Sequencing Services

Illumina sequencing flowcell for HiSeq X system

Whole Genome Research Sequencing

The Kinghorn Centre for Clinical Genomics (KCCG) WGS sequencing service provides a minimum mean whole genome at 30X coverage [1], as defined by Illumina [2]. The HiSeq X™ Ten system is exclusively for use in whole genome sequencing.

Sequencing services are currently available for research purposes only and researchers are responsible for ensuring that all relevant ethics approvals have been obtained prior to providing samples. Data will be delivered via Cloud (DNAnexus) or external hard drive (at an additional cost)[3].

From here, you can:

Why Whole Genome Sequencing?

The recent dramatic decrease (~67%) in cost of whole genome sequencing (WGS) prompts a reconsideration of the value equation of WGS compared to whole exome sequencing (WES).

Key advantages of WGS compared to WES and other forms of targeted sequencing are as follows:

  • Consistent coverage. Coverage across the exome is highly variable: although WES is typically undertaken at high mean coverage (>100X), >20X coverage achieved over only ~85% of targeted coding regions [4]. WGS provides very consistent coverage - at 40X mean coverage, >96% is covered at >20X depth.
  • Copy number variation (CNV). e consistent and genome-wide coverage provided by WGS makes it straightforward to call copy number variants. Variable coverage – including gaps over noncoding regions – makes CNV detection challenging with WES.
  • Structural variation. WES can seldom define structural variation. Chromosomal modifications, such as translocations and inversions, can be precisely defined by WGS, often with single-nucleotide precision.
  • Comprehensive coverage. WGS covers all regulatory regions, noncoding RNAs, and every exon of every protein, regardless of annotation (i.e. the mappable genome). Whole genome data can be re-queried as new functional elements are identified or as answers to new questions are sought.
  • Research value. Whole genomes are agnostic to our currently limited understanding of genome function and are therefore much more valuable for research purposes
  • Diagnostic yield. Diagnostic yield from clinical whole genomes is significantly higher than exomes.

Notes

[1] Higher coverage is also available (e.g. equivalent to 60X, 90X, etc.).
[2] 100 Gb raw data; >75% bases above Q30 at 2x 150bp. See the Illumina Product Sheet and Illumina Sequencing Coverage Technical Note for details.
[3] AARNET provides internet to most academic institutions in Australia. Please check with
your IT provider. The end user is responsible for any additional network charges imposed by their host institution.
[4] 20X coverage is commonly regarded as the minimum coverage to call a heterozygous SNP.

 

Header image credit: P. Morris/Garvan


© Garvan Institute 2017