genotype data from sequenom massarray (iplex)  (Sequenom)

Journal: PLoS ONE

Article Title: SNPflow: A Lightweight Application for the Processing, Storing and Automatic Quality Checking of Genotyping Assays

doi: 10.1371/journal.pone.0059508

Figure Lengend Snippet: This figure shows the 4 steps of the SNPflow data analysis wizard. In brief, the first step allows the uploading of either SDS files (ABI 7900HT) or TyperAnalyzer 4.0 (MassARRAY) files. For TyperAnalyzer files, a second input field asks for the name of the result group under which results shall be grouped. The second step checks the validity of the IDs found in the uploaded and reports IDs, which are not found in the study definition and shall thus be deleted. Step 3 converts the found genotype designations to standard genotypes and allows entering the name of the result, the operator name, an optional comment and the rs-number of the SNP in HapMap and the 1000 Genomes Project. This is useful in case that a SNP ID changed between the current dbSNP release and the dbSNP release used in HapMap, as happened for some SNPs. For convenience, the result name is automatically pre-set as HapMap lookup. In multiplex assays, pagination allows navigating through the single SNPs. For quality reasons a manual confirmation of each conversion is required (Checkbox “All settings are correct”). Finally, step 4 confirms the successful analysis and brings the user to the report. Exemplary abbreviation used in this figure: NTC, Non-template control; ER, annulled samples (“error”), i.e. DNA samples present on the plates, but known to be flawed. The IDs of these samples were thus replaced with “ER” in order to avoid data collection for these samples.

Article Snippet: SNPflow is a lightweight, intuitive and easily deployable application, which processes genotype data from Sequenom MassARRAY (iPLEX) and ABI 7900HT (TaqMan, KASPar) systems and is extendible to other genotyping methods as well.

Techniques: Multiplex Assay

Journal: BMC Oral Health

Article Title: Family and case–control genetic study of MSX1 polymorphisms in peg-shaped teeth Jordanian population

doi: 10.1186/s12903-022-02051-2

Figure Lengend Snippet: The basic information of the selected SNPs in this study

Article Snippet: The haplotype program revealed that one SNP (rs6446693) out of the six SNPs from Sequenom Massarray data was not associated with peg-shaped teeth.

Techniques: Variant Assay

Journal: BMC Oral Health

Article Title: Family and case–control genetic study of MSX1 polymorphisms in peg-shaped teeth Jordanian population

doi: 10.1186/s12903-022-02051-2

Figure Lengend Snippet: The MSX1 SNPs with their minor allele frequencies and HWE P -values for cases and controls at each locus based on the (36) families

Article Snippet: The haplotype program revealed that one SNP (rs6446693) out of the six SNPs from Sequenom Massarray data was not associated with peg-shaped teeth.

Techniques:

Journal: BMC Oral Health

Article Title: Family and case–control genetic study of MSX1 polymorphisms in peg-shaped teeth Jordanian population

doi: 10.1186/s12903-022-02051-2

Figure Lengend Snippet: Haploview plot of linkage disequilibrium (r 2 ) between (rs8670, rs12532, and rs4464513) within MSX1 located on chromosome 4p16.2 represent SNP-SNP relationship. A black diamond without a number represents complete linkage disequilibrium between SNPs (r 2 = 1)

Article Snippet: The haplotype program revealed that one SNP (rs6446693) out of the six SNPs from Sequenom Massarray data was not associated with peg-shaped teeth.

Techniques:

Journal: Journal of Southern Medical University

Article Title: 焦磷酸测序和MassARRAY定量检测DNA甲基化在年龄推断中的差异

doi: 10.12122/j.issn.1673-4254.2020.12.21

Figure Lengend Snippet: 基于65样本集的MassARRAY和焦磷酸测序两种方法的相关性分析 Correlation analysis of MassARRAY and pyrosequencing based on 65 samples

Article Snippet: A , B : Plots based on data without Z-score transformation typed from MassARRAY and pyrosequencing., : Plots based on data after Z-score transformation typed from MassARRAY and pyrosequencing.

Techniques:

Journal: Journal of Southern Medical University

Article Title: 焦磷酸测序和MassARRAY定量检测DNA甲基化在年龄推断中的差异

doi: 10.12122/j.issn.1673-4254.2020.12.21

Figure Lengend Snippet: 基于62样本集的MassARRAY和焦磷酸测序两种方法的相关性分析 Correlation analysis of MassARRAY and pyrosequencing based on 62 samples

Article Snippet: A , B : Plots based on data without Z-score transformation typed from MassARRAY and pyrosequencing., : Plots based on data after Z-score transformation typed from MassARRAY and pyrosequencing.

Techniques:

Journal: Wellcome Open Research

Article Title: Interferon-gamma polymorphisms and risk of iron deficiency and anaemia in Gambian children

doi: 10.12688/wellcomeopenres.15750.2

Figure Lengend Snippet: The IFNG single nucleotide polymorphisms (SNP) are designated according to the nucleotide position relative to the transcriptional starting site of IFNG .

Article Snippet: Agena Biosciences (formerly SEQUENOM) MassARRAY ® primer-extension definitions data for the five IFNG polymorphisms Extended datafile 3.

Techniques:

Journal: BMC Plant Biology

Article Title: Genetic identification of SNP markers linked to a new grape phylloxera resistant locus in Vitis cinerea for marker-assisted selection

doi: 10.1186/s12870-018-1590-0

Figure Lengend Snippet: Validation of 42 SNPs at the RDV2 locus

Article Snippet: A comparison of the genotype data from Sequenom MassARRAY and the TASSEL SNP calling pipeline was performed to validate SNPs.

Techniques:

Journal: BMC Plant Biology

Article Title: Genetic identification of SNP markers linked to a new grape phylloxera resistant locus in Vitis cinerea for marker-assisted selection

doi: 10.1186/s12870-018-1590-0

Figure Lengend Snippet: Genotyping errors detected in F 1 individuals after Sequenom MassARRAY genotyping

Article Snippet: A comparison of the genotype data from Sequenom MassARRAY and the TASSEL SNP calling pipeline was performed to validate SNPs.

Techniques:

Journal: Nucleic Acids Research

Article Title: A primary role of TET proteins in establishment and maintenance of De Novo bivalency at CpG islands

doi: 10.1093/nar/gkw529

Figure Lengend Snippet: TET2 overexpression induces DNA demethylation of hypermethylated CGIs. ( A ) Western blot analysis of TET2 expression in Mock, TET2-WT and TET2-Mut 293T cells. β-Actin was used as loading control. ( B–C ) Total 5hmC (B) and 5mC (C) in Mock, TET2-WT and TET2-Mut 293T cells were detected by mass spectrometry. Data are presented as mean ± SD (n = 3). * P < 0.05. ( D–E ) Number of peaks in whole genome and CGIs gaining 5hmC (left) or losing 5mC (right) in 293T cells overexpressing TET2-WT. ( F ) hMeDIP-qPCR analysis for 5hmC at four representative hypermethylated CGI promoters. The ID1 CGI promoter was used as a negative control. Data are presented as mean ± SD (n = 3). * P < 0.05. ( G ) Representative data of Sequenom MassARRAY analysis of ‘5mC + 5hmC’ at CpG sites within four representative hypermethylated CGI promoters. The ID1 CGI promoter was used as a negative control.

Article Snippet: Sequenom MassARRAY data showed a significant decrease in the percentage of ‘5mC + 5hmC’ within these CGIs in TET2-WT but not TET2-Mut 293T cells (Figure ).

Techniques: Over Expression, Western Blot, Expressing, Control, Mass Spectrometry, Negative Control