WHOLE HUMAN GENOME SEQUENCING KINGHORN CENTRE FOR CLINICAL GENOMICS 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 Specifications Sample 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 Sampless There is no minimum order size (volume orders may attract a discount) Ethics Research sequencing conditional on appropriate ethical approvals Contacts 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] 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). 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. Notes 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