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Sequencing and analysis of an Irish human genome.
- Source :
-
Genome biology [Genome Biol] 2010; Vol. 11 (9), pp. R91. Date of Electronic Publication: 2010 Sep 07. - Publication Year :
- 2010
-
Abstract
- Background: Recent studies generating complete human sequences from Asian, African and European subgroups have revealed population-specific variation and disease susceptibility loci. Here, choosing a DNA sample from a population of interest due to its relative geographical isolation and genetic impact on further populations, we extend the above studies through the generation of 11-fold coverage of the first Irish human genome sequence.<br />Results: Using sequence data from a branch of the European ancestral tree as yet unsequenced, we identify variants that may be specific to this population. Through comparisons with HapMap and previous genetic association studies, we identified novel disease-associated variants, including a novel nonsense variant putatively associated with inflammatory bowel disease. We describe a novel method for improving SNP calling accuracy at low genome coverage using haplotype information. This analysis has implications for future re-sequencing studies and validates the imputation of Irish haplotypes using data from the current Human Genome Diversity Cell Line Panel (HGDP-CEPH). Finally, we identify gene duplication events as constituting significant targets of recent positive selection in the human lineage.<br />Conclusions: Our findings show that there remains utility in generating whole genome sequences to illustrate both general principles and reveal specific instances of human biology. With increasing access to low cost sequencing we would predict that even armed with the resources of a small research group a number of similar initiatives geared towards answering specific biological questions will emerge.
- Subjects :
- Base Sequence
Chromosome Mapping
Codon, Nonsense
Gene Duplication
Genetic Association Studies
Genetic Predisposition to Disease
Genetic Variation
Geography
Haplotypes
Human Genome Project
Humans
INDEL Mutation
Inflammatory Bowel Diseases genetics
Ireland
Male
Polymorphism, Single Nucleotide
Selection, Genetic
Genome, Human
Sequence Analysis, DNA
White People genetics
Subjects
Details
- Language :
- English
- ISSN :
- 1474-760X
- Volume :
- 11
- Issue :
- 9
- Database :
- MEDLINE
- Journal :
- Genome biology
- Publication Type :
- Academic Journal
- Accession number :
- 20822512
- Full Text :
- https://doi.org/10.1186/gb-2010-11-9-r91