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
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 algor...
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| Tipo de recurso: | tesis doctoral |
| Estado: | Versión publicada |
| Fecha de publicación: | 2021 |
| País: | España |
| Institución: | CBUC, CESCA |
| Repositorio: | TDR. Tesis Doctorales en Red |
| OAI Identifier: | oai:www.tdx.cat:10803/671600 |
| Acceso en línea: | http://hdl.handle.net/10803/671600 |
| Access Level: | acceso abierto |
| Palabra clave: | Population genomics Rural areas Whole-genome sequencing Batch effect Genòmica de poblacións Zones rurals 1,000 Genomes project 575 |
| Sumario: | 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. |
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