Massarray genotyping platform

Manufactured by Labcorp

Sourced in United States

The MassARRAY genotyping platform is a high-throughput, cost-effective genetic analysis system. It utilizes mass spectrometry technology to accurately determine genetic variations and provide reliable genotyping results.

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Lab products found in correlation

Genomic dna purification kit, by Promega (3 mentions) Taqman assay, by Thermo Fisher Scientific (1 mentions) Amplitaq gold dna polymerase, by Thermo Fisher Scientific (1 mentions) Spectroclean resin, by Labcorp (1 mentions)

Close spelling variants of this product

MassARRAY platform (248 citations) MassARRAY (137 citations) MassARRAY SNP genotyping platform (11 citations) IPlex MassARRAY genotyping platform (2 citations)

8 protocols using massarray genotyping platform

Genetic Variants and Platinum-Based Chemotherapy Toxicity

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All of the common genetic variants in MLH1, MSH2, MSH3, MSH4, MSH5, SAPCD1 and MSH6 were selected by Haploview (Broad Institute, Cambridge, MA, USA) using pair-wise tagging with default settings (pairwise r² threshold = 0.8). SNPs with a minor allele frequency (MAF) ≥ 5% in the Han Chinese population were selected. Finally, Thirty-five SNPs were genotyped in the patients (Table 1). In our previous studies, the SNPs were investigated to be associated with platinum-based chemotherapy toxicity 30 (link).
ALL blood samples were collected in the morning and stored in EDTA tube. Genomic DNA was isolated using a Genomic DNA Purification Kit (Promega, Madison, WI, USA) and stored at -20°C before use. Genotyping was analyzed using a Sequenom Mass ARRAY Genotyping Platform (Sequenom, San Diego, CA, USA) through polymerase chain reaction (PCR) system.

Liu J.Y., Zou T., Yin J.Y., Wang Z., Wang Y., Liu Z.Q., Chen J, & Chen Z.W. (2020). Genetic Variants in DNA Mismatch Repair Pathway predict prognosis of Lung Cancer patients with receiving Platinum-Based Chemotherapy. Journal of Cancer, 11(18), 5281-5288.

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Genetic Polymorphisms in CRC miRNA

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Common polymorphisms within miRNA involved in CRC turmorigenesis or metastasis were selected in accordance with the following included criteria: (1) miRNA was reported to associate with CRC carcinogenesis and prognosis; (2) SNP was located at mature sequence of hsa-miRNA, flanking sequence of pre-, pri-miRNA which showed to be of biological function by F-SNP database (http://compbio.cs.queensu. ca/F-SNP/) [37 (link)]; (3) frequency of minor allele was more than 5% in Chinese Han population; (4) there was no or few reports between the selected miRNA and CRC risk, drug response and prognosis; (5) the reported results concerning the selected SNP were contradictory. Consequently, a total of fifteen CRC related miRNA polymorphisms were retrieved, and only six polymorphsims (rs4919510 within miR-608, rs3746444 within miR-499a, rs2910164 within miR-146a, rs41291957 within pre-miR-143, rs531564 within pre-miR-124-1, rs7372209 within pre-miR-26a-1) were selected in accordance with the criteria. Human genomic DNA was extracted from each peripheral blood sample using Tiangen kit (Tiangen, Beijing, China) according to the manufacturer's protocol. Genotypes of all the selected SNPs were detected by PCR-based MassARRAY genotyping platform (Sequenom lnc, San Diego, USA). Meanwhile, 5% of random selected sample was tested for second time to validate the result.

Ying H.Q., Peng H.X., He B.S., Pan Y.Q., Wang F., Sun H.L., Liu X., Chen J., Lin K, & Wang S.K. (2016). MiR-608, pre-miR-124-1 and pre-miR26a-1 polymorphisms modify susceptibility and recurrence-free survival in surgically resected CRC individuals. Oncotarget, 7(46), 75865-75873.

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Genotyping of Tagging SNPs in Blood

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DNA was isolated from whole blood using a commercial kit (NucleoSpin, Macherey & Nagel, Düren, Germany). Genotyping of the tagging SNPs was performed by mass spectrometry using the massARRAY genotyping platform (Sequenom, Hamburg, Germany) and the manufacturer’s iPLEX software. SNPs rs849405, rs2037718, and rs10216210 resisted massARRAY multiplex assay design and were, therefore, genotyped by allelic discrimination using commercial TaqMan assays (Applied Biosystems, Foster City, CA, USA). The call rates were ≥96%. The genotyping results were validated in 50 randomly selected subjects by bidirectional sequencing, and no deviations were observed.

Kächele M., Hennige A.M., Machann J., Hieronimus A., Lamprinou A., Machicao F., Schick F., Fritsche A., Stefan N., Nürnberg B., Häring H.U, & Staiger H. (2015). Variation in the Phosphoinositide 3-Kinase Gamma Gene Affects Plasma HDL-Cholesterol without Modification of Metabolic or Inflammatory Markers. PLoS ONE, 10(12), e0144494.

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Genetic Polymorphism Analysis of DNA Repair Genes

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The SNPs genotyped in our study were ERCC1 SNPs (rs2298881), ERCC2 SNPs (rs1052555, rs238406), ERCC4 SNP (rs1799801), ERCC6 SNPs (rs2228527, rs3793784), XPC SNPs (rs2228000, rs2228001), XRCC1 SNP (rs25489), XRCC3 SNPs (rs1799794, rs861539), BRCA1 SNP (rs799917), BRCA2 SNPs (rs543304,rs206118), RAD51 SNPs (rs12593359, rs1801320, rs1801321), RAD52 SNPs (rs1051669, rs7963551), POLH/POLR1C SNP (rs6941583), MAD2L2 SNPs (rs2233004, rs746218, rs2233006), NFKB1 SNPs (rs230529, rs1585215, rs4648068), NFKBIA SNP (rs2233406), TNF SNP (rs1800629), TNFRSF1A SNPs (rs4149570, rs2234649), TNFRSF1B SNP (rs1061622), and FASN SNPs (rs1140616, rs2228309, rs4246445, rs4485435). Haploview was used to choose pair-wise tagging SNPs with pair wise r² threshold ≥0.8, and all SNPs had a minor allele frequency (MAF) greater than 0.05 (Table 1).
All blood samples were collected and stored in EDTA tubes. We used a genomic DNA Purification Kit (Promega) to extract genomic DNA. Genotyping of all SNPs was performed using the Sequenom MassARRAY Genotyping Platform (Sequenom, San Diego, CA, United States).

Liu J.Y., Zou T., Yin J.Y., Wang Z., Liu C., Huang H.X., Ding F.X., Lei M.R., Wang Y., Liu M., Liu Z.Q., Tan L.M, & Chen J. (2022). Genetic Variants in Double-Strand Break Repair Pathway Genes to Predict Platinum-Based Chemotherapy Prognosis in Patients With Lung Cancer. Frontiers in Pharmacology, 13, 915822.

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Genetic Variants Impact CYP2C9 Enzyme Activity

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Well-known genetic variants of the CYP2C9 gene, namely, CYP2C9*2 (Arg144Cys) and CYP2C9*3 (Ile359Leu), were selected to assess its role in SIH. These variants are known to cause amino acid substitutions in the CYP2C9 enzyme, leading to decreased enzyme activity. The genotyping of the selected variants was performed using the Sequenom MassARRAY genotyping platform at the Centre of Genomics, Rehman Medical Institute (RMI), Peshawar, via collaboration. The Sequenom MassARRAY genotyping method is a high-throughput genotyping technology that utilizes matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to accurately and efficiently genotype genetic variations.

Jan A., Saeed M., Mothana R.A., Muhammad T., Rahman N., Alanzi A.R, & Akbar R. (2023). Association of CYP2C9*2 Allele with Sulphonylurea-Induced Hypoglycaemia in Type 2 Diabetes Mellitus Patients: A Pharmacogenetic Study in Pakistani Pashtun Population. Biomedicines, 11(8), 2282.

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SNP Selection and Genotyping Protocol

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All single nucleotide polymorphisms (SNPs) were selected by Haploview (Broad Institute, Cambridge, MA, USA) using pair-wise tagging with default settings (pair-wise r² threshold = 0.8). The following SNPs were eligible for further study: SNPs with a minor allele frequency (MAF) ≥ 5% in the Han Chinese population and SNPs in Hardy–Weinberg equilibrium (HWE) (P > 0.05).
All blood samples were collected in the morning and stored at −20°C for 4 h. Genomic DNA was isolated using a Genomic DNA Purification Kit (Promega, Madison, WI, USA) and stored at −20°C before use. Genotyping was conducted using a Sequenom MassARRAY Genotyping Platform (Sequenom, San Diego, CA, USA).

Liu J.Y., Qian C.Y., Gao Y.F., Chen J., Zhou H.H, & Yin J.Y. (2017). Association between DNA mismatch repair gene polymorphisms and platinum-based chemotherapy toxicity in non-small cell lung cancer patients. Chinese Journal of Cancer, 36, 12.

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HBV Genotyping by MALDI-TOF MS

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The MALDI-TOF MS-based HBV genotyping assay started with amplification of 754 bp DNA fragment containing 12 codons: 80, 169, 173, 180, 181, 184, 194, 202, 204, 233, 236, and 250 [27 (link)–35 (link)]. The PCR reaction mixture contained (25 μl): 200 nmol/l of each primer [25 (link)], 5 μl of HBV DNA, 1x chelating buffer, 1.2 mM Mg(OAc)₂, 0.2 mM dNTP and 0.5 U of AmpliTaq Gold DNA polymerase (Applied Biosystems, Germany). Amplification conditions of HBV pol/S region analysis are shown in Table 1.
PCR products were then purified from non-incorporated dNTPs by treating with shrimp alkaline phosphatase (SAP) solution (40 min at 37°C and 5 min at 85°C). The iPLEX Gold assay was done in 4 separate primer-extension reactions on the Mass Array genotyping platform (Sequenom Inc., USA) with a standard procedure following the iPLEX kit protocol (Sequenom Inc., USA). To desalt the iPLEX reaction products, a resin kit was used (SpectroCLEAN resin, Sequenom Inc., USA), then cleaned extension products were dispensed onto a 384-element SpectroChip using the Nanodispenser, and mass differences were detected with MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry). All data analyses were carried out with TyperAnalyzer Application, version 4 (Sequenom Inc., USA).

Stalke P., Rybicka M., Wróblewska A., Dreczewski M., Stracewska E., Smiatacz T, & Bielawski K.P. (2014). An initial assessment of correlations between host- and virus-related factors affecting analogues antiviral therapy in HBV chronically infected patients. Medical Science Monitor : International Medical Journal of Experimental and Clinical Research, 20, 321-328.

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DNA Extraction and Genotyping for AMD Risk

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DNA was extracted from whole blood using standardized protocols. Blood was drawn via venipuncture and DNA extraction was extracted from whole blood using the Pure Gene method and standard protocols [48 ] and frozen at –80 ºC until use. Genotyping was performed at Vanderbilt University’s Center for Human Genetics Research. The Sequenom MassARRAY genotyping platform (Sequenom, San Diego, CA) was used to genotype samples at 19 common (MAF>1%) SNVs significantly associated with the risk of advanced AMD in a GWAS meta-analysis (Appendix 1) [35 (link)].

Sardell R.J., Bailey J.N., Courtenay M.D., Whitehead P., Laux R.A., Adams L.D., Fortun J.A., Brantley MA J.r., Kovach J.L., Schwartz S.G., Agarwal A., Scott W.K., Haines J.L, & Pericak-Vance M.A. (2016). Whole exome sequencing of extreme age-related macular degeneration phenotypes. Molecular Vision, 22, 1062-1076.

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