Sequenom bruker massarray nanodispenser electronics by. The region analysed and the cpg sites of mglur1 promoter are shown in fig 1. The massarray system simplifies the process of design and implementation of new testing. Statistical analysis the comparisons between two groups were performed with students t test or nonparametric mannwhitney u tests. The launch of the service function allows researchers worldwide to access the massarrayr solution for the quantitative analysis and profiling of dna methylation and gene expression. Analysing and interpreting dna methylation data nature.
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. Sequenom massarray methylation analysis was performed using the massarray compact system sequenom, san diego, ca. Introduction to dna methylation analysis using the massarray. Research paper a pilot study of aberrant cpg island. The search for specific biological markers is of great importance to advance the method of diagnosis for depression. We have previously used this program to design bisulfite pcr. The sequenom massarray sequenom, san diego, ca, usa was used for quantitative dna methylation analysis of the cpgs within the amplicons of fancc, svopl, and wdr27 using conditions described. Epidesigner is a tool for designing quantitative dna methylation experiments for agena biosciences epityper technology. Association of promoter methylation statuses of congenital. Pdf archived guthrie blood spots as a novel source for. Quantitative methylation analysis software is scheduled. Mshrm followed by sangerbased dna sequencing is a fast, simple method for methylation analysis that can measure methylation levels as low as 0. Epityper is scalable and allows you to analyze multiple cpgs on a single amplicon without compromising accuracy, sensitivity, or reproducibility. Additionally, the software is customizable for the advanced user and enables detailed exploration of raw spectral data.
Massarray qge is scalable, allowing you to perform assays without compromising, accuracy, sensitivity, or reproducibility, thus solving the multiplate replication gap seen with other quantitative gene expression technologies. Cpg island shore methylation of zfpm2 is identified in. If a cpg dinucleotide was methylated and protected from bisulfite. Sqnm, a leading provider of fine mapping genotyping, methylation and gene expression analysis solutions, today announced the sequenom launches typer 4. The epityper software minimizes manual design and assay optimization, with no need to design cpgspecific primers. L format on 384well microplates view table 1, with 10 ng bisulfitetreated dna, 0. The proprietary software for masscleave analysis epityper currently provides both graphical and tabular readout of cg methylation calls. Highthroughput quantitative dna methylation analysis.
The methylated and nonmethylated cytosine residues in the original genomic dna are easily distinguished using epityper software. In this chapter, we have analyzed in depth the sequenom massarray technology for the analysis of dna methylation with special emphasis on its applications in clinical practice. Sequenom introduces the massarray analyzer 4 system. A custom twomultiplexed genotyping assay was designed and optimized for a panel of 40 snps using the assay design suite 1. This system is based on mass spectrometry ms analysis for qualitative and quantitative detection of dna methylation using homogeneous masscleave hmc basespecific cleavage and matrixassisted laser. Epityper uses the agena bioscience previously sequenom inc. Sequenom massarray iplex gold platform bioinformatics analysis. The massarray r package supports assay design and data analysis for the massspectrometrybased sequenom epityper assay 106, and primegens 107, in combination with biq analyzer ht 108, provides.
Mass spectrometry methylation assays provide a sensitive method of detection based on difference in fragment weights that have been cleaved based upon methylation status. Agena biosciences epityper dna methylation analysis technology allows you. In recent years, the sequenom epityper system technology has emerged as a novel technique for methylation analysis that offers a high range of options with great performance and several advantages. Massarray qge from sequenom combines competitive pcr with malditof mass spectrometry ms analysis to offer a highly accurate, sensitive, and highthroughput method for the quantitative analysis of gene expression in multiple samples. The sequenom massarray platform was used for the quantitative methylation analysis of the upstream sequence of mglur1 gene promoter.
Archived guthrie blood spots as a novel source for. Dna methylation profiles of the brainderived neurotrophic. The sequenom massarray nanodispenser can run quick sample transfers onto a spectrochip assay and is configured to hold up to two microplates plates. Design, measurement and processing of regionspecific dna. Quantitative methylation analysis can be applied to many cg sites. Highthroughput, quantitative dna methylation analysis is crucial for the study of the normal physiology of the epigenome and its dysregulation in disease. Diagram depicts the cpg sites analyzed within the assay by seqeunom massarray epityper red circles, while. The demonstration of archived dna blood spots as a suitable template for dna methylation analysis represents a unique resource for the retrospective analysis of epigenetic status of. Major depression is still diagnosed on the basis of clinical symptoms in patients. A pipeline for the quantitative analysis of cg dinucleotide methylation using mass spectrometry. The sequenom massarray are ideally suited for assays such as snp genotyping, methylation analysis, comparative sequence analysis, quantitative gene expression and snp genotyping. Methylation analysis epidesigner is an online tool for designing quantitative dna methylation experiments for agena biosciences epityper technology. With the capability for quantitative gene expression analysis, epigenetic nucleic acid methylation analysis as well as highthroughput genotyping and snp fine mapping applications, the massarray analyzer 4 is designed to empower the basic and translational research community to advance.
To test if dna methylation has contributed to the evolution of human brain, with the use of medipchip. Asanindustryinnovatorindnadetection technology,sequenomdevelopedthebench. Dna methylation is a key epigenetic mechanism regulating gene expression and chromatin structure. Massarray epityper for quantitative dna methylation analysis uses basespecific enzymatic cleavage. The methylation status of a detected pattern was then analyzed using epityper software version 1. The epityper software minimizes manual design and assay optimization, with no. Highthroughput quantitative dna methylation analysis the epityper massarray assay sequenom inc.
Instrumentation the foundation of the massarray system is the massarray malditof mass spectrometer. Epityper biochemistry starts with bisulfite treatment of genomic dna, followed by pcr amplification of target regions. The assay uses bisulfitetreated dna in which unmethylated cytosines have been. The epityper software provides convenient solutions for data analysis and export. Quantitative methylation analysis for zfpm2 gene was performed using the epityper by massarray sequenom based upon basespecific cleavage and malditof mass spectrometry, as recommended by the. A pipeline for the quantitative analysis of cg dinucleotide. The sequenom massarray platform was used to perform the quantitative methylation analysis of line1 element. Agena biosciences epityper dna methylation analysis technology allows you to interrogate tens to hundreds of cpgs in amplicons of up to 600 bp and detect down to 5% differences in methylation. The massarray instrument is able to quantitatively determine the. Recently, several largescale studies reported the evolutionary roles of dna methylation.
Massarray epityper is scalable and allows you to analyze multiple cpgs on a single amplicon without compromising accuracy, sensitivity, or reproducibility. The latter assay has been commercialized using sequenoms massarray platform. Introduction to dna methylation analysis using the massarray system 1. Massarray system with epityper dna methylation analysis. Sqnm is an american company based in san diego, california. Genomewide dna methylation analyses in the brain reveal. Quantitative mass array analysis of gene methylation status. The sequenom massarray platform was used to perform the quantitative methylation analysis for the promoter regions of 71 chd candidate genes. It requires the use of bisulfite converted dna, and primers designed in regions without. It develops enabling molecular technologies, and highly sensitive laboratory genetic tests for nipt. A new approach to imprinting mutation detection in gnas by. Tofmstoprovideadirectphysicalmeasurementofthegenetictargetmaterial andvariationstherein. Pdf a pipeline for the quantitative analysis of cg. The dna methylation analysis technology, epityper massarray, provided by.
The highly improved cognitive function is the most significant change in human evolutionary history. Analysis of multiple cpgs in amplicons up to 600 bp length depends on dna quality and bm compatible with formalinfixed paraffinembedded tissue samples individual methylation ratios for cpgs within a target sequence detection. This system, which combines basespecific enzymatic cleavage with malditof mass spectrometry, is a highly accurate, sensitive and highthroughput method for the quantitative analysis of dna methylation at cpg sites 28. Identification and analysis of an early diagnostic marker. Comparative sequence analysis snp genotyping quantitative gene expression methylation analysis massarray. The sequenom massarray mass spec has it all including the ability to scale up as your laboratory needs continue to grow. Several system options are available depending on throughput requirements. Introduction to dna methylation analysis using the massarray system 2 april 15, 2005 doc. Sequenom developed the massarray malditof ms analyzer systems to specifically meet the requirements of moderate to high throughput quantitative genetic analysis. Sequenom massarray technology for the analysis of dna. Sequenom also intends to launch dna methylation and qge as new application products available to all massarray system customers in the first quarter of 2006.
The benchtop system can be used with any of sequenoms applications and assays, including. Methylation analysis using methylationsensitive hrm and dna sequencing. The methylation status of dna can be analyzed by many different. We further demonstrated the utility of this approach by examining the methylation levels at the h19 imprinted region using the sequenom massarray epityper analysis. Highthroughput quantitative dna methylation analysis the. Analyzing the cancer methylome through targeted bisulfite. The dna methylation analysis technology, epityper massarray, provided by agena bioscience previously sequenom inc. Sequenoms massarray system facilitates a number of nucleic acid analysis applications including snp genotyping and allelotyping, somatic mutation analysis, cnv. Introduction to dna methylation analysis using the. The bench top massarray compact system is a multiapplication platform that addresses the following applications. This program allows simple design of primers for bisulfite treated genomic dna and recommends primer pairs for individual assays.
The massarray system is a complete system for discriminating methylated vs. Quantitative realtime polymerase chain reaction qrt pcr was used to analyze spred1 mrna levels. Quantitative methylation analysis snp genotyping somatic mutations quantitative gene expression. The quantitative methylation data for each cpg site or aggregates of multiple cpg sites obtained from massarray were analyzed on the epityper software sequenom. Here, we present an r package massarray that assists in assay design. A sequenom massarray quantitative methylation analysis using the massarray compact system sequenom, san diego, ca was performed for the quantitative dna methylation analysis.
This system is based on ms for the detection and quantitative analysis of dna methylation using homogeneous masscleave hmc, basespecific cleavage and malditof ms 11. Long cycling incubation was applied to further optimize the conversion reaction. Expands massarrayr platform utility with launch of quantitative methylation and gene expression analysis products read this article along with other careers information, tips and advice on biospace. The massarray system and all products and services listed on this. Pyrosequencing pyromark, qiagen and massarray epityper, sequenom have now largely.1291 1280 1547 787 930 1458 342 758 236 1426 334 469 1283 435 71 303 195 829 1559 1312 1241 1189 248 1411 903 1108 1143 991 460 991 1526 199 1230 897 940 394 919 17 46 1074 693 182 1162 1085 953