In silico prædiktion af skizofrenirelaterede varianter: In silico prediction of schizophrenia related variants

Camilla Schütt Nielsen, Mathias Mørup-Lendal, Mikkel Garly Hansen & Sebastian Niemeier

Studenteropgave: Semesterprojekt

Abstrakt

Background: Schizophrenia is a severe and lifelong mental disorder caused by genetic and environmental components as well as interaction between the two. Genomewide association studies (GWAS) have successfully associated a large number of genetics variants, known as single nucleotide polymorphisms (SNPs), with schizophrenia. The associated SNPs are likely a part of a larger region of linkage disequilibrium and further analysis is therefore necessary to identify and predict putative functional SNPs. Method: In this study we perform an in silico prediction of schizophrenia-related variants. We base our analysis on reported schizophrenia-associated SNPs from GWAS with a p-value of 10-8 or lower. Information from web-based genomic databases is used to identify genetically linked SNPs (proxySNPs) and investigate their regulatory and transla-tional features. The identification of proxySNPs is based on R2 values (LD-measure) of at least 0.8 (SNAP) and the examined regulatory and translational features of interest include eQTL, TF-binding sites, sequence motifs, DNase peaks and –footprints (RegulomeDB) as well as missense/nonsense mutations (UCSC genome browser). Subsequently the SNPs of interest and their genomic origin are further studied in relation to schizophrenia. Results: Initially 56 leadSNPs was mapped which lead to identification of 2012 proxySNPs. These proxySNPs was by means of regulatory or translational characteristics reduced to a total of 8 putative functional SNPs. Conclusion: The SNPs of most interest were rs200981, rs33932084, rs34788973 and rs61742093 which based on our study are predicted to be of functional importance in the development of schizophrenia.

UddannelserMedicinalbiologi, (Bachelor/kandidatuddannelse) Bachelor el. kandidat
SprogDansk
Udgivelsesdato19 jun. 2014
VejledereThomas Hempel Sparsø

Emneord

  • GWAS
  • Schizophrenia
  • SNPs
  • Genetics