A bird's-eye view of Italian genomic variation through whole-genome sequencing

The genomic variation of the Italian peninsula populations is currently under characterised: the only Italian whole-genome reference is represented by the Tuscans from the 1000 Genome Project. To address this issue, we sequenced a total of 947 Italian samples from three different geographical areas....

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Bibliographic Details
Published in:European journal of human genetics : EJHG 2020-04, Vol.28 (4), p.435-444
Main Authors: Cocca, Massimiliano, Barbieri, Caterina, Concas, Maria Pina, Robino, Antonietta, Brumat, Marco, Gandin, Ilaria, Trudu, Matteo, Sala, Cinzia Felicita, Vuckovic, Dragana, Girotto, Giorgia, Matullo, Giuseppe, Polasek, Ozren, Kolčić, Ivana, Gasparini, Paolo, Soranzo, Nicole, Toniolo, Daniela, Mezzavilla, Massimo
Format: Article
Language:English
Subjects:
Databases, Genetic
Female
Gene Frequency
Genetic diversity
Genome, Human
Genome-Wide Association Study - methods
Genome-Wide Association Study - standards
Genomes
Humans
Italy
Male
Natural selection
Polymorphism, Genetic
Population - genetics
Population structure
Reference Standards
Selection, Genetic
Whole genome sequencing
Whole Genome Sequencing - methods
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Summary:The genomic variation of the Italian peninsula populations is currently under characterised: the only Italian whole-genome reference is represented by the Tuscans from the 1000 Genome Project. To address this issue, we sequenced a total of 947 Italian samples from three different geographical areas. First, we defined a new Italian Genome Reference Panel (IGRP1.0) for imputation, which improved imputation accuracy, especially for rare variants, and we tested it by GWAS analysis on red blood traits. Furthermore, we extended the catalogue of genetic variation investigating the level of population structure, the pattern of natural selection, the distribution of deleterious variants and occurrence of human knockouts (HKOs). Overall the results demonstrate a high level of genomic differentiation between cohorts, different signatures of natural selection and a distinctive distribution of deleterious variants and HKOs, confirming the necessity of distinct genome references for the Italian population.
ISSN:1018-4813
1476-5438
DOI:10.1038/s41431-019-0551-x