The first entire genome of an Irish individual has been sequenced by a team of scientists led by UCD Conway's Professor Brendan Loftus. The sequence, published today in BioMed Central's open access journal, Genome Biology, provides insight into the evolutionary history of this distinct lineage.
The UCD Conway research team used data from a previous genotyping study to select an Irish male representative with a confirmed Irish ancestry over three generations for DNA sequencing. Then, using a next generation sequencing approach, the team created nine DNA sequence libraries, which were overlaid to generate a high quality genome sequence with 11-fold coverage.
Analyses were then carried out in conjunction with collaborators from Trinity College Dublin, the Royal College of Surgeons of Ireland (RCSI), Beaumont hospital, the MRC Human Genetics Unit and University of Edinburgh.
Although the first human genome was identified a decade ago, scientists have been reading genome sequences of many different species and lineages in an effort to identify how life forms differ from each other and if one group are more susceptible to disease than another based on the differences in their genetic makeup.
The UCD researchers focused on identifying new DNA variants such as insertions/deletions (indels) and single nucleotide polymorphisms (SNPs). Nearly 200,000 indels and over 3 million SNPs were identified in the Irish genome sequence.
Of the SNPs, 13 % were novel, potentially including markers specific to Irish ancestry or indicators of disease. In particular, one of the new SNPs interferes with the production of a macrophage-stimulating protein, thought to be associated with inflammatory bowel disease and chronic liver disease.
"Our findings show that there remains utility in generating whole genome sequences to illustrate both general principles and reveal specific instances of human biology", says Loftus, adding, "The Irish population is of interest to biomedical researchers because of its isolated geography, ancestral impact on further populations and the high prevalence of a number of diseases".
The authors also describe a new way to improve SNP calling accuracy at low genome coverage by using haplotype data from the current Human Genome Diversity Panel and they identify gene duplication events that may show recent positive selection in the human lineage.
The DNA variants in this study have been uploaded to the Galaxy computing platform, facilitating the continued full analysis of this genome. The authors hope that this sequence will compliment the ongoing '1000 genomes' project, which currently lacks an Irish representative.
Science Foundation Ireland funded this research, which forms part of the doctoral thesis of PhD graduate student Pin Yong, through a research professorship grant award to Brendan Loftus.
For more see:
Irish person's genetic code sequenced for first time (UCD News)
