SUPR
Final haplotype assignment of the functional SNP for fatty-acids metabolism
Dnr:

sens2018598

Type:

SNIC SENS

Principal Investigator:

Stefan Enroth

Affiliation:

Uppsala universitet

Start Date:

2018-10-15

End Date:

2025-04-01

Primary Classification:

30107: Medical Genetics

Webpage:

Allocation

  • Castor /proj/nobackup at UPPMAX: 1000 GiB
  • Castor /proj at UPPMAX: 1000 GiB
  • Cygnus /proj/nobackup at UPPMAX: 1000 GiB
  • Cygnus /proj at UPPMAX: 1000 GiB
  • Bianca at UPPMAX: 1 x 1000 core-h/month

Abstract

I propose to apply targeted sequencing using the Pacific Biosciences instrumentation completely resolving the individual sequences over the repetitive region (Alu-repeat) harbouring rs174557 in the whole HGDP-panel consisting of 1050 individuals and additional individuals from the arctic region. This will complement the functional data with worldwide frequencies and provide the necessary data for evaluating the evolutionary history of the repeat in relation to the FADS-region and finally tie the functional SNP to the known haplotype structures in the region. The amplified region covers the entire Alu-repeat and anchored on each side in non-repetitive regions encompassing two A/D haplotype-tag SNPs, rs174556 and rs174560. rs174556 was also one of the SNPs reported by Fumagalli et al as positively selected in the Inuites. The core region to be sequenced consists of ~3.5kb and has over 100 reported SNPs in public databases. This will allow us to not only to completely resolve the linkage of rs174557 to the A/D haplotypes but also to address questions pertaining to the evolutionary history of the Alu-repeat overall and in particular in relation to the A/D haplotypes.