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Massarray iplex platform

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The MassARRAY iPLEX platform is a high-throughput genotyping system used for genetic analysis. It employs matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry technology to detect and analyze DNA sequence variations.

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Lab products found in correlation

Nanodrop 2000, by Thermo Fisher Scientific (14 mentions) Typer version 4, by Agena (7 mentions) Massarray nanodispenser, by Agena (4 mentions) Assay design suite v2, by Agena (4 mentions) Nanodrop 2000c spectrophotometer, by Thermo Fisher Scientific (3 mentions) Typer 4, by Agena (2 mentions) Dna investigator kit, by Qiagen (1 mentions) Qiaamp dna blood mini kit, by Qiagen (1 mentions) Typer software version 4.0, by Agena (1 mentions) Assay design software, by Agena (1 mentions) Dna blood mini kit, by Qiagen (1 mentions) Qiaamp dna ffpe tissue kit, by Qiagen (1 mentions) Magbind blood dna kit, by CWBIO (1 mentions) Assay design suite software, by Agena (1 mentions) Nanodrop 2000 platform, by Thermo Fisher Scientific (1 mentions)

39 protocols using massarray iplex platform

1

Genotyping EBV variants and human SNPs in NPC

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To genotype the EBV variants in the 990 cases and 1105 controls from
Zhaoqing, the customized primers and the protocol recommended by the Agena
Bioscience MassArray iPLEX platform were used. A fixed position in the human
albumin gene was used as a positive control. Because the genotyping success rate
strongly correlates with the EBV DNA abundance (Supplementary Fig. 15), about half
of the validation samples (483 of the cases and 605 of the controls) could be
successfully genotyped for all the three GWAS candidate markers (i.e., SNPs
162215C>A, 162476T>C and 163364C>T). The slightly lower
success rate in the cases is consistent with the fact that the EBV DNA abundance
was lower in the saliva from patients than from controls. For detailed
information, see Supplementary
Note.
Seven previously reported human SNPs in HLA (rs2860580,
rs2894207 and rs28421666), CDKN2A/2B (rs1412829),
TNFRSF19 (rs9510787), TERT (rs31489) and
MECOM (rs6774494) were genotyped using customized primers
and following the protocol recommended by the Agena Bioscience MassArray iPLEX
platform in the 990 cases and 1105 controls from Zhaoqing. A fixed position in
the human albumin gene was used as a positive control. The genotyping completion
rate for all seven human SNPs was > 95%. Associations with NPC were
assessed with logistic regression under an additive model adjusted for sex and
age.
Xu M., Yao Y., Chen H., Zhang S., Cao S.M., Zhang Z., Luo B., Liu Z., Li Z., Xiang T., He G., Feng Q.S., Chen L.Z., Guo X., Jia W.H., Chen M.Y., Zhang X., Xie S.H., Peng R., Chang E.T., Pedergnana V., Feng L., Bei J.X., Xu R.H., Zeng M.S., Ye W., Adami H.O., Lin X., Zhai W., Zeng Y.X, & Liu J. (2019). Genome sequencing analysis identifies Epstein-Barr virus subtypes associated with high risk of nasopharyngeal carcinoma. Nature genetics, 51(7), 1131-1136.
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2

Genotyping EBV variants and human SNPs in NPC

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To genotype the EBV variants in the 990 cases and 1105 controls from
Zhaoqing, the customized primers and the protocol recommended by the Agena
Bioscience MassArray iPLEX platform were used. A fixed position in the human
albumin gene was used as a positive control. Because the genotyping success rate
strongly correlates with the EBV DNA abundance (Supplementary Fig. 15), about half
of the validation samples (483 of the cases and 605 of the controls) could be
successfully genotyped for all the three GWAS candidate markers (i.e., SNPs
162215C>A, 162476T>C and 163364C>T). The slightly lower
success rate in the cases is consistent with the fact that the EBV DNA abundance
was lower in the saliva from patients than from controls. For detailed
information, see Supplementary
Note.
Seven previously reported human SNPs in HLA (rs2860580,
rs2894207 and rs28421666), CDKN2A/2B (rs1412829),
TNFRSF19 (rs9510787), TERT (rs31489) and
MECOM (rs6774494) were genotyped using customized primers
and following the protocol recommended by the Agena Bioscience MassArray iPLEX
platform in the 990 cases and 1105 controls from Zhaoqing. A fixed position in
the human albumin gene was used as a positive control. The genotyping completion
rate for all seven human SNPs was > 95%. Associations with NPC were
assessed with logistic regression under an additive model adjusted for sex and
age.
Xu M., Yao Y., Chen H., Zhang S., Cao S.M., Zhang Z., Luo B., Liu Z., Li Z., Xiang T., He G., Feng Q.S., Chen L.Z., Guo X., Jia W.H., Chen M.Y., Zhang X., Xie S.H., Peng R., Chang E.T., Pedergnana V., Feng L., Bei J.X., Xu R.H., Zeng M.S., Ye W., Adami H.O., Lin X., Zhai W., Zeng Y.X, & Liu J. (2019). Genome sequencing analysis identifies Epstein-Barr virus subtypes associated with high risk of nasopharyngeal carcinoma. Nature genetics, 51(7), 1131-1136.
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3

High-Throughput Genotyping of Dried Blood Spots

Cited 2 times
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The dried blood spots on filter paper were sent to the Wellcome Sanger Institute for processing. DNA extraction was carried out using the Qiagen DNA Investigator Kit (No. 56504, Qiagen, Crawley, UK) for high-throughput robotic processing. DNA was eluted in 100 μl TE buffer and stored at − 20 °C for later use. Extracted DNA underwent whole genome amplification (WGA) by primer-extension pre-amplification [37 (link)] or selective WGA [38 (link)] prior to genotyping. Genotyping was performed according to manufacturer’s instruction on the Agena MassARRAY® iPLEX platform (Agena Bioscience, Hamburg, Germany). This system is able to accurately genotype large numbers of samples for multiple SNPs simultaneously. It previously been used in P. falciparum for sequencing validation of novel SNPs [39 (link)]. All genotypes were called from background adjusted peak intensities, which were normalized and called by batch. In brief, batches underwent calling using a heuristic algorithm which identifies intensity ranges for each SNP in single infection samples, and called mixed base loci (“heterozygous”) based on those range thresholds, adjusting for background intensity. Batches were plate based and contained between 96 and 384 samples. These are necessary to generate per assay ranges of intensities to calculate background intensity levels.
Diakité S.A., Traoré K., Sanogo I., Clark T.G., Campino S., Sangaré M., Dabitao D., Dara A., Konaté D.S., Doucouré F., Cissé A., Keita B., Doumbouya M., Guindo M.A., Toure M.B., Sogoba N., Doumbia S., Awandare G.A, & Diakité M. (2019). A comprehensive analysis of drug resistance molecular markers and Plasmodium falciparum genetic diversity in two malaria endemic sites in Mali. Malaria Journal, 18, 361.
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4

Genomic DNA Extraction and Genotyping

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Genomic DNA was isolated from peripheral blood leukocytes using the QIAamp DNA Blood Mini Kit (Qiagen, Germany). The polymorphism rs1256031 was genotyped using the Agena MassARRAY iPLEX platform (Agena Inc., CA). Primers are listed in Supplementary Table S1. For quality control we randomly tested 5% of samples using the same sets of primers, and the results were 100% consistent.
Li X., Su J., Zheng K., Lin S., Chen S., Wang B., Lai L, & Duan S. (2020). Assessment of the association between the polymorphism rs1256031 of the estrogen receptor β gene and GDM susceptibility. Nagoya Journal of Medical Science, 82(4), 703-709.
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5

Genetic Association of Statin Myopathy

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All 585 CPRD statin‐tolerant controls and 19 patients with myopathy from the EUDRAGENE cohort were genotyped for statistically significant association signals identified in the case‐control discovery GWAS (P < 5 × 10−5) using either the Agena MassArray iPLEX platform (Agena Biosciences, San Diego, CA) or TaqMan real‐time polymerase chain reaction SNP genotyping assay (Life Technologies, Paisley, UK), according to the manufacturer's protocols.
Carr D.F., Francis B., Jorgensen A.L., Zhang E., Chinoy H., Heckbert S.R., Bis J.C., Brody J.A., Floyd J.S., Psaty B.M., Molokhia M., Lapeyre‐Mestre M., Conforti A., Alfirevic A., van Staa T, & Pirmohamed M. (2019). Genomewide Association Study of Statin‐Induced Myopathy in Patients Recruited Using the UK Clinical Practice Research Datalink. Clinical Pharmacology and Therapeutics, 106(6), 1353-1361.
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6

MIR31HG Polymorphisms Genotyping

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Seven functional SNPs in MIR31HG (rs1332184, rs72703442, rs2025327, rs55683539, rs2181559, rs10965059 and rs10965064) were selected from the 1000 Genomes Project (http://www.1000genomes.org/), with the minor allele frequency (MAF) of each SNP greater than 0.05. Peripheral blood genomic DNA was extracted from all subjects according to the operating procedures of Whole Blood Genomic DNA Isolation Kit (Xi’an GoldMag Biotechnology, China). Agena MassARRAY iPLEX platform was used for genotyping. Agena Bioscience Assay was used to design PCR primers for amplification (Supplementary Table 1). Finally, Agena Bioscience TYPER application software 4.0 was performed to analyze the genetic data.
Wang Y., Wang Y., Liang D., Hu H., Li G., Meng X., Zhu B, & Zhong W. (2022). MIR31HG polymorphisms are related to steroid-induced osteonecrosis of femoral head among Chinese Han population. BMC Musculoskeletal Disorders, 23, 836.
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7

Genotyping of CDKN2B-AS1 SNPs

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Genomic DNA was extracted from peripheral blood stored with EDTA using blood DNA kit (GoldMag Co. Ltd.). The concentration of the DNA samples was measured with Nanodrop 2000 (Thermo Scientific). In this study, five SNPs in CDKN2B‐AS1 were selected from UCSC database and each candidate SNP had larger than 5% minor allele frequency in Chinese Han population. The primers used in this study were designed using MassARRAY Assay Design 3.0 software (Table S1), and the genotyping was performed on the MassARRAY iPLEX platform (Agena Bioscience) (Sun et al., 2017). We checked the quality of the genotype determination by the same method. We predicted functions of selected polymorphisms by HaployReg v4.1. Agena Bioscience TYPER version 4.0 software was used to perform data management and analyses.
Huang K., Zhong J., Li Q., Zhang W., Chen Z., Zhou Y., Wu M., Zhong Z., Lu S, & Zhang S. (2019). Effects of CDKN2B‐AS1 polymorphisms on the susceptibility to coronary heart disease. Molecular Genetics & Genomic Medicine, 7(11), e955.
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8

STOX1 Genotyping by MassARRAY

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In this study, six SNPs (rs10998449, rs10762244, rs10998461, rs10998468, rs7903209, and rs4472827) in the STOX1 were selected from the DbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/) and 1,000 genome (http://www.internationalgenome.org/). All the SNPs were selected at a minor allele frequency >5% in Han Chinese from the 1,000 Genome Projects.
According to the manufacturer's protocol, GoldMag‐Mini Whole Blood Genomic DNA Purification Kit (GoldMag Co. Ltd.) was used to isolate the total genomic DNA from peripheral blood. The Agena Bioscience Assay Design Suite V2.0 software (http://agenacx.com/online-tools) was used to design the extended primer. The MassARRAY Nanodispenser (Agena Bioscience) and MassARRAY iPLEX platform (Agena Bioscience) were used to genotype, and the Agena Bioscience TYPER software (version 4.0) was used to analyze the data. We randomly selected about 10% of the sample to repeat genotyping, and the reproducibility was 100% indicating that our result is reliable.
Yang X., Li F., Xin D., Huang Z., Xue J., Wang B., Da Y., Xing W, & Zhu Y. (2019). Investigation of the STOX1 polymorphism on lumbar disc herniation. Molecular Genetics & Genomic Medicine, 8(1), e1038.
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9

Genotyping of Genetic Variants

Cited 1 time
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Peripheral blood samples were collected from the participants and were stored at −80°C until analysis. Genomic DNA was extracted from EDTA-containing blood via a blood DNA kit (GoldMag Co. Ltd., Xi'an, China). DNA concentration was measured by Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA) (15 (link)). Combined with previous studies and the criteria of minor allele frequency (MAF) ≥ 0.05, five SNPs (rs2531995, rs879620, rs2230742, rs2230741, and rs2531992) were selected in this study based on the dbSNP database (https://www.ncbi.nlm.nih.gov/snp/) and HapMap database (http://www.hapmap.org). Primers were designed by MassARRAY Assay Design 3.0 software and were listed in Supplemental Table 1. SNP genotyping was performed by the MassARRAY iPLEX platform (Agena Bioscience, San Diego, CA, USA) (16 (link)). Finally, the data analysis was accomplished by Agena Bioscience TYPER version 4.0 software (17 (link)).
Chao X., Jia Y., Feng X., Wang G., Wang X., Shi H., Zhao F, & Jiang C. (2020). A Case–Control Study of ADCY9 Gene Polymorphisms and the Risk of Hepatocellular Carcinoma in the Chinese Han Population. Frontiers in Oncology, 10, 1450.
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10

Genotyping of BDNF-related SNPs

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Blood samples were obtained close to the neuropsychological assessment. The Tagger tool of Haploview v.4.244 (link) was used to select tagSNPs in linkage disequilibrium (LD) (r2 > 0.7) with the remaining SNPs at minor allele frequency (MAF) > 10% from the HapMap phase III European samples. Functional SNP rs6265 and SNPs most commonly associated with mental disorders or cognitive dysfunction from the literature (rs2030324, rs12273363, rs908867, and rs1491850) were prioritized as tagSNPs45 (link)–48 (link). In addition, rs11030094, rs11602246, and rs4923463, which were absent from the HapMap data, were included following Hennings, Honea, and Neves49 (link)–51 (link). In total, 11 SNPs were selected (Fig. S1).
Genotyping of the selected SNPs was performed using the MassARRAYiPLEX platform (Agena Bioscience, formerly Sequenom, Inc.; San Diego, California). We used mean methylation levels from the performed technical replicas and discarded outlying values (standard deviation >10%) as a quality control method. The genotyping assays were performed at the genotyping facilities of CeGen in the Santiago de Compostela Node (‘Centro Nacional de Genotipado’).
Ferrer A., Labad J., Salvat-Pujol N., Barrachina M., Costas J., Urretavizcaya M., de Arriba-Arnau A., Crespo J.M., Soriano-Mas C., Carracedo Á., Menchón J.M, & Soria V. (2019). BDNF genetic variants and methylation: effects on cognition in major depressive disorder. Translational Psychiatry, 9, 265.
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