Whole blood was taken from all subjects in the Lund cohort and DNA was extracted. All patients were genotyped for the SUMF1 SNPs identified to be top hits in the eQTL analysis and Lifelines using Agena iPLEX genotyping. Genotyping was performed at the Mutation Analysis Facility at Karolinska University Hospital (Huddinge, Sweden) using iPLEX® Gold chemistry and MassARRAY® mass spectrometry system [31 (link)] (Agena Bioscience, San Diego, CA, U.S.A.). Multiplexed assays were designed using MassARRAY® Assay Design v4.0 Software (Agena Bioscience). Protocol for allele-specific base extension was performed according to Agena Bioscience’s recommendation. Analytes were spotted onto a 384-element SpectroCHIP II array (Agena Bioscience) using Nanodispenser RS1000 (Agena Bioscience) and subsequently analyzed by MALDI-TOF on a MassARRAY® Compact mass spectrometer (Agena Bioscience). Genotype calls were manually checked by two persons individually using MassARRAY® TYPER v4.0 Software (Agena Bioscience).
Massarray typer v4
Manufactured by Agena
Sourced in United States
The MassARRAY Typer v4.0 Software is a laboratory instrument designed to perform genetic analysis. It is used for the detection and identification of genetic variants in samples. The software provides the core functionality to operate the MassARRAY system and analyze the generated data.
Automatically generated - may contain errors
Lab products found in correlation
Iplex gold chemistry, by Agena (4 mentions)
Massarray mass spectrometry system, by Agena (2 mentions)
Massarray assay design v4, by Agena (2 mentions)
Autopure ls system, by Qiagen (2 mentions)
Qiaamp 96 dna blood kit, by Qiagen (2 mentions)
Massarray system, by Agena (2 mentions)
Nanodispenser rs1000, by Agena (1 mentions)
Iplex genotyping, by Agena (1 mentions)
Assay design suite v2, by Agena (1 mentions)
5 protocols using massarray typer v4
1
SUMF1 SNP Genotyping in Lund Cohort
2
Genetic Profiling of Osteoporosis Risk
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We recruited AIS subjects from six hospitals in Sweden and one in Denmark as with previously described inclusion criteria22 (link)–25 (link). We recruited control subjects from the Osteoporosis Prospective Risk Assessment cohort and PEAK-25 cohort26 (link),27 (link). Dual-energy X-ray absorptiometry (DXA) scan was performed in both cohorts and subjects with any sign of scoliosis on DXA were excluded. We extracted genomic DNA from blood or saliva using the QIAamp 96 DNA Blood Kit and Autopure LS system (Qiagen, Hilden, Germany). We used iPLEX Gold chemistry and MassARRAY system (Agena Bioscience, CA, USA) for genotyping. Two persons checked genotype calls using the MassARRAY Typer v4.0 Software (Agena Bioscience).
3
Scoliosis Genetics in Scandinavia: Recruitment and Genotyping
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AIS subjects were recruited from six hospitals in Sweden and one in Denmark as described previously to the Scoliosis and Genetics in Scandinavia (ScoliGeneS) study15 (link),38 (link)–40 (link). Individuals with a history or clinical sign of a non-idiopathic scoliosis and with neural abnormalities in a MRI of the spine were excluded. All control subjects were females and recruited from the Osteoporosis Prospective Risk Assessment cohort and PEAK-25 cohort41 (link),42 (link). Dual-energy X-ray absorptiometry (DXA) scan was performed in both cohorts and subjects showing any sign of a curved spine on DXA were excluded. Genomic DNA was extracted from blood or saliva using the QIAamp 96 DNA Blood Kit and the Autopure LS system (Qiagen). iPLEX Gold chemistry and the MassARRAY system (Agena Bioscience, CA, USA) were used for genotyping. Genotype calls were checked by two persons individually using the MassARRAY Typer v4.0 Software (Agena Bioscience).
4
Genotyping of Oesophagitis-Related SNPs
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Genomic DNA was extracted according to manufacturer recommendations from peripheral blood (collected at the visit prior to the start of RT) with the automatic Chemagen Robot (Chemagen Biopolymer-Technolgie AG, Beasweiler, Germany) at the Fundación Pública Galega de Medicina Xenómica (FPGMX) in Santiago de Compostela, Spain. Genotyping was conducted with the Agena Bioscience MassARRRAY® technology; PCR primers for multiplex assays were designed using Assay Design Suite v2.0 software (Agena Bioscience®. San Diego, CA, USA). The SNPs rs3819721 (TAP1) and rs204993 (AGER) were excluded due to genotyping design reasons. Genotype calling was performed with MassARRAY® Typer v4.0 software (Agena Bioscience®. San Diego, CA, USA) by pooling all the study data simultaneously. Only SNPs with a genotyping call rate of over 95% were included in the study.
Twenty-one SNPs related to oesophagitis passed quality control and were in Hardy–Weinberg equilibrium. The very low minor allele frequency of three SNPs located in the BRCA1 gene (rs12516, rs1799966, rs8176257) made it impossible to investigate them as described in the reference study (recessive genetic model).
Twenty-one SNPs related to oesophagitis passed quality control and were in Hardy–Weinberg equilibrium. The very low minor allele frequency of three SNPs located in the BRCA1 gene (rs12516, rs1799966, rs8176257) made it impossible to investigate them as described in the reference study (recessive genetic model).
5
Genotyping Variants in Idiopathic Scoliosis
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We genotyped the previously reported variants rs10510181, rs11190870, rs12946942, and rs6570507 in 1,739 patients with idiopathic scoliosis and in 1,812 controls from the OPRA and PEAK-25 cohorts [4] [5] [6] [7] . Genotyping was performed at the Mutation Analysis Facility at Karolinska University Hospital (Huddinge, Sweden) using iPLEX Gold chemistry and MassARRAY mass spectrometry system (Agena Bioscience, San Diego, CA, USA) [19] . Multiplexed assays were designed using the MassARRAY Assay Design v4.0 Software (Sequenom, Agena Bioscience, San Diego, CA, USA). Genotype calls were manually checked by two persons individually using the MassARRAY Typer v4.0 Software (Agena BioScience, San Diego, CA, USA).
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