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Sequenom sequenom genotyping data
Sequenom Genotyping Data, supplied by Sequenom, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/sequenom+genotype+data/sequenom+genotype+data/pmc02245971-185-9-8
Average 90 stars, based on 1 article reviews
sequenom genotyping data - by Bioz Stars, 2026-09
90/100 stars

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Related Articles

Sequencing:

Article Title: Estimation of allele frequency and association mapping using next-generation sequencing data
Article Snippet: Both the estimates using the ML method and the genotype calling method without filtering are highly correlated with the estimates made from the Sequenom genotype data (i.e., a small standardized difference between the two estimates in Figure ). .. However, estimates based on genotype calling with filtering show poor correspondence to the frequencies estimated from the Sequenom genotype data, especially when sequencing depth is low. .. Interestingly, there is one SNP where the estimated MAF from the resequencing data is very different from the estimate obtained from the Sequenom genotype data, even though the sequencing depth is very high (14×).

Article Title: Estimation of allele frequency and association mapping using next-generation sequencing data
Article Snippet: However, estimates based on genotype calling with filtering show poor correspondence to the frequencies estimated from the Sequenom genotype data, especially when sequencing depth is low. .. Interestingly, there is one SNP where the estimated MAF from the resequencing data is very different from the estimate obtained from the Sequenom genotype data, even though the sequencing depth is very high (14×). .. Specifically, the estimated MAF from the Sequenom genotype data is 22.5%, but is 17.2% when estimated using the ML approach.

other:

Article Title: A prezygotic transmission distorter acting equally in female and male zebra finches Taeniopygia guttata.
Article Snippet: The two parental alleles at a specific locus are usually inherited with equal probability to the offspring.. However, at least three processes can lead to an apparent departure from fair segregation: early viability selection, biased gene conversion and various kinds of segregation distortion.. Here, we conduct a genome-wide scan for transmission distortion in a captive population of zebra finches (Taeniopygia guttata) using 1302 single-nucleotide polymorphisms (SNPs) followed by confirmatory analyses on independent samples from the same population.

Article Title: Monoallelic expression determines oncogenic progression and outcome in benign and malignant brain tumors.
Article Snippet: The authors thank all of the patients and their families who were involved with the study, as well as the Canadian Virtual Brain Tumor Bank and its affiliate members for the adult tumor tissues and also thank staff at TCAG for assistance and advice with themicroarray processing, and staff at AGTC for assistance with processing and analysis of the Sequenom genotype data.

Article Title: Association between in vivo alcohol metabolism and genetic variation in pathways that metabolize the carbon skeleton of ethanol and NADH reoxidation in the Alcohol Challenge Twin Study
Article Snippet: Correction for sex, age, age 2 , sex*age andsex*age 2 was performed by fitting covariates in theregression model. Phenotypes were also adjusted for possible effects ofpopulation stratification in our sample by fitting the first ten eigenvectors(PC1-PC10) from European-only principal components analysis of ancestry in theregression model ( McEvoy et al., 2009 ).Sequenom genotype data and phenotypes were available for 366 twins(40.0% male) from 187 families comprising 77 MZ pairs (42 female and 35male), 102 DZ pairs (37 female, 27 male and 38 opposite sex) and 8 unpaired DZtwins.

Control:

Article Title: ABO blood group associations with markers of endothelial dysfunction in the Multi-Ethnic Study of Atherosclerosis
Article Snippet: Additional genotyping of key functional ABO genetic variants necessary for ABO blood type prediction was conducted using a custom Sequenom (San Diego, CA) panel that included 10 ABO variants as part of a 27 variant panel design, three of which (rs8176746, rs1053878, rs7853989) were previously assayed by the Illumina arrays. .. Quality control for the Sequenom genotype data was based upon sample call rate (>90%), genotype call rate (>85%), and Hardy-Weinberg equilibrium ( p >0.05/40=0.00125; evaluated separately by race/ethnicity and adjusted for multiple testing). ..



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Image Search Results


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.

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

Validation of 42 SNPs at the RDV2 locus

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:

Genotyping errors detected in F 1 individuals after Sequenom  MassARRAY  genotyping

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: