Italian Genome Biodiversity Project (IGBP)
Giuseppe Matullo, Alberto Piazza, Davide Pettener, Donata Luiselli
HuGeF-Università di Torino: Giovanni Fiorito, Cornelia Di Gaetano, Simonetta Guarrera, Clara Viberti, Barbara Pardini, Alessandra Allione, Alessia Russo
Università di Bologna: Paolo Garagnani, Marco Sazzini, Alessio Boattini, Stefania Sarno, Cristina Giuliani, Guido Alberto, Gnecchi Ruscone
Characterization of the genomic variability of the Italian population from well-selected samples.on the basis of biodemographic studies and surname origins / distributions.
Two studies are currently on going and share the same aim the Italian Genome Project (IGP) (HuGeF, Turin) and the Italian Biodiversity Project (IBP) (University of Bologna).
During the first step the two datasets will be merge, creating a new project called "Italian Genome Biodiversity Project" (IGBP). The purpose is to achieve a better cover of Italian territory. (Figure above)
Other samples may be added from existing studies.
- Reconstructing Genetic structure Italian
- Creating a database of gene frequencies, haplotype and Copy Number Variants (CNV) within the Italian population
- Expanding the IGDB (Italian Database Genome-Wide)
- Identifying genomic regions subjected possibly to the action of natural selection
- Checking the effectiveness of methods of imputation of SNPs from a well-characterized samples
- Study the implications of genetic stratification in Italian association studies
Criteria for selection of the samples
The selection of samples is based on:
1. Identification of macro-geographical areas potentially homogeneous genetic point of view based on analysis of local surnames
2 Father and mother born in the same province or region, maternal and paternal grandparents originating from the same province/region
3. The absence of kinship between individuals and / or IBD <1/16
Figure shows the distribution of samples analyzed with the following genotyping platforms: Chip Illumina SNP by 1-2.5 million SNPs in the project IGP (N = 314), the Y chromosome and mitochondrial DNA within the project IBP (N = 880).
A first collaborative paper concerning IGBP with about 250,000 common SNPs (Illumina Core Chip), and 250,000 rare SNP (Illumina Chip exome) is in preparation
Our purpose is obtaining an optimal cover of the Italian territory (analyzing about 30-50 individuals for each administrative division, within Italy). We plan to integrate the database reaching 4567 individuals. During the step 2 our purpose is to explore the rare genetic variants distribution in Italian population using whole-exome sequencing and rare-variant genotyping chips. We will use the observed patterns of variation to estimate population growth parameters, the proportion of variants in a given frequency class that are putatively deleterious, and we will study how these variant are geographically localized .
We are aware that many of these rare variants are deleterious and may have relevance to understanding disease risk.
An integration with sequencing data is planned to take place during the step 2 of this project thanks to the collaboration with Prof. D. Toniolo and P. Gasparini who are involved in whole genome sequencing projects on Italian genetic isolates .