WGS information sheet - Garvan Institute of Medical Research

The Garvan Institute’s Kinghorn Centre for
Clinical Genomics (KCCG) is offering low
cost, large scale whole human genome
sequencing using the Illumina
HiSeq X™ Ten system.
Research sequencing
The Kinghorn Centre for Clinical Genomics (KCCG) is providing
access to whole genome sequencing on the Illumina HiSeq
X Ten platform for research purposes [1]. Our whole genome
sequencing service provides a minimum mean whole genome
at 30X coverage [2], as defined by Illumina [3].
The Illumina HiSeq X Ten system is exclusively for use
in whole human genome sequencing. The sequencing
services are presently available for research purposes only.
Researchers are responsible for ensuring
that all relevant ethics approvals have been obtained prior
to providing samples.
Clinical sequencing
We anticipate providing whole genome sequencing for clinical
use in 2015, once clinical accreditation is in place.
Further information
Visit: http://www.garvan.org.au/research/clinical-genomics
2 µg high-quality genomic DNA
Turn-around Time
4 – 6 weeks for 90% of samples from
date of acceptance to date of data
delivery. Remaining samples may take
up to 4 additional weeks to complete.
Data Format
FASTQ (BAM and VCF available for
additional charge
Data Delivery
SFTP download via AARNET [4] or
hard drive (additional charge)
Number of
There is no minimum order size
(volume orders may attract a discount)
Research sequencing conditional
on appropriate ethical approvals
For sequencing services within Australia:
AGRF (Australian Genome Research Facility)
URL: http://www.agrf.org.au/campaigns/whgs
T 03 9321 3716 E [email protected]
Ramaciotti Centre for Genomics
URL: http://www.ramaciotti.unsw.edu.au/
T 02 9385 1658 E [email protected]
For international sequencing enquiries:
URL: http://www.garvan.org.au/research/clinicalgenomics/WGSservices E [email protected]
Collaborations and commercial partnerships:
A/Prof Marcel Dinger, Head of Clinical Genomics
and Genome Informatics
T +612 9355 5860 E [email protected]
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).
The key advantage of WGS compared to WES and other forms of targeted sequencing are as follows:
1. Consistent coverage
4. Comprehensive 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 [5]. WGS provides very consistent
coverage – at 40X mean coverage, >96% of the mappable
genome is covered at >20X depth.
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.
2. Copy number variation (CNV)
The 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.
3. Structural variation
WES can seldom define structural variation. Chromosomal
modifications, such as translocations and inversions,
can be precisely defined by WGS, often with singlenucleotide precision.
5. Research value
Whole genomes are agnostic to our currently limited
understanding of genome function and are therefore
much more valuable for research purposes.
6. Diagnostic yield
Diagnostic yield from clinical whole genomes is significantly
higher than exomes, due to their consistent coverage
across exons, splice sites, and the detection of noncoding
variants and CNVs.
1Pricing is subject to capacity and agreed terms and conditions from AGRF or Ramaciotti Centre (for orders from within Australia) and KCCG (for international orders). Orders are
now being accepted.
2 Higher coverage also available (e.g. equivalent to 60X, 90X, etc.).
3 >100 Gb raw data; >75% bases above Q30 at 2x 150bp. See the Illumina Product Sheet (http://tinyurl.com/oyfjav8) for details.
4AARNET (http://www.aarnet.edu.au/) 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.
5 20X coverage is commonly regarded as the minimum coverage to call a heterozygous SNP.
Information Sheet v2.1, 30 September 2014. DNA image by Kate Patterson/Garvan Institute, used with permission; laboratory photographs by Paula Morris/Garvan Institute. Illumina HiSeq X Ten image courtesy of
Illumina Inc., used with permission. Remainder ©2014, KCCG, all rights reserved.
Garvan Institute Of Medical Research 384 Victoria Street Darlinghurst Sydney NSW 2010 Australia