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Characterization of the micro-substructure of a rural population from the Pyrenees from a geodesic and technical point of view using NGS data : Quantification of batch effects in whole genome sequence data

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dc.contributor.author Maceda Porto, Iago, 1986-
dc.contributor.other Lao Grueso, Oscar, 1976-
dc.contributor.other Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut
dc.date.accessioned 2022-04-29T01:30:32Z
dc.date.available 2022-04-29T01:30:32Z
dc.date.issued 2021-04-28
dc.identifier http://hdl.handle.net/10803/671600
dc.identifier.uri http://hdl.handle.net/10230/47405
dc.description.abstract In this work we present a new whole genome sequencing dataset with samples gathered from the Spanish Eastern Pyrenees (SEP) with more than 40x coverage. We apply both classical and new methods to unveil their particular demographic histories and we present the use of a newly in-house developed algorithm to detect genetic barriers taking into account the use of geo-statistics. With these analyses we detect fine population substructure for the first time in this region. We also report the presence of an important batch effect in one of the most important datasets used in genomics: the 1,000 Genomes Project. We find this batch effect when considering very low frequency variants, such as loss of function mutations and the amount of singletons (both ancestral and derived) detected in each sample.
dc.description.abstract En aquest treball presentem un nou dataset de whole genome sequencing amb mostres recollides del Pirineu Oriental espanyol (SEP) amb un coverage superior a 40x. Apliquem mètodes clàssics i nous per descobrir les seves particulars històries demogràfiques i presentem l’ús d’un algorisme desenvolupat recentment en el nostre laboratori per detectar barreres genètiques tenint en compte l’ús de geoestadística. Amb aquestes anàlisis detectem, per primera vegada, una delicada subestructura de poblacions en aquesta regió. També informem de la presència d’un important batch effect en un dels datasets més importants utilitzats en genòmica: the 1.000 Genomes Project. Trobem aquest batch effect quan considerem variants rares, com per exemple mutacions que comporten pèrdua de funció i la quantitat de singletons (tant ancestrals com derivats) detectats en cada mostra.
dc.format application/pdf
dc.format 217 p.
dc.language.iso eng
dc.rights L'accés als continguts d'aquesta tesi queda condicionat a l'acceptació de les condicions d'ús establertes per la següent llicència Creative Commons:http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights info:eu-repo/semantics/openAccess
dc.source TDX (Tesis Doctorals en Xarxa)
dc.title Characterization of the micro-substructure of a rural population from the Pyrenees from a geodesic and technical point of view using NGS data : Quantification of batch effects in whole genome sequence data
dc.type info:eu-repo/semantics/doctoralThesis
dc.type info:eu-repo/semantics/publishedVersion
dc.date.modified 2022-04-28T00:00:28Z
dc.subject.keyword Population genomics
dc.subject.keyword Rural areas
dc.subject.keyword Whole-genome sequencing
dc.subject.keyword Batch effect
dc.subject.keyword Genòmica de poblacións
dc.subject.keyword Zones rurals
dc.subject.keyword 1,000 Genomes project
dc.subject.keyword 575


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