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Title: Reconstructing pedigrees using RNA-seq data
Author: Blay Magriñá, Natàlia
Director: Ventura Royo, Carles  
Tutor: Vavouri, Tanya
Keywords: RNA-seq
Issue Date: Jun-2018
Publisher: Universitat Oberta de Catalunya (UOC)
Abstract: The aim of this work is to develop a method to determine and represent kinship relationships between individuals using RNA-seq data. Currently, there are methods to reconstruct pedigrees based on data from genotyping arrays, although there is no effective method based on RNA-seq. Pedigree reconstruction has several applications such as detecting labeling mistakes. The methodology is as follows: (i) perform a quality control of raw data, (ii) map the reads to the reference genome, (iii) filter the mapped reads by eliminating duplicates and multi-mapping reads, (iv) select common SNPs that are not in repeats nor imprinted genes, (v) filter the SNPs in reads and obtain the genotypes, (vi) determine and represent the relationship between pairs of individuals and (vii) represent the whole pedigree. After the selection of filters and their thresholds, a method that allows to discriminate between different kinship relationships and to represent them has been obtained. First-degree relationships (parent-offspring and full siblings) are the most easily detected, while more distant relationships (grandparent-grandchild or uncle-nephew) are more difficult to differentiate from unrelated individuals.
Language: Spanish
Appears in Collections:Bachelor thesis, research projects, etc.

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