and flexibility for massarray system through single base primer extension with mass modified terminators 1 april 28, 2005 doc. Malditof msbased analyses have the potential to become a useful approach in clinical diagnoses, as they are very. Here, we provide a guide to using the massarray system, from assay design. Study dna samples were tested at two different times using cyp2d6 iplex genotyping assays agena bioscience, san diego, ca. The massarray platform has several advantages for the users who desire an accurate custom snp genotyping assay. The sequenom brisbane, australia massarray iplex snp typing platform uses matrixassisted laser desorption ionization timeof.
A schematic representation of massarray hme and iplex assays. Snp genotyping with iplex reagents and the massarray system two iplex reagent versions are available iplex gold for routine genotyping, and iplex pro for more demanding applications that require high performance and sensitivity, such as somatic mutation analyses. Genotyping of single nucleotide polymorphisms in dna isolated. Depending upon the complexity of the assay, a single multiplex reaction can contain up to 40 markers. The assay consists of an initial locusspecific pcr reaction, followed by. Single nucleotide polymorphism detection with the iplex assay and the massarray system efficient, scalable, and costeffective snp genotyping and somatic mutation analysis.
Malditof msbased snp genotyping assay using the iplex. This article appeared in a journal published by elsevier. Laboratory personnel were blinded to the identity and source of the dna sample. Taqman probes are designed to hybridize to a specific snp allele, with a different 5. A sixmember snp assay on the iplex massarray platform. In this context, we developed a 16plex iplex assay based on an allelespecificprimer singlebaseextension reaction using the iplex gold kit sequenom, followed by matrixassisted laser desorption ionizationtime of flight mass spectrometry malditof ms analysis on the commercially available sequenom massarray platform.
Efficient, scalable, and costeffective snp genotyping and somatic mutation analysis. Extension probes are designed in such a way that 40 different snp assays can be amplified and analyzed in a pcr cocktail. The sequenom brisbane, australia massarray iplex snp typing platform uses matrix. This study evaluated the discriminatory power, cost of and time required for genotyping kenyan staphylococcal isolates using iplex massarray compared to conventional methods. Highthroughput informative single nucleotide polymorphism. The agena bioscience massarray system is one such platform. Call frequencies, expressed as percentages, were calculated for each snp. The use of genomewide snp genotyping arrays has become increasingly more commonplace for gene discovery. Singlenucleotide polymorphisms snps are the most common type of. In this study, we have developed a reliable mediumthroughput genotyping platform using the sequenom massarray system to provide a simultaneous screening of the most relevant cyp2d6 gene variants in several hundreds of subjects. The method for snp genotyping described in this unit is based on the commercially available sequenom massarray platform.
Dna preparation for sequenom malditof based human snp genotyping using the prepgem universal storage card blood harsh jayesh sheth. However, taqman assays, as with other single snp genotyping methods, are time consuming and costly, which limits their usefulness for largescale studies. This process combines the technologies of mass spectrometry, polymerase chain reaction pcr, and primer extension to determine each allele. Combined iplex and taqman assays to screen for 45 common. Snp genotyping with iplex reagents and the massarray. This study explores the use of sample id plus snp assay technology sequenom bioscience, san diego, ca in generating complete genotype profiles from ffpe tissue dna. Genotyping using the sequenom massarray system iplex gold.