We used two reference panels: (1) the public 1000 Genomes Project Phase 3 haplotypes, version 20130502, (1KGP) (Sudmant et al. 2015 (link)); and (2) The EPIGEN-5M+1KGP reference panel, which is the merge of the 1KGP panel and our unpublished EPIGEN-5M panel, bearing 14,970 more SNPs than the public panel solely. The EPIGEN-5M data set was genotyped with the Illumina HumanOmni5-4v1 array. After quality control, the data set comprises 4,102,271 SNPs for 265 Brazilians from the three cohorts (90, 88, and 87 individuals from Salvador, Bambuí, and Pelotas, respectively) (Supplemental Table S2 ). We used SHAPEIT2 (Delaneau et al. 2013 (link)) to infer the chromosome phase of the EPIGEN-5M data set (Supplemental Tables S4–S8 ).
Protocol detail
Constructing a Comprehensive Brazilian Genetic Reference Panel
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 :
Other organizations : Universidade Federal de Minas Gerais, Instituto de Ensino e Pesquisa Santa Casa, Fundação Oswaldo Cruz, Universidade Federal da Bahia, Instituto de Saúde, Universidade Federal de Pelotas, Universidade de São Paulo, Brazilian Society of Computational and Applied Mathematics
Top 5 similar protocols
Protocol cited in 4 other protocols
Variable analysis
independent variables
- The public 1000 Genomes Project Phase 3 haplotypes, version 20130502, (1KGP)
- The EPIGEN-5M+1KGP reference panel, which is the merge of the 1KGP panel and the unpublished EPIGEN-5M panel
- The chromosome phase of the EPIGEN-5M data set
- The 4,102,271 SNPs for 265 Brazilians from the three cohorts (90, 88, and 87 individuals from Salvador, Bambuí, and Pelotas, respectively)
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!