Cargando…
Whole-Exome Sequencing in the Isolated Populations of Cilento from South Italy
The present study describes the genetic architecture of the isolated populations of Cilento, through the analysis of exome sequence data of 245 representative individuals of these populations. By annotating the exome variants and cataloguing them according to their frequency and functional effects,...
Autores principales: | , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6411969/ https://www.ncbi.nlm.nih.gov/pubmed/30858532 http://dx.doi.org/10.1038/s41598-019-41022-6 |
_version_ | 1783402494799380480 |
---|---|
author | Nutile, T. Ruggiero, D. Herzig, A. F. Tirozzi, A. Nappo, S. Sorice, R. Marangio, F. Bellenguez, C. Leutenegger, A. L. Ciullo, M. |
author_facet | Nutile, T. Ruggiero, D. Herzig, A. F. Tirozzi, A. Nappo, S. Sorice, R. Marangio, F. Bellenguez, C. Leutenegger, A. L. Ciullo, M. |
author_sort | Nutile, T. |
collection | PubMed |
description | The present study describes the genetic architecture of the isolated populations of Cilento, through the analysis of exome sequence data of 245 representative individuals of these populations. By annotating the exome variants and cataloguing them according to their frequency and functional effects, we identified 347,684 variants, 67.4% of which are rare and low frequency variants, and 1% of them (corresponding to 319 variants per person) are classified as high functional impact variants; also, 39,946 (11.5% of the total) are novel variants, for which we determined a significant enrichment for deleterious effects. By comparing the allele frequencies in Cilento with those from the Tuscan population from the 1000 Genomes Project Phase 3, we highlighted an increase in allele frequency in Cilento especially for variants which map to genes involved in extracellular matrix formation and organization. Furthermore, among the variants showing increased frequency we identified several known rare disease-causing variants. By different population genetics analyses, we corroborated the status of the Cilento populations as genetic isolates. Finally, we showed that exome data of Cilento represents a useful local reference panel capable of improving the accuracy of genetic imputation, thus adding power to genetic studies of human traits in these populations. |
format | Online Article Text |
id | pubmed-6411969 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-64119692019-03-13 Whole-Exome Sequencing in the Isolated Populations of Cilento from South Italy Nutile, T. Ruggiero, D. Herzig, A. F. Tirozzi, A. Nappo, S. Sorice, R. Marangio, F. Bellenguez, C. Leutenegger, A. L. Ciullo, M. Sci Rep Article The present study describes the genetic architecture of the isolated populations of Cilento, through the analysis of exome sequence data of 245 representative individuals of these populations. By annotating the exome variants and cataloguing them according to their frequency and functional effects, we identified 347,684 variants, 67.4% of which are rare and low frequency variants, and 1% of them (corresponding to 319 variants per person) are classified as high functional impact variants; also, 39,946 (11.5% of the total) are novel variants, for which we determined a significant enrichment for deleterious effects. By comparing the allele frequencies in Cilento with those from the Tuscan population from the 1000 Genomes Project Phase 3, we highlighted an increase in allele frequency in Cilento especially for variants which map to genes involved in extracellular matrix formation and organization. Furthermore, among the variants showing increased frequency we identified several known rare disease-causing variants. By different population genetics analyses, we corroborated the status of the Cilento populations as genetic isolates. Finally, we showed that exome data of Cilento represents a useful local reference panel capable of improving the accuracy of genetic imputation, thus adding power to genetic studies of human traits in these populations. Nature Publishing Group UK 2019-03-11 /pmc/articles/PMC6411969/ /pubmed/30858532 http://dx.doi.org/10.1038/s41598-019-41022-6 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Nutile, T. Ruggiero, D. Herzig, A. F. Tirozzi, A. Nappo, S. Sorice, R. Marangio, F. Bellenguez, C. Leutenegger, A. L. Ciullo, M. Whole-Exome Sequencing in the Isolated Populations of Cilento from South Italy |
title | Whole-Exome Sequencing in the Isolated Populations of Cilento from South Italy |
title_full | Whole-Exome Sequencing in the Isolated Populations of Cilento from South Italy |
title_fullStr | Whole-Exome Sequencing in the Isolated Populations of Cilento from South Italy |
title_full_unstemmed | Whole-Exome Sequencing in the Isolated Populations of Cilento from South Italy |
title_short | Whole-Exome Sequencing in the Isolated Populations of Cilento from South Italy |
title_sort | whole-exome sequencing in the isolated populations of cilento from south italy |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6411969/ https://www.ncbi.nlm.nih.gov/pubmed/30858532 http://dx.doi.org/10.1038/s41598-019-41022-6 |
work_keys_str_mv | AT nutilet wholeexomesequencingintheisolatedpopulationsofcilentofromsouthitaly AT ruggierod wholeexomesequencingintheisolatedpopulationsofcilentofromsouthitaly AT herzigaf wholeexomesequencingintheisolatedpopulationsofcilentofromsouthitaly AT tirozzia wholeexomesequencingintheisolatedpopulationsofcilentofromsouthitaly AT nappos wholeexomesequencingintheisolatedpopulationsofcilentofromsouthitaly AT soricer wholeexomesequencingintheisolatedpopulationsofcilentofromsouthitaly AT marangiof wholeexomesequencingintheisolatedpopulationsofcilentofromsouthitaly AT bellenguezc wholeexomesequencingintheisolatedpopulationsofcilentofromsouthitaly AT leuteneggeral wholeexomesequencingintheisolatedpopulationsofcilentofromsouthitaly AT ciullom wholeexomesequencingintheisolatedpopulationsofcilentofromsouthitaly |