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: CNS Neuroscience & Therapeutics

Article Title: BST1 rs4698412 allelic variant increases the risk of gait or balance deficits in patients with Parkinson’s disease

doi: 10.1111/cns.13099

Figure Lengend Snippet: Genotype frequencies for BST1 rs4698412 in PD and HC groups

Article Snippet: The BST1 rs4698412 data were processed and analyzed using MassARRAY TYPER 4.0 software (Agena Bioscience, San Diego, CA, USA) via the Beijing Genomics Institute (BGI).

Techniques:

Journal: CNS Neuroscience & Therapeutics

Article Title: BST1 rs4698412 allelic variant increases the risk of gait or balance deficits in patients with Parkinson’s disease

doi: 10.1111/cns.13099

Figure Lengend Snippet: Groups × genotypes ANCOVA of ALFF. (A) Main effect of diagnostic groups on ALFF in PD and HC was shown in the left cerebellum_8 and cerebellum_9. (B) Interaction between BST1 rs4698412 alleles and diagnostic groups was found in the right lingual gyrus. These findings were obtained via two‐way factorial analysis of covariance (ANCOVA: groups × genotypes; groups: PD and HC, genotypes: GG carriers and GA/AA carriers) adjusting for age, gender, and education years. Thresholds were set at a corrected P < 0.001, determined by Monte Carlo simulation. The color bar indicates the F values from ANCOVA. ALFF, amplitude of low‐frequency fluctuations; PD, Parkinson’s disease; HC, healthy control; BST1, bone marrow stromal cell antigen‐1; R, right; L, left

Article Snippet: The BST1 rs4698412 data were processed and analyzed using MassARRAY TYPER 4.0 software (Agena Bioscience, San Diego, CA, USA) via the Beijing Genomics Institute (BGI).

Techniques: Diagnostic Assay, Control

Journal: CNS Neuroscience & Therapeutics

Article Title: BST1 rs4698412 allelic variant increases the risk of gait or balance deficits in patients with Parkinson’s disease

doi: 10.1111/cns.13099

Figure Lengend Snippet: The interaction of groups (PD or HC) and genotypes (GG or GA/AA) on ALFF values. ***Post hoc tests were corrected by Bonferroni correction with a significant different P < 0.008 (0.05/6 [number of pair‐comparisons]). The ALFF values were decreased in the right lingual gyrus in PD patients with GA/AA carriers compared to GG carriers and increased in HC subjects. ALFF, amplitude of low‐frequency fluctuations; PD, Parkinson’s disease; HC, healthy control; BST1, bone marrow stromal cell antigen‐1

Article Snippet: The BST1 rs4698412 data were processed and analyzed using MassARRAY TYPER 4.0 software (Agena Bioscience, San Diego, CA, USA) via the Beijing Genomics Institute (BGI).

Techniques: Control