Pyromark q96 id software

Manufactured by Qiagen

Sourced in Sweden

The PyroMark Q96 ID Software is a software application designed for the analysis and interpretation of DNA pyrosequencing data generated by the PyroMark Q96 ID system. The software provides tools for analyzing DNA sequences, detecting sequence variations, and generating reports.

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Lab products found in correlation

Pyromark q96 id system, by Qiagen (2 mentions) Amplitaq gold buffer, by Thermo Fisher Scientific (1 mentions) Goldengate genotyping assay, by Illumina (1 mentions) Amplitaq gold, by Thermo Fisher Scientific (1 mentions) Dneasy blood tissue kit, by Qiagen (1 mentions) Psq96ma system, by Biotage (1 mentions) Pyromark assay design 2, by Qiagen (1 mentions) Pyromark q96 id instrument, by Qiagen (1 mentions) Pyromark gold q96 reagent, by Qiagen (1 mentions) Pmd18 t vector, by Takara Bio (1 mentions) Tianamp genomic dna kit, by Tiangen Biotech (1 mentions)

Spelling variants of this product

PyroMark Q96 ID (106 citations) PyroMark Q96 (70 citations) PyroMark ID (9 citations) PyroMark Q96 ID System and software (5 citations) PyroMark Q96 ID software version 1.0 (3 citations) PyroMark Q96 ID Software 2.5 (2 citations)

6 protocols using pyromark q96 id software

SNP Genotyping and Kras Repeat Analysis

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Genomic DNA from urethane-treated ABF4 mice was used for genome-wide SNP genotyping carried out with the GoldenGate Genotyping Assay according to the manufacturer's protocol (Illumina, San Diego, CA, USA), using the Mouse MD Linkage Panel representing 1449 mouse loci.
Additionally, the Pas1 locus in untreated ABF4 mice was genotyped for nine genetic markers, including eight SNPs (rs6349084, rs33863668, rs31000839, rs31005929, rs13479063, rs33893742, rs13479082, rs3711088) and a 37-bp tandem repeat in Kras[21] (link). Briefly, a genomic fragment surrounding each marker was PCR-amplified in reactions containing 30 ng genomic DNA, 1 U AmpliTaq Gold (Applied Biosystems, Life Technologies), 1× AmpliTaq Gold buffer (Applied Biosystems, Life Technologies), 1.5 mM MgCl₂, 200 µM dNTPs and 5 pmol of each of a pair of specific primers (Table S1) in a total volume of 25 µl. To genotype the eight SNPs, PCR products were pyrosequenced on a PyroMark Q96 ID system running PyroMark Q96 ID Software (Qiagen). To genotype the Kras 37-bp repeat, PCR amplicons were analyzed by 3% agarose gel electrophoresis for fragment size.

Dassano A., Colombo F., Trincucci G., Frullanti E., Galvan A., Pettinicchio A., De Cecco L., Borrego A., Martinez Ibañez O.C., Dragani T.A, & Manenti G. (2014). Mouse Pulmonary Adenoma Susceptibility 1 Locus Is an Expression QTL Modulating Kras-4A. PLoS Genetics, 10(4), e1004307.

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Genetic Profiling of Nicotinic Receptors

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DNA was extracted from peripheral blood using the DNeasy Blood & Tissue Kit (Qiagen) and was quantified by spectrophotometry (ND-2000c, NanoDrop Products, Wilmington, DE, USA). SNP-containing fragments were PCR-amplified using SNP-specific primers (Supplementary Table S1). Then, six SNPs were genotyped by pyrosequencing: rs2072661 in CHRNB2 (chr. 1), four SNPs mapping to CHRNA5 (rs503464, rs55853698, rs55781567 and rs16969968 on chr. 15q25), and rs2236196 mapping in CHRNA4 (chr. 20q13). Pyrosequencing was performed on a PSQ96MA system (Biotage, Uppsala, Sweden) running PyroMark Q96 ID Software (Qiagen). Additionally, a 22-bp insertion/deletion (ins/del, rs3841324), 71 bp upstream of the CHRNA5 transcription start site, was genotyped by 3% agarose gel electrophoresis.

Pintarelli G., Galvan A., Pozzi P., Noci S., Pasetti G., Sala F., Pastorino U., Boffi R, & Colombo F. (2017). Pharmacogenetic study of seven polymorphisms in three nicotinic acetylcholine receptor subunits in smoking-cessation therapies. Scientific Reports, 7, 16730.

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Pyrosequencing for Allele Fraction Validation

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To validate the presence and allele fraction of the candidate pSNMs detected by our pipeline, pyrosequencing was performed on the genomic DNA obtained from all available samples and family members. The PCR and sequencing primers were designed using PyroMark Assay Design (2.0; Qiagen, Venlo, the Netherlands) and listed in Supplementary information, Table S6. The PCR amplification, product processing and pyrosequencing were performed using the PyroMark Q96 ID System (Qiagen) with the corresponding reagents. The raw data were analyzed using the PyroMark Q96 ID Software (Qiagen) for allele quantification. Pyrosequencing has a detection limit of 5% allele fraction^{35 (link),36 (link)}, and any sites with an alternative signal < 5% were usually considered technical noise. The differences in allele fraction between different samples within the same individuals were assessed using the Euclidean distance of the minor allele fractions for all the validated sites, and the six samples were further clustered using Ward's method.

Huang A.Y., Xu X., Ye A.Y., Wu Q., Yan L., Zhao B., Yang X., He Y., Wang S., Zhang Z., Gu B., Zhao H.Q., Wang M., Gao H., Gao G., Zhang Z., Yang X., Wu X., Zhang Y, & Wei L. (2014). Postzygotic single-nucleotide mosaicisms in whole-genome sequences of clinically unremarkable individuals. Cell Research, 24(11), 1311-1327.

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Genetic Mutation Analysis in FAP

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FAP samples were tested for mutations in BRAF (1799) and KRAS (34, 35, 37, and 38) by pyrosequencing using PyroMark Gold Q96 reagents (Qiagen) and a PyroMark Q96 ID instrument, as previously reported [39 (link)] (Figure 3B). Primer sequences are described in Supplementary Table 2. Pyrogram outputs were analyzed with PyroMark Q96 ID Software (Qiagen) using the allele quantification mode. The cut-off value for positive results of mutations was set at 20% on the sequencer and was based on the tumor cell content (≥40%).

Takane K., Fukuyo M., Matsusaka K., Ota S., Rahmutulla B., Matsushita K., Miyauchi H., Nakatani Y., Matsubara H, & Kaneda A. (2018). The frequency of promoter DNA hypermethylation is decreased in colorectal neoplasms of familial adenomatous polyposis. Oncotarget, 9(66), 32653-32666.

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Epigenetic Regulation of Hippocampal Genes

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The genomic DNA of the hippocampus was extracted using the TIANamp Genomic DNA Kit (TIANGEN BIOTECH, China). Genomic DNA bisulfite conversion was performed using the EpiTeck Bisulfite Kit (QIANGEN), which was ready for bisulfite sequencing PCR (BSP) analysis. The primers of IL-6, IL-1β, TNF-α, and BDNF were designed using PyroMark Assay Design 2.0 (BGI, China). The target promoter sequences of IL-6, IL-1β, TNF- α, and BDNF were amplified from the converted DNA performed through touch-down PCR, and then the purified PCR products were cloned into pMD-18 T vector (Takara, China) for sequencing. Pyrosequencing was performed using PyroMark Q96 ID software (QIAGEN), and the CpG Island level was analyzed automatically.

Yang Y., Yang T., Zhou J., Cao Z., Liao Z., Zhao Y., Su X., He J, & Hua J. (2022). Prenatal exposure to concentrated ambient PM2.5 results in spatial memory defects regulated by DNA methylation in male mice offspring. Environmental Science and Pollution Research International, 30(12), 35142-35152.

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Validation of Promoter Methylation in GBC-OSCC

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The promoter methylations of HOXB13, GLDC, and FAT1 were validated by bisulfite pyrosequencing in an independent 127 GBC-OSCCs and 20 normal samples. In order to cover more CpG sites, we designed two primer sets for each gene targeting CpG locus represented by the 850 K BeadChip. The details of PCR amplification and bisulfite pyrosequencing are given in Additional file 3: Additional informations and Additional file 1: Table S18. The methylation percentages for each CpG locus in controls and GBC-OSCC cases were calculated by the PyroMark Q96ID Software (Qiagen).

Inchanalkar M., Srivatsa S., Ambatipudi S., Bhosale P.G., Patil A., Schäffer A.A., Beerenwinkel N, & Mahimkar M.B. (2023). Genome-wide DNA methylation profiling of HPV-negative leukoplakia and gingivobuccal complex cancers. Clinical Epigenetics, 15, 93.

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