The use of genome-wide SNP genotyping arrays has become increasingly more commonplace for gene discovery. We report on the development, validation and testing of a Sequenom MassARRAY iPLEX method for multilocus sequence typing (MLST)-style genotyping . . 12, 1-16. doi: 10.1002/0471142905.hg0212s60. DPYD, OPRT, ERCC1, ERCC2 and XRCC1 genotyping by MassARRAY. Protoc. The MassARRAY system is widely used for fine mapping, linkage studies and routine genetic testing of SNP panels of interest. 题目: SNP Genotyping Using the Sequenom MassARRAY iPLEX Platform- Introduction & Troubleshooting 主讲: 王蒙 时间: 2013年10月16日(周三)下午14：00 地点: Bio-X研究院徐汇校区小白楼二楼会议室 MassARRAY combines the benefits of a simple, reproducible primer extension reaction chemistry with state of the art MALDI-TOF mass spectrometry - Operation of the Sequenom MassARRAY Analyzer and RoboDesign SpectroCHIP Spotter. Another significant advantage of using the iPLEX Gold assay for SNP genotyping is the ability to obtain highly precise, quantitative results. - SNP Genotyping using the Sequenom MassARRAY iPLEX Platform. Anthropometric and blood lipid profiles were measured. Ziaugra L, Tabbaa D. SNP genotyping using the Sequenom MassARRAY iPLEX platform. Nowadays, new technologies such as Illumina GoldenGateTM [15] and Sequenom iPLEX MassARRAYH [16] allow researchers to generate high-throughput genotyping data from SNPs. Two duplicate positive and 2 negative controls for quality assurance were genotyped for . Sequenom MassARRAY iPLEX Gold - CD Genomics Sequenom MassARRAY iPLEX Gold iPLEX® Gold is a . Protoc. Two different genotyping chips were used and only the 42,230 SNPs present on both chips were initially pre-selected for evaluation. We utilize the MassARRAY iPLEX™ platform by Sequenom™ for high-throughput SNP analysis. Primers flanking the gene region of the SNPs were designed in the AgenaCx platform (GRCh38/hg38) . Accuracy studies were performed by comparing the genotypes of the variants determined by the OA-PGx panel with at least one of 2 reference genotyping methods, next-generation sequencing (NGS), and/or Sequenom MassARRAY iPLEX platform (MassARRAY). Sequenom Typer 4.0 software was used for data management and analyses (Thomas et al. SNP genotyping using the Sequenom MassARRAY® system (iPLEX GOLD) (Sequenom, San Diego, CA, USA) (Sequenom, San Diego, CA, USA) was performed according to the manufacturer's recommendations (Sequenom, San Diego, CA, USA). 题目: SNP Genotyping Using the Sequenom MassARRAY iPLEX Platform- Introduction & Troubleshooting 主讲: 王蒙 时间: 2013年10月16日(周三)下午14：00 地点: Bio-X研究院徐汇校区小白楼二楼会议室 MassARRAY platform with the iPLEX Gold genotyping assay . f.) using a combined Next Generation Sequencing approach on the Illumina MiSeq system with genotyping on the Agena MassARRAY iPLEX™ platform. This process combines the technologies of mass spectrometry, polymerase chain reaction (PCR), and primer extension to determine each allele. While data generation is straightforward, the subsequent data . The Sequenom MassARRAY iPLEX single-nucleotide polymorphism (SNP) typing platform uses matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) coupled with single-base extension PCR for high-throughput multiplex SNP detection. Both STR and SNP genotyping methods of sample identification are evaluated, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS), to enable cost savings by reducing rework. Curr Protoc Hum Genet. Genotyping using the Sequenom MassARRAY® iPLEX platform. Co740 NCo310 RB835089 SP71-6163 9. The parasite genotype is determined by the SNP allelic intensity ratios, ranging between 0 and 1. "SNP genotyping using the Sequenom MassARRAY iPLEX platform," Current Protocols in Human Genetics, chapter . Curr Protoc Hum Genet Chapter 2:Unit 2.12. doi: 10.1002/0471142905.hg0212s60; Fox CH, Johnson FB, Whiting J, Roller PP (1985) Formaldehyde fixation. The validation studies consisted of accuracy, precision, and sensitivity evaluation. Hum. Curr. Parentage SNP panel selection. . Chapter 11 Genotyping with Sequenom Martina Bradic´, João Costa, and Ivo M. Chelo Abstract Often in evolutionary genetics research, one needs to analyze polymorphisms in populations for which cost-efficient high-throughput arrays are nonexistent, either because the species is not a model . Relative to the standard multiplexing assay for homogenous MassEXTEND® (hME)1, the iPLEX genotyping assay has been modified with regards to: • Assay design • PCR amplification conditions • Primer extension conditions and . Protoc. Then, four selection steps were applied successively: . Since its introduction in 2000, the MassARRAY system (previously named Sequenom) has been widely adopted for a variety of genomic applications. The NAT2 tag SNP rs1495741 correlates with the susceptibility of antituberculosis drug-induced hepatotoxicity Hsin-Tien Hoa, Teng-Hsu Wangb, Cheng-Huei Hsiongb, Wann-Cherng Perngd, Stacey B. Gabriel is an American geneticist and Senior Director of the Genomics Platform at the Broad Institute.With Eric Lander, she is also the co-director of the National Human Genome Research Institute's sequencing center at the Broad Institute. Recent high-throughput 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. SNP ID is shown on the right and distance in cM on displayed on the left side of the linkage group. MassARRAY SNP Genotyping amplifies the DNA sequence across the SNP site by PCR, and then uses a single extension primer to amplify PCR products, ensuring that the primer extends only one base. The assay consists of an initial locus-specific PCR reaction, followed by single base extension using mass-modified dideoxynucleotide terminators of an oligonucleotide primer whic … The method for SNP genotyping of all samples was based on the Sequenom Massarray® platform . Available in 96 and 384-well plate formats. Skip to main content. The assay consists of an initial locus-specific PCR reaction, followed by single base extension using mass-modified dideoxynucleotide terminators of an oligonucleotide primer which anneals immediately upstream of the polymorphic site of interest. Curr. Now . Genomic DNA was extracted from peripheral blood lymphocytes using the ClotBlood DNA Kit (Cwbio, Beijing) and detected using an ultraviolet spectrophotometer (Beckman, USA), OD260/OD280: 1.6-1.9. . (2009) [Gabriel, S. , Ziaugra, L. and Tabbaa, D. (2009), SNP Genotyping Using the Sequenom MassARRAY iPLEX Platform. 2009 Chapter 2:Unit 2 12 28. View Article SNP genotyping was performed using the Sequenom iPlex® MassARRAY platform according to manufacturer's instructions (Sequenom, San Diego, CA. SNP genotyping using the Sequenom MassARRAY iPLEX platform. SNP genotyping employing the Agena MassARRAY offers a robust, sensitive, cost-effective method to assess multiple SNPs and samples simultaneously. Gabriel S, Ziaugra L, Tabbaa D (2009) SNP genotyping using the Sequenom MassARRAY iPLEX platform. Ziaugra L, Tabbaa D. SNP genotyping using the Sequenom MassARRAY iPLEX platform. Curr Protoc Hum Genet. . 37 Full PDFs related to this paper. iPLEX® Reagents is the leading technology for SNP Genotyping. Research fields like routine genetic analysis of SNPs, linkage studies and validation of genome-wide association studies took advantage of this technology. Current genotyping technologies such as Sequenom iPLEX, ABI TaqMan and KBioscience KASPar made the genotyping of huge SNP sets in large populations straightforward and allow the generation of hundreds of thousands of genotypes even in medium sized labs. Single nucleotide polymorphisms (SNPs) play a prominent role in modern genetics. Abstract. . Novel single nucleotide polymorphism loci were identified for teak (Tectona grandis Linn. SNP genotyping analysis on 100 ng of toenail DNA (as measured with NanoDrop) was carried out by Sequenom in Hamburg using the MassARRAY iPLEX SNP genotyping platform (Sequenom; ref. Single nucleotide polymorphism genotyping was performed with a fifty-four SNPs panel identified in the earlier work (Zbawicka et al., 2012, Zbawicka et al., 2014, 2022; Wenne et al., 2016, Wenne et al., 2020) using the Sequenom MassARRay iPLEX platform (Gabriel et al., 2009). SNP genotyping using the Sequenom MassARRAY iPLEX platform. The method for SNP genotyping described in this unit is based on the commercially available Sequenom MassARRAY platform. She was named the "hottest researcher" on Thomson Reuters' list of the World's Most Influential Scientific Minds in 2014. 王蒙的学术报告-SNP Genotyping Using the Sequenom MassARRAY iPLEX Platform- Introduction & Troubleshooting. The Agena Bioscience MassARRAY System is one such . MassARRAY SNP Genotyping combines the benefits of a simple and accurate primer extension chemistry with state of the art MALDI-TOF mass spectrometry to quickly and cost effectively characterize genotypes with the highest levels of reproducibility. In this study, an iPLEX MassARRAY method (iPLEX14SNP) was developed targeting 14 informative SNPs across six (abcZ, aroE, fumC, gdh, pdhC and pgm) of the seven gonococcal housekeeping genes that are commonly used for MLST investigations. Genotyping was performed using Agena MassArray platform, a robust and highly sensitive tool for genotyping of SNPs 47 available in the Central Analyzer Mass Array facility at SMVDU. The major applications of SNP genotyping are in the treatment of disease and pharmacogenomics studies. Four aliquots from each of the 82 DNA samples (100 ng each, as measured by NanoDrop) were taken and genotyped. 2009; (Chapter 2:Unit 2.12) SNP genotyping was performed using the standard protocol recommended by the manufacturer with a Sequenom Mass-ARRAY ® RS1000 (Sequenom, Inc.). 3). SNP genotyping was performed using the Sequenom MassARRAY RS1000 (Sequenom Inc., San Diego, CA) with standard protocol recommended by the manufacturer. Sequenom platform as per the manufacturer's procedure without and the other with post-PCR purification using silica columns. SNPs at the MJR1 locus were validated using the Sequenom MassARRAY [ 51 ]. Using MALDI-TOF mass spectrometry, the distinct mass of the extended primer identifies the SNP allele. J Histochem Cytochem 33(8):845-853 . The SNP most associated with PV, rs1003879, is located in a motif with a binding site for many transcription factors (TF) and considered by some genomic databases as a promoter flanking region for. 上一篇：王蒙的学术报告-SNP Genotyping Using the Sequenom MassARRAY iPLEX Platform- Introduction & Troubleshooting; 下一篇：阮云凤的学术报告-Enzyme 's Trade-off between Specificity and Generality during Evolution Appropriate molecular typing methods are important for understanding the emergence and spread of N. gonorrhoeae AMR. Gabriel, S., Ziaugra, L. & Tabbaa, D. SNP genotyping using the Sequenom Co449 NA56-79 RB835054 SP71-1406 MassARRAY iPLEX platform. Hum. The method for SNP genotyping described in this unit is based on the commercially available Sequenom MassARRAY platform. Sequenom MassARRAY iPLEX Gold - CD Genomics Sequenom MassARRAY iPLEX Gold iPLEX® Gold is a . MassARRAY SNP Genotyping combines the benefits of a simple and accurate primer extension chemistry with state of the art MALDI-TOF mass spectrometry to quickly and cost effectively characterize genotypes with the highest levels of reproducibility. Mass differences were detected with matrix . Ten SNP multiplex PCR amplification products were visualized using an Invitrogen 2% E-gel (Figure 1). 2007). What is SNP genotyping? Genotyping was performed using Sequenom MassARRAY((R)) iPLEX platform. The first step in this process is to perform PCR to amplify the region surrounding the SNP. Bortolin, S Black, M Modi, H Analytical validation of the tag-it high-throughput microsphere-based universal array genotyping platform: application to the multiplex detection of a panel of thrombophilia-associated single-nucleotide polymorphisms Clin Chem 2004 50 2028Google Scholar Statistical analysis. Relative to the standard multiplexing assay for homogenous MassEXTEND® (hME)1, the iPLEX genotyping assay has been modified with regards to: • Assay design • PCR amplification conditions • Primer extension conditions and . CD Genomics offers a rapid and accurate custom SNP validation on the Sequenom MassARRAY iPLEX Gold Platform that contains the MassARRAY SNP Genotyping system, combining mass spectrometry, sensitive and robust chemistry, and advanced data analysis software to meet researchers' SNP genotyping needs. Flexibility of iPLEX® Gold Genotyping Platform Forensic SNP Analysis. Curr. Gidaro, T., Servais, L . Credit: Sequenom TaqMan and iPLEX Gold, for instance, require an initial amplification step. However, smaller-scale genotyping platforms capable of efficiently genotyping tens to hundreds of SNPs are still crucial for many aspects of this work, including replication of associations. For one SNP, FCRL3-169*C/T (fclr3_3, rs7528684), a subset of the samples were genotyped using a 5'-allelic discrimination assay as described previously . DNA Extraction and SNP Genotyping. Genet. The iPLEX GOLD reactions consisted of three parts: the iPLEX PCR reaction, the SAP reaction, and the iPLEX Extend reaction. SNP allele is determined by variations of MALDI-TOF mass spectrometry at SNP site . The SNP genotyping was analyzed using the Sequenom MassARRAY iPLEX platform . Eight iPLEX assays, each carrying 28-36 SNP markers, were developed with the software SpectroDesinger v3.0 [ 39 ]. 16 PDF View 1 excerpt, cites methods A large number of technologies and commercial platforms have been developed for SNP genotyping. For laboratories that require CE-IVD systems or are seeking to develop CE-IVD tests . Hum. a clinical platform to guide personalized cancer medicine. Non-polymorphic GBS-predicted SNPs and incorrectly genotyped SNPs were removed before mapping MJR1 using the 380 SNP set. Genotyping was performed using the iPLEX™ Gold Assay (Sequenom ® Inc.) . The MassARRAY assay identified 14 unique SNP genotypes, while spa typing and MLST revealed 22 spa types and 21 sequence types (STs) that displayed unique r egional distribution. Statistical analysis Statistical analysis for the clinical parameters was per-formed using STATA software, version 14.1 . High-throughput SNP genotyping can also be done on the Sequenom MassARRAY iPLEX platform, which is capable of multiplexing up to 40 SNPs per single reaction. 5 In brief, the iPLEX14SNP assay was an adaption to the Sequenom platform of a previous real-time PCR 14 SNP . . Primers were designed from 100 bp of sequence flanking the SNP or indel of interest; FVB/NJ SNPs and indels in the flanking . Laboratory personnel were blinded to the identity and source of the DNA sample. The Sequenom (Brisbane, Australia) MassARRAY iPLEX SNP typing platform uses matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) coupled with single-base extension PCR for high-throughput multiplex SNP detection, which is capable of multiplexing up to 40 SNPs per single reaction ( 19, 20, 21 ). The MassARRAY ® System is an open platform that can grow with your lab and simplify the genetic testing process with easy-to-interpret data, fast turn-around times, and broad genetic coverage. Sequenom validation. iPLEX Gold is a SNP genotyping assay that runs on Sequenom's MassArray mass spectrometer. However, this SNP genotyping platform is a promising and suitable alternative to STR profiling for NGS sample identification, especially for FFPE tissue DNA of lower integrity. Product SPECIFICATIONS MassARRAY System with CPM 96 Dimensions (WxHxD) 37x43x27 in (104x110x68 cm) Capacity 2 x Microtiter plates (96 . CE-IVD SYSTEM AVAILABLE. In this study, we investigated the use of iPLEX MassARRAY technology for methicillin-resistant Staphylococcus aureus (MRSA) genotyping. Genotyping was performed mainly using the Sequenom MassArray platform according to the manufacturer's instructions . The Agena iPLEX assay is a robust platform for the detection of many genetic variations, which has been approved for clinical diagnosis. 10148-2) Gabriel et al. The method for SNP genotyping described in this unit is based on the commercially available Sequenom MassARRAY platform. . Objectives: Neisseria gonorrhoeae antimicrobial resistance (AMR) is a global problem heightened by emerging resistance to ceftriaxone. " Our MassARRAY platform and iPLEX Gold assay already provide rapid, high-throughput genotyping in fine mapping studies at the lowest cost per data point for a typical fine mapping study. The assay consists of an initial locus-specific PCR reaction, followed by single base extension using mass-modified dideoxynucleotide terminators of an oligonucleotide primer which anneals immediately upstream of the polymorphic site of interest. Read Paper. SNP genotyping refers to the determination of SNP loci on a whole-genome scale or within genomic regions of interest. Curr Prot Human Genet 60: 2.12.1-2.12.18. The Sequenom (Brisbane, Australia) MassARRAY iPLEX SNP typing platform uses matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) coupled with single‐base extension PCR for high‐throughput multiplex SNP detection, which is capable of multiplexing up to 40 SNPs per single reaction ( 19 - 21 ). Three hundred and forty four putative loci were identified through sequencing of DNA fragments following a modified double digest Restriction Associated DNA . Results and Discussion Extracted genomic DNA quantity measured using PicoGreen was found to be 238.6 pg/µl. About us . The design of all amplification primers of 4 SNPs of the LRCH1 gene was followed by gene sequencing using the dbSNP database and added to the 5′ 10-mer tag (ACGTTGGATG), as shown in Table 1. The whole process was performed according to the manufacturer's 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., San Diego, USA). Data management and analyses were performed using Sequenom Typer 4 . CrossRef Full Text | Google Scholar. Relative to the standard multiplexing assay for homogenous MassEXTEND® (hME)1, the iPLEX genotyping assay has been modified with regards to: • Assay design • PCR amplification conditions • Primer extension conditions and . Chapter 2, Unit 2. Single nucleotide polymorphism genotyping Co997 PO88-62 RB835205 SP71-6949 in polyploid wheat . - Genotyping on the GenMarkDx eSensor XT-8 System . EMBO Mol Med. . incorporate allele dosage using more efficient marker systems. Analysis of Genetic and Epigenetic Variation Using MassARRAY® Compact from Sequenom® . spa type t355. Akhunov, E., Nicolet, C. & Dvorak, J. Results: MC4R rs571312 SNP was associated with logBMI (p = 0.008) and systolic blood pressure (p = 0.005), while MC4R rs2229616 SNP was associated with total cholesterol (TC) levels (p = 0.016). SNP genotyping using the Sequenom MassARRAY iPLEX platform. A total of 17 SNPs (eTable 1 in the Supplement) were genotyped by a custom-designed Sequenom MassARRAY iPLEX assay (Agena Bioscience GmbH), as previously described, 15 and 1 SNP was genotyped using a TaqMan SNP Genotyping Assay (Fisher Scientific-UK Ltd). Accurate genotyping is essential for building genetic maps and performing genome assembly of polyploid species. All genotyping was performed with the MassARRAY iPLEX platform (Sequenom Inc, San Diego, California, USA). 2009; (Chapter 2: . 234 samples genotyped at 40 loci using the MassArrayiPLEX genotyping assay using the iPLEX Gold genotyping kit (Agena Biosciences, cat. The assay consists of an initial locus-specific PCR reaction, followed by single base extension using mass-modified dideoxynucleotide terminators of an oligonucleotide primer which anneals immediately upstream of the polymorphic site of interest. using a MassARRAY nano-dispenser and assayed on the MassARRAY platform. Genet . Genotype analyses for SNPs determination were performed with the single‐base extension polymerase chain reaction Sequenom iPLEX‐Gold and the mass spectrometry‐based platform MassARRAY MALDI‐TOF (Sequenom, San Diego, CA, USA) at the Spanish Genotyping National Centre (CEGEN‐ISCIII). About Us ; This is Broad; History; Leadership; Director . . The development of modern genotyping technologies, such as the Sequenom iPLEX MassARRAY® 8, Illumina GoldenGate™ 9 and protocols such as Genotyping by Sequencing (GBS 10) or RAD seq 11, allows . SNP genotyping using the Sequenom MassARRAY iPLEX platform. Genotyping of the other genes was carried out using the Sequenom MassARRAY Iplex Platform at the Center for Genomic Sciences of the University of Hong Kong. We used Sequenom MassARRAY Assay Design 3.0 Software (Sequenom Inc., San Diego, CA) to design Multiplexed SNP MassEXTEND assay. In: Current . 2010; 2: 146-158. . Genotype analysis was performed using the MassARRAY iPLEX system (Sequenom, San Diego, CA) according to manufacturer's instructions. SEQUENOM presents here a newly developed genotyping assay termed iPLEX™ for use with the MassARRAY platform. In this S., Ziaugra, L., and Tabbaa, D. (2009). The genotyping design software generated three multiplex reactions: 29 SNPs (plex1), 28 SNPs (plex 2), and 24 SNPs (plex 3). . 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