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genotype data  (Perlegen Sciences)

 
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    Perlegen Sciences genotype data
    Genotype Data, supplied by Perlegen Sciences, 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/massarray%C2%AE+genotyping+data/genotype+data/pmc02880976-136-2-10
    Average 90 stars, based on 1 article reviews
    genotype data - by Bioz Stars, 2026-10
    90/100 stars

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    Article Title: Predicting functionally important SNP classes based on negative selection
    Article Snippet: As a source for the allele frequencies, we use the publicly available genotype data from the Perlegen project populations--African Americans (AFR), European Americans (EUR), and Han Chinese from the Los Angeles area (CHN) [ ].

    Article Title: SNPs in PTGS2 and LTA Predict Pain and Quality of Life in Long Term Lung Cancer Survivors
    Article Snippet: To accomplish this, genotype data from the HapMap consortium, Seattle SNPs, Perlegen Sciences, and Panel 2 of the National Institute for Environmental Health Sciences were analyzed with ldSelect to bin SNPs with European American MAF >0.05 at a pairwise linkage disequilibrium (LD) threshold of r 2 ≥ 0.8.

    Article Title: A survey of airway responsiveness in 36 inbred mouse strains facilitates gene mapping studies and identification of quantitative trait loci
    Article Snippet: We obtained genotype data consisting of 70,000 SNPs from the Broad Institute, Perlegen, GNF, Oxford, and Merck, selecting SNPs that were highly polymorphic and that were located approximately 40,000 base pairs apart.

    Article Title: Ensembl variation resources
    Article Snippet: For example, in release 56 Ensembl has genotype data for 8335 individuals from a number of reference data sets including the HapMap [ ], Perlegen [ ] and the 1000 Genomes Project [ ].

    Article Title: Evaluation of 6 candidate genes on chromosome 11q23 for coeliac disease susceptibility: a case control study
    Article Snippet: For these, genotype data were downloaded from the NCBI and Perlegen databases and gametic phase was assigned.

    Article Title: IMPROVING POPULATION-SPECIFIC ALLELE FREQUENCY ESTIMATES BY ADAPTING SUPPLEMENTAL DATA: AN EMPIRICAL BAYES APPROACH
    Article Snippet: In this section we examine the performance of the empirical Bayes estimates using genotype data collected from the International HapMap Project [ International HapMap Consortium (2005) ] and by the Perlegen Sciences [ Hinds et al. (2005) ].

    Selection:

    Article Title: Highly Punctuated Patterns of Population Structure on the X Chromosome and Implications for African Evolutionary History
    Article Snippet: .. Conclusions By analyzing genotype data from both the International HapMap Project and Perlegen Biosciences, we discovered a punctuated distribution of population differentiation on the human X chromosome, and additional analyses suggest that patterns of X-linked variation are mediated in bulk by neutral forces such as genetic drift, but in the extremes by natural selection. ..

    Article Title: Highly Punctuated Patterns of Population Structure on the X Chromosome and Implications for African Evolutionary History
    Article Snippet: .. By analyzing genotype data from both the International HapMap Project and Perlegen Biosciences, we discovered a punctuated distribution of population differentiation on the human X chromosome, and additional analyses suggest that patterns of X-linked variation are mediated in bulk by neutral forces such as genetic drift, but in the extremes by natural selection. ..



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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.

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    Validation of 42 SNPs at the RDV2 locus

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    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.

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    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.

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    Table 1.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

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    Figure Lengend Snippet: Table 1.

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