Sequencing and analysis of an Irish human genome.

Hdl Handle:
http://hdl.handle.net/10147/125891
Title:
Sequencing and analysis of an Irish human genome.
Authors:
Tong, Pin; Prendergast, James G D; Lohan, Amanda J; Farrington, Susan M; Cronin, Simon; Friel, Nial; Bradley, Dan G; Hardiman, Orla; Evans, Alex; Wilson, James F; Loftus, Brendan
Affiliation:
Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
Citation:
Sequencing and analysis of an Irish human genome. 2010, 11 (9):R91 Genome Biol.
Journal:
Genome biology
Issue Date:
2010
URI:
http://hdl.handle.net/10147/125891
DOI:
10.1186/gb-2010-11-9-r91
PubMed ID:
20822512
Abstract:
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.; 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.; 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.
Item Type:
Article
Language:
en
MeSH:
Base Sequence; Chromosome Mapping; Codon, Nonsense; European Continental Ancestry Group; Gene Duplication; Genetic Association Studies; Genetic Predisposition to Disease; Genetic Variation; Genome, Human; Geography; Haplotypes; Human Genome Project; Humans; INDEL Mutation; Inflammatory Bowel Diseases; Ireland; Male; Polymorphism, Single Nucleotide; Selection, Genetic; Sequence Analysis, DNA
ISSN:
1465-6914

Full metadata record

DC FieldValue Language
dc.contributor.authorTong, Pinen
dc.contributor.authorPrendergast, James G Den
dc.contributor.authorLohan, Amanda Jen
dc.contributor.authorFarrington, Susan Men
dc.contributor.authorCronin, Simonen
dc.contributor.authorFriel, Nialen
dc.contributor.authorBradley, Dan Gen
dc.contributor.authorHardiman, Orlaen
dc.contributor.authorEvans, Alexen
dc.contributor.authorWilson, James Fen
dc.contributor.authorLoftus, Brendanen
dc.date.accessioned2011-03-28T14:50:41Z-
dc.date.available2011-03-28T14:50:41Z-
dc.date.issued2010-
dc.identifier.citationSequencing and analysis of an Irish human genome. 2010, 11 (9):R91 Genome Biol.en
dc.identifier.issn1465-6914-
dc.identifier.pmid20822512-
dc.identifier.doi10.1186/gb-2010-11-9-r91-
dc.identifier.urihttp://hdl.handle.net/10147/125891-
dc.description.abstractRecent 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.-
dc.description.abstractUsing 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.-
dc.description.abstractOur 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.language.isoenen
dc.subject.meshBase Sequence-
dc.subject.meshChromosome Mapping-
dc.subject.meshCodon, Nonsense-
dc.subject.meshEuropean Continental Ancestry Group-
dc.subject.meshGene Duplication-
dc.subject.meshGenetic Association Studies-
dc.subject.meshGenetic Predisposition to Disease-
dc.subject.meshGenetic Variation-
dc.subject.meshGenome, Human-
dc.subject.meshGeography-
dc.subject.meshHaplotypes-
dc.subject.meshHuman Genome Project-
dc.subject.meshHumans-
dc.subject.meshINDEL Mutation-
dc.subject.meshInflammatory Bowel Diseases-
dc.subject.meshIreland-
dc.subject.meshMale-
dc.subject.meshPolymorphism, Single Nucleotide-
dc.subject.meshSelection, Genetic-
dc.subject.meshSequence Analysis, DNA-
dc.titleSequencing and analysis of an Irish human genome.en
dc.typeArticleen
dc.contributor.departmentConway Institute, University College Dublin, Belfield, Dublin 4, Ireland.en
dc.identifier.journalGenome biologyen

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