After a whirlwind of spring conferences and U.S. and European Illumina User Group Meetings we rounded out our April with the Illumina Asia Pacific Summit on the beautiful Phuket Island in Thailand. The summit provided presentations on an exciting variety of topics including: the ENCODE project and recent findings on regulatory elements, ovarian cancer and varying treatment profiles, the use of NGS for criminal justice/forensic science, the microbiome of your gut (and a following presentation on the microbiome of waste treatment plants), non invasive prenatal testing in China, and the translational application of next-generation sequencing for identifying rare diseases.
Mike Snyder of Stanford presented recent findings of regulatory elements and described genomic phasing. He summarized that only 50% of regulatory elements have been found to date using current techniques (GWAS) and there is a need to assess linkage and compound heterozygosity. Dr. Snyder introduced RegulomeDB to help identify regulatory elements in non-coding regions and make further predictions on linkage.
David Botwell of Peter Mac in Australia discussed clinical outcomes in ovarian cancer patients. David presented data indicating that there are four different types of ovarian cancer based on clinical response. By employing NGS, his team conducted a re-evaluation of the disease over the last 5 years and found that while the condition is treated as a single disease, the genomic profiles indicate that in fact there are many distinct diseases just sharing a single anatomical location.
Switching gears from patient treatment to criminal justice, Bruce Budowle, director of the UNT Health Science Center‘s Institute of Investigative Genetics and vice chair of the Department of Forensic and Investigative Genetics, presented on the recent uptake of NGS in the forensic sciences. As the cost of this technology has decreased and the capacity of the instruments has increased, the technology has been able to be utilized in several cases where genomic evidence is warranted and WGS can provide a complete picture. He, of course, also mentioned the infamous blue dress…
As a lunch symposium on the first day, we hosted a seminar on our new product, BaseSpace Clarity 2.0 and its applicability in Next gen omics labs. David Miller, Sequencing Manager at Queensland Center for Medical Genomics, was a co-presenter and covered how the QCMG lab is using the LIMS to further their clinically focused research. The first half of the talk covered the newly released module – Lab Manager dashboard – the first module of its kind in the LIMS market. The Dashboard allows a Lab Manager to oversee all activity within the lab and get real time information to allow for planning and immediately catch blockers within the lab. During the second half of the talk, David Miller discussed how the QCMG lab made use of the preconfigured workflows within the LIMS as well as extended the LIMS through the application programming interface (API) to automate analysis pipelines and specific lab tasks. The QCMG lab runs Illumina Hiseqs and Miseqs and uses the LIMS to track all workflows and analysis done through these instruments. The research focus of the lab is a systemic approach to analyzing cancer using ngs, sequencing, and array technologies.
Immediately after lunch we were treated to two talks regarding microbiomes. Starting with the human gut microbiome, Peer Bork of EMBL presented data on the consequences of diet and drug intake on the microbiome of our gut. Dr. Bork presented data on the differing types and levels of antibiotic resistance observed in populations across different countries and explained how these differences can be attributed to the use of antibiotics in the regions, as well as, variations in local food production.
Following Dr. Bork was Dr. Stephan Shuster of SCELSE who discussed the microbiome of a tropical waste treatment system. The talk focused on urban sustainability and how best to manage waste through a better understanding of water cycles. Dr. Shuster stressed the importance of a balanced waste ecosystem in waste management and presented data to suggest that the most active organisms may not always need to be the most abundant.
Ryan Taft of Queensland Institute for Molecular Bioscience gave an inspiring talk on the life-saving capabilities brought to medicine from the translational use of NGS technologies. Dr. Taft presented four case studies wherein next-generation sequencing was used to diagnose a previously undiagnosed disease. All cases were rare diseases in children, and all these cases were a great representation of how beneficial whole genome and exome sequencing is in clinical practice. You can read more about Dr. Taft’s work on his post “Deciphering the Unconventional Genetics of Complex Life and Inherited Disease.”
As expected, the level of E.coli on the restroom door handle increased exponentially between pre and post flight… Conclusion: wash your hands and don’t touch anything on the plane!
Back to microbiomes for a moment, Dr. Shawn Levy of Hudson Alpha presented several different areas of microbiome research. These topics included a focus on using individualized probiotics to treat disease and combat aging, as well as, a deeper understanding than you ever wanted to know of the microbiome of a plane (pre and post flight) (for which I had to cover my ears). As expected, the level of E.coli on the restroom door handle increased exponentially between pre and post flight… Conclusion: wash your hands and don’t touch anything on the plane!
Daixing Zhou of Berry Genomics gave an interesting talk regarding the rate of adoption of non-invasive pre-natal testing in China. Dr. Zhou discussed the primary challenge associated with these tests, namely false positives (sometimes due to maternal mosaicism), as well as, the impact of false negatives. Take a look at this BioIT article on the company for more information.
All in all, we’d like to thank Illumina for inviting us to participate in this great event! I also encourage you to take a look at the Illumina blog for Brett Kennedy’s summary of the presentations as well. We look forward to seeing those of you attending the NGS Translate meeting in Cambridge, Mass. this month.