Dataset and Genome Reference:



Gene Name (ex: HBB), Region (ex: 11:5246696-5248301 or chr11:5246696-5248301), Position (ex: 11:5248232 or chr11:5248232) or Variant ID (ex: rs334).
Search HLA variants (SABE-1171-WGS hg38).












ABraOM

Support

Arquivo Brasileiro Online de Mutações

Online Archive of Brazilian Mutations

The ABraOM repository contains genomic variants obtained with whole-exome and whole-genome sequencing from SABE, a census-based sample of elderly individuals from São Paulo, Brazil's largest city. Brazilian population is constituted by ~500 years of admixture between Africans, Europeans, and Native Americans. Additionally, the cohort presents ~3% of individuals with non-admixed Japanese ancestry (early 20th century migration).

The latest dataset, SABE-WGS-1171(hg38), deposited in September 2020, comprehends genomic variants from 1,171 unrelated individuals from SABE cohorts enrolled in 2010-2012. A total of 77,236,632 variants (SNVs and short Insertions/Deletions) were called. From that, a total of 61,174,462 are high confidence variants (flagged as PASS by GATK and not flagged as FDP/FAB/LowCall by our in-house quality control filter CEGH-USP). Over 2,000 variants in HLA class I genes were identified with a separate mapping method and can be searched here. In addition, over 7,000 mobile element insertions (MEIs) were identified, described and can be searched here.

SABE609 (hg19) comprehends exomic variants from 609 individuals from SABE cohorts. A total of 2,382,573 variants were called. From that total, 1,264,224 are high confidence variants (flagged as PASS by GATK and not flagged as FDP/FAB/LowCall by our in-house quality control filter CEGH-USP).

Whole-exome or whole-genome datasets can be chosen within the search engine.

There is an overlap of 574 individuals between the two datasets, therefore refrain from combining allelic frequencies.

Please refer to the about page and to Naslavsky, Yamamoto et al. (2017) for more information on the cohorts, flags, counts and summary statistics.


Terms of Use

For Academic use only. Licensing for commercial use might be available under request and agreement.

Whole-genome sequencing dataset flagship paper is under submission in a peer-review journal. Meanwhile, by using this resource you agree to cite our preprint on BioRXiv:

Naslavsky, Scliar, Yamamoto, et al., 2020. Whole-genome sequencing of 1,171 elderly admixed individuals from the largest Latin American metropolis (São Paulo, Brazil).
https://www.biorxiv.org/content/10.1101/2020.09.15.298026v1

Signed consent forms from all subjects were obtained prior to this publication. No data from any given individual was shared. Collaborations are welcome. Contact us for any further information.


Human Genome and Stem Cell
Research Center - HUG-CELL

The University of Sao Paulo
Rua do Matão - Travessa 13, n. 106
Cidade Universitária, São Paulo, SP
CEP: 05508-090
HUG-CELL Website


Support:

Contact


abraom@ib.usp.br