Michael W. Hunkapiller
Analyst · Maxim Group
Thanks, Trevin. Good afternoon, and thank you for joining us today. We are pleased with our third quarter results and the continued progress we're making in driving the adoption of our products. Highlights of our third quarter are as follows: we booked new orders for 5 PacBio RS II systems and installed 6 systems, which brings our install base up to 83 and our backlog of systems to 9 as of September. We booked 7 new orders for RS II upgrades, which brings our total system upgrades to 61 out of a possible 74 RS systems that were installed prior to our release of the RS II. All but 1 of those 61 upgrades were installed as of September 30. Consumable revenue for the quarter was $2.1 million, which is up 64% from Q3 of last year, and up 10% sequentially from our second quarter revenue, signaling continued strong utilization in our install base. Total revenue grew sequentially from $6 million in Q2 to $7.4 million in Q3. Last month, we signed an agreement with Roche Diagnostics to make them our partner for developing and commercializing products for the in-vitro diagnostic market, and we received $35 million in cash upfront from Roche as part of that agreement. We ended the quarter with $127 million in cash, which is up $20 million from our cash balance at the end of June. And finally, we launched our latest chemistry and software release earlier this month. This P5-C3 chemistry release features photo-protected dyes, which enables extra long read lengths. We have already seen customers achieving N50 read lengths in excess of 10,000 bases, which means that more than half the data they get from run is comprised of reads longer than 10,000 bases and the longest reads they're getting are over 30,000 bases long. In addition to these highlights, we have also seen a significant increase in the number, recently averaging 1 paper per week of customer publications based on the use of our SMRT sequencing technology. We're excited about all of these, but I will highlight a few that illustrates some of the key advantages of the SMRT technology. In particular, its extraordinary read lengths and lack of sequence context bias enable analysis of important genomic regions that are frequently missed entirely using short read technologies. Either because they cannot span DNA repeat regions or because of the use of DNA amplification biases against low complexity sequences. The first paper I'll highlight is a publication in the American Society for Microbiology Journal, Genome Announcements, entitled De Novo Assembly of the Streptomyces Strain in G1 Genome Using PacBio Single Molecule Sequencing. Streptomyces species have approximately 8.7 megabase genomes that contain numerous long repeat structures in key gene clusters and have greater than 70% average GC content. Genome assembly based on combinations of short reads, both Illumina HiSeq and Roche 454 data gave an assembly in 466 pieces with over 10% of the sequence missed entirely. Using data from the PacBio RS, the researchers were able to generate an assembly that overcame these problems and result in genomic regions key to the medical and industrial significance of these bacteria. The second publication is from Genome Biology entitled, Reducing Assembly Complexity of Microbial Genomes with Single Molecule Sequencing. The authors of this paper describe the inability of first and second generation sequencing platforms to completely reconstruct bacterial chromosomes, which has resulted in most bacterial genomes being left unfinished. In this study, the author sequenced 6 bacteria with PacBio and analyzed the repeat complexity of 2,267 other genomes. Based on the results, the authors conclude that they can assemble most known bacteria at finished grade quality without gaps using only a single library with the PacBio RS, and that accuracy of these assemblies with quality values greater than 60 is much better than what they could achieve with either short read technologies or hybrid assembly techniques. The authors went on to state that automated assembly of long single molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes and continuing improvement should drive that cost even lower. The next publication is from BMC Genomics entitled, An Evaluation of the PacBio RS Platform for Sequencing a De Novo Assembly of a Core Plast Genome. The researchers were studying the genome of a close relative of strawberry plants. This chloroplast genome is relatively low in GC Content, with an average of 37%, and has several very long and almost identical repeat structures. Using the PacBio platform, the researchers were able to obtain the full sequence of the 155 kilobase genome in a single contig from as little as 35x coverage. In contrast, using high speed data, up to 9,100x coverage, they were only able to get an assembly with 7 contigs with almost 10% of the sequence missing entirely due to very low GC content in the repeats. The last publication I'll highlight is one that appeared in the American Journal of Respiratory Cell and Molecular Biology entitled, Genome Reference in Sequence Variation in the Large Repetitive Central Exon of human MUC5AC. Last quarter, I mentioned that researchers at the University of North Carolina were working on studying samples from cystic fibrosis patients to better understand the relationship between expanding repeat regions in this gene and the severity of disease. This publication highlights some of that work and describes the region as one that contains the gap known in the human genome reference comprised of a highly repetitive and complex central exon. This exon region has not been successfully sequenced in the past by any other sequencing technology. They noted that the entire region was in general disarray prior to using SMRT sequencing. In the paper, the researchers described how they used SMRT sequencing to obtain long sequence reads and robust coverage that allowed for de novo sequence assemblies spanning the entire gene. They also identified genetic variation in the 4 patient samples that were studied. The study illustrates and the authors concluded: "That SMRT sequencing can be used successfully to perform de novo assemblies of large repetitive sequences to fill in gaps in important regions of the human genome." This past month, we attended the second Annual International Conference on Genomics in the Americas, which was held in Sacramento. There were several presentations at the conference highlighting PacBio technology. In the keynote presentation, Nobel Laureate, Rich Roberts, described his recent work on bacterial methylomes using the PacBio RS II. His team at New England Biolabs has been studying methyltransferase systems to better understand how certain bacterial organisms evolve and acquire pathogenic genes. For instance, his team used the PacBio RS to study the epigenetics of the E. coli strain responsible for the outbreak in Germany in 2011, and found that it was missing genes found in other bacterial strains, which restrict incoming DNA that is methylated. Without that protection, the strain had picked up the phage with the gene that encoded shiga toxin, causing it to be pathogenic. Another presentation I'll highlight was made by Ken Dewar from McGill University in Montréal. His talk focused on the analysis of complete bacterial genomes in less than 24 hours in response to outbreaks of infectious diseases. His team at McGill University has developed protocols to rapidly sequence and analyze outbreak samples using the PacBio RS II platform. Dr. Dewar highlighted the PacBio RS II's ability to generate high-quality, complete bacterial genomes in a very short timeframe. McGill also uses the Illumina MiSeq for studying bacterial genomes. However, while the MiSeq data is useful, McGill cannot produce completely finished genomes with the MiSeq data alone, due to repetitive elements in the bacterial genomes, which were not spanned by short read sequences. Dr. Dewar concluded that with sequencing cost coming down from product improvements and streamlining protocols, sequencing is becoming an attractive option for outbreak monitoring. The last presentation I will highlight was from our Chief Scientific Officer, Jonas Korlach, entitled Finished Microbial Genomes and Epigenomes on a Large Scale. Jonas described the results from a joint study with the Centers for Disease Control, Cornell University, New England Biolabs and the University of California at Davis, involving the study of the food-borne pathogen Lysteria monocytogenes. In this study, the researchers were able to easily assemble 16 different strains down to single contigs or approximately 3 million bases each. Furthermore, they discovered mobile elements in certain strains, which should only be identified using SMRT sequencing. Finally, when looking into the strain's epigenomes, they identified modified bases that are likely to have regulatory roles in the expression of the genes that cause the strains to be pathogenic. This past month, we hosted a West Coast user group meeting, UGM, and a bioinformatics training session here in the Bay Area. We had 85 attendees at the UGM and 36 attendees at the training session. We found these types of meetings to be very effective in sharing the latest customer accomplishments and sequencing approaches in an informal fashion that is much closer to realtime than peer-reviewed publications. At the UGM, there were 12 diverse customer presentations covering a wide range of sequencing applications with the PacBio RS II platform. I'll highlight 3 of these presentations. The Joint Genome Institute has been and continues to be a leader in microbial sequencing with their PacBio RS II systems. For the past few months, they have assembled genomes using between 3 and 10 SMRT cells each. And now, they are down to using just 2 SMRT cells each. Alex Copeland at JGI presented an interesting historical recount of their cost to sequence bacterial genomes over the past decade. 10 years ago, when all they had was Sanger sequencing, they would spend up to $85,000 to sequence a genome to a high level of quality. In order to reduce cost, they adopted the use of second-generation systems, such as HiSeq, to sequence many more genomes at a lower cost per genome but the drawback was that the genomes were lower quality and never finished. Now with PacBio, they were able to produce high quality finished genomes at low cost. Furthermore, with all the improvements and throughput we have delivered over the past year, the team at JGI has expanded their work with the PacBio platform in the fungal and plant genomes, which are one to several orders of magnitude larger than microbial genomes. At the Salk Institute, scientists have been studying Arabidopsis thaliana, which is one of the model organisms used for studying plant biology. Its genome consists of approximately 120 megabases and researchers have spent millions of dollars attempting to assemble it. Dr. Luo from the Salk Institute shared some of the early analysis of the genome using SMRT sequencing and the results were very impressive. As example, previous assemblies with short read technologies combined with Sanger sequencing yielded contigs or pieces with a maximum length of 460,000 bases. In comparison, the assembly with PacBio alone yielded contigs with a maximum length of close to 13 million bases, or a 28x improvement. The contig N50, which describes the contig length at the halfway point of the distribution was only 66,000 bases for the reference short read assembly compared with 6 million bases for the PacBio assembly, which represents a 93x improvement. It's results such as this that we believe will lead to much more work in the area of plant genomics with their technology. Mount Sinai presented some of their latest data on a variety of projects ranging from studying the spread of MRSA infections in the hospital to sequencing human genes with disease association. With respect to monitoring MRSA, they have created a pipeline using PacBio to generate data from a patient sample in approximately 48 hours at a cost of less than $300. In the area of human sequencing, they are focused on previously ignored regions of the genome that have not been well fed in the past because other sequencing technologies cannot read through them. In particular, they are studying genes with complex tandem repeat regions, which are associated with diseases such as hemiplegic migraines and episodic ataxia. And now, I'll highlight our most recent product announcement, the P5-C3 chemistry and software enhancement, which we released earlier this month. This is our latest in a series of product enhancements over the past 2 years that improves the performance of the PacBio RS II platform for both existing and new customers. We are committed to systematically delivering product improvements in short timeframes, and this allows our customers to take full advantage of their PacBio equipment. We believe this latest release will have a significant impact in our customer's ability to assemble larger-sized genomes and to close existing gaps on partially completed genomes. For example, Mount Sinai is one of our customers that had early access to the P5-C3 chemistry. At our UGM, they shared some of their latest results using a combination of 20,000 base libraries and our P5-C3 chemistry. They reported achieving read length N50 of 12,500 bases and their longest reads were over 34,000 bases. Our latest release also includes 20,000 base size selected library protocols optimized for use with the Sage Science and BluePippin DNA size selection system, along with an upgraded version of SMRT analysis, which introduces an update to the popular HGAP assembler. The new HGAP II assembler significantly decreases the time required to perform the noble genome assembly and extends the range of genome sizes that can be assembled. Additional software features include deployed aware set detection, as well as haplotype phasing of amplicons, which provide users the opportunity to utilize the platforms for applications such as HLA analysis. Now I'll make a few comments on our partnership with Roche, which we announced last month. As I mentioned on a recent conference call, we believe this partnership accelerates our ability to participate in a large and growing molecular diagnostics market. Roche is the world leader in in-vitro diagnostics. They bring a wealth of knowledge and experience in bringing products to market in this space. They have the sales and marketing infrastructure to accelerate sales once the products are available. We received an initial $35 million in funding from the agreement, and we expect to receive an additional $40 million in the future, provided that we achieve certain development milestones. Our development activities are up and running and while we do not plan on reporting on the details of the development activities, we look forward to updating you when we reach significant milestones. Now switching back to our commercial activities. During the third quarter, we were pleased to see our consumable revenues growing despite the impact of summer seasonality. Consumable revenues were up 64% year-over-year and up 10% from last quarter. We believe this is a strong testament to the value we are bringing to our customers. As we mentioned in the past, we believe that strong customer references fuel ongoing consumer purchases. On the capital sales side, our instrument bookings for the quarter were 5 units, compared with 4 units in Q3 last year, and compared with 7 in Q2 of this year. While we were a bit disappointed with the sequential decrease, we continue to have a healthy pipeline. And for the year, we continue to target a doubling of total 2013 bookings compared with our bookings from last year. That said, I would like to briefly comment on how the U.S. government funding environment is impacting our short term look at our business. A number of our existing customers in the U.S. are either federal agencies or laboratories funded by government grants or contracts. When the government shut down this quarter, a number of our U.S. customers were forced to temporarily shut down their systems while their labs were closed. Many government scientists were not allowed to come to work or even check their e-mail. This has impacted our current quarter consumable sales and has disrupted the dialogue we're having with certain government agencies concerning future Instrument business. Therefore, we are being somewhat cautious about providing near-term forecast until we better understand the full implications of the recent shutdown and ongoing U.S. budget negotiations. We still feel positive about the overall trajectory of our business. Finally, many of you are aware that the annual American Society of Human Genetics Conference is being held this week in Boston. For those of you attending, we are hosting a lunchtime workshop at the conference this Thursday, entitled Characterizing Structural Variation in the Human Genome using Long Read SMRT Sequencing. The workshop will include 3 presentations that illustrate the use of SMRT sequencing to characterize important and complex genome regions that have been refractory to satisfactory analysis by short read technologies. We hope to see some of you there. With that, I'll turn the call over to Susan.