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Analysis of qualitative and quantitative expressed traits in the Sardinian population using Next Generation Sequencing

Pala, Mauro (2014) Analysis of qualitative and quantitative expressed traits in the Sardinian population using Next Generation Sequencing. Doctoral Thesis.

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Genome Wide Association Studies (GWAS) have revolutionized the genetic analysis of complex traits but the functional consequences of most of the over one thousand detected genetic associations remain unknown. Whole transcriptome sequencing followed by expression quantitative trait loci (eQTL) analysis represents a powerful tool to help overcome, this limitation by systematically assessing the impact of the associated variants on gene expression. Accordingly, different large-scale transcriptome efforts have been conducted in the last few years to define a catalog of variants affecting gene expression. The vast majority of these studies focused on the PolyA(+) fractions of the RNA which may provide more robust data but also miss transcript that lack the polyA tail. In this thesis, we performed a pilot study sequencing the transcriptome using both PolyA(+) selection and whole transcriptome rRNA-depletion libraries in 68 individuals to compare these two protocols in the context of an eQTL study. All the individuals were enrolled in the SardiNIA longitudinal project and were already sequenced at the genomic level and phenotyped for over 500 quantitative variables. We mapped genomic variances associated with the expression levels of protein coding genes, long non-coding RNAs, splice site and isoforms ratios. The PolyA(+) selection resulted in a greater number of discoveries and was hence adopted for the transcriptome characterization of a larger dataset (608 individuals).

Item Type:Doctoral Thesis
ID Code:9458
Contributors:Cucca, Francesco
Publisher:Università degli studi di Sassari
Uncontrolled Keywords:EQTL, RNA-seq, CountSeq, COViewer, Splicing, Sardinia
Subjects:Area 06 - Scienze mediche > MED/03 Genetica medica
Divisions:001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Scienze Biomediche
Cicli, scuole e corsi:Ciclo 26 > Scienze biomediche > Genetica medica, Malattie metaboliche e Nutrigenomica
Deposited On:02 Apr 2014 08:19

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