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dc.contributor.authorTong, Pin
dc.contributor.authorPrendergast, James GD
dc.contributor.authorLohan, Amanda J
dc.contributor.authorFarrington, Susan M
dc.contributor.authorCronin, Simon
dc.contributor.authorFriel, Nial
dc.contributor.authorBradley, Dan G
dc.contributor.authorHardiman, Orla
dc.contributor.authorEvans, Alex
dc.contributor.authorWilson, James F
dc.contributor.authorLoftus, Brendan J
dc.date.accessioned2012-05-22T15:38:04Z
dc.date.available2012-05-22T15:38:04Z
dc.date.issued2010-09-07
dc.identifier.citationGenome Biology. 2010 Sep 07;11(9):R91
dc.identifier.urihttp://dx.doi.org/10.1186/gb-2010-11-9-r91
dc.identifier.urihttp://hdl.handle.net/10147/225334
dc.description.abstractAbstract 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. 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. 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.
dc.titleSequencing and analysis of an Irish human genome
dc.typeJournal Article
dc.language.rfc3066en
dc.rights.holderTong et al.; licensee BioMed Central Ltd.
dc.description.statusPeer Reviewed
dc.date.updated2012-05-22T15:02:36Z
refterms.dateFOA2018-08-08T14:09:05Z
html.description.abstractAbstract 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. 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. 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.


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