The whole process was performed according to the manufacturers instructions for the multiplex reactions, including the pcr amplification, the shrimp alkaline phosphatase sap treatment, and the primer extension reactions using the iplex gold assay sequenom inc. Briefly, pcr and single base extension primers sbe were designed using massarray assay design 3. This represents customer savings of approximately 25% per study compared to the original iplex assay and improves project efficiency. The software is used in conjunction with sequenom s iplex. 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. Genotyping using the sequenom massarray iplex platform. Snp genotyping using the sequenom massarray iplex platform. A simple workflow takes you from sample to result in less than 8 hours. The iplex adme pgx panel enables the analysis of 192 polymorphisms across 36 pharmacogenetically relevant genes. The massarray system is offered in two different configurations to meet your throughput needs. In this study, we investigated the use of iplex massarray technology for methicillinresistant. Highthroughput detection of fusion genes in cancer using. From targeted discovery utilizing 10s to 100s of multiplexed assays to validation of select markers against 100s to s of samples, the massarray system.
Our massarray snp genotyping system combines mass spectrometry. A 16plex massarray iplex gold assay mrsaiplex was developed that targets a set of informative snps and binary genes for mrsa characterization. Massarray snp genotyping combines the benefits of a simple and accurate primer extension. Inherited common variants in mitochondrial dna and. Massarray iplex gold snp genotyping for research use only. Single nucleotide polymorphism detection with the iplex assay. The sequenom massarray system iplex gold was used to genotype 49 single nucleotide polymorphisms snps within 8 genes drd1, drd2, drd3, drd4, drd5, bdnf, slc6a3 and comt. Home products massarray system software agena biosciences software provides simple, flexible, and robust capabilities, from designing your own assays to obtaining userfriendly reports for downstream data analysis. Wholegenome sequencing and iplex massarray genotyping.
Pdf development and research validation of the iplex adme. Sequenoms wholly owned subsidiarity, sequenom center for molecular medicine scmm, offers multiple clinical molecular genetics tests to patients, including maternit21, plus a noninvasive. This software was created specifically for use with the massarray system and has. The massarray system from agena bioscience is a scalable platform. Snp genotyping was performed for the 27 populations included in dataset 3 using the iplex gold chemistry following 52 on a massarray system agena. The sequenom massarray iplex singlenucleotide polymorphism snp typing platform uses matrixassisted laser desorption ionization timeofflight mass spectrometry malditof ms coupled with singlebase extension pcr for highthroughput multiplex snp detection. The massarray analyzer 4 can resolve mass differences of approximately 16 daltons and process two 96 or 384pad spectrochip arrays per. Sequenom oncocarta oncomap identifies 396 unique druggable or actionable mutations in 33 cancer genes. Comparison of a multiplexed massarray system with real. Pdf development and research validation of the iplex. The first step in this process is to perform pcr to amplify the region surrounding the snp. Sqnm is an american company based in san diego, california.
Highthroughput detection of fusion genes in cancer using the. The iplex gold assay conveniently runs on sequenoms currently available massarrayr compact system and is also available as a service offering through sequenoms genetic analysis services business unit. With a 1well panel, such as the iplex pro sample id panel, up to 768 samples per day can be typed in 96well. Snp genotyping is easy with massarray of agena labclinics. The dedicated typer 4 software was used for automatic allele calling.
Snp genotyping was performed for the 27 populations included in dataset 3 using the iplex gold chemistry following 52 on a massarray system agena bioscience. The method for snp genotyping described in this unit is based on the commercially available sequenom massarray platform. Sequenom introduces iplex adme pgx panel on massarray system. Each complete iplex genotyping reagent set includes. The iplex extension reaction is a universal method for detecting insertions, deletions, substitutions, and other polymorphisms in amplified dna. Increased plexing efficiency and flexibility for massarray system through single base primer extension with massmodified terminators. This is performed using a design software package from agena. Two iplex reagent versions are available iplex gold for routine genotyping. Odds ratios ors and 95% confidence intervals cis were used to evaluate the association between the usf2 gene rs916145 polymorphism and ba susceptibility. Results this study revealed six new associations involving snps within drd2 gene on chromosome 11. Cell competition, the conditional loss of viable genotypes only when surrounded by other cells, is a phenomenon observed in certain genetic mosaic conditions.
Agena biosciences malditofbased scalable massarray system combines sensitive and robust chemistry with sophisticated analysis software. Oct 04, 2011 after detection on the massarray ruo system, the proprietary software solution is then used to score and qualify polymorphisms to create a unique haplotype report. Assay design suite ads software from agena, we can design the pcr and iplex. The specifics of these new conditions are described in the materials and methods section. Chips plex 1 5 10 20 24 9,216 46,080 92,160 184,320 36,824 69,120 8,240 276,480 40 15,360 76,800 153,600 307,200 60 23,040 115,200 230,400 460,800 8h workday.
The throughput of the massarray system depends upon the well format for a given panel. The massarray system, combined with iplex chemistry, enables molecular biology labs to perform high quality assays for single nucleotide variationspolymorphisms snps, insertions and deletions indels, and copy number variation cnv. The massarray system simplifies the process of design and implementation of new testing paradigms in the laboratory. The sequenom massarray compact system at the dna sequencing and genotyping core facility is designed for moderate to highthroughput primarily finemapping genotyping needs. The massarray analyzer 4 is a bench top matrixassisted laser desorptionionization timeofflight malditof mass spectrometer that supports all agena bioscience massarray genetic analysis applications. Cd genomics offers a rapid and accurate custom snp validation on the massarray malditof instrument provided by agena bioscience. Massarray spectrometry is more sensitive than pretect hpvproofer and consensus pcr for typespecific detection of highrisk oncogenic human papillomavirus genotypes in cervical cancer. Sequenoms massarray designer software automatically designs pcr and extension. The pgx panel consists of 200 assays in 8 wells requiring 10 ng of input dna per well from fresh or frozen whole blood or cells. The iplex gold system is an accurate and fast technology for genotyping of. San deigo, california using the iplex biochemistry on massarray system 23. The iplex adme pgx panel screens for 192 polymorphisms snp, indel, and cnv in 36 genes and 200 assays using typer assay designer software version 3.
The assays are set up in multiplexed reactions with primer pairs designed to. Using iplex reagents you could amplify, extend and detect your snps. Overall, no difference was observed in the sensitivity, measured as call rate, for the. Dont switch off the instrument as it may take a whole day to create the vacuum when switched on again acrf sequenom iplex gold snp detection sop created on 14072008 11. Massarray genetic analysis system massarray advantage massarray genotyping facilitates identification and prioritization of genetic targets within each stage of biomedical research. It develops enabling molecular technologies, and highly sensitive laboratory genetic tests for nipt. A total of 66 samples from unrelated individuals with minimum three generations of danish ancestors were genotyped with global 15 using the iplex gold kit sequenom. Gold assay, a multiplexing assay that runs on sequenom s proprietary massarray system for fine mapping genotyping applications including studies validating the association of single nucleotide polymorphisms snps with specific diseases. 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. This process combines the technologies of mass spectrometry, polymerase chain reaction pcr, and primer extension to determine each allele.
Oct 04, 2011 the iplex adme pgx panel enables the analysis of 192 polymorphisms across 36 pharmacogenetically relevant genes. Using the present iplex gold chemistry, 28 snps can be analyzed in a single pool, i. The massarray system by agena bioscience combines mass spectrometry, sensitive and robust chemistry, and advanced data analysis software to meet the assay design, validation, and performance needs of genomic laboratories a flexible, scalable genetics platform. An assay was designed for typing 29 of the 52 snps in the snpforid multiplex on the sequenom massarray analyzer 4 system. Oct 16, 2017 two iplex reagent options are available. We conducted a chemical mutagenesis and screen to recover new mutations that affect cell competition between wildtype and rps3 heterozygous cells. We utilize the massarray iplex platform by sequenom for highthroughput snp analysis. It consists of a liquid handler, a nanodispenser, and a mass spectrometer. Sequenom customers have been successful in developing assays for a wide variety of adme biomarkers, and numerous highimpact studies have been published using sequenom technology. The software has a proven design efficiency of 95% with a. The method was evaluated with 147 mrsa isolates, and the results were compared with those of an established sybr greenbased realtime pcr system utilizing the same snpbinary markers. Screening of genetic alterations related to nonsyndromic.
Genotyping using the sequenom massarray system iplex gold. A 16plex massarray iplex gold assay mrsaiplex was developed. The software has a proven design efficiency of 95% with a throughput of more than 10,000 assays per day. Sequenoms iplex gold assay is a leading technology for snp genotyping and fine mapping for sub. In this study, we investigated the use of iplex massarray technology for methicillinresistant staphylococcus aureus mrsa. This software was created specifically for use with the massarray system and.
Irrelevance of usf2 rs916145 polymorphism with the risk of. Snp genotyping on the massarray system combines the robust multiplexed primer extension chemistry with highly sensitive mass spectrometry. Pcr reagents for amplification iplex gold or iplex pro reagents for primer extension spectrochip arrays and clean resin ordering information published studies using the massarray system. This generates throughput in excess of 10,000 genotypes per day. Contents introduction to sequenom overview massarray system iplex.
The massarray system, massarray liquid handler, massarray rs nanodispenser, massarry qge, epityper, iplex gold, oncocarta panels, melacarta panel, iseq and spectrochip arrays are for research use only. Using the massarray online assay design software, snp assays can be designed as multiplexes, where maximally up to 40 snps can be analysed simultaneously within a single well of a 384 well plate. The massarray system with iseq software sets a new precedent for rapid, accurate molecular identification of microbes, viruses, and other haploid organisms. Implementation of the snpforid multiplex on the sequenom. After use, stop the rtprocesses dont shut down each software but use this button on the desktop dont shut down the computers. We examined the usf2 rs916145 genotype in a large casecontrol study consisting of 506 ba patients and 1473 healthy controls, using the massarray iplex gold system sequenom. A panel of 64 mtsnps designed to tag all common european mtdna variation minor allele frequency maf.
The iplex gold assay conveniently runs on sequenoms currently available massarray r compact system and is also available as a service offering through sequenoms genetic analysis services business unit. The panel uses sequenoms iplex gold biochemistry together with specific adme oligonucleotides. The iplex gold assay combines the benefits of simple and robust single. A custom twomultiplexed genotyping assay was designed and optimized for a panel of 40 snps using the assay design suite 1. Ads software to design the pcr and iplex extension. Sep 18, 2007 the software is used in conjunction with sequenom s iplex gold assay, a multiplexing assay that runs on sequenom s proprietary massarray system for fine mapping genotyping applications. Development and optimisation of five multiplex assays with. Comparison of a multiplexed massarray system with realtime. Snp genotyping on the massarray system combines the robust. Custom genotyping for substance addiction susceptibility. The method was evaluated with 147 mrsa isolates, and the results were compared with those of an established sybr green. The software is used in conjunction with sequenom s iplex gold assay, a multiplexing assay that runs on sequenom s proprietary massarray system for fine mapping genotyping applications. Briefly, pcr and singlebase extension primers sbe were designed using the massarray assay design 3.
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