Typer analyzer software

Manufactured by Labcorp

Sourced in United States

The Typer Analyzer software is a powerful tool designed for efficient genetic analysis. It provides a comprehensive suite of features to assist in the identification and characterization of genetic markers. The software is capable of analyzing and interpreting data from various genetic testing platforms.

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Lab products found in correlation

Massarray platform, by Labcorp (6 mentions) Genomic dna kit, by Corning (6 mentions) Mass array rs1000 system, by Labcorp (3 mentions) Iplex gold assay, by Labcorp (2 mentions) Massarray system, by Labcorp (2 mentions) Ezna blood dna midi kit, by Omega Bio-Tek (2 mentions) Sequenom massarray rs1000 system, by Labcorp (1 mentions) Massarray compact system, by Labcorp (1 mentions) Infinium hd human610 quad beadchip, by Illumina (1 mentions) Qiamp blood mini kit, by Qiagen (1 mentions) Assay design software, by Labcorp (1 mentions)

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TYPER software (15 citations) Typer analyzer (5 citations) MassARRAY Typer Analyzer software (4 citations) Typer Analyzer Software package (2 citations)

15 protocols using typer analyzer software

Genetic Variants in Bone Genes

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All SNPs with minor allele frequencies (MAF) ≥ 0.01 were searched for between 15 kb upstream and 15 kb downstream of the IBSP and PTHLH genes in the HapMap HCB database by Haploview v4.225 (link). A total of 27 SNPs in the IBSP gene and 24 SNPs in the PTHLH gene were identified. Three additional SNPs in the IBSP gene were included from previous reports17 (link)24 (link). Based on the above criteria, 54 SNPs were included in further analyses (Supplementary Table S1). Peripheral blood was drawn from a vein into a sterile tube containing ethylenediamine tetraacetic acid (EDTA). Genomic DNA was extracted from peripheral blood leukocytes according to the manufacturer’s protocol (Genomic DNA kit, Axygen Scientific Inc., California, USA). DNA was stored at −20 °C for SNP analysis. Genotyping was performed for all SNPs using the MassARRAY platform (Sequenom, San Diego, California, USA). Briefly, SNPs were genotyped using high-throughput, matrix-assisted laser desorption ionization–time-of-flight (MALDI–TOF) mass spectrometry. The resulting spectra were processed using Typer Analyzer software (Sequenom), and genotype data were generated from the samples. As the final genotype call rate of each SNP was greater than 98% and the overall genotyping call rate was 99.6%, the reliability of further statistical analysis was ensured.

Zhang Y., Liu H., Zhang C., Zhang T., Zhang B., Li L., Chen G., Fu D, & Wang K. (2015). Endochondral ossification pathway genes and postmenopausal osteoporosis: Association and specific allele related serum bone sialoprotein levels in Han Chinese. Scientific Reports, 5, 16783.

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Genotyping of WLS Gene SNPs

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WLS tagging SNPs (tagSNPs) were selected from the 1000 Genomes Chinese Han Beijing population (CHB) using Haploview^{23 (link)}. SNPs with minor allele frequencies (MAF) ≥0.05 were selected based on pairwise tagging with an r² threshold of 0.5. A final set of 40 tag SNPs was selected within the WLS gene (Supplemental Table S1). Genomic DNA was extracted from peripheral blood leukocytes according to the manufacturer’s protocol (Genomic DNA kit, Axygen Scientific Inc., California, USA). Genotyping was performed for all SNPs using the Sequenom Mass ARRAY RS1000 system (Sequenom, San Diego, California, USA). The results were processed using Typer Analyzer software (Sequenom), and genotype data were generated from the samples^{24 (link)}.

Zhang D., Ge Z., Ma X., Zhi L., Zhang Y., Wu X., Yao S, & Ma W. (2017). Genetic association study identified a 20 kb regulatory element in WLS associated with osteoporosis and bone mineral density in Han Chinese. Scientific Reports, 7, 13668.

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Genotyping Breast Cancer Pharmacogenetics

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Approximately 30 μL of DNA from whole blood, FFPE-T and FFPE-LN was submitted to the University of Michigan DNA Sequencing core. Assays were designed using standard Sequenom software (both online Assay Design Suite tools and desktop Assay Design 4.0) and assays were performed using a Sequenom MassARRAY Compact instrument, according to manufacturer’s standard protocols. Results were processed to generate SNP calls automatically, using Sequenom TyperAnalyzer software, and then manually reviewed by the operator to validate the allele calls. Automatic SNP calls that were of concern, based on questionable spectra, were removed. A total of 304 unique SNPs were genotyped on 8 Sequenom MassARRAY plexes with up to 40 SNPs each. These SNPs were not selected specifically for this project, but represent a collection of candidate SNPs relevant to the metabolism, mechanism, or toxicity of breast cancer treatments, for genotyping in prospective-retrospective pharmacogenetic analyses of breast cancer clinical trials. Sample concentration was determined using a Nanodrop spectrophotometer. Ideal sample concentrations for Sequenom are between 50–100 ng/μl. DNA concentrations were less than optimal from FFPE-T (median=10.09, range: 0.78–88.0) and FFPE-LN (median=57.00, range 2.57–97.29).

Hertz D.L., Kidwell K.M., Thibert J.N., Gersch C., Regan M.M., Skaar T.C., Henry N.L., Hayes D.F., Van Poznak C.H, & Rae J.M. (2015). Genotyping concordance in DNA extracted from formalin‐fixed paraffin embedded (FFPE) breast tumor and whole blood for pharmacogenetic analyses. Molecular Oncology, 9(9), 1868-1876.

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Genotyping Chinese Han Population

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We searched for all SNPs with minor allele frequencies (MAFs) ≥ 0.02 within the region of the MDM4 gene in the 1000 Genomes Project Chinese Han Beijing population database. MAF ≥ 0.02 and tagging r² ≥ 0.8 were used as a screening standard in the selection of tag SNP, which generated 24 tag SNPs for our study. As a result, these 24 tag SNPs (rs3014610, rs2169137, rs117139931, rs137991330, rs4252707, rs190876924, rs12024619, rs72644182, rs117137314, rs76605997, rs76432362, rs116854458, rs12138846, rs61421373, rs191840558, rs116907825, rs115517182, rs12567161, rs150337092, rs80242302, rs3789044, rs3789043, rs884108 and rs61817485) were included in further analyses. All our selected SNPs had P values greater than 0.05 by the HWE test. Commercial kits were used to extract genomic DNA from peripheral blood leukocytes (Genomic DNA kit, Axygen Scientific Inc., CA, USA). Genotyping was conducted for 24 selected SNPs by using the platform of Sequenom Mass ARRAY RS1000 system (Sequenom, San Diego, CA, USA). Typer Analyzer software (Sequenom, San Diego, California, USA) was used to process signal results to ultimately generate genotype data^{20 (link)}. Case and control statuses were blinded during all genotyping processes for quality control. Five percent of the random samples were repeated, and the results were 100% concordant.

Sun P., Yan F., Fang W., Zhao J., Chen H., Ma X, & Song J. (2018). MDM4 contributes to the increased risk of glioma susceptibility in Han Chinese population. Scientific Reports, 8, 11093.

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SNP Genotyping of GZMB Gene

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SNPs with a minor allele frequency (MAF) >0.01, heterozygosity >0.2 and located within the GZMB gene region were extracted for genotyping based on the 1000 genome CHB data. Overall, 15 SNPs were obtained. Genomic DNA was extracted from peripheral blood leukocytes according to the manufacturer’s protocol (Genomic DNA kit, Axygen Scientific Inc., CA, USA). Genotyping was performed for all SNPs using the MassARRAY platform (Sequenom, San Diego, CA, USA). The genotyping results were generated and processed by using Typer Analyzer software (Sequenom)^{22 (link)}. The final genotyping call rate for each SNP was greater than 99%, and the overall genotyping call rate was 99.9%. The quality of our genotyping results ensured the reliability of further statistical analyses.

Xu M., Liu Y., Liu Y., Li X., Chen G., Dong W, & Xiao S. (2018). Genetic polymorphisms of GZMB and vitiligo: A genetic association study based on Chinese Han population. Scientific Reports, 8, 13001.

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Genotyping of Tag SNPs in TLR10 and NFKBIA

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Tag SNPs covered the gene regions of TLR10 and NFKBIA and were selected for genotyping based on the 1,000 genome data of Chinese Han populations. Minor allele frequency (MAF) > 0.01 and r² > 0.6 were utilised as criteria for tagging. A total of 23 tag SNPs, 14 from TLR10 and 9 from NFKBIA, were selected for genotyping. Genomic DNA was extracted from peripheral blood leukocytes according to the manufacturer’s protocol (Genomic DNA kit, Axygen Scientific Inc., California, USA). Genotyping was performed for all SNPs using the Sequenom Mass ARRAY RS1000 system (Sequenom, San Diego, California, USA). The results were processed using Typer Analyzer software (Sequenom)^{29 (link)}, and the genotype data were generated from the samples. To ensure the accuracy of the genotyping, we have randomly chosen 5% of our study subjects and repeated the genotyping process for them. The concordance rate of this process was 100%, which indicates that the genotyping results of our study were reliable.

Tang H., Cheng Z., Ma W., Liu Y., Tong Z., Sun R, & Liu H. (2018). TLR10 and NFKBIA contributed to the risk of hip osteoarthritis: systematic evaluation based on Han Chinese population. Scientific Reports, 8, 10243.

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Genotyping of GNL3 SNPs in Chinese Han

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SNPs in the GNL3 gene were selected from the 1000 Genomes Chinese Han Beijing population (CHB) using Haploview. In total, 11 SNPs with minor allele frequencies (MAF) ≥ 0.01 were selected to be included in the study, including rs1108842, rs11177, rs3774349, rs117150867, rs35911561, rs183781382, rs75373137, rs35315313, rs13076193, rs6762813, and rs2289247. Genomic DNA was extracted from peripheral blood leukocytes according to the manufacturer’s protocol (Genomic DNA kit, Axygen Scientific Inc., California, USA). Genotyping was performed for all SNPs using the Sequenom Mass ARRAY RS1000 system (Sequenom, San Diego, California, USA). The results were processed using Typer Analyzer software (Sequenom), and genotype data were generated from the samples^{21 (link)}. To ensure the accuracy of genotyping, we randomly chose 5% of our study subjects and repeated the genotyping process for those individuals. The concordance rate of this process was 100%, which indicated that the genotyping results of our study were reliable.

Liu B., Cheng H., Ma W., Gong F., Wang X., Duan N, & Dang X. (2018). Common variants in the GNL3 contribute to the increasing risk of knee osteoarthritis in Han Chinese population. Scientific Reports, 8, 9610.

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Validation of Germline Variant Panels

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After filtering, 58 variants in 35 target genes (listed in Tables S2–S4) were selected for validation which was performed on germline DNA from 2216 subjects, including 1293 cases and 923 population controls. The majority of the cases (1105 individuals) represented unselected PrCa patients from the Pirkanmaa Hospital District, Tampere, Finland. In addition, 188 index cases from Finnish HPC families^{10 (link)} were included in the study. The control DNA samples from anonymous male blood donors were provided by the Finnish Red Cross Blood Transfusion Service. Genotyping was performed at the Technology Centre, FIMM using the Sequenom MassARRAY system and iPLEX Gold assays (Sequenom, Inc., San Diego, CA, USA). Genotyping reactions were performed with 20 ng of dried genomic DNA according to manufacturer’s recommendations and with their reagents. The genotypes were called using TyperAnalyzer software (Sequenom). For quality control (QC) reasons, the genotype calls were also checked manually. Genotyping quality was examined using a detailed QC procedure that included success rate checks, duplicated samples and water controls.

Laitinen V.H., Rantapero T., Fischer D., Vuorinen E.M., Tammela T.L., Wahlfors T, & Schleutker J. (2014). Fine-mapping the 2q37 and 17q11.2-q22 Loci for Novel Genes and Sequence Variants Associated with a Genetic Predisposition to Prostate Cancer. International journal of cancer. Journal international du cancer, 136(10), 2316-2327.

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Genomic DNA Genotyping and QC

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Genomic DNA was extracted from peripheral blood and genotyped by Illumina arrays: the Finnish discovery sample and the Dutch replication cases by CNV370k DUO chip; the HBCS and YFS controls by Illumina Human670K customBeadChip; and the H2000 controls by Illumina Infinium HDHuman610-Quad BeadChip.
In the Finnish replication sample, DNA was genotyped using Sequenom MassARRAY system and iPLEX Gold assays (Sequenom Inc., San Diego, USA). The data was collected using the MassARRAY Compact System (Sequenom) and the genotypes were called using TyperAnalyzer software (Sequenom). Genotyping quality was examined by a detailed QC procedure consisting of success rate checks, duplicates, water controls and Hardy-Weinberg Equilibrium (HWE) testing. SNPs were filtered if genotype missingness >0.05 or if HWE p<0.001.

Kurki M.I., Gaál E.I., Kettunen J., Lappalainen T., Menelaou A., Anttila V., van 't Hof F.N., von und zu Fraunberg M., Helisalmi S., Hiltunen M., Lehto H., Laakso A., Kivisaari R., Koivisto T., Ronkainen A., Rinne J., Kiemeney L.A., Vermeulen S.H., Kaunisto M.A., Eriksson J.G., Aromaa A., Perola M., Lehtimäki T., Raitakari O.T., Salomaa V., Gunel M., Dermitzakis E.T., Ruigrok Y.M., Rinkel G.J., Niemelä M., Hernesniemi J., Ripatti S., de Bakker P.I., Palotie A, & Jääskeläinen J.E. (2014). High Risk Population Isolate Reveals Low Frequency Variants Predisposing to Intracranial Aneurysms. PLoS Genetics, 10(1), e1004134.

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Quality Control for Genetic Associations

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Each run of 25 multiplexed assays was carefully inspected with TyperAnalyzer software (Sequenom Inc.), and evident errors, according to the manufacturer’s guidelines, were manually corrected to ensure optimal genotyping. Before the association analysis, quality control was applied with PLINK.^{28 (link)} The SNPs with P < 1 × 10⁻⁴ in a Hardy-Weinberg equilibrium test, genotype call rate less than 90%, concordance rate less than 90%, or MAF less than 1% were excluded. Samples with genotyping rate less than 90% and families and SNPs with Mendelian error rates greater than 10% also were excluded.

Huertas-Fernández I., Gómez-Garre P., Madruga-Garrido M., Bernal-Bernal I., Bonilla-Toribio M., Martín-Rodríguez J.F., Cáceres-Redondo M.T., Vargas-González L., Carrillo F., Pascual A., Tischfield J.A., King R.A., Heiman G.A, & Mir P. (2015). GDNF Gene Is Associated With Tourette Syndrome in a Family Study. Movement disorders : official journal of the Movement Disorder Society, 30(8), 1115-1120.

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