The Pro12Ala single nucleotide polymorphism in the study participants was genotyped at the Broad Institute (Cambridge, Massachusetts) using the Affymetrix GeneChip SNP Array 6.0® and the Birdseed calling algorithm17 (link). These data were extensively quality-controlled according to accepted standards18 (link), including checks for genetic outliers via average identity-by-state statistics and EIGENSTRAT-generated principal components19 (link). The Pro12Ala (rs1801282) variant was directly measured; we imputed the genotypes for missing values (≤5% of the sample) by exploiting a scaffold containing all variants with ethnic-specific missing rates ≤0.05, minor allele frequencies≥0.01, and Hardy-Weinberg Equilibrium tests >10−5. After pre-phasing with ShapeIt (v1.r532), we employed IMPUTE2 and the 1,000 Genomes haplotypes-Phase I integrated variant set release (v3) reference panel (NCBI Build 37) to impute the missing genotypes20 (link), 21 (link).
Protocol detail
Genotyping and Imputation of the Pro12Ala Variant
Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link:
Access Free Full Text.
Corresponding Organization : General Department of Preventive Medicine
Other organizations : University of Mississippi Medical Center, Johns Hopkins University, The University of Texas Health Science Center at Houston, British Geriatrics Society
Top 5 similar protocols
Variable analysis
independent variables
- Pro12Ala single nucleotide polymorphism
- Not explicitly mentioned
- Genetic outliers via average identity-by-state statistics and EIGENSTRAT-generated principal components
- Ethnic-specific missing rates ≤0.05, minor allele frequencies≥0.01, and Hardy-Weinberg Equilibrium tests >10^-5
Annotations
Based on most similar protocols
Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.
Sign up for free or login to display all annotations
As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!