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Typer software

Manufactured by Agena
Sourced in United States

Typer software is a lab equipment product designed for data analysis and processing. It provides core functionality for managing and interpreting experimental data. The software's primary purpose is to facilitate efficient data handling and analysis within the laboratory environment.

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7 protocols using typer software

1

Mosaic Mutation Detection using iPLEX and MALDI-TOF MS

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The mosaic mutation was confirmed by using iPLEX and MALDI-TOF MS (Agena Bioscience, Hamburg, Germany). The iPLEX reaction was performed according to the standard protocol recommended by the system supplier (21 (link)). The homogeneous MassEXTEND (hME) and iPLEX process reley on a small volume PCR amplifying the target regions including the SNP position in a multiplex fashion. The basic principle of hME and iPLEX reaction is identical. Both methods use a third, so-called MassEXTEND primer, which anneals directly adjacent to the SNP position. In an enzymatic primer extension reaction, this primer will be elongated. During that process the allele-specific analytical products are generated. The products differ by mass according to the incorporated bases. Primers were designed: ACGTTGGATGCTGTGAGCACCAATTTGGAC (PHEX-ex21_PCR1) and ACGTTGGATGTTCTCTTCTAGGTGAGGTGC (PHEX-ex21_PCR2), with the tag-sequences in italics. For the iPLEX-reaction the primer sequences were: ACAGACCAGAAGCTGCC (left) and CCAATTTGGACTTGTTCTC (right). The sample carrier was introduced into the mass spectrometer (MassARRAY Analyzer Compact, Agena Bioscience) and data are fully automatically acquired and analyzed in a real-time setting and revised using Typer software (Agena Bioscience).
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2

Genotyping by Mass Spectrometry

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DNA was extracted from blood samples using DNeasy Blood and Tissue kit (Qiagen). The genotyping was performed using a multiplexed primer extension (SBE) chemistry of the iPLEX assay with detection of the incorporated allele by mass spectrometry with a MassARRAY analyzer from Agena Bioscience. Raw data from the mass reader was converted to genotype data using the Typer software (Agena Bioscience). Reproducibility was controlled to be 100%. The tool PLINK (version 1.07)64 (link) was used for Chi-square calculations to test for association between SNV allele and phenotype. The experiment was performed twice.
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3

Genotyping of CA6 gene SNPs

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Single nucleotide polymorphisms in the region of the CA6 gene were selected and genotyped on DNA isolated from whole stimulated saliva. The criteria for SNP selection were a) minor allele frequency (MAF) ≥ 5% in the CEU population b) not in complete linkage disequilibrium (r2 ≤ 0.8) and c) in the 10,000 bp up-stream to 10,000 bp down-stream region of the CA6 gene. Using the NIH snptag resource (https://snpinfo.niehs.nih.gov/snpinfo/snptag.html) 30 SNPs met these criteria. Genotyping was performed using a multiplexed primer extension chemistry of the iPLEX assay with detection of the incorporated allele by mass spectrometry using a MassARRAY analyzer (Agena Bioscience, Hamburg, Germany). Raw data from the mass reader was converted to genotype data using the Typer software (Agena Bioscience)39 –41 (link). Two SNP markers had sample call rate 0%, rs2274333 and rs17032942, the reasons for the failure was low allele signals resulting in inaccurate genotype calls. An additional SNP (rs6697763) was excluded from analysis for deviation from Hardy-Weinberg equilibrium (p = 0.033), leaving 27 SNPs with valid genotype data, where the average call rate per sample was 99.4% and overall call rate was 99.8% (Table S1). Genotyping data are uploaded and available at figshare 10.6084/m9.figshare.6948020.
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4

Genotyping of MIR17HG SNPs

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We selected four SNPs (rs75267932, rs72640334, rs7318578 and rs17735387) in MIR17HG with a minor allele frequency (MAF) >5% in the global population from the HapMap database. The primers for polymerase chain reaction (PCR) amplification and single base extension of the three SNPs were designed by the Agena Bioscience Assay Design Suite V2.0 software (https://agenacx.com/online-tools/). The four SNPs genotyping were performed using the Agena MassARRAY platform with iPLEX gold chemistry (Agena Bioscience, San Diego, CA, U.S.A.) according to the manufacturer’s instructions. Data were managed and analyzed using the version 4.0 Agena Bioscience TYPER software.
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5

Genotyping of COMT polymorphism

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DNA was extracted from peripheral blood samples and stored at Karolinska Institutet Biobank. DNA samples were transferred on PCR plates and sent to the SNP&SEQ Technology Platform, Uppsala University [National Genomics Infrastructure (NGI), SciLifeLab Sweden]. The genotyping was performed using a multiplexed primer extension (SBE) chemistry of the iPLEX assay with detection of the incorporated allele by mass spectrometry with a MassARRAY analyser from Agena Bioscience (Ross et al., 1998 (link); Gabriel et al., 2009 (link); Storm et al., 2019 ). Raw data from the mass reader was converted to genotype data using the Typer software (Agena Bioscience). The COMT genotype distributions were in Hardy-Weinberg equilibrium (ps > 0.1). Of the full sample, 9 were missing genotype information and were treated as missing at random. Genotype distributions are reported in Table 1.
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6

Genotyping SLCO1B1 and SLCO1B3 Variants

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A QIAamp DNA Blood Mini Kit was used to perform genomic DNA extraction from blood samples for genotyping of SLCO1B1 (463 C>A, 388 A>G, 11187 G>A, rs4149015, 521 T>C and 1436 G>C) and SLCO1B3 (334 T>G). Genotyping was performed by multiplexed primer extension chemistry of an iPLEX assay with detection of the incorporated allele by MS with a MassARRAY analyser (Agena Bioscience, San Diego, CA, USA).17 (link),18 The output data were converted into genotype data using Typer software (Agena Bioscience).
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7

Genotyping HFE Mutations via MassARRAY

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DNA samples were transferred on PCR plates and sent to the SNP&SEQ Technology Platform, Uppsala University (National Genomics Infrastructure [NGI], SciLifeLab Sweden). The genotyping was performed using a multiplexed primer extension (SBE) chemistry of the iPLEX assay with detection of the incorporated allele by mass spectrometry with a MassARRAY analyzer from Agena Bioscience.28 , 29 (link), 30 (link) Raw data from the mass reader were converted to genotype data using the Typer software (Agena Bioscience). Both HFE C282Y (rs1800562) and H63D (rs1799945) genotype distributions were in Hardy‐Weinberg equilibrium (Ps > .1).
Given the limited number of individual carriers of H63D or C282Y, we pooled the participants in 2 groups: non‐carriers of any of the mutations (HFE‐neg) and carriers of either the H63D and/or C282Y (HFE‐pos).
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