Sequencing Finishing and Analysis in the Future Meeting 2014
Arguably, one of the top genome conferences, the annual SFAF meeting began this year in Santa Fe with a great line up of speakers from genome centers, academia and industry. Frankly, what’s amazing is that the meeting is completely supported by outside funding, there is no registration fee (hope that last comment doesn’t spoil the intimate, small size of the meeting next year).
Rick Wilson kicked off SFAF with his keynote titled, ‘Recent Advances in Cancer Genomics’. He discussed a few clinical cases where the combination of whole genome sequencing, exome-seq and RNA-seq were used to help diagnose and guide targeted drug cancer therapy. He emphasized that this combination based sequencing approach would be required to identify actionable genes and that WGS or exome-seq alone wasn’t enough.
Jonathan Bingham from Google announced the release of a simple web-based API to import, process, store, and collaborate with genomic data: https://gabrowse.appspot.com/. He mentioned that Google thinks of computing in terms of data centers, where is there availability? At any given time their idle computers pooled together are larger than any single data center. His new genomics team is looking to harness this and use it for genome analysis. He made the comparison of a million genomes adding up to more than 100 petabytes, on the scale of their web search index.
Steve Turner from Pacific Biosciences discussed platform advances that have led to higher quality assemblies that rival pre-second generation clone by clone sequencing. He made an analogy to the current state of transcriptome assembly: like putting a bunch of magazines in the shredder, the gluing pieces together. He described a method that is now available for construction of full length transcripts, cDNA SMRTbell™ libraries for single molecule sequencing. Finally, he announced that there were >100 Pacbio instruments installed in the field. At Genohub, we already have several listed, with service available for purchase: https://genohub.com/shop-by-next-gen-sequencing-technology/#query=f64db717ac261dad127c20124a9e1d85.
Kelly Hoon from Illumina was next up. She described a series of new updates, the most notable being the submission of the HiSeq2500 for FDA approval by the end of the year. Other points included updates to basespace, the 1T upgrade (1T data in 6 days), Neoprep allows 1 ng of input, coming this summer, new RNA capture kits and a review of Nextseq optics.
Thermo Fisher’s presentation was immediately after Illumina. Most of the discussion was on Ion Torrent’s new Hi-Q system, designed to improve accuracy, read-length and error-rates.
Right after the platform talks was a panel discussion with Pacbio, Illumina, Roche and Thermo Fisher. Main points from that discussion were:
- Steve Turner from Pacbio declined to discuss or entertain discussion on benchtop platform. This was met with lots of audience laughter
- Illumina had no response for ONT except to say they’re not going to respond to ONT until after they launch…ouch.
- Pacbio said that right now read length is not being limited by on board chemistry but rather quality of input DNA.
- Roche 454 is phasing out 454 but looking to compete on 4-5 other possibilities (very interesting news)
Ruth Timme from the FDA discussed implementation of an international NGS network of public health labs to collect and submit draft genomes of food pathogens to a reference database. Data coming in from these sites provides the FDA with actionable leads in outbreak investigations. Currently Genome Trakr consists of six health state labs and a series of FDA labs.
Sterling Thomas discussed Noblis’ Center for Applied High Performance Computing (CAHPC) suite of high speed algorithms called BioVelocity. BioVelocity basically performs reference based multiple sequence alignment (MSA) and variant detection on human raw reads. High speed variant finding in adenocarcinoma using whole genome sequencing was used as an example.
Sean Conlan from NHGRI discussed sequence analysis of plasmid diversity amongst hospital-associated carbapenem-resistant Enterobactericeae. Using finished genome sequences of isolates from patients and the hospital, he was able to better understand transmission of bacterial strains and plasmids encoding antibiotic resistance.
David Trees examined the use of WGS to determine molecular mechanisms responsible for decreased susceptibility and resistance to azithromycin in gonorrhoeae. Predominant causes of resistance included mutations in the promotor region or structure gene of mtrR and mutations in 23S rRNA alleles located on the gonococcal chromosome.
Darren Grafham from Sheffield Diagnostic Genetics Services emphasized the importance of consensus in the choice of an analytical pipeline along side Sanger confirmation of variants for diagnostics. He described his pipeline that is currently being use in a clinical diagnostic lab for regular screening of inherited, pathogenic variants. He stated that 30x coverage is the point at which false positives are eliminated with >99.9% confidence.
Other talks during the first day (that we likely missed enjoying the beautiful Santa Fe weather):
Heike Sichtig: Enabling Sequence Based Technologies for Clinical Diagnostic: FDA Division of Microbiology Devices Perspective
Christian Buhay: The BCM-HGSC Clinical Exome: from concept to implementation
Dinwiddie: WGS of Respiratory Viruses from Clinical Nasopharyngeal Swabs
Karina Yusim: Analyzing TB Drug Resistance
Colman: Universal Tail Amplicon Sequencing
Roby Bhattacharyya: Transcriptional signatures in microbial diagnostics
Eija Trees: NGS as a surveillance tool
Helen Cui: Genomics Capability Development and Cooperative Research with Global Engagement
Raphael Lihana: HIV-1 Subtype Surveillance in Kenya: the Puzzle of Emerging Drug Resistance and Implications on Continuing Care
Gvantsa Chanturia: NGS Capability at NCDC
The night ended with a poster and networking session. The entire agenda is posted here: http://www.lanl.gov/conferences/sequencing-finishing-analysis-future/agenda.php
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