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Operator
Greetings, and welcome to the Halozyme Therapeutics third quarter 2012 financial results conference call. At this time, all participants are in a listen-only mode. A brief question-and-answer session will follow the formal presentation. (Operator Instructions) As a reminder, this conference call is being recorded.
It is now my pleasure to introduce your host, Anne Erickson, Executive Director of Investor Relations at Halozyme Therapeutics. Thank you, Ms. Erickson, you may begin your conference.
Anne Erickson - Executive Director, Corporate Communications and IR
Good afternoon, everyone. Thank you for joining Halozyme's quarterly update conference call. With me on the call today are Gregory Frost, President and Chief Executive Officer; and Kurt Gustafson, Chief Financial Officer.
This afternoon, Halozyme released third quarter 2012 financial results. If you've not received this news release or if you'd like to be added to the Company's distribution list, please e-mail me directly at aerickson@halozyme.com. This call is also being webcast live over the Internet at www.halozyme.com, and a replay will be available on the Company's website for the next 14 days.
Before we begin, let me remind you that during this conference call, we will be making forward-looking statements. The Private Securities Litigation Reform Act of 1995 provides a Safe Harbor for forward-looking statements. The Company's actual results may differ materially from those expressed in or indicated by such forward-looking statements. All statements made during this conference call that are not statements of historical fact constitute forward-looking statements.
The matters referred to in forward-looking statements could be affected by the risks and uncertainties of Halozyme's business, both known and unknown. Such risks inherent in the Company's business are described in our filings with the Securities and Exchange Commission, as well as in our news releases.
With that, I'd like to turn the call over to Gregory Frost, Halozyme's President and CEO.
Greg Frost - President and CEO
Thanks, Anne, and good afternoon to everyone. We're glad that you joined us for our third quarter call for 2012. Today, I'll provide you with an update on the business and a recap of the quarter's highlights; and then, Kurt Gustafson, Halozyme's CFO, will review the quarter's underlying financial results with you.
Halozyme is continuing into the fourth quarter on track and progressing very well toward some important milestones for 2013. Let's begin focusing first on the late-stage programs with our partner, Roche. The subcutaneous formulations of Herceptin and MabThera Roche has developed with Halozyme's enhanced technology, represent near-term revenue streams for us, with the European Medicines Agency or EMA's decision on Herceptin estimated for early next year and the MabThera marketing application anticipated to be filed with the EMA by the end of this year.
As you may have seen, the abstracts on subcu MabThera now available on the American Society of Hematology or ASH website, Roche will be presenting data from three subcu MabThera studies at the meeting in early December. Roche continues to reiterate their intent to file the marketing authorization application for subcu MabThera to EMA by the end of this year. This could be an important opportunity for patients with non-Hodgkin's lymphoma, as this therapy could reduce infusion times from several hours with the IV formulation to just 5 to 7 minutes with the subcu formulation, providing an easier, less-invasive and more-efficient route of administration, without compromising the established safety and efficacy of the intravenous product.
It's worth noting that Roche continues to make significant investments in the clinical development programs for both subcu Herceptin and MabThera, with numerous studies that range in focus from efficacy and safety to health economics and patient preference. As many of you have seen, Roche presented half a dozen posters on the subcu Herceptin program at the European Society for Medical Oncology Meeting a few weeks ago in Vienna. They presented additional data from the HannaH registration trial as well as detail on the 2,500-patient SafeHer trial, which we believe should adequately answer any questions physicians may have about self-administration of the subcutaneous therapy for eligible patients.
Roche is putting significant resources behind this program to help patients make the transition from IV to subcutaneous administration as smooth as possible and we look forward to being able to provide women with HER2-positive breast cancer a more convenient treatment option for this disease. On our side, we continue working closely with the Roche-Genentech-CMC teams to ensure adequate pre-launch bulk-enzyme inventories to support potential launches.
In summary, subcu Herceptin and MabThera are progressing on track and we're working with Roche to advance these programs through their final stages. Both of these subcutaneous products could be very important to Halozyme, as combined worldwide sales of the intravenous-administered forms are $13 billion in sales. Royalty streams and milestone payments from the subcu formulations of these products, once approved, will drive our near-term profitability and help fund future growth and innovation.
To round out updates on our partner programs, I'll quickly touch on HyQ and Cinryze, the development programs with our partners, Baxter and ViroPharma, respectively. To summarize, FDA has requested additional preclinical data to complete their review of the HyQ Biologics License Application. This request came in August in the form of a complete response letter. We're currently working with Baxter to meet with the agency and propose studies we believe can address their questions.
Additionally, at the time of the HyQ CRL, FDA placed a temporary clinical hold on the subcu Cinryze study that included our enzyme rHuPH20. That hold has since been released and ViroPharma will be initiating the Phase II Cinryze plus PH20 combination study in Europe shortly and will be phasing in the US [sites] as quickly as they can. On their latest earnings call, ViroPharma indicated that they'll have data available from this study in 2013. We're committed to both HyQ and subcu Cinryze and look forward to working with our partners to enhance these important programs on behalf of the patients who can benefit from these lifesaving therapies.
Now, switching over to our proprietary programs, as you may have heard at our Analyst/Investors Day, Halozyme is putting an experienced commercial organization in place to support our proprietary recombinant human hyaluronidase product, Hylenex. We're seeing success with the first wave of commercialization with an initial focus on hospitals, emergency departments for regional anesthesia, drug extravasations, and fluid administration in patients with difficult venous access.
In just 10 months, we've captured a quarter of the hyaluronidase market and are forecasting a 50% share by the end of the year. While we've always said the initial targeted markets are not large, we expect that Hylenex will be profitable in these domains by the end of the year, which really sets the stage for future growth.
In order to continue to grow the Hylenex brand, we recently announced that we're pursuing an additional market opportunity for the product. We believe the pre-administration of Hylenex in insulin pumps is a large, attractive and obtainable market opportunity. While this indication is on label today, there are a number of elements we're currently putting in place to ensure a successful commercial launch in the insulin pump market. These activities include gaining approval of the simple tubing and vial connector that would be required for administration, scaling up drug product manufacturing processes and ensuring there's enough supply to support market demand and, finally, completing Phase IV studies that will support effective commercialization and provide healthcare providers with the exposure data in relevant patient populations they need in order to prescribe.
You can expect that we'll be providing definitive timing on product introduction by the beginning of next year. The decision to pursue this commercial opportunity supports our strategy of complementing the partnered revenue streams we've discussed with our own products in order to drive sustained growth. We believe that this will put the Company on a growth trajectory beyond what it could achieve if only focused on proprietary or partnered programs alone. We're confident that guiding some of our own programs through approval and onto commercial success will be the best way to transform our innovations into reality and will ultimately result in greater returns for our shareholders.
Lastly, our Phase II PEGPH20 with chemotherapy study in patients with Stage IV previously untreated pancreatic cancer continues to progress steadily. We expect to complete the run-in cohorts of this trial before year-end and then we'll progress into the randomized portion of the trial. We expect to present data from the run-in cohorts in the first half of 2013.
There is a significant unmet medical need with pancreatic cancer and the standard of care is evolving. For patients presenting with metastatic disease, unfortunately, gemcitabine has been the only tool available for many years, with a median survival rate around just one year. However, there are some chemotherapy backbones that could change the future therapeutic landscape.
FOLFIRINOX, for example, is a regimen, which demonstrates superior activity but is today limited to patients that can tolerate the aggressive regimen. The gemcitabine and ABRAXANE combination is being watched closely as results of the randomized Phase III trials should be announced this year. As we look at the future of care with this devastating disease, we're monitoring the treatment landscape carefully to see how it evolves and whether or not gemcitabine plus ABRAXANE is going to become the backbone of therapy for patients that cannot tolerate FOLFIRINOX. We expect to integrate the most current standard of care when we initiate the randomized Phase II portion of our ongoing trial in 2013.
In addition to our current Phase II trial, we're also considering two additional investigator-sponsored trials with PEGPH20 in pancreatic cancer with the FOLFIRINOX regimen in metastatic and with gemcitabine and ABRAXANE for locally advanced disease in an effort to advance our knowledge regarding the right therapeutic approach to make significant advancements against this devastating disease.
Now, before I turn the call over to Kurt, I want to re-emphasize that we're very excited by all the programs we have in our pipeline and the future of our organization. We've had many significant scientific breakthroughs that have brought us to this point, but I look forward to the future breakthroughs that will take Halozyme to the next level.
I'll now turn the call over to Kurt.
Kurt Gustafson - VP and CFO
Thanks, Greg, and hello to everyone. Earlier today, we announced our financial results for the third quarter of 2012. The net loss for the third quarter of 2012 was $20 million or $0.18 per share compared with a net income for the third quarter of 2011 of $5.2 million or $0.05 per share. The net loss for the nine months ended September 30, 2012 was $49.1 million or $0.44 per share compared to a net loss of $1.4 million or $0.01 per share for the comparable period in 2011.
Revenue for the third quarter of 2012 was $5.3 million compared to $22.9 million for the third quarter of 2011. Revenue in the third quarter of 2012 primarily consisted of research and development reimbursements from partners. The third quarter last year was an unusually high quarter due to the recognition of deferred revenue associated with the termination of the Hylenex agreement with Baxter.
Research and development expense for the third quarter of 2012 was $19.5 million compared with $13.5 million for the third quarter of 2011, primarily due to an increase in manufacturing activities, most of which relates to building launch inventory for Roche. As I've indicated before, this material will be expensed as R&D expense until the product is approved, at which point it will be put on the balance sheet as inventory.
SG&A expense for the third quarter of 2012 was $5.6 million compared to $4.3 million for the third quarter of 2011. Cash and cash equivalents were $87.6 million as of September 30, 2012, compared with $66.3 million as of September 30 last year. And net cash used in the third quarter was $14.4 million.
With regards to our cash burn guidance, we are leaving this unchanged at $60 million to $65 million for the year.
Greg Frost - President and CEO
Thanks, Kurt. We appreciate your support of Halozyme. Over the next few months leading up to the year-end and beginning of 2013, we anticipate hitting some key milestones. In addition to what I've already updated you on, we also expect to have topline results from the Phase II portion of the HTI-501 trial in cellulite. That trial is progressing nicely and we look forward to sharing data with you.
Thanks for listening and I'll now hand the call over to the operator for managing Q&A.
Operator
Thank you. (Operator Instructions) Matthew Harrison, UBS.
Matthew Harrison - Analyst
Hi, good afternoon. Thanks for taking the question. A question on cellulite. Could you help us think about what the data is that we're going to get from that trial and how you're going to decide on the decision to move forward with that?
Greg Frost - President and CEO
Oh, sure. So, as you may recall, we started a single-arm escalation phase of this last year and that was to go through and it's an evaluation of two different modulators, the concentration of the drug and the activator, if you will. And that came up with a recommended Phase 2 dose, which then folded out into a multi-field injection of either placebo or the active agent.
So those are dual-arm blinded studies and we will have a read out on that, that has both pharmacologic end points with regards to imaging-based sensitivity as well as clinical outputs. So from this, essentially, what we'll have is a good read in a randomized design that will allow us to establish both the safety of the product from the standpoint of local tolerability as well as the pharmacodynamic and pharmacologic activity as assessed by the clinicians and patients.
Matthew Harrison - Analyst
And then, just in terms of the efficacy, can you give us any sense for what sort of hurdle you're looking for there?
Greg Frost - President and CEO
Sure. Well, if you take a look at the simplest level, there is a 5-point scale that's involved on these and essentially, there is -- we've done some ad boards and others have kind of weighed in on this of what sort of magnitude of change is clinically relevant, that's typically looked at as far as a two-point change in median. So obviously, the first point is safety, number one, and then the secondary point is the pharmacologic activity. And from there, we then make our strategic decisions on that specific product between regional partnering discussions, as well as development activities from there, but that's essentially kind of the key driving point as far as what puts us in a position of deciding go/no-goes and opportunities for that program.
Matthew Harrison - Analyst
Great. Thanks very much.
Greg Frost - President and CEO
Sure.
Operator
Thank you. Ying Huang, Barclays.
Ying Huang - Analyst
Hey, good afternoon. Thanks for taking my questions as well. So first of all, can you categorically speaking talk about the antibody levels that were observed in the SABRINA trial? Because we looked for that information in the abstract and it's conspicuously not there. And then, secondly, in terms of the HyQ update, I know Greg, you were talking about the gap analysis. Can you confirm whether you guys have finished that analysis or not, and does FDA have this information in hand or not? And then, lastly, on HTI-501, do you think the imaging endpoint will be accessible by FDA as an approval endpoint? Thanks.
Greg Frost - President and CEO
All right. So three different questions in there. As far as the first component regarding the MabThera abstracts, obviously, those are live on the ASH website, but as far as the details that go into those presentations, we're embargoed from any speculation outside of the four corners of the published abstract until ASH. So unfortunately, up to this point, all I can tell you is that the teams are very confident that the data being generated keeps us on track to the planned regulatory filings and we look forward to seeing obviously the trials continuing and further results from these studies, but there's not something conspicuously absent from the standpoint of a safety concern or anything of that nature.
With regards to your HyQ question, all I can tell you at this point obviously is that we're working very carefully from the standpoint of the gap analysis components, but that Baxter has not provided an update on scheduling of any meetings with FDA and so we can't provide any additional information at that time. Other than that, we continue to work with them to define those preclinical studies that will address the questions raised by FDA this year, but I do feel that we've made very good progress as far as the overall gap analysis.
And finally, regarding HTI-501, between imaging versus clinical assessment scores, I don't think there's any established path that we can talk to at this point as far as registration pathways except that the clinical assessment scores are probably the -- are more valid than imaging, if you will, as far as just historically when you look at the sorts of things from a drug development perspective.
Ying Huang - Analyst
So you're talking about the 5-point scale scores, I guess?
Greg Frost - President and CEO
The global assessment scores are typically the sorts of things that come into play there.
Ying Huang - Analyst
Got it. Thank you, Greg.
Greg Frost - President and CEO
But I think it's early to be talking about regulatory endpoints for this as far as in POC-type studies.
Ying Huang - Analyst
Got it, thanks.
Greg Frost - President and CEO
Sure.
Operator
Thank you. Jim Birchenough, BMO Capital.
Jim Birchenough - Analyst
Yes, hi guys, congrats on all the progress. Just a few questions. In terms of the R&D expense, it jumped up about $3.4 million sequentially. Is that all due to building inventory and supply for Herceptin subcu and MabThera subcu? And then, just on the cellulite program, are you going to be looking at antibody levels and inflammatory mediators, I think those have been important things for other drugs that are being developed for cellulite.
Greg Frost - President and CEO
Sure, Jim. I'll let Kurt take the first question there.
Kurt Gustafson - VP and CFO
Yes, I think it's good question, Jim. And as I said, yes, the vast majority of the increase in R&D expense that you're seeing there is related to building inventory, or inventory is probably the wrong word, but -- because we're not putting on the balance sheet, you're seeing it as an R&D expense, but it's building material for our partners.
Jim Birchenough - Analyst
And maybe just before the second question, Kurt, how do you -- how is that expensed, does it add cost or can you maybe take us through the accounting of what does that represent exactly?
Kurt Gustafson - VP and CFO
Yes, sure. And I think I've said, a really good, probably about a third of our R&D expense this year is based on building this material for our partners. The way it's expensed is we will expense this material over the course of the batch, if you will. So it's expensed kind of along the way. Then, once the batch is finished and released by us, it's then shipped out to our partners and when it is shipped, it -- you'll see the revenue come in through the reimbursement in our corporate partner revenues and that will change once the product is approved, so we'll still make the same stuff, but then it will be inventory on the balance sheet and what you'll see when we actually ship it is you'll see sales and associated cost of goods for that.
Jim Birchenough - Analyst
And just so I understand, when you ship it to Roche and it's recorded as revenue, you're selling it to Roche?
Greg Frost - President and CEO
That's correct.
Jim Birchenough - Analyst
And when you book the R&D cost associated with it now, is that booking it at the prescribed selling price that you sell to Roche at?
Kurt Gustafson - VP and CFO
No, it's not.
Jim Birchenough - Analyst
Any detail on what drives that expense?
Kurt Gustafson - VP and CFO
Well, as we are making the batch, we amortize the batch costs over the life of the batch. So, we're booking the expense. The revenue that comes in through our -- you'll see the line, revenues under collaborative agreements, that's where it's coming in today and we earn a markup on that. And I think as I said at Analyst Day, I want to be sure that you understand this, Jim, that this is not stuff that we're making based on kind of a guess at what Roche will want or Baxter will want. We are making this material based on firm purchase orders from these guys.
Jim Birchenough - Analyst
Got it. Okay. And the second question on the cellulite.
Greg Frost - President and CEO
Sure, Jim. So obviously, there are two components regarding laboratory assessments for these types of programs. Obviously, both for ADA as well as looking at any changes from the standpoint of serum chemistry, those are monitored throughout. So you'll have those pieces coming up as well. But from a challenge perspective and the mechanism of action of this conditionally active biologic, one, as far as a very precise nature of how the enzyme works when it's turned off outside of the site of injection and secondly, from the standpoint, it's a recombinant human enzyme, there is some differences there maybe from some other products that you might be thinking of.
Jim Birchenough - Analyst
Great, thanks, guys.
Kurt Gustafson - VP and CFO
Sure.
Greg Frost - President and CEO
Sure.
Operator
Thank you. Jason Butler, JMP Securities.
Jason Butler - Analyst
Hi, guys, thanks for taking the question. Understanding that this is new information and you're probably still digesting it, could you maybe talk about the outcome today from the endo division and the apparent move towards requiring cardiovascular outcome studies for insulin drugs and how you think that might impact how you partner the pen component of that market?
Kurt Gustafson - VP and CFO
Sure. Jason, it's clear you were listening to that too. First and foremost, from the cardiovascular standpoint, the answer is no, because as you know, the compound that was reviewed today is a new molecular entity. So the insulin APIs that we've evaluated as previously -- are previously approved entities that have a long history of use in patients with Type 1 and Type 2 diabetes. So the agency has given us guidance towards insulin mixes for our co-formulations with enzyme.
And then, obviously, in the case of insulin pump therapy where the initial focus is on the Type 1 population, the safety concerns are usually more directed towards hypoglycemia risk with glycemic control. So with regards to partnership-related elements there, that's not something that we've seen coming up as a challenge from that perspective, as far as the MDI market.
Jason Butler - Analyst
Okay, great. Thanks for taking the question.
Greg Frost - President and CEO
Sure.
Operator
Thank you. (Operator Instructions) Thank you. Richard Reznick, William Blair.
Rich Reznick - Analyst
Hi, everyone. This is Rich Reznick, William Blair for John Sonnier. Thanks for taking my question.
Greg Frost - President and CEO
Sure.
Rich Reznick - Analyst
It has to do with the ASH abstract for MabThera subcutaneous. We were intrigued by the differences, although not significant in complete response rates between MabThera subcutaneous and MabThera IV and SABRINA trial. We also remember that from the Phase III trial with Herceptin subcutaneous and Herceptin IV that there was a similar trend, even though it's less pronounced. So I was wondering if you could talk about that trend and what you think might be driving it, if you have any thoughts on that.
Greg Frost - President and CEO
Thanks, Rich. Obviously, you're referring to data that's in the ASH abstracts, but -- and obviously, we're enthusiastic about the datasets that are tracking for filing but unfortunately, as you kind of mentioned, we're embargoed from really getting into any speculation outside the four corners of the published abstracts until ASH. But we're certainly confident that the data is keeping us on track. So certainly, I think we can go through and it's -- from a dataset perspective isn't something we can really speculate on right now.
Rich Reznick - Analyst
Okay, thanks.
Operator
Dr. Frost, there are no further questions at this time. I'd like to turn the floor back over to you for closing comments.
Greg Frost - President and CEO
Thanks. This concludes today's conference call and thank you for joining us.
Operator
Thank you. This concludes today's teleconference. You may disconnect your lines at this time and thank you for your participation.