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Página principal > Artículos > Artículos publicados > Assessment of kinship detection using RNA-seq data |
Fecha: | 2019 |
Resumen: | Analysis of RNA sequencing (RNA-seq) data from related individuals is widely used in clinical and molecular genetics studies. Prediction of kinship from RNA-seq data would be useful for confirming the expected relationships in family based studies and for highlighting samples from related individuals in case-control or population based studies. Currently, reconstruction of pedigrees is largely based on SNPs or microsatellites, obtained from genotyping arrays, whole genome sequencing and whole exome sequencing. Potential problems with using RNA-seq data for kinship detection are the low proportion of the genome that it covers, the highly skewed coverage of exons of different genes depending on expression level and allele-specific expression. In this study we assess the use of RNA-seq data to detect kinship between individuals, through pairwise identity by descent (IBD) estimates. First, we obtained high quality SNPs after successive filters to minimize the effects due to allelic imbalance as well as errors in sequencing, mapping and genotyping. Then, we used these SNPs to calculate pairwise IBD estimates. By analysing both real and simulated RNA-seq data we show that it is possible to identify up to second degree relationships using RNA-seq data of even low to moderate sequencing depth. |
Ayudas: | Ministerio de Economía y Competitividad BFU2015-70581 Ministerio de Economía y Competitividad ADE10-00026 Agència de Gestió d'Ajuts Universitaris i de Recerca 2017SGR1262 Agència de Gestió d'Ajuts Universitaris i de Recerca 2017SGR529 |
Nota: | Altres ajuts: Research at the IJC was supported by the 'La Caixa' Foundation, the Fundació Internacional Josep Carreras and Celgene Spain. Funding for open access charge: Catalan Agency for Management of University and Research Grants. |
Derechos: | Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original. |
Lengua: | Anglès |
Documento: | Article ; recerca ; Versió publicada |
Materia: | Base Sequence ; Databases ; Genome ; Humans ; Pedigree ; Polymorphism, Single Nucleotide genetics ; RNA ; Sequence Analysis |
Publicado en: | Nucleic acids research, Vol. 47 (september 2019) , p. e136, ISSN 1362-4962 |
9 p, 3.1 MB |