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Tesi etd-08102009-152716

Thesis type
Tesi di laurea specialistica
Characterization, through re-sequencing, of genetic variants associated with high altitude adaptation in North Caucasian ethnic groups.
Corso di studi
relatore Prof. Paoli, Giorgio
correlatore Dott. Tyler-Smith, Chris
correlatore Dott. Bulayeva, Kazima
controrelatore Prof. Landi, Stefano
correlatore Dott. Tofanelli, Sergio
Parole chiave
  • Laks
  • Perl
  • non synonymous SNP
  • HIF1
  • EPOr
  • ACE
  • NOS3
  • Haemoglobin
  • Avars
  • Kubachians
  • candidate gene
  • Encode
  • HapMap
  • Illumina
  • Solexa
  • allignment
  • MAQ
  • positive selection
  • environmental stress
  • neutral region
  • Sanger
  • resequencing
  • daghestan
  • high altitude
Data inizio appello
Data di rilascio
Riassunto analitico
The proposed Master Thesis refers to the results of the research work carried out at the Wellcome Trust Sanger Institute, Hinxton, UK, under the direct supervision of Dr. Chris Tyler-Smith, Head of the Human Evolution Team.
The aim of the study is to ascertain signals of positive selection in human populations living at high altitude using targeted next-generation DNA re-sequencing of candidate genes and control regions in 96 individuals. For this purpose 55 Daghestani from three ethnic groups were selected as case populations living at high altitudes (>2,000 msl). Adygei (n = 20), CEU (n = 20) and 1 chimpanzee sample were used as controls.
The Daghestani populations have a long history of permanence (>10.000 years) at high altitudes and their peculiar demographic history make them suitable for hypoxia adaptation studies. In order to disentangle selective and demographic effects on the genome, fifteen candidate genes involved in oxygen metabolism (HIF1α; PHD1; PHD2; PHD3; VHL; EPO; EPOr; VEGF; EDN1; NOS3; ACE; α,β,γ,δ-Hb) were sequenced together with twenty-seven “control regions” selected among those used in the Hominid Project (Wall, Cox et al. 2008) and the ENCODE3 Project

DNA samples obtained from whole blood or cell cultures were used to amplify the targeted genomic regions by long-template PCR. The amplimers were visualized by gel electrophoresis and those belonging to the same individuals were pooled together and subsequently purifiedusing the QIAquick PCR Purification Kit. Each pooled sample was indexed by adding an eight nucleotides tag, and 8 samples were combined and sequenced on each lane of an Illumina flow-cel. The sequenced DNA was sorted and aligned to the reference sequence using the MAQ algorithm (Li, Ruan et al. 2008). Parameters checking the goodness of the sequencing outputs as well as summary statistics and neutrality tests (Tajima’s D, Fu and Li’s D and F, Fay and Wu’s H) were calculated on “PHASED” haplotype data. Candidate targets of positive selection (re-sequenced genes) and neutral regions were analyzed for putative signals of adaptation to hypoxia and several novel SNPs characterized. Particularly, four non synonymous mutations were found responsible for altering the functionality of HIF1α, ACE, EPOr and NOS3 and could be considered as putative candidate for hypoxia adaptation.