massarray® genotyping data  (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 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: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Population, genetic, and antigenic diversity of the apicomplexan Eimeria tenella and their relevance to vaccine development

doi: 10.1073/pnas.1506468112

Figure Lengend Snippet: Table 1.

Article Snippet: Returning to the Sequenom MassARRAY genotyping data, we found 46% of all samples submitted for typing to be polyclonal as determined by a multiple SNP identity at one or more loci.

Techniques: Genome Wide