Genomics Research Centre (IHBI)

Lab Head: Prof Lyn Griffiths
Lab Manager: Dr Larisa Haupt
Head Bioinformatics: A/Prof Rod Lea
Research Staff: Miles Benton, Heidi Sutherland, Saras Menon, Robert Smith, Bisha Roy, Bushra Nasir, Carlos Aya Bonilla, David Eccles

We used an integrative genomics approach to explore expression and SNP data.

• Mapped expression to genomic loci
• Identified markers associated with CVD-related traits
• Work published in American Journal of Human Genetics (Dec 2013)

Completed phenome scan study in NI:

• multi-phenotype GWAS to identify pleiotropic genes
• identified new locus associated with kidney function traits

• supported by replication and gene expression data

  Preparing for submission to Nature

GWAS of commonly measured blood-based markers:

• large association peak on chr 2 with bilirubin
• tight LD forms risk haplotypes
• genotypes associated with increased bilirubin levels

• protective against T2D and MetS

  Manuscript in final draft for PLoS Genetics

Extreme gender biased admixture:

• mt & Y chr analysis
• strong support for written history
  • Manuscript ready for submission to Nature.

NI core-pedigree genomic struture:

• unique RoH and Locus-specific admixture
• appears to be associated with metabolic traits
  • Manuscript ready for submission to Investigative Genetics.

The NI data set is rich and multi-layered:

• we have SNP, expression and methylation data
  • have just finsihed imputing more SNPs against 1000Genomes (now ~8M per sample)
• working with QUT bio-statisticians to further explore this data with novel methods
• preliminary work with methylation and expression looks promising
  • BMI/weight associations (Dr. Jules Hernandez-Sanchez)
• algorithm to infer CNVs from 450k methylation in development

We have undergone development and processing of full mitochondrial genome sequencing in the NI core-pedigree

• Ion Torrent platform
  • Shani Stuart
• ~315 mt genomes
• associations with complex traits and disease
• population genetics
  • Several manuscripts ready for submission to AJHG & other journals.

Illumina 450K methylation arrays

• developed custom workflow
• have ability to run in-house (Illumina HiScan)

Several projects underway in NI cohort

• obesity methylation
• longitudinal and aging

Collaboration with ESR NZ

• epigenetic response to gastric-bypass
  • under review at Genome Biology

ROHGen (team from UK [Oxford])

• many cohorts from across the globe (>100K individuals)

• exploring homozygosity across the genome and the potential influences on complex traits

  Manuscript under review at Nature.

Greg Gibson (Georgia Tech, USA)

• similar population, gene expression axes

• replication for Phenomescan paper

  NI Phenomescan manuscript in final draft for Nature.

GIANT 1000Genomes (Broad Institute)

• incorporate data for between 500K and 1M individuals, across multiple continental ancestries.
  
• anticipate new discoveries from: - increased sample sizes,
  - increased diversity of ancestries, - and imputation to a better reference panel.

Wellcome Trust Centre for Human Genetics

• epistasis & quantitative trait variation

Have just finished selection for the first round of WGS in the Norfolk Island population.

• WGS and WGBS for a selected large pedigree
• two initial projects:
  • epigenetics (inheritance and heritability)
  • Ocular (Glaucoma)
• using Illumina X10 (Garven Institute)