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EARNINGS CALL TRANSCRIPT
EARNINGS CALL TRANSCRIPT 2016 - Q1
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Executives

Rebecca Chambers - Vice President-Investor Relations & Treasury Jay T. Flatley - Chairman & Chief Executive Officer Francis A. deSouza - President & Director Marc A. Stapley - Executive Vice President, Chief Financial Officer & Chief Administrative Officer.

Analysts

Tycho W. Peterson - JPMorgan Securities LLC Doug Schenkel - Cowen & Co. LLC Derik De Bruin - Bank of America Merrill Lynch Daniel Arias - Citigroup Global Markets, Inc. (Broker) Jonathan Groberg - UBS Securities LLC Ross Muken - Evercore ISI Amanda L. Murphy - William Blair & Co. LLC Alexander D. Nowak - Piper Jaffray & Co. (Broker) Dan L.

Leonard - Leerink Partners LLC Steve C. Beuchaw - Morgan Stanley & Co. LLC Dane Leone - BTIG LLC Jack Meehan - Barclays Capital, Inc..

Operator

Good day, ladies and gentlemen, and welcome to the Illumina, Inc. Q1 2016 Earnings Conference Call. At this time, all participants are in a listen-only mode. Later, we will conduct a question-and-answer session and instructions will be given at that time. As a reminder, this call is being recorded.

I would now like to turn the conference over to Rebecca Chambers. Please go ahead..

Rebecca Chambers - Vice President-Investor Relations & Treasury

Thank you, operator, and good afternoon, everyone. Welcome to our earnings call for the first quarter of fiscal year 2016. During the call today, we will review the financial results released after the close of the market and offer commentary on our commercial activity, after which we will host a question-and-answer session.

If you have not had a chance to review the earnings release, it can be found in the Investor Relations section of our website at illumina.com.

Participating for Illumina today will be Jay Flatley, Chairman and Chief Executive Officer; Francis deSouza, President; and Marc Stapley, Executive Vice President, Chief Financial Officer and Chief Administrative Officer.

Jay will focus on our Q1 results, Francis will provide the outlook for our business, and Marc will review our financial results and updated guidance. This call is being recorded and the audio portion will be archived in the Investors section of our website.

It is our intent that all forward-looking statements regarding our expected financial results and commercial activity made during today's call will be protected under the Private Securities Litigation Reform Act of 1995. Forward-looking statements are subject to risks and uncertainties.

Actual events or results may differ materially from those projected or discussed. All forward-looking statements are based on current information available and Illumina assumes no obligation to update these statements.

To better understand the risks and uncertainties that could cause actual results to differ, we refer you to the documents that Illumina filed with the Securities and Exchange Commission, including Illumina's most recent Forms 10-Q and 10-K.

Before I turn the call over to Jay, I would like to let you know that our Q1 earnings presentation will be available on the Investors section of our website shortly. We plan to reference this document during today's call. With that, I will now turn the call over to Jay..

Jay T. Flatley - Chairman & Chief Executive Officer

orders we booked that were not recognizable as revenue; and instrument orders that we were expecting, but did not receive. Additionally, after quarter-end, we received a disappointing outlook from Europe, which is central to the guidance reduction for the remainder of the year.

I will address the Q1 factors, and Francis will address our outlook and action plan. The majority of the shortfall in Q1 resulted from orders booked that did not translate to revenue.

A combination of factors contributed, including capacity constraints in array manufacturing resulting in back orders; orders that were received late in the quarter, resulting in systems in transit and therefore not converted to revenue; customer initiated requests for delayed shipment or conditions outside our control delayed revenue recognition; and partial revenue deferrals due to increase in complexity of large deal structures, particularly in the case of high-throughput instruments, including the HiSeq X.

Some of these deferrals will be recognized in Q2, while others will convert to revenue over the rest of the year. Some were controllable by us and some were not, but none are related to fundamental market demand.

Individually, each was less than 1% of revenue, and that happens to a degree every quarter, but the combined effect was larger than we expected. The second factor was HiSeq orders that were forecasted but were not received, accounting for $9 million of the shortfall.

As a consequence, we shipped 19 fewer HiSeq 2500, HiSeq 3000 and HiSeq 4000 instruments than anticipated, valued at $14 million, which was partially offset by strength in other portions of the portfolio. We had anticipated sequential growth of 11 units rather than a decline of eight units, which led to flat placements year-over-year.

Over the last several weeks, we've gone through a detailed analysis of the underlying drivers deal by deal.

There were no dominant themes, but we did see a collection of factors, including delays in funding release, customers opting to purchase NextSeqs, and one-off situation such as pending lab moves, financing deliberations, contract reviews, or an upcoming regulatory audit.

While outsourcing to service providers was also cited by a few customers, this is not a significant driver of our forward projection. This feedback confirmed our view on questions of competition and market capacity.

While we can never be certain a few customers did not delay purchases to assess other platforms, our win rates remained stable; and to our knowledge, we did not lose a competitive deal in Q1. We also did not get any information to indicate that excess market capacity was a factor.

As you can see in our investor deck, high-throughput utilization as a percentage of available sequencing capacity has been on an upward trend since Q3 2014 when normalized for one large order that we shipped in Q3 2015.

Run data collected from BaseSpace, which represents about a third of the high-throughput installed base, confirms this analysis, showing roughly flat utilization for legacy HiSeq instruments like HiSeq X, HiSeq 3000 and HiSeq 4000.

Newly announced initiatives, like the Chinese precision medicine program to sequence millions of genomes and the AstraZeneca project to access 2 million genomes, create the confidence that today's sequencing capacity represents but a small fraction of that necessary to meet the growing demand for population sequencing programs.

Focusing now on products. Orders for HiSeq X exceeded our expectations and we added four new customers, bringing the total to 31. Our outlook remains robust, at 20 to 30 instrument orders per quarter. HiSeq X Consumables also beat our forecast despite the timing of customer shipments lowering pull-through to below the guidance range.

On a four quarter basis, which normalizes the impact of shipment timing, X utilization averaged $650,000 to $750,000 annually, a range we feel comfortable with going forward. HiSeq pull-through is in our projected range of $300,000 to $350,000.

For modeling purposes, we've removed 95 HiSeqs from our installed base, bringing the figure to just over 2,000 instruments, reflecting the units taken offline due to adoption of newer machines. Our benchtop instrument portfolio performed well in the quarter, and the outlook is consistent with our expectations coming into the year.

This is being driven by lower than expected cannibalization of MiSeq, strong initial interest in MiniSeq and NextSeq adoption for NIPT in China. Benchtop consumables were strong in Q1, as both MiSeq and NextSeq saw utilization above their respective guidance ranges.

Microarrays were also an emerging bright spot this quarter, as revenue grew 1% versus the prior year period to almost $90 million and orders dramatically exceeded our expectations with growth of 85%. A new Consortium Array, which will begin shipping in Q4, and demand from DTC customers, contributed to the strong order result.

Shipments to our clinical customers grew approximately 20% in the quarter. As we've noted on multiple earnings calls, we've been expecting some NIPT services customers to shift to running samples in-house on our sequencers, and a significant part of that shift occurred this quarter.

Normalizing for the effect of the lower revenue, because we're not getting the full service revenue, our remaining clinical customer base revenue grew 24%. NIPT shipments grew 10%, or 28% after adjusting for the shift, versus the prior year.

We now believe most payers will next assess average risk coverage decisions in 2017, which is later than we had anticipated. Despite this, the rate of adoption is meeting our forecast, and we expect further acceleration as reimbursement decisions are made.

We believe the delay is a matter of focus by the labs that are working to obtain a network designation for existing coverages, as opposed to driving incremental average risk coverage for a faster return on investment. Oncology shipments grew 9% adjusted for the large HiSeq X shipments seen in the first quarter of last year.

This growth rate is lower than that we typically see from this market, due to a large number of orders shipped in the prior year period. We continue to expect expanded adoption in 2016, which will be fueled in part by the launch of TruSight Tumor 170 later this year.

In summary, while we're not happy with our performance in Q1, we do not believe our results are related to a change in fundamental market demand.

Instead, timing of instrument orders is creating late quarter revenue uncertainty, some of which we can and will take specific actions to mitigate, and unique customer situations impacting the HiSeq order rate. With the lower European forecast, it was important that we realign our full-year expectations.

We continue to believe that demand for next-generation sequencing is far more robust than our first quarter results or the outlook our European forecast suggests. I'll now turn the call over to Francis..

Francis A. deSouza - President & Director

Thanks, Jay, and good afternoon everyone. Today, I plan to provide further details on our outlook and action plan. Europe revenue declined 2% year-over-year in Q1, missing our projections, and we are forecasting low-to-mid single-digit growth for the full-year.

Revenue from the Americas grew 14% representing a slightly slower start than we anticipated for the reasons Jay outlined, but we remain confident in the region's full-year projection of mid-teens growth. Asia Pacific revenue declined 5% as forecasted due primarily to a large HiSeq X comparable.

During the quarter, we began to see customer purchasing patterns in Japan improved as research funds are now being released. It's too early to call this a resurgence, but the signs are certainly more positive. Our Asia Pacific region is also forecasting mid-teens growth for the year.

The Q1 challenges are responsible for a minimal change in full-year outlook. With the benefit of two additional weeks of analysis since our pre-announcement, we are more confident that Q1 was a result of operational challenges and not market demand.

By far, the largest driver of our lowered guidance is our lack of visibility in Europe, as evidenced by the drop in the region's full-year forecast three months after we completed our budget. We're taking steps to enhance visibility and improve our execution in the region.

In the meantime, we have incorporated the reduced outlook from Europe into our projection. We're focusing on three areas to deliver on our full-year. First, we're making improvements to our sales process.

To address the variability in instrument orders and shipments during the last months of the quarter, we're focusing the sales team on early closure of instrument orders. In addition, large instrument contracts including those for HiSeq X have become more complex, particularly in Europe. And so we are simplifying and standardizing deals.

Finally, we're building out our manufacturing capacity for arrays, so that we're able to clear the back orders, and meet the increasing demand. Second, we are committed to improving the execution and outlook in Europe.

As we mentioned a few weeks ago, we recently brought in an interim sales leader in Europe, who has already established accountability and ownership for the revised forecast and is driving to the updated expectations. He has already put in place greater discipline around opportunity management, accuracy of our CRM data and quoting.

In addition, we're making good progress in our search for a permanent general manager with large global company experience to ensure that our European organization realizes its full potential. The last step in our plan is focused on expense management.

Last year we added close to 900 employees, 500,000 square feet of real estate commitments and a new global ERP system. While these investments were necessary to support both the growth we have experienced and our ongoing market opportunities, we recognize the need to meaningfully slow down the pace of investment in 2016, given our updated outlook.

We do not expect to have broad changes to our product portfolio or development pipeline but do have other opportunities to delay initiatives that are less impactful to the long-term outlook. We're working on a 2016 re-plan, and have incorporated those improvements into our guidance for the remainder of the year.

As a result excluding GRAIL and Helix, our operating margin target for the year is expected to be 34.5%. While disappointing our Q1 results have not dampened our conviction and our market opportunity or our ability to deliver innovative technology to capture those markets.

I am personally committed and excited to move this organization to realize our mission, benefit patients and deliver shareholder value. I will now turn the call over to Marc, who will provide a detailed overview of our first quarter results..

Marc A. Stapley - Executive Vice President, Chief Financial Officer & Chief Administrative Officer

Thanks, Francis. While revenue for the quarter missed our guidance, orders of over $700 million significantly beat our expectations. We built more than 100 million in sequencing consumable backlog, most of which is expected to be delivered this year.

As a reminder, we typically see higher sequencing consumable orders in the first quarter, ahead of annual list price increases. Instrument revenue declined 20% year-over-year to $118 million, given the large HiSeq X shipments in the first quarter last year, which accounts for more than $30 million of decline.

Consumable revenue was of $361 million, an increase of 17% compared to the first quarter of 2015. Sequencing consumable revenue grew 24% over Q1 of last year to approximately $300 million.

Services and other revenue, which includes genotyping and sequencing services as well as instrument maintenance contracts, grew approximately 12% versus Q1 2015 to $89 million.

This improvement was driven by extended maintenance contracts associated with the largest sequencing installed base and genotyping services, partially offset by a decline in NIPT service revenue, given the shift to in-house testing as expected.

Going forward, we expect (14:29) to at least partially offset the further impact from the transition of these two customers. Turning now to gross margin, operating expenses, I will highlight on our adjusted non-GAAP results, which exclude non-cash stock compensation expense and other items.

I encourage you to review the GAAP reconciliation of non-GAAP measures as well as our GAAP EPS guidance, both of which can be found in today's earnings release and presentation. Please note that all subsequent references to net income and earnings per share refer to the results attributable to Illumina stockholders.

Our adjusted gross margin for the first quarter was 71.7%, flat compared to the fourth quarter as the benefit of favorable consumables mix was offset by lower absorption.

Year-over-year, adjusted gross margins contracted 50 basis points as the positive impact of consumables mix was more than offset by lower instrument margin associated with fewer HiSeq X shipments as well as the decline in services margin.

Adjusted research and development expenses for the quarter were $113 million or 19.8% of revenue, including $5 million attributable to GRAIL and Helix.

This compares to $103 million or 17.5% of revenue in the fourth quarter, higher due to head count additions and investments in GRAIL, Helix, and development projects including projects including Project Firefly. Adjusted SG&A expenses for the quarter were $125 million, or 21.9% of revenue, including $3 million attributable to GRAIL and Helix.

This compares to $124 million, or 20.9% of revenue, in Q4. Adjusted operating margins were 30.1% compared to 33.4% in the fourth quarter and 39.3% in the prior-year period. Excluding GRAIL and Helix, operating margins were 31.6% in the first quarter.

The year-over-year decline is attributable to the lower gross margins and increased employee-related expenses. Stock-based compensation expense equaled $35 million, flat compared to Q4. Our non-GAAP tax rate for the quarter was 25.5%, compared to 24.5% in the first quarter of last year and non-GAAP net income was $106 million.

This resulted in Q1 non-GAAP EPS of $0.71, which included approximately $0.04 and $0.02 of dilution from GRAIL and Helix respectively. This quarterly result compares to non-GAAP net income and EPS of $135 million and $0.91 in the first quarter of 2015 respectively.

We reported first quarter GAAP net income of $90 million, or $0.60 per diluted share, compared to net income of $137 million, or $0.92 per diluted share, in the prior-year period.

As a reminder, prior-period results include a pre-tax gain of $15 million from the partial sale of our minority interest in Sequenta when acquired by Adaptive Biotechnologies. Cash flow from operations equaled $40 million, lower versus the prior year due to the impact of the operating expense growth.

Q1 DSO totaled 64 days, equal to last quarter, and inventory rose to $288 million, given the quarterly shortfall in sequencing instruments, and a continued build-up of consumable safety stock. Capital expenditures in Q1 were $53 million, higher than the $37 million in the prior-year quarter, due primarily to our real estate build-outs.

Consequently Q1 free cash flow was a negative $14 million. During the quarter, we retired the remaining $76 million of the 0.25% 2016 convertible notes and ended the quarter with approximately $1.34 billion in cash and short-term investments including the cash balances of GRAIL and Helix.

Looking forward, we now expect total company revenue growth of 12% year-over-year.

Beyond the first quarter miss (18:09), the additional decline versus our original expectation of 16% is due to the lowered outlook for Europe, which went from high-teens growth to low-single digits to mid-single digits, including a smaller contribution than planned from the Genome England (sic) [Genomics England] (18:19) project.

Our outlook in the Americas and Asia Pacific regions is much more robust as both are expected to grow in the mid-teens for the full year, roughly in line with our expectations due in part to strong orders in the first quarter. For these regions in the second half, we expect to see HiSeq sales increase but remain short of our original expectation.

We believe this will be more than offset by (18:40) MiSeq placements, given lower than expected cannibalization, as well as an increase in the rate revenue (18:45), NextSeq consumables and HiSeq X placements. We also continue to expect strong adoption across our four clinical markets in 2016.

We are forecasting Q2 revenue of $590 million to $595 million driven by sequential seasonality in Japan and roughly flat HiSeq X shipment. We're not forecasting an uptick in other HiSeq instrument shipments until the second half. This Q2 revenue guidance implies a meaningful back half acceleration.

Our confidence in delivering for this projection stems from our existing backlog, a third of which is shippable in Q3 and Q4, and our pipeline.

We are projecting Q2 non-GAAP EPS to be in the range of $0.72 to $0.74 as higher revenue is expected to be largely offset by a sequential increase in operating expenses both from the head count additions in the first quarter and additional GRAIL and Helix spend.

The steps we are taking to reduce spending will have a marginal impact in Q2 and a more meaningful impact in the second half of the year. We anticipate significant EPS leverage in the second half, driven by the acceleration of the revenue growth and our spending action.

For the full year, non-GAAP EPS is expected to be $3.35 to $3.45, which includes GRAIL dilution of $0.20, an increase of $0.05 versus our prior estimate.

Illumina is retaining almost all of the GRAIL losses in net income attributable to Illumina shareholders, significantly greater than our majority ownership percentage, due to an unexpected accounting treatment. We are in discussions with GRAIL regarding updating the equity structure.

Our updated non-GAAP EPS guidance and GRAIL dilution commentary includes our expectation that we will continue to recognize most of the losses in the second quarter and that drops substantially in the second half to closer to our ownership, based on the structural changes that are being contemplated in Q2 and the accounting treatment we are anticipating.

Any delays in this timeline could have a negative impact of up to $0.04 per quarter in the second half. In closing, as a management team, we have a number of matters to address that we have outlined today, including our in quarter linearity, our execution in Europe, and rate of investment and GRAIL equity structure.

Resetting our outlook so significantly is uncharacteristic of our company and unacceptable to us as a team. We are committed to delivering strong results consistent with our track record and our confidence in the long-term opportunity for our business remains high. Thank you for your time. We will now move to the Q&A session.

To allow full participation, please ask one question and rejoin the queue if you have additional questions. Operator, we will now open the line..

Operator

Thank you. Our first question comes from the line of Tycho Peterson of JPMorgan. Your line is now open. Your line is now open..

Tycho W. Peterson - JPMorgan Securities LLC

Hey, thanks. Sorry to hone in on the Europe issues, but I just would love to hear from you a little bit more about the steps you're taking to improve your forecasting ability. Obviously, you had issues in Europe in 3Q last year as well.

So if you could just talk a little bit about how you intend to improve visibility there? And really what gives you the confidence that the problems are going to be fixed by 3Q since the back half estimates are essentially unchanged to get to the midpoint of the new guidance range..

Francis A. deSouza - President & Director

Sure, Tycho. This is Francis. There are a number of things we are doing. We started by moving one of our strong leaders from the U.S., who ran Western region, Scott Thomas out to Europe. And he was out there at the beginning of this quarter and has already started rolling out a much more disciplined sales process.

And that starts all the way from capturing the opportunities and tracking the opportunities as well as managing our visibility into the opportunities that are in various stages of the process. He is also instituted, a process that frankly we use in the U.S., around managing the pipeline for some of our lower-end instruments.

And so that alone has started to give us better visibility into when deals are expected to close over the course of this quarter and allowed us to add urgency and also manage more for a weekly close process, rather than a close process that's so heavily tailored towards the end of the quarter.

That does a few things; one, it gives us much better visibility into what we're working for the course of the quarter, it helps drive urgency into the team, and it helps make sure that we understand whether we have the pipe to get the deals we need.

Additionally, Tycho, the execution challenges that we've talked about in Europe, much of that related to this deferral challenge that I talked about in the script, where we had a surprisingly large amount of revenue that was not recognizable, and part of the discipline we need in the team is to pull in the orders to make sure that we don't have a lot of systems that don't get shipped in time to be recognized as revenue, or there are small contractual issues at the end of the quarter that wind up having a revenue recognition question and therefore can't be counted.

And that's all the discipline of making sure that those deals get closed earlier in the quarter, and Scott is going to make a big difference there as well, we believe..

Tycho W. Peterson - JPMorgan Securities LLC

Okay..

Marc A. Stapley - Executive Vice President, Chief Financial Officer & Chief Administrative Officer

Tycho, I would just add one point to your question about confidence in the outlook for the rest of the year. As I mentioned in the script, or Francis mentioned, we've got Europe in our outlook currently at the revised number that they've committed to and provided recently, which is a lot lower than it was previously.

And so that gives us an opportunity to get these changes and improvements baked in, and start to get some positive impacts from them..

Tycho W. Peterson - JPMorgan Securities LLC

Okay. That's helpful. And then just on the other side, on spending, I know you talked about maybe pulling back on some of the hiring. Can you just get us comfortable that – I mean, you're such an innovation-driven company that you're not necessarily going to be kind of pushing off stuff that could impact the pipeline and really, future growth..

Jay T. Flatley - Chairman & Chief Executive Officer

Sure. I mean, that's an important tradeoff for us to analyze, and we're in the process of doing that right now. And, of course, the most important programs that are the largest revenue generators, the ones with the highest ROI, will continue to be fully staffed and fully funded.

What we'll be looking for are other areas outside of the core product development activity. For example, we may re-staff some of our research at a bit slower rate, because we moved a lot of those people over into GRAIL, and much of that research work has an effect three years to five years from now.

So those are the kinds of things we can slow down for some short number of quarters until we get back to the revenue growth rates that we believe we should be at. And clearly, we're going to do that in some of the other support organizations as well, without impacting customer support and the core product development activity.

So we're pretty confident we can make a big impact without hitting the core..

Francis A. deSouza - President & Director

Yeah. Another example of something we're doing there, Tycho, is look, we've already kicked off an initiative to drive more focus and prioritization.

And one of the things that we'd identified was that look, there's this terrific strategic planning process that kicks off the project that we want to focus on for the future and leads to the new products we put out. One element that we hadn't focused on historically is to look at all the initiatives we have underway and see what we could stop doing.

So we had already kicked off an effort to look at all the things we had going on and prune that portfolio, if you like. So that's an effort we already had underway. We're accelerating that to sort of complete over the course of this quarter, and expect to roll that out starting over the next quarter..

Operator

Thank you. And our next question comes from the line of Doug Schenkel of Cowen & Co. Your line is now open..

Doug Schenkel - Cowen & Co. LLC

Good afternoon. I guess, first, just a – I guess a couple quick ones, and then maybe a slightly longer answer question after that. So the first one is, maybe as a follow-up to Tycho, regarding your guidance for the year, some seem to be focused on what seems to be some back-end loading of the guidance.

Does your guidance reflect an assumption that demand gets better, or execution gets a lot better in the second half? Or is your guidance simply reflecting that comparisons get a lot more favorable in the second half, keeping in mind first half growth last year was around 30% and second half growth was 17%? It doesn't seem like you're baking in a whole lot more for the second half than the first half.

It seems like it's more comps driven.

Is that fair?.

Jay T. Flatley - Chairman & Chief Executive Officer

Hello..

Marc A. Stapley - Executive Vice President, Chief Financial Officer & Chief Administrative Officer

Doug. Yes, can you hear me? It's Marc..

Operator

We're back guys. Sorry, we lost the call there for a minute..

Doug Schenkel - Cowen & Co. LLC

Okay..

Jay T. Flatley - Chairman & Chief Executive Officer

Doug, I lost you about two-thirds the way through your question, I think..

Doug Schenkel - Cowen & Co. LLC

Yeah. It's really just your guidance for the year and the pacing doesn't seem to reflect a whole lot in the way of herculean assumptions for an improvement in the second half in terms of demand or execution.

It seems on the surface to be more a function of just changes in year-over-year comparisons, first half to second half, is that fair?.

Jay T. Flatley - Chairman & Chief Executive Officer

Well, there's a couple of elements, comparisons are better or easier in the back half, for sure.

We're not anticipating any radical changes in the European outlook, because we've actually factored in the disappointing European outlook into the guidance numbers that we've given, and obviously we'll be working to do better than those numbers and are working hard to achieve that.

But the single biggest factor that gives us a lot of confidence in the back half is the backlog, the strength of the backlog, the incoming order rate that we had in Q1 and the pipeline that we see for business in the Americas and Asia-Pacific in the back half.

So that's what really gives us confidence in the increasing revenue rates in the back half of the year..

Francis A. deSouza - President & Director

Yeah. I'd say very strongly that the numbers we've put out for the rest of the year were driven from a bottoms-up look at what the regions were forecasting, based on what they had in the pipeline and had visibility into. And so that's what gives us the confidence..

Doug Schenkel - Cowen & Co. LLC

Okay. Another area of focus has been clinical growth, you grew 20% in the quarter, oncology growth was 9%. These on the surface jump out as being light. That being said, what you didn't point out was that clinical growth was up against a tough compare. I think you grew 60% in Q1 of last year, the oncology comp I think is 37% growth.

Can you just share any data on backlog, or really anything else, that will help address concerns about a moderation in clinical demand?.

Jay T. Flatley - Chairman & Chief Executive Officer

Yeah. I think, as we tried to indicate in the script, we didn't see any fundamental demand factors in our business. We did very deep analysis, as you might imagine, over the last few weeks and so that did not pop out from anywhere. The clinical comparisons were very difficult against Q1 last year for sure, as you pointed out.

And so I think that's the single biggest driver in the numbers that we saw in Q1.

So we continue to feel very positive about the clinical adoption rates going through the year, and a lot of the key inflections in our markets, whether it's average risk (29:54) coverage, whether it's oncology reimbursement, those affect us largely in the clinical markets over the next year..

Doug Schenkel - Cowen & Co. LLC

Okay. And one last one. Q1 was not your best quarter, and it's been a tough two out of three.

That said, you made it really clear in your prepared remarks that nothing occurred in the quarter that heightened concern about overcapacity, competitive dynamics, the clinical outlook or market potential, but one of the big debates in the investment community is about Illumina's long-term growth outlook.

Given some recent developments, and clearly the moderation in revenue growth over the last few quarters, we didn't hear anything in your remarks that would suggest there is a change in how you think about the market opportunity or your ability to drive growth via innovation.

Could you just help us with some commentary in terms of how you're thinking about things on the longer-term growth potential, and why we shouldn't think differently about Illumina, given what we've seen over the last few quarters?.

Jay T. Flatley - Chairman & Chief Executive Officer

Sure.

Hey, if anything (30:58) I'd say that there is nothing that happened in Q1, despite our disappointment, your disappointment, and obviously our investors' disappointment in our actual performance there, that caused us to change our thinking or our conviction in any way about the sequencing opportunity, the market position we have, the competitive prospect, or the future growth and (31:21) of our business.

So there are no fundamental changes there, we clearly didn't think it was appropriate to emphasize those points in the script, on the back of a disappointing quarter for all of us. So we didn't highlight that, but I can assure you that there is – this is something we consider to be a short-term issue with us and we're going to come through it.

And there is no fundamental changes in our outlook to the market or our pace of innovation over the next couple of years..

Doug Schenkel - Cowen & Co. LLC

Okay. Thank you..

Jay T. Flatley - Chairman & Chief Executive Officer

Yeah..

Operator

Thank you. Our next question comes from the line of Derik De Bruin of Bank of America. Your line is now, open..

Derik De Bruin - Bank of America Merrill Lynch

Hi, good afternoon..

Jay T. Flatley - Chairman & Chief Executive Officer

Hi, Derik..

Derik De Bruin - Bank of America Merrill Lynch

Hey, just one short question which is stock option expense for the full year and then a longer question which is sort of following up on Doug's question I think, we've had a lot of incomings from investors questioning the outlook and just the numbers.

But I think, in particular, we had a lot of questions on GRAIL and Helix and the fact that those are dilutive to earnings right now and when they would start to potentially be more accretive, I guess.

The question been is like when are potentially we going to see some return on those investments and it's more of a question about valuation support for the stock, relative to some of the other names in the MedTech space, that are trading at similar types of top-line growth levels right now.

So basically give us some clarity or some indication when do you think you're going to see some benefits from – be able to get some benefits from Helix and GRAIL?.

Jay T. Flatley - Chairman & Chief Executive Officer

What was the stock comp question exactly?.

Derik De Bruin - Bank of America Merrill Lynch

What is the update for the full year, is there – what's the number for the full year..

Jay T. Flatley - Chairman & Chief Executive Officer

So, Marc, do you want to cover....

Marc A. Stapley - Executive Vice President, Chief Financial Officer & Chief Administrative Officer

Yeah. Derik, let me talk to that one really quickly. I'm not giving that specific number at this point, but we're on a path here that isn't going to accelerate that substantially through the second half. There are going to be some upticks, part of which is related to Helix and GRAIL and part of which is related to core Illumina.

But it's not going to be that vastly different from what you've seen so far..

Jay T. Flatley - Chairman & Chief Executive Officer

With respect to GRAIL and Helix, Derik, those are incredibly important, strategic bets for our company. We think they both represents, on their own, massive markets, as we've talked, about in cancer screening, gigantic opportunity, probably the single biggest market segment that we can imagine.

We continue to believe that there is going to be a strong market for consumer genomics, but it's going to take some work to create the ecosystem to really unleash that, and that's the goal of Helix.

And as a company, it is critically important that we take a long-term view and that $0.05 a share in a quarter, even $0.10 a share in a quarter, compared to the opportunities that these two ventures portend for us in the next five years, is insignificant.

And so, we're not prepared today to talk about when these are going to turn profitable, and begin to contribute to the bottom-line, but GRAIL, as we mentioned, is a long-term bet and they're not going to be seeing product on the market for some time.

Helix will be quicker and so once we get into 2017, we'll begin to get the earliest indications of revenue ramp, but I certainly wouldn't expect that to be a profitable enterprises in 2017..

Derik De Bruin - Bank of America Merrill Lynch

Great. I'll get back in the queue. Thank you..

Operator

Thank you. Our next question comes from the line of Dan Arias of Citigroup. Your line is now open..

Daniel Arias - Citigroup Global Markets, Inc. (Broker)

Yeah. Hi, good afternoon, guys..

Jay T. Flatley - Chairman & Chief Executive Officer

Hi, Dan..

Daniel Arias - Citigroup Global Markets, Inc. (Broker)

Jay or Francis, just to go back to Europe, as you've digested the issue a little bit, have you found that the shortfall on the HiSeq side was due more to installs that didn't materialize on the clinical or on the non-clinical side of things? And then if I could just ask a follow-up for Marc.

Marc, what are you forecasting instrument revenues to be down year-over-year at this point? Thank you..

Jay T. Flatley - Chairman & Chief Executive Officer

Yeah. There was nothing in the European numbers that was market specific. And so these were revenue recognition issues of various sorts as I highlighted in the script. None of those were particularly related to specific markets within the clinical sector or the research sector..

Francis A. deSouza - President & Director

Right, they are two very different issues, right. If we look at Q1 HiSeq story and that was the HiSeq story across regions and we talked about the fact that a lot of that was the HiSeq shortfall (35:47) in the orders that came in that we weren't able to recognize as revenue. So that's really what the Q1 story was.

Looking forward the issue is around the forecasted shortfall in Europe and there we believe a lot of it is around sales execution.

And that's really what we are focused on, driving more discipline and generating the pipeline, getting visibility into the pipeline and urgency in working the deals through the process and that's across instruments and across markets in Europe..

Daniel Arias - Citigroup Global Markets, Inc. (Broker)

Okay.

So, Francis, if I could just sort of crystallize from both your thoughts on the issue itself in Europe, is it your estimation that what took place in Europe was pretty much 100% personnel-related?.

Francis A. deSouza - President & Director

I think personnel and then the knock-on effect on the process we're running in Europe. I feel like, we have – and you're not going to put all this on one person and we have definitely good people on the team.

What we are seeing is that we don't run as disciplined a process in Europe as we do in the other regions, and already we're starting to see in the last few weeks an improvement in the visibility of the pipeline through this quarter and we're seeing more urgency in our sales process.

So that we believe were the biggest drivers in what we're seeing in Europe..

Marc A. Stapley - Executive Vice President, Chief Financial Officer & Chief Administrative Officer

And Dan, on the instrument revenue, yeah, we are not bifurcating the guide for the year into the individual component pieces, but I gave some specific commentary, I mean clearly we've given commentary around Q1. I gave some specific commentary around Q2 there as well.

So definitely a slower start for the year, driven by the high throughput and then as I mentioned we're seeing uptick towards the second half of the year, but not giving out specific commentary on breaking down the revenue growth by category at this point..

Daniel Arias - Citigroup Global Markets, Inc. (Broker)

Okay. Thanks, so much..

Operator

Thank you. Our next question comes from the line of Jon Groberg of UBS. Your line is now open..

Jonathan Groberg - UBS Securities LLC

Thanks a million.

So, (37:57) just correct me if I'm wrong, Jay or Francis, but it feels a little bit it was like, two misses out of three quarters, that maybe you – just given the size of the company, you have a pretty segmented market in terms of the products that you're in, it feels to me like there is a transition happening, kind of away from being necessarily your products story and a little bit more a market development story, and I'm just wondering, do you feel like you have a little less control or visibility into your quarterly results and if you need to, but just more broadly, if you're thinking about, how you need to approach forecasting?.

Francis A. deSouza - President & Director

Yeah. I maybe wouldn't characterize it exactly like that, Jon, but I think your points are important ones.

I've highlighted over the past year or 18 months that much of the market development that has to happen now in sequencing falls on Illumina, that we don't have a lot of other large companies who are spending marketing dollars developing markets and so that is key for us to do, more than it ever has been.

And the big markets we're opening up now have each their own unique set of issues, whether it's reimbursement or regulatory or in the case of GRAIL, clinical trial work. And so it does take some time to open up those new markets.

Having said that, there is no question that Illumina is so driven by product innovation and in all of our businesses, we analytically see, a cycle that's related to product cycles and that, whenever we launch new platforms, we get a surge of new orders for those instruments and then the following year, the consumables begin to catch up and then that platform begins to level out over time.

So, every platform has an S curve associated with it. It is true that we are a larger company now and therefore, each individual S curve has a smaller effect on the total revenue of the company.

So, there is no getting around that fact and so we've – we have much greater diversity in our business now, which is a good thing, but each individual product launch probably is less of an impact that it might have been back when we had only one sequencer.

For example when we replaced the GA with the HiSeq everybody bought a HiSeq, because it was the only product in the market. That's not quite where we are today..

Jay T. Flatley - Chairman & Chief Executive Officer

Yeah. And as we look to operationalize those dynamics, as I said, there are two dynamics playing out.

One is, there is an opportunity for us to get more actively involved in the development of those markets, so we can accelerate the adoption of MGS into the different markets we play in and work with our customers to help them with things like, the trial that we're doing, the STAR trial we're doing in the PGS space, in the IVF world for example.

We're also getting more engaged with our customers in the payer community and market access programs, and part as Jay said, what we do to develop the market is actually bring new instruments into the market which can catalyze the market through the access to a lower price point.

So, certainly, a set of things we are going to operationalize, developing those markets. Separate from that, there is a change in how you sell at this scale.

And that, in addition to sort of tracking the big deals that get a high level of visibility at the executive level, a scalable sales process needs to make sure that we're taking care of the flow business and that we do have really good visibility into the pipeline, how pipelines are progressing, the opportunities and that's what we're putting in place in Europe for example right now..

Jonathan Groberg - UBS Securities LLC

And that's helpful. And then, just as a quick follow-up, I think you were minus 5% in Asia Pac where you said you're guiding to mid-teens, I know you had a solid book-to-bill, is there anything else that the kind of – gives you the confidence in that acceleration in Asia Pac for the rest of the year? Thanks..

Jay T. Flatley - Chairman & Chief Executive Officer

Yeah, that's exactly right. So, we did see, as expected a decline in Asia in Q1, but as we look at the forecast for the rest of the year, we do believe we have the opportunities and pipeline to support a mid-teens growth in the year.

The things that are driving those are one, there is activity around the Chinese PMI that is causing purchasing to happen. We saw that already start and we expect that to play out. We're continuing to see incremental improvement in Japan for example.

And while that is slow and steady, it's slow and steady in the right direction and we're seeing that show up in our pipeline as well..

Marc A. Stapley - Executive Vice President, Chief Financial Officer & Chief Administrative Officer

And Jon, obviously Japan was a challenge quarter-after-quarter for us last year and so that's reflected in the (42:39-43:49)..

Rebecca Chambers - Vice President-Investor Relations & Treasury

Operator, we're ready for the next question..

Operator

And the next question comes from the line of Ross Muken of Evercore. Your line is now open..

Ross Muken - Evercore ISI

Good afternoon, guys.

So, can you just go back to that capacity utilization slide and sort of help us understand exactly sort of what we're looking at and how we should sort of interpret the peaks and dips in terms of how you relate that or if it's at all relatable to how you think about your instrument forecasts or managing at least sort of that (43:22)?.

Jay T. Flatley - Chairman & Chief Executive Officer

Yeah. Marc, you want to walk through that or you want me to or....

Marc A. Stapley - Executive Vice President, Chief Financial Officer & Chief Administrative Officer

I just want to, yeah, Ross, guess what, I missed the first part.

You were saying in relation to the utilization slide?.

Ross Muken - Evercore ISI

Yeah, I'm just trying to exactly understand how we should interpret sort of the various levels of capacity utilization across the base, and then, how we should think about certain points. Typically, if you think about capacity utilization, it sort of signals capital purchasing depending on what level it is.

So how do we interpret what levels for you to signal that you should see an increase in instrumentation demand versus maybe a moderation at a certain level and how you sort of attempt to manage it. I'm just trying to exactly interpret what we are supposed to gain from those..

Marc A. Stapley - Executive Vice President, Chief Financial Officer & Chief Administrative Officer

Yeah. So I think a couple of things. Firstly, the capacity calculation itself, which is based on the actual mix of types of kit that our customers buy and run.

Clearly, that's increasing quarter-over-quarter as a result of both the installed base, a little bit of the change in mix and that's coming up with higher throughput instruments, which I will come back to, when I look at the capacity utilization chart.

If you think about the percentages, what you probably – what you don't want to see is a very low percentage of utilization. That would reflect a lot of spare capacity in the market, which would have a read-through, I think, to future instrument purchases.

You're obviously not going to see utilizations based on our trajectory of past history and our trajectory of much over 50% on an ongoing basis due to the decentralization of market. Only in a centralized market would you see it much, much higher than this.

So, if you look at the data, what you're seeing is – well, you see a couple of inflection points where the utilization tends to stabilize.

That happens to coincide, in fact in one case, go down, if you look at 3Q 2014, that coincides with when we put new capacity in the market, so back then was the v4 run kit and that created an instant increase in available capacity, which caused the dip in utilization, you can see that recovered.

Same thing as, when we introduced the HiSeq 4000, that had an effect on the growth and utilization because we introduced new capacity into the market, with that instrument as well.

And then what you're seeing if you see it normalize without one large order is they have a fairly consistent growth rate, which is exactly what you would want to see, which I believe – we believe reflect that the capacity is not – there is not excess capacity in the market, it's being utilized at a rate that is increasing over time, in spite of the increased volumes or capacities that we're putting out there with the higher throughput instruments and kits, does that safe? (46:11).

Jay T. Flatley - Chairman & Chief Executive Officer

The takeaway of course, from this, Ross, is that, to the concern that there is always extra capacity being generated in the market, I think this analysis and what we've gotten from our base analytics show that that's just not the case.

That the average instrumentation utilization, if anything, is on a slightly upward trend, which is exactly what we would hope to see. And expect to see..

Ross Muken - Evercore ISI

Right. And I guess regionally, would Europe look any different, I'm sure you've probably cut the data at some point..

Jay T. Flatley - Chairman & Chief Executive Officer

Well, Europe would be lower on the averages, the trend line probably isn't too much different, but we clearly see highest utilization in the U.S. Europe tends to be significantly lower on average utilization across almost all the platforms..

Ross Muken - Evercore ISI

That's helpful. Jay, you started off talking about the various reasons for sort of the HiSeq miss, and you have that nice little pie chart which sort of breaks down the components. I guess, as you stated, typically in a quarter, maybe one or two will happen, but not as many.

I mean, as you think about the complexity of your business and what you can sort of manage versus what is just market-oriented and the like – and I guess, what period in the company's history, or what prior experience in all the years you've been doing this, would you sort harken back to and say oh, this reminds me of X, and because of Y, we feel confident.

I'm just trying to figure out it – what this most looks like, in terms of any of the few sort of periods of challenge that the company has had. I mean, there hasn't been very many..

Jay T. Flatley - Chairman & Chief Executive Officer

Well, and I think from a sort of magnitude of the challenge, Q3 2011 was the other big one for us, driven by very different factors, that was a collection. It was one of those, again, rare quarters where you had the convergence of a whole bunch of factors all at once, which I think we had this quarter as well.

The specific factors that were different than the ones we had in Q1, but it was one of those of sort of convergence effects that sometimes happens, and that's what happened to us in Q1. So I'd say that's the closest analogy, in terms of lots of things going in the wrong direction in one quarter..

Ross Muken - Evercore ISI

Got it. Thanks..

Operator

Thank you. Our next question comes from the line of Amanda Murphy from William Blair. Your line is now open..

Amanda L. Murphy - William Blair & Co. LLC

Hi, good afternoon.

So I just had a follow-up to your answer to Jon's question earlier about sort of the R&D pipeline, and I appreciate your comment about enabling markets and smaller S curves but I'm wondering, if you think about technical – or advancements that could further move the market forward, I was just curious if you can give us some high-level perspective there.

So, obviously, you mentioned the innovation at the lower kind of CapEx portion of the market, but is there anything in the works? Obviously, ordered arrays is quite meaningful in terms of the improvement in performance, is there anything like that in the works that you could talk to obviously, with respect to your R&D pipeline (49:21) obviously?.

Jay T. Flatley - Chairman & Chief Executive Officer

Well, I mean, we can't give you specifics on that of course, but if you think about it, ordered arrays have only been implemented on the very highest end of our product line, HiSeq X and the HiSeq 3,000, HiSeq 4,000.

So, we could put ordered arrays on other products in the product line, when and if that becomes important for a throughput and cost reason and is the highest return R&D program for us to invest in.

And so, that technology can be applied to the other instruments, we've not done that yet, because we don't think it's the most important factor in increasing the overall revenue from those segments.

But we have a broad product line now, and over time, various portions of that product line will age out and they will be replaced by brand new products that we bring into the market, that of course will have dramatic new innovations built into them.

And we've been working on the fundamental technologies around this (50:16) continued improvements in what we did in NextSeq and then how we learned from MiSeq and NextSeq and made a MiniSeq.

And many of those kinds of improvements will get bundled into whatever the next system architecture is, and clearly, we're working across the entire product portfolio, and we'll launch products into the segments we think are the richest opportunities therein.

And we think that, none of those segments is, I guess – I described it as permanently saturated, meaning that people won't change out their boxes if we bring something brand new in, and that can be dramatically different in cost, it could be dramatic improvements in ease of use and usability, dramatic improvements in speed, there is all kinds of vectors that we're working on and prioritizing in our R&D pipelines.

And then, instruments aside, we have very exciting stuff going in the sample prep area and the informatics area, and it's a very broad product development portfolio..

Francis A. deSouza - President & Director

Yeah. One thing to highlight is, look, in addition to looking to, over time, refresh everything we've got, one of the other things you can expect is, look, we are keenly focused on addressing the biggest impediments to getting NGS adopted in the different segments.

Some of that is through our own offerings and you can expect innovations where customers are telling both you and us that there are the biggest bottlenecks. So for example, one of the things we heard early on when we launched the X was that, the informatics around was a problem and a challenge for our customers, and you saw us launch C cloud (51:45).

So you can expect that, across the different segments, the biggest impediment is that customers are telling you about, they're telling us too, and through a combination of our own innovations and partner innovations, you should expect us to be looking to address those..

Amanda L. Murphy - William Blair & Co. LLC

Got it. Super helpful. And then, just I guess a more specific question on one of the reasons that you cited around the HiSeq miss was related to people evaluating the NextSeq.

So I was curious, I know that's not that many of them, but was that an NIPT-driven factor, and so, if so, then how should we think about product mix maybe changing, to the extent that average risk gains more traction next year?.

Francis A. deSouza - President & Director

Well, there was an underlying factor where one or a couple perhaps of our NXP (52:36) customers are converting to NextSeqs, but that was something we were aware of. And so that was in the plan, we knew that going in (52:40) forecast. We did exactly what we thought we were going to do in those examples.

The ones that we cited and referred to in the script and in the table were ones that essentially stalled the HiSeq quarter we expected to get at the very last minute, where we thought that those orders were coming in, and they didn't come in because the customer was considering that and we didn't know about it. That's the execution issue..

Amanda L. Murphy - William Blair & Co. LLC

Got it. Okay. Thanks very much..

Operator

Thank you. Our next question comes from the line of Bill Quirk of Piper Jaffray. Your line is now open..

Alexander D. Nowak - Piper Jaffray & Co. (Broker)

Great. Thanks. Good afternoon, everyone. This is actually Alex Nowak filling in for Bill today.

So going back to the first quarter, just trying to understand what happened following the preannouncement that changed the commentary from saying that the Q1 shortfall is predominantly due to customer outsourcing to now being a myriad of different issues that you really had no control over.

Just trying to understand, what was the change there?.

Jay T. Flatley - Chairman & Chief Executive Officer

So if you go back and look at the exact script, we didn't say primarily outsourcing, we did cite the example of outsourcing as one factor that we knew about at the preannouncement date.

You can imagine, in those two weeks before the preannouncement, we were scrambling hard to try to get as much data together as we could and have a preannouncement that was timely.

We didn't want to wait another week to do a preannouncement to have more data, and so we've learned a lot in the last two weeks when all of the analytics from the Q1 have really come in and we've been able to digest them, talk to the regions, get the new forecast, understand all of the background detail.

And so we've been able to go order by order and look at every one of the circumstances and break it into the pie chart that you see in the deck that we provided. And so there were a lot of different issues, and no singular thing to (54:28) dominate.

And so I think what happened is because we mentioned that one comment, people jumped on that one thing we mentioned as the cause, and it clearly wasn't and we didn't intend to imply that it was. So we probably should have said among many causes this was one we knew about at that time..

Francis A. deSouza - President & Director

Yeah. Lead (54:44) factor was a shortfall in HiSeq, that's the (54:48)..

Alexander D. Nowak - Piper Jaffray & Co. (Broker)

Okay. That's helpful. And then just switching to a little bit longer term....

Francis A. deSouza - President & Director

In addition to getting the orders that didn't convert into revenue, so those were the two issues that we talked about in the preannounce, and those are the two issues still..

Alexander D. Nowak - Piper Jaffray & Co. (Broker)

Okay. That's helpful. And then on the China Precision Medicine Program, just a two part question, sounds like you're starting to see the program move in the country. I'm just wondering if you could provide some more color on what you're seeing, what you're hearing from customers.

And then the second part of the question is, is there any risk that several customers in China are buying instruments, specifically, HiSeq Xs in anticipation for sequencing volume, and just because of the timing of a program ramp, you could have some idle (55:32) instruments sitting throughout China?.

Jay T. Flatley - Chairman & Chief Executive Officer

Well, we are seeing a number of customers gearing up to try to be participants in the PMI, we don't know who will win that ultimately, and I don't think they do either frankly. There's obviously a couple of some very strong candidates to participate, and those are large entities, some of which own instruments already, some of which don't.

So we think they will buy in advance to have some installation, and perhaps the pull through will be a little bit lower on those in early stages, but they should get very highly utilized once the program begins to ramp up.

So sure, we could have a little bit lower utilization locally on some instruments, but that's not atypical, I mean, people sometimes do that for other programs as well, and we'll take that into account in our forecast and our planning..

Alexander D. Nowak - Piper Jaffray & Co. (Broker)

Okay. Great. Thanks..

Operator

Thank you. And our next question comes from the line of Dan Leonard of Leerink. Your line is now open..

Dan L. Leonard - Leerink Partners LLC

Thank you. This overlaps a little bit with the last question, but Jay or Francis, I was hoping you could characterize the incremental X customers, I think you grew to 31 in the quarter.

And then also the funnel, in terms of are these (56:46) customers that have samples, have projects or are they buying Xs in anticipation of some missionary sales, some different kind of business model?.

Jay T. Flatley - Chairman & Chief Executive Officer

Sure. So one of the things we talked about is, we did have the four Xs that came in in Q1. We did see some interest from the – wanting to participate in the Chinese PMI that is driving some of the X interest. We haven't gone public with the customers that have come online in Q1.

So I can say that there is definitely demand generated from the Chinese PMI, but we can't talk about specific customers associated with that..

Rebecca Chambers - Vice President-Investor Relations & Treasury

Yeah. The only one that's public is GENEWIZ..

Dan L. Leonard - Leerink Partners LLC

Well, I know, at least early in the HiSeq X program, you were careful to deliver instruments to folks that had samples and had projects.

Is that still the case or are you more (57:42) shipping orders as they come?.

Jay T. Flatley - Chairman & Chief Executive Officer

No, that's still a factor. We still use the access to samples as a criteria for the purchase.

And what we've really seen in probably the past year is more of the X customers are metering out their instrument deliveries, we're in the very early phases of X, people converting their entire large existing programs over to the X, if you're abroad or an NHI (58:10).

What we see now is, someone will place an X order and say, okay, I want two units for now and then a quarter or two quarters from now, I'll take another three and so we're not – that's one way that we deal with sample access problem and they do as well..

Dan L. Leonard - Leerink Partners LLC

Thank you..

Operator

Thank you. Our next question comes from the line of Steve Beuchaw of Morgan Stanley. Your line is now open..

Steve C. Beuchaw - Morgan Stanley & Co. LLC

Hi. Good afternoon. Just a couple of clarifications. Marc, I wonder given the $700 million order figure that you provided, if you could give us just a little bit more context around it.

Could you give us any sense for maybe what the backlog growth was exiting Q1 or maybe how the growth in orders compares to what you saw in 2015, just so we can again put it in a little bit more context? And then Jay, I wanted to follow up on a couple of comments you made in the prepared remarks around clinical.

First on NIPT, I was a little surprised given that we're here in May of 2016, that you talked about some reimbursement decisions around NIPT getting delayed out to 2017, maybe I'm just overly optimistic there, but I wondered if there might be some hope for the second half of 2016, curious what is it that you're seeing there.

And then, just to round it out on clinical, on the clinical cancer side, I just want to make sure I understand the narrative, is it stable reimbursement, new products, drives (59:32) reacceleration, is that the way to think about it. Thanks..

Jay T. Flatley - Chairman & Chief Executive Officer

Hey, Marc do you want to start?.

Marc A. Stapley - Executive Vice President, Chief Financial Officer & Chief Administrative Officer

Yeah. So I'll start with the orders conservation. Steve, obviously a large part of the orders that we booked in the first quarter were shipped in the first quarter, as you would normally expect.

But we built significant backlog, and I quote out specifically sequencing consumable backlog, and that will ship mostly through this year, in fact, almost entirely, there is some that carries over into 2017 and beyond. But most of that is going to ship this year.

So the way I would think about that, is it's kind of an advanced ordering of reagent purchases that we're going to get, or we should get anyway throughout the year. So it gives us some confidence, but I wouldn't think of it as necessarily incremental. It is relative to last year and prior year, it is larger than we've traditionally seen.

And so it gives us a little bit more of the backlog than we would normally have at this time. And then, I also mentioned that we have about a third of our ending backlog for the quarter, rolling over into the second half which gives us some added confidence. Obviously, that includes a portion of those sequencing consumables that I just talked about.

So it's nothing more kind of quantitative than that at this point. But other than the sequencing consumables, I would say pretty pleased with the array business and the consumer driven activity there, which has been another helpful part of building backlog.

What it wasn't necessarily was a significant proportion of instrument backlog that's not, it's become much more of a – instruments have become much more of a turn in the quarter type of activity. We don't necessarily come into the quarter with significant levels of backlog like you saw us have in Q1 of 2015, and it's much more normalized now..

Jay T. Flatley - Chairman & Chief Executive Officer

Yeah, I would just add the math on the backlog growth is pretty simple. So it's $700 million plus minus the revenue that we get in. So that growth in the backlog was more than we've typically seen in Q1. So we felt really good about the incoming order rate.

With respect to NIPT, what we're seeing is that the large payers, the majors there tend to assess coverage decisions on specific dates. So they are on a cycle, and so if they're not on a cycle to do this in 2016, there is little to no chance they are going to go off cycle to approve this.

And so as we've mapped out all those cycles, there still remains a possibility of some of them late in 2016, but the majority of them fall in 2017, which is why we cited that we think that the bolus of these coverage decisions will be made in 2017.

With respect to cancer, the narrative really isn't about stable reimbursement, because the vast majority of the cancer tests aren't reimbursed today, even foundation medicine. So most of that market is being driven by labs running these tests for market share reasons. Most of the labs are losing money on the cancer tests.

So the reimbursement opportunity in oncology lies ahead of us, and it's something that many of our customers are working on. It's an area that I'll be spending a fair amount of my time on in the next year, and it's related to the standardization challenges that I think exist here.

We're in the phase of the oncology market where it's becoming increasingly fragmented with lots and lots of different panel products, and one of the things that Illumina needs to do is to begin to re-converge that market into a more standard set of products and more standard set of processes so that payers can get their heads around, what is a – something they should be paying for, and that's something our TST 15 is attempting to do initially in (01:03:30).

Our TST 170 will begin to move in that direction as well, but remember those are REO (01:03:35) products as we can't sell those for clinical use. And so we are evaluating what's happening with the FDA before we begin to push those toward regulatory approval..

Steve C. Beuchaw - Morgan Stanley & Co. LLC

Thanks so much..

Operator

Thank you. And our next question comes from the line of Dane Leone of BTIG. Your line is now open..

Dane Leone - BTIG LLC

Hi, thank you. I just had a quick one on how MiniSeq and MiSeq performed.

Could you kind of give us color because historically, you commented that there would be some degree of cannibalization in sales, can you just kind of give us a basket idea of collectively how MiniSeq and MiSeq kind of performed as a group this quarter versus maybe last year, which would have only been MiSeq, and kind of how you expect that ramp and MiniSeq specifically to continue over the course of this year?.

Jay T. Flatley - Chairman & Chief Executive Officer

If you recall we had projected nominally a 20% to 25% cannibalization rate of MiSeq.

We're seeing a rate so far at least that's less than that, and part of it is an interesting phenomenon where the low price point of the MiniSeq opens the door to a new customer, and then as we begin to engage with that customer we use it as an up-selling opportunity to sell them a MiSeq rather than a MiniSeq.

And so we're seeing that phenomenon working well for our sales people because they love to sell $100,000 instrument rather than $50,000 one, if they have the option to do so. Having said that, the MiniSeq product did well in its first quarter. We've got a great pipeline there, and we're continuing to be optimistic about MiniSeq.

And the data we have today at least indicates a lower cannibalization rate of MiSeq than we would have expected previously..

Dane Leone - BTIG LLC

Okay. Thanks..

Operator

Thank you. And our final question comes from the line of Jack Meehan of Barclays. Your line is now open..

Jack Meehan - Barclays Capital, Inc.

Thanks. Thanks for squeezing me in. Just a follow up one on MiniSeq. Do you have sense at this point for what we should be building in as a range for quarterly replacements? And I know there is the long tail of labs that would like to do sequencing.

Have you found this customer class is more responsive to an instrument sale approach versus reagent rental?.

Jay T. Flatley - Chairman & Chief Executive Officer

(01:05:48) too early for us to have any data on that Jack. So we're continuing to look at this, and the number of customers that actually crossed the finish line, got it installed, and actually running these at any volume is still a relatively small number. So it's too early for us to put an estimate out there.

In general, what we've used across the product line is about half of the purchase price, I think in this product, or probably less than that. So I've modeled something less, significantly less than half....

Rebecca Chambers - Vice President-Investor Relations & Treasury

12 to 15 (01:06:18)..

Jay T. Flatley - Chairman & Chief Executive Officer

Yeah, yes, exactly. So we'll be looking probably three or four quarters out before we actually start quoting what the actual range is running..

Jack Meehan - Barclays Capital, Inc.

Got it. That's helpful. And then, just one for modeling out. I know here in May, you're not ready to be talking about 2017, let alone 2018 or 2019, but I think one of the moving pieces of the income statement across the Street is the R&D line item, just given some of the expenses you're planning for both GRAIL and Helix.

Can you just give us a framework for what we should be building in, in terms of long-term expenditures in R&D is closer to revenue growth, or do you think some of these new products we should be building in something more than that? Thank you..

Jay T. Flatley - Chairman & Chief Executive Officer

Well, I think, clearly, GRAIL and Helix in many ways are incremental to what we're doing before, and we should be thinking about them as such. These are very important strategic bets that we think are the most important market opportunities for us to be working on.

But the base level of R&D and the growth rates you've seen over the past couple of quarters will begin to moderate based on the absolute number, will begin to moderate based on the the absolute (01:07:29) asset growth rate will moderate in the R&D lines because of the actions we're taking to slowdown hiring, and that's important to more closely match what's happening in R&D with the recast revenue growth rate.

And so we'll be analyzing this over the next quarter and probably give you a little bit more update next quarter, not guidance for 2017 or 2018, but probably a little more qualitative statement about what you can think about R&D and sales and marketing..

Francis A. deSouza - President & Director

Yeah. One of these we have studied, and if you take out GRAIL and Helix over any three-year time horizon, there is enough leverage in our operating model organically. So we continue to believe that..

Rebecca Chambers - Vice President-Investor Relations & Treasury

Thanks, Jack..

Operator

Thank you. And I would like to now turn the call back to Rebecca Chambers for closing remarks..

Rebecca Chambers - Vice President-Investor Relations & Treasury

Thank you operator. As a reminder, a replay of this call will be available as a webcast in the Investors section of our website, as well as through the dial-in instructions contained in today's earnings release. Thank you all for joining us today.

This concludes our call and we look forward to our next update following the close of the second fiscal quarter..

Operator

Ladies and gentlemen, thank you for participating in today's conference. This does conclude the program. You may all disconnect. Everyone have a great day..

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