Illumina Inc. (NASDAQ: ILMN) Q3 2020 earnings call dated Oct. 29, 2020
Corporate Participants:
Juliet Cunningham — Vice President, Investor Relations
Francis deSouza — President and Chief Executive Officer
Sam Samad — Senior Vice President and Chief Financial Officer
Analysts:
Doug Schenkel — Cowen — Analyst
Tycho Peterson — JPMorgan — Analyst
Derik De Bruin — Bank of America — Analyst
Puneet Souda — SVB Leerink — Analyst
Dan Arias — Stifel — Analyst
Tejas Savant — Morgan Stanley — Analyst
Vijay Kumar — Evercore ISI — Analyst
Catherine Schulte — Baird — Analyst
Dan Leonard — Wells Fargo Securities — Analyst
Patrick Donnelly — Citigroup — Analyst
David Westenberg — Guggenheim Securities — Analyst
Dan Brennan — UBS — Analyst
Presentation:
Operator
Good day, ladies and gentlemen, and welcome to the Third Quarter 2020 Illumina Earnings Conference Call. [Operator Instructions] Thank you. As a reminder, this conference call is being recorded.
I would now like to introduce your host for today’s conference call, Ms. Julia Cunningham, VP, Illumina Investor Relations. Please go ahead.
Juliet Cunningham — Vice President, Investor Relations
Good afternoon, everyone, and thanks for joining us for our third quarter 2020 results conference call. During the call today, we will review the financial results released after the close of market and offer commentary on our commercial activity, after which we will host a question-and-answer session. If you’ve 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 Francis deSouza, President and Chief Executive Officer; and Sam Samad, Chief Financial Officer. Francis will share an update on our business and Sam will review our financial results. Similar to last quarter, we are hosting our call from a number of different locations, so please bear with us if there are any technical issues or pauses.
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 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 upon current available information 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 documents that Illumina files with the Securities and Exchange Commission, including Illumina’s most recent forms 10-Q and 10-K.
With that, I’ll turn the call over to Francis.
Francis deSouza — President and Chief Executive Officer
Thank you, Juliet. Good afternoon, everyone, and thank you for joining us today. We saw a strong rebound in our business in the third quarter with a faster recovery than we expected in both our clinical and research customers. Total revenue for the third quarter was $794 million, up 26% sequentially and down 12% compared to the prior year period.
I’ll share the third quarter highlights and Sam will provide more detailed financials. Sequencing revenue grew 25% compared to the second quarter of 2020. Sequencing consumables grew 29% sequentially with strength across our high, mid and low throughput product portfolio. NextSeq momentum continued to build with mid-throughput consumables growing both sequentially and 3% year-over-year. And we expect continued growth in the fourth quarter. Sequencing instruments also outperformed expectations with revenue up 24% sequentially. This growth was primarily driven by increased shipments of NovaSeq and NextSeq platforms. NovaSeq purchases have rebounded nicely from Q1 when some customers delayed purchases as shelter-in-place policies took effect.
We have been pleased with the sequential growth in NovaSeq shipments in each quarter since Q1. We’re entering the fourth quarter with a strong NovaSeq pipeline and expect the sequential growth to continue in Q4. In addition, we had another successful quarter for our mid-throughput portfolio with both NextSeq 2000 and NextSeq 550 exceeding our expectations.
Strong demand for these flexible sequencers led to record mid-throughput shipments in the third quarter. We’re especially pleased with the success of the NextSeq 2000 launch, reflecting positive customer feedback and demand. Approximately one-third of the NextSeq 2000 placements are coming from new to Illumina customers. Consistent with our expectations, we’ve seen little cannibalization of NovaSeq conversions among the remaining HiSeq customers.
Sequencing service and other revenue grew 9% sequentially and was 28% lower compared to the prior year due to one-time IVD licensing and development revenue of over $30 million in the third quarter of last year. Total microarray revenue of $86 million was up 28% sequentially as direct-to-consumer customers and other applications began recovering from pandemic-related headwinds.
Turning to our customer segments. We saw solid improvement in both clinical and research activity. As a reminder, we track sequencing run rates as an indicator of general activity. Run volumes are based on sampling and do not directly correlate with revenue. The intend to providing this metric is to help investors understand customer sequencing activity. Clinical sequencing run volumes increased from an average of 84% in the second quarter to 96% during the third quarter compared to pre-pandemic levels.
In oncology, we are encouraged by signs of point to continued adoption of NGS in cancer treatment. The European Society for Medical Oncology, or ESMO, became the first scientific society to issue recommendations for the use of NGS in oncology. Depending on the cancer type, the society recommends NGS for large multi-gene panels for the determination of tumor mutation burden and to screen patients for clinical trials. To-date, TSO500, which is for research use only, provides comprehensive genomic profiling that has been adopted by approximately 250 customers. We’re excited to release a CE-IVD mark TSO comprehensive assay in 2021 to ensure labs can follow ESMO guidelines and continue to improve cancer patient outcomes.
Growing payer adoption will continue to broaden the availability of these tests. Last month, Aetna, covering 19 million lives, announced coverage for large panel comprehensive genomic profiling for both solid and liquid, including testing for TMB. We’re also encouraged by the increasing availability and adoption for NGS-based liquid biopsy tests. The recent FDA approval for Guardant360 and FoundationOne Liquid CDx demonstrates the clinical utility of these technologies that detect cell free DNA from the tumor in the blood and can provide comprehensive genomic profiling when tumor tissue is not available. Liquid biopsy panels like these broaden access to more patients who can benefit from NGS in their cancer treatment.
Reproductive Health showed strength in the quarter, growing sequentially and year-over-year. In fact, during the third quarter, Reproductive Health averaged over 100% of its pre-pandemic run rate. We expect sustained growth as reimbursement prospects have never looked more promising. Recently, ACOG updated its guidance to recommend that NIPT be made available to all pregnant women, regardless of maternal age or baseline risk. This is a major milestone and we expect payers to continue to follow ACOG’s guidance, adding to the already 130 million plus lives covered for average risk in the U.S. Centene, for example, recently aligned its guidelines, adding average risk coverage to an additional 23 million lives in the U.S. Centene is also the largest Medicaid managed care organization in the U.S., meaning this coverage decision will bring NIPT as an option to more medically underserved areas and populations.
In Genetic Disease Testing, physicians, insurance companies and governments around the globe are increasingly adopting sequencing to diagnose children suspected of having genetic conditions. We’re seeing solid progress on the reimbursement front. Payer adoption in the U.S. continues to grow with more than double the lives covered for whole genome sequencing than at the start of the year. And Australia recently announced that it will reimburse whole exome or genome sequencing to identify the genetic cause of intellectual disabilities. These positive developments give us confidence in sustained long-term growth in this underpenetrated market.
Turning to Research, sequencing runs show continued improvement and increased from an average of 65% in the second quarter to 82% in the third quarter compared to its pre-pandemic run volumes. We’re encouraged to see researchers returning to their labs and reopening. And this level of improvement exceeded our expectations.
Within Research, we’re seeing the role of NGS take shape in infectious disease. We believe the most likely near-term use case for sequencing is in research and surveillance for projects like Australia’s First National COVID-19 Tracking System, which aims to sequence the virus genomes of all positive COVID-19 tests in Australia and track COVID-19 using genomics across the country. NIH is also increasing its funding for understanding COVID-19 and the transmission pathway using genomic testing. We continue to believe COVID-19 testing will be primarily served by PCR and antigen tests, with NGS providing supplemental testing capacity. As such, we’re not factoring in a material contribution to revenue in the fourth quarter from COVID-19 testing.
On the Population Genomics front, we’re seeing promising signs of progress. All of Us received its IDE approval from the FDA in the second quarter. And as expected, samples started to flow from the biobank to partner genome centers. We expect the project to ramp in the fourth quarter and into 2021. During the third quarter, sequencing for the UK biobank continued and we expect levels to gradually return to normal and sequencing to continue into 2021. And we expect whole genome sequencing services for the NHS Genomic Medicine Service to commence later this quarter. Given the NHS’s current focus on COVID, we expect this program to gradually ramp over the next few quarters.
Perhaps one of the most resilient PopGen programs in the face of the pandemic has been the Million Veteran Program, or MVP. The project aims to provide insights on how genetics, lifestyle and military exposures affect health and illness and has recently expanded its targeted enrollment from 1 million to 2 million veterans. The U.S. Department of Veteran’s Affairs, through its sequencing partner Personalis, expects to cross the 100,000 whole genome milestone before the end of the year. We believe these and other initiatives will expand our markets and create exciting new opportunities for Illumina. We are committed to continue to lead through innovation with new product launches to support the markets and customers we serve, including: NovaSeq 6000 v1.5 reagents, which were launched during the third quarter. This release offers increased shelf-life, improved quality scores, longer indexes and, most importantly, it makes the $600 genome more broadly available to help smaller labs be successful and provides additional incentives for labs to upgrade from HiSeqs to NovaSeq. NovaSeq 6000 v1.5 reagents have been extremely well received by our customers.
For example, the Princess Maxima Center, the largest national pediatric oncology center in Europe, was outsourcing its genome sequencing to a collaborator, but with the new reagents, they were able to purchase a NovaSeq and can now start to perform testing in-house, meaning potential care-altering genomic information will reach children with cancer faster and performed closer to the patient.
The longer read lengths, combined with high throughput scale, enabled a Canadian biotech company to adopt the NovaSeq 6000 for the development of antibody products for potential COVID19 therapy. We’re preparing to launch NextSeq 1000 this quarter. NextSeq 1000 enables lower throughput customers to adopt our newest platform as an entry point with the ability to field-upgrade to the NextSeq 2000.
We’re also launching the P3 flow cell this quarter. Early access P3 customers, including academic core labs, are already using the flow cell for routine sequencing methods in mid-sized research projects to enable faster turnaround times. Other customers are using P3 to develop workflows in single cell, epigenetics and spatial transcriptomics. These are examples of how we continue to execute on our current and future plans throughout these challenging times to advance our mission and create long-term shareholder value.
Now, I’ll hand the call over to Sam to discuss the third quarter financials.
Sam Samad — Senior Vice President and Chief Financial Officer
Thanks, Francis. As discussed, third quarter 2020 revenue was $794 million, a 12% decline year-over-year, but a 26% increase compared to the second quarter of 2020. While the global pandemic continued to impact our business, we saw encouraging signs of recovery within both clinical and research customers.
Sequencing consumables revenue of $500 million was up 29% sequentially and down 5% compared to the prior year period. Quarter-over-quarter growth of $113 million reflected significant improvement across high, mid and low-throughput platforms with NovaSeq pull through returning to over 1 million per system per year. Our mid-throughput sequencing consumables grew in the quarter versus the same period last year.
Total sequencing system revenue of $109 million was ahead of our expectations with both NovaSeq and our mid-throughput platforms exceeding our expectations at the start of the quarter. The third quarter was also a record quarter for mid-throughput shipments driven by customer demand for NextSeq 2000 and the NextSeq 550 Dx platform. In fact, NextSeq Dx shipments represented over 40% of NextSeq 550 shipments year-to-date. Since 2013, Illumina has shipped over 1,000 Dx instruments, reflecting the growing clinical nature of our customer base.
Sequencing service and other revenue of $99 million was lower compared to the third quarter of 2019. Total sequencing revenue was $708 million and represented 89% of total revenue. Finally, total microarray revenue of $86 million was down 16% from the third quarter of 2019, reflecting lower consumables and services revenue primarily driven by COVID-19-related headwinds.
Turning to the regions, Americas revenue of $436 million was ahead of expectations and grew over $100 million or 30% compared to the second quarter of 2020. Sequential growth was driven by both research and clinical customers as labs continued to reopen and clinical activity increased. In fact, clinical sequencing consumables grew modestly compared to the prior year period as demand started to recover after delays in testing in the second quarter.
EMEA revenue of $213 million was up $45 million compared to the second quarter of 2020 with strength in sequencing consumables, which grew compared to the third quarter of 2019 driven by a strong rebound in both clinical and research customers. China revenue grew sequentially to $83 million, driven by strength in instrument placements. APJ revenue was roughly flat year-over-year at $62 million and increased $11 million compared to the second quarter of 2020 with NIPT helping to lead the recovery with sequential and year-over-year growth.
Moving through the P&L, I will highlight non-GAAP results that include stock-based compensation. I encourage you to review the GAAP reconciliation of these non-GAAP measures, which can be found in today’s release and the supplementary data available on our website. Please note that all subsequent references to net income and earnings per share refer to the results attributable to Illumina shareholders.
Non-GAAP gross margin of 67.4% was lower, as expected, on both a year-over-year and sequential basis. The year-over-year decline was driven by IVD partnership revenue in the third quarter of 2019 not repeating this year and lower volume and higher freight costs associated with the pandemic. Non-GAAP operating expenses of $365 million were higher compared to the second quarter of 2020 and the same quarter last year. Sequential growth was driven, as expected, by an increase in R&D project spend and higher compensation expenses. Compared to the third quarter of 2019, operating expenses were higher primarily due to compensation-related expenses and increased project spend, partially offset by decreased travel. Non-GAAP operating margin was 21.4%, up from 15.8% last quarter. The non-GAAP tax rate of 14.8% was lower compared to last quarter and prior year due to discrete tax benefits related to prior year return adjustments and release of tax reserves.
For the third quarter of 2020, GAAP net income was $179 million or $1.21 per diluted share and non-GAAP net income was $150 million or $1.02 per diluted share. Other income was the main driver for the difference between GAAP and non-GAAP net income due to net gains from mark-to-market adjustments on our strategic investments, primarily from our marketable equity securities.
Additionally, in the third quarter, cash flow from operations was $153 million. Capital expenditures were $48 million and free cash flow was $105 million. DSO of 53 days compared to 55 days last quarter, in part, due to increased collections. We repurchased $125 million of common stock in the third quarter with $295 million remaining for repurchase under our current plan. We ended the quarter with approximately $3.3 billion in cash, cash equivalents and short-term investments. Our weighted average diluted share count for the quarter was approximately 148 million.
As we continue to navigate this pandemic, there are still uncertainties around the virus resurgence and rate of recovery. And therefore, we will not provide guidance for the remainder of the year. Additionally, we are closely monitoring developments in the pandemic given the risk of new shutdowns in the U.S. and Europe. In the fourth quarter, we expect that sequencing run volumes will continue to improve modestly for clinical and research customers from the 96% and 82% levels respectively in the third quarter. Again, we caution that this does not directly correlate to revenue, but data from the third quarter suggests customers are steadily returning to their labs, which will lead to increased activity. Consistent with the third quarter, we expect fourth quarter sequential growth across all regions with China and APJ showing flat to modest growth year-over-year.
For the fourth quarter of 2020, we currently expect continued sequential improvement in revenue, resulting from sequencing consumables being up modestly on a sequential basis as clinical and research activity continues to gradually improve. Sequencing instruments increasing sequentially and the fourth quarter is expected to be the strongest quarter of the year for instrument placements. Sequencing service and other flat sequentially and microarrays up modestly on a sequential basis as we continue to see a gradual recovery in direct-to-consumer and genotyping applications
For the rest of the P&L, we expect sequential decline in non-GAAP gross margin, in part, driven by product mix with higher contribution from instrument sales. Sequential increase in non-GAAP operating expenses, primarily driven by R&D project-related expenses, compensation related expenses and an extra week in the fourth quarter compared to the prior quarter and prior year. Non-GAAP EPS to be roughly flat compared to the third quarter of 2020, reflecting revenue improvement offset by lower gross margins and a sequential increase in operating and tax expenses.
With that, I’ll hand the call back over to Francis for some closing remarks.
Francis deSouza — President and Chief Executive Officer
Thanks, Sam. As the global leader for sequencing platforms and consumables, we’ve seen our products enable groundbreaking research programs and transformative clinical tests that have the potential to shift the paradigm in patient care. One of the largest opportunities for patient impact and revenue potential for years to come is the ability for NGS to detect cancer early.
Last month, we announced a definitive agreement to acquire GRAIL and we expect the acquisition to close in the second half of 2021. We believe our planned acquisition of GRAIL will accelerate a new era of early cancer detection, transforming cancer survivability and opening up the largest clinical application of genomics we’ve seen. We look forward to welcoming our GRAIL colleagues to Illumina when the acquisition closes. Upon close, we expect to operate GRAIL as a division within Illumina. We remain committed to supporting all of Illumina’s customers and ensuring that innovators who wish to develop NGS-based tests have continued access to our technologies.
To conclude, the recovery of our business accelerated in the third quarter with significant sequencing consumables revenue growth compared to the second quarter of 2020 and we expect continued consumables growth in the fourth quarter. Importantly, we’re also making good progress incorporating genomics into the standard of care in oncology therapy selection, NIPT and genetic disease testing. And most importantly, we believe that we’re laying a strong foundation for Illumina’s near- and long-term growth.
With that, we’ll open the call up to Q&A.
Questions and Answers:
Operator
Thank you. [Operator Instruction] Your first question comes from the line of Doug Schenkel with Cowen. Your line is open.
Doug Schenkel — Cowen — Analyst
Good afternoon, guys. And thank you for taking the questions. The quarter was clearly better than most expected, I think, even better than you guys probably thought in a lot of instances. I’m just wondering if you have a sense for how much of this was catch-up versus reflecting a new base to build off of moving forward. Based on your prepared remarks on Q4, both yours, Sam, as well as yours, Francis, it does seem like this is kind of a new base to build off of, given the momentum you’ve described heading into Q4. Is that fair?
Francis deSouza — President and Chief Executive Officer
Hi, Doug. I think that’s fair. If we look at how this quarter played out, it certainly played out better than we expected based on how the first few weeks of the quarter were looking. So what we saw over the course of the quarter was an acceleration in the recovery in terms of the sequencing activity in both our clinical and research customers. And so, as we exited the quarter, I think we’re at a new baseline that we will keep going into Q4. So I think it’s fair to say that the recovery accelerated to create a new baseline for us going forward.
Operator
Your next question comes from the line of Tycho Peterson with JPMorgan. Your line is open.
Tycho Peterson — JPMorgan — Analyst
Hey, thanks. Want to kind of hit on two things. Just the elasticity on the consumable pricing cut. You highlighted couple of examples for customers that have come forward on the $600 genome and use it as a reason to buy NovaSeq. But I’m just curious as we think ahead into next year. How much incremental demand do you think that that will drive and to what degree will it catalyze some of the projects that you hope it would. And then, on the instruments side, instruments were still down 23%. I’m just mentioning if you could comment a little bit on when you think they’re really going to get back to growth?
Francis deSouza — President and Chief Executive Officer
Yeah, sure. So let me take both of those questions. So first around the elasticity point associated with the launch of version 1.5 reagent. So what version 1.5 and to do and we saw the effect in the quarter, was there any catalyze some of the smaller core labs by giving them access to the $600 genome. The larger labs already had access to the $600 genome. So this is really a released targeted at the smaller core labs and the incentives to do two things, one to unlock the elasticity and that part of the market. And so we saw customers that were, I think you bigger projects we saw customers that are moving to insource and I talked about an example of that in the prepared remarks.
The other thing that the this release was intended to do was catalyze upgrade cycle in that segment of the market, the smaller core labs. And so we started to see examples of customers that were either on older instruments or didn’t have, so they could get HiSeq, for example, or they didn’t have sequencers. And because of this release they were able to buy a NovaSeq, both of those dynamics so capitalizing the elasticity of demand in terms of bigger projects as well as driving an upgrade cycle our dynamics, we expect to continue to play out into Q4 and going into next year. As you know, typically when we release a new price point into the market a lower price point. Initially, there is a bit of a headwind in this case, though, we expect it to be very short and that’s how it’s playing out, where very quickly we’re starting to see both of those positive dynamic start to play out.
The second question, you talked about was around instruments and maybe I’ll start and Sam, you can add to it and I talked a little bit in the prepared remarks that we saw really good activity from an instrument perspective. We were really pleased that throughout the course of the year. Q2, we saw an increase in NovaSeq shipments compared to Q1. Q3 was bigger than Q2. And so we continue to see growth in NovaSeq shipments play out over the course of this year from the base of Q1 and we saw strong demand in the mid-throughput instruments too.
Maybe Sam, I’ll turn it over to you to provide more color.
Sam Samad — Senior Vice President and Chief Financial Officer
Yeah. I would say, in fact we’ve been pleased with the sequencing instrument performance both in Q3 and the resilience that we’ve seen through the pandemic. You would expect that there would be a year-over-year decline, especially given the pandemic, given some pause on instrument purchases. But as we look towards Q4, we’re expecting growth in instruments, our strongest quarter of the year, we’re expecting growth in terms of NovaSeq sequentially as well. And when I say growth in Q4, I mean, sequentially in terms of instruments revenues, and then the pipeline looks really strong for both NextSeq 2000 and for NovaSeq.
Operator
Your next question comes from the line of Derik De Bruin with Bank of America. Your line is open.
Derik De Bruin — Bank of America — Analyst
Hi, good afternoon. Couple of questions. I think the first one, obviously there has been a big ramp in the operating expense in the second half of the year. As we think about going forward, is this something we should think about rolling into ’21, but even higher as some of the T&E comes back in, some of the [Indecipherable] back in.
And I guess, on the fall, a negative question the, on the NIPT space, can you give us a sense of how many women that were covered under high-risk actually were taking advantage. I mean, the women that were eligible for doing high-risk, how many actually went and do NIPT testing. And the reason why I ask is, I’m just trying to get a sense of what the penetration would be for average risk and sort of expanding coverage. Just trying to get some feel for the dynamics and how we can think about the NIPT business expanding. Thank you.
Francis deSouza — President and Chief Executive Officer
Yeah. Maybe I’ll start and then Sam can add some color too. In terms of operating expenses, our philosophy over the course of the year has been to review our operating expenses very closely. And one of the things we want to do is make sure we continue to protect the high priority thing that we were working on. So, that includes our rich innovation pipeline. And so we’ve protected our projects associated with upcoming products as well as some long-term investments in the business. So we protected those, but we’ve looked for other areas where we could make savings. Some of those sort of naturally played out over the course of the pandemic in the form of reduced travel, for example. And some of those, you’re right, we’ll come back next year.
And so Sam will comment a little bit more about that. In terms of NIPT, obviously it’s a very regional story. But in the US, for example, you have a reasonably good penetration in terms of the women who are eligible for NIPT going to get it. So the majority of women who are eligible for the test do get it as part of their pregnancy. And so, the opening up of that market in the average risk segment does represent meaningful upside in terms of the actual demand for the test.
Sam Samad — Senior Vice President and Chief Financial Officer
Yeah, Derik, with regards to opex, I would add, just maybe a couple of points. And thanks for the question by the way. The one thing I would say is, we’ve been incredibly focused and diligent in terms of managing our operating expenses. But at the same time, really focused on Francis’ point about not in any way undercutting our innovation and then our investment in innovation and in any way impacting our R&D pipeline. But for three quarters of the year, up until the end of Q3, I would say, we’re about $150 million below our own internal budget in terms of operating expense. So we have been very careful in terms of managing operating expenses were about 10% below.
And as we look forward, yes, there will be some things that start to ramp back up, things like, again, as employees come into the labs, we will have R&D projects start to scale back up that will continue into next year. And we’ll have certain expenses as hopefully this pandemic eases, like travel that increase as well, but I would say in general, we’ve been extremely diligent and disciplined in terms of managing our expenses through our year-to-date.
Operator
Your next question comes from the line of Puneet Souda with SVB Leerink. Your line is open.
Puneet Souda — SVB Leerink — Analyst
Hi, Francis, thanks. And thanks for providing comments on 4Q as well, appreciate that. First question, recently just in the last 24 hours, we have seen locked down in France and Europe and these lockdowns can potentially spread. Just wondering, is that contemplated in your expectations for the fourth quarter? And also, do you expect customers in Europe to be more adept at this time around in terms of managing research and diagnostic sequencing operations now versus before? I just wanted to get your thoughts on that, given that sequencing run rates which you described earlier is 96% of pre-pandemic levels. Could we see a different standard here and is this baked into your guidance?
And then, if you — second question, if I could ask around GRAIL, one of the key questions that has emerged last week, since this week actually, is the approach that Illumina took to GRAIL’s acquisition in light of another multi-cancer liquid biopsy acquisition this week. I totally recognize that the acquisitions are pre-revenue, but it appears that GRAIL is valued significantly higher versus Thrive. So, could you elaborate, if there is anything in terms of the overall market opportunity of the pan cancer test or technical performance of the gallery [Phonetic] or scale of the studies or anything here that gives you a greater confidence and a higher valuation. I appreciate it.
Francis deSouza — President and Chief Executive Officer
Yeah. Thanks, Puneet. So, I will start with your question around the potential restrictions in Europe, maybe even the US. As we mentioned on the prepared remarks, we’re monitoring that closely. Obviously we all want to see the pandemic get under control, but there are definitely some signs in Europe that there are some potential shutdowns taking place, so at least additional restrictions. And so, for Q4, we’re monitoring that closely. We factored that in as we look forward in terms of our expectations for Q4. In fact, we said clinical sequencing activity in Q3 was 96% of pre-pandemic levels, research was 82% of pre-pandemic levels. And we expect both of those to improve modestly because of the fact that we’re really tracking kind of how this pandemic evolves in Q4 and not to improve more than that.
With regards to your other point about customers being more adept, I do think they are getting a bit more adept in terms of learning to work with the virus. Not to say that they’re not obviously very careful and cautious about that. But at the same time, when you look at, for instance, a number of labs that are now based on our Q3 data that are either completely open or in sort of some level of operation, it’s about 90% of the labs compared to about 50% back in April. So that doesn’t mean that 90% is all full systems ahead and they’re all open. But they are either fully open or and restricted operations, it’s about 90% of the total labs globally. So they are really gradually ratcheting back up, but in a cautious way. And that was factored into our expectation.
Sam Samad — Senior Vice President and Chief Financial Officer
And then, Puneet, if I could comment on your GRAIL question. We start about the fact that early detection of cancer represents by far the largest clinical application of genomics. We’re likely to see over the next decade or two. And we’ve also talked about the fact that we expect many players in this market because it’s such a large opportunity and we expect to take different approaches, whether it’s single cancer versus multi-cancer or different technological approaches. And certainly we have a number of customers, including Thrive, Exact but also Phenom and Garden and other liquid biopsy players like Foundation Medicine that we expect to play a role in this market going forward. And we will continue to support all of those customers going forward.
What attracted us to GRAIL was its unique position in that market in terms of being the closest to having a commercial test and in terms of having the performance characteristics, consistent with being closer to having a commercial test. So, GRAIL is looking to launch its test next year and that will likely make them the first player into the market. We have also undertaken by far some of the largest clinical studies in that space. And so, they have over 100,000 people enrolled in the studies that they’ve done and generated quite a remarkable bolus of data associated with their test. And then the performance characteristics of their tests are very strong. So, for the 12 deadliest cancers, they have a sensitivity in the high-60% with a false-positive rate of less than 1%, which really does represent our best-in-class product at this time in the market.
What we also like to is that the only player at this point that has FDA approval in terms of being able to run an IDE study to return results to patients and so they are working with some of the premier healthcare systems, including the Mayo Clinic, Cleveland, Oregon Health System, the Intermountain Health System, Dana-Farber, Sutter Health and so they already have their gallery test in the hands of doctors returning results to patients as part of the study. And so, having that FDA approval is also very attractive is and all of that obviously factored into the price associated with GRAIL.
Operator
Your next question comes from the line of Dan Arias with Stifel. Your line is open.
Dan Arias — Stifel — Analyst
Good afternoon, guys. Thank you. Francis, on the All of Us sample that should begin to flow this quarter, is there a material consumables assumption that’s built into that work for 4Q? And assuming that things do get going there, you thinking that that should be all sequencing? Or might there be some genotyping that makes it into the mix there? And if I could ask a quick follow-on. It sounds like you’re ticking modest growth in China. Is in the picture for 4Q? Did you say a year over year, that would be a sequential step up there that we haven’t seen in a while. So What’s driving the confidence in the move, I guess back up to the mid-$19 billion? Thanks.
Francis deSouza — President and Chief Executive Officer
Yeah. So let’s starts with All of Us. For all of those, we expect the All of Us samples to start flowing to partner genome centers in Q4 and to start to see both sequencing in genotyping activity. From our perspective, the actual revenue contribution into Q4 we’re expecting modest. But it’s a very important step, because it then sets us up well for All of Us to ramp up more meaningfully going into next year. And so it means that the [Technical Issues] setup, workflow has been setup and machine is going into like. And so again, modest contribution in Q4, but that’s a big step and sets us up we believe well going into next year. And then Sam, maybe you can talk about China.
Sam Samad — Senior Vice President and Chief Financial Officer
Yeah. So, again, thanks for the question, first of all. With regards to China, we were expecting, I would say, flattish year-over-year performance in Q4. So we’ve said on the prepared remarks for China and APJ, flat to slightly increasing. So for China, specifically it’s flattish performance year-over-year. In fact, China, the clinical performance has been strong year-to-date and growing year-over-year. Research, as we’ve talked about on previous calls, has been impacted definitely by the pandemic, repurposing some of the work towards PCR testing and just the general impact of that on research. But we’re pleased with the clinical performance that we’ve had in China. Q3 had strong instrument placements as well in China, which bodes well for future activity. And so, pleased with the clinical performance there for sure and that’s what gives us confidence.
Operator
Your next question comes from the line of Tejas Savant with Morgan Stanley. Your line is open.
Tejas Savant — Morgan Stanley — Analyst
Hey, guys. Thanks for the time here. So, a couple of questions for you, Francis and Sam. So, on the sequencing consumables line, you had some destocking in the second quarter. Did some sort of a restocking dynamic here play into that 29% quarter-over-quarter growth at all? And then, in oncology, how are you thinking about sort of the bolus here in the fourth quarter and in the first half of ’21 as the missed screenings come back online?
Francis deSouza — President and Chief Executive Officer
Yeah. Thanks, Tejas. With regards to stocking levels and restocking, yes, in Q2, we had some customers that destocked specifically in AMR. So that was an impact on our performance in Q2. We have not seen from our data that there has been an increase in inventories or restocking back in Q3. So essentially what we’ve seen and we’ve really looked at this with a lot of our customers, we’ve seen that customers are really purchasing to the demand that they have but have not restocked back some of the destocking that occurred in Q2 nor are we expecting in Q4 that there is restocking either. But they’re going to continue. Based on the activity levels that we track and triangulating that back with revenues, we can see that essentially they’re buying to their demand.
Sam Samad — Senior Vice President and Chief Financial Officer
And then quickly — yeah, if you look at oncology, I mean, I think you bring up a really important point. I think one of the tragedies associated with the pandemic is that there are people who frankly aren’t going in to get screened for cancer. And so, they are walking out with cancer developing. I think there are sort of two dynamics that will play out. One is, there will be at some point a catch up, right. Unfortunately of those individuals, that means that cancer has progressed, but whether that plays out in Q4 or next year, there will be a catch-up associated with people who haven’t had their diagnosis yet.
In addition, the other dynamic that’s playing out is, we’re seeing that blood-based tests are actually doing better through the course of the pandemic. So, if we look at how the market is playing out, the service providers that offer blood-based tests have proved that their business is more resilient through the pandemic than the service providers that do tissue-based analysis. And so, I think one of the things that’s playing out through the course of the pandemic is you’re starting to see an acceleration of blood as a sample type for cancer testing. So you’re seeing an acceleration in the growth of liquid biopsies, which we think is a durable dynamic and it’s not just as a result of the pandemic, but we think that will continue to play out in the coming years.
Operator
Your next question comes from the line of Vijay Kumar with Evercore ISI. Your line is open.
Vijay Kumar — Evercore ISI — Analyst
Hey, guys. Thanks for taking my question. I guess two quick ones. One, maybe I misheard this, but did GRAIL deal close? Is that a second half of next year? And then, I’m curious how we should be thinking about investments here. And then, when you think about the system placements here, given the razor-razorblade model, maybe perhaps elaborate on how the lower systems this year should play out next year. I do realize the comps for consumables are easier. Should that offset the system declines for this year? I’m curious.
Francis deSouza — President and Chief Executive Officer
Yeah. So let me touch on both. And maybe Sam can add some color. If we — so on GRAIL, yes, we are expecting the deal to close in the second half of 2021 as we go through the regulatory process. We’ve talked a little bit about the dilution associated with GRAIL, but frankly we’ll have more information for you as the deal closes. And again, that’s the second half of 2021.
Sam Samad — Senior Vice President and Chief Financial Officer
In terms of the instrument placements, we — obviously you’re right, it is a razor–razor blade model. And that’s why it’s important — that’s why we’re so encouraged by the recovery we’re seeing in instruments placements after we got out of Q1. And so, the strength in NovaSeq placements through Q2, Q3 and certainly the pipeline as we walk into Q4 is a very — is very important. Similarly, the strength that we’re seeing in the mid-throughput part of the portfolio, specifically NextSeq both the new NextSeq 2000 as well as the 500 and the DX boxes are a good sign for us as we look going into next year.
Operator
Your next question comes from the line of Catherine Schulte with Baird. Your line is open.
Catherine Schulte — Baird — Analyst
Hi. Thanks for the questions. A two-parter on the GRAIL studies. What’s the timing next year in terms of when we can expect to see data from Pathfinder? And do you expect any performance degradation as you move into an all-comer screening population for that study? And then, second, for the STRIVE study, I believe GRAIL completed enrollment in late 2018 and was following patients for 30 months. So, is that something where we could see a readout at some point next year or is it likely end of 2022?
Francis deSouza — President and Chief Executive Officer
Yeah, so let me talk about the GRAIL studies. The easy answer is we don’t expect the Pathfinder study to provide substantially different performance data then we have seen so far. And the reason for that is that GRAIL has done a number of other large-scale studies. So the CCGA study have 15,000 people enrolled in the study. The second phase of that study was a prospective study, an all comers study. And so, given the size of the studies they’ve done with the same test, the performance they’ve published externally is based on statistically significant data and so we didn’t expect the Pathfinder data to reveal anything different.
And in fact before we signed the deal, we had a small group of people look at some of the early results at the mid-term results associated with Pathfinder. And while we won’t talk broadly, they’re generally consistent with what we expected. And so we don’t expect when the final study results get published next year, them to be significantly different from the performance characteristics that you’ve seen so far. What was the second part of that question?
Catherine Schulte — Baird — Analyst
It’s Strive, Francis.
Francis deSouza — President and Chief Executive Officer
Yeah. So, Strive is a prospective study. It’s a 100,000 women and it was fully enrolled about 18 months ago. So it’s again pretty far down its path. And again, similarly, given the size of the studies that have gone before, we expect this to be further validation in terms of the performance characteristics and not significantly different.
Operator
Your next question comes from the line of Patrick Donnelly with Citi. Your line is open.
Dan Leonard — Wells Fargo Securities — Analyst
Great. Thanks, guys. Maybe just one on the PopSeq side. It’s encouraging to see some of those bigger projects gaining momentum to get flowing here in the near-term. Obviously the timelines have slipped a few times now. Can you just talk to your confidence on these taking off on time, I guess, with the new 4Q timelines particularly All of Us. Now the trajectory is similar to kind of what we’ve talked about before, All of Us, I think, for example, at the beginning of the year. We kind of talked about 60,000 whole genomes in the first six months. Are we still thinking that the trajectories are the same once they do get launched? Thank you.
Patrick Donnelly — Citigroup — Analyst
Yeah. It’s a good question. And as we look at where we are with those population studies now, I’ll touch on sort of the four big ones, right. So, the UK Biobank, the Million Veterans, All of Us and the UK NHS. And where we are now is that walking into next year, the majority of them have already been stood up, and it’s a matter of just either getting back to where they were, which is, for example, the UK Biobank, or just ramping up volumes of samples. That’s a much better place to be than we were last year, for example, where All of Us still have to get FDA approval, and then work out the workflows to get the samples flowing to its partner genome centers.
And so if I look at all of them, the UK Biobank it actually they entered the year, equencing at a high capacity, they pulled back in March because of the pandemic, and they’re starting to ramp back up going into next year. And so, assuming conditions are good, we have high confidence in their ability to ramp up quickly. We talked about the fact that the million veterans program has been remarkably resilient over the course of the year, and in fact, has increased its scope over the course of this year. All of us we took samples of are flowing in Q4. And so really, it is all about just scaling up next year, which is a pretty good place to be in terms of actually getting it going.
And then the UK NHS for this year, has been on hold primarily as the NHS has been dealing with the pandemic testing that they’re doing. But they are expected also to start sequencing later this quarter. And so, that puts us we believe in a good position to start to see the scale up going into next year. So across all four, we feel really good that as we end this year, all of them will be in a position where they are processing samples and ready to scale up and deal with the pent up demand that they’ve had.
Operator
Your next question comes from the line of Dan Leonard with Wells Fargo. Your line is open.
Dan Leonard — Wells Fargo Securities — Analyst
Thank you. Just a couple on the expense side. One, can you elaborate on what’s happening on the gross margin line, both the driver of the sequential downtick and the further downtick expected in the fourth quarter. And then, secondly, can you talk about the anticipation of the GRAIL acquisition, philosophically change any of your thinking around base Illumina budgeting as you roll in the 2021? Thank you.
Francis deSouza — President and Chief Executive Officer
Yeah. Thanks, Dan, for the question. So with regards to gross margin, first of all, the downtick from Q2 to Q3 was really expected per our expectation. So, gross margin came in at slightly better than our expectation. And that was driven by some additional — we have some additional freight expenses, some additional compensation expenses in our operations organization. And also some of the ramp on the project as well had some additional impact on gross margin or cost. So that’s the expectations.
The Q4 downtick sequentially versus Q3 is really mostly driven by mix. And the fact that we have an instrument quarter that’s strong, that outweighs some of the benefit from the consumables, mix is impacted negatively by that. With regards to the expectations for ’21, really when we think about the core business in Illumina, there is really not a material change in terms of our budget philosophy and approach. We are absolutely focused on continuing to invest in the core business and also generating the shareholder returns that we were committed to in the core business to continue to drive that over time. But at the same time, we have a really compelling opportunity with GRAIL and we’re going to continue. We’re going to invest behind that opportunity. It’s going to be dilutive in the next few years, but we are committed. So not a major change in terms of our budgeting philosophy for ’21 on the core businesses.
Operator
Your next question comes from the line of David Westenberg with Guggenheim Securities. Your line is open.
David Westenberg — Guggenheim Securities — Analyst
Hi. Thanks for taking the question. So we appreciate kind of your long-term expectations of double-digit growth in consumables, sequencing consumables. Can you quantify how much of that is clinical and specifically oncology as a component of growth. And then, as kind of a follow-up to that, can you quantify or maybe just qualify the opportunity of moving from panels to our — two panels from hotspot testing in terms of just growth there. Thank you.
Francis deSouza — President and Chief Executive Officer
Yeah. Sure, David. So maybe I’ll start by saying, look, as we entered this year, we talked about the fact that the clinical business represents just under half of our sequencing consumables. But we also talked about the fact that that part of our business is growing significantly faster than the research side of our business. And so, you should expect those lines to cross. And once they cross, they aren’t going back. Sequencing consumables from the clinical business is going to be the majority of our sequencing consumables both in dollars and in growth going forward.
Of those sequencing consumables in the clinic oncology testing for therapy selection represents the biggest part of that market. And so, we haven’t — you should expect that to continue going forward. We have long-term numbers there, but you should expect that to continue to be the biggest part of the sequencing tools in the clinic going forward. We do expect, for a number of reasons, to continue to see the migration from hotspots to larger panels and frankly from — not just hot — but the smaller panels and larger panels too and that’s driven by a number of things, including the increasing use of TMB as a biomarker for therapies. And so, if you look at what happened with Keytruda for example, in the last few months, that continues to add momentum to stay, it’s not enough just to look at gene hotspots to prescribe a therapy. But you need to look at things like TMD and that will require the use of larger panels.
And so you take that, you take the fact that you’re seeing, I talked about ESMO for example, you’re seeing momentum in guidelines to use biomarkers like TMB and all of that will continue to drive momentum to the larger panels, which will then drive more sequencing and will make oncology testing grow even faster, and therefore be a bigger component of the sequencing consumable revenue going forward.
Operator
Your next question comes from the line of Dan Brennan with UBS. Your line is open.
Dan Brennan — UBS — Analyst
Great. Thanks. Thanks for taking the question. Francis, could you just give us a sense of the upgrade opportunity that still remains ahead of you for your smaller customers that are in the HiSeq. I guess, we haven’t gotten to that the new long, particularly in light of the price cuts and the comments this quarter about the strong demand on that you saw. So any color regarding the size of that opportunity. If you look at early traction look like this quarter and kind of how do you think that upgrade opportunity evolves as we look out? Thanks.
Francis deSouza — President and Chief Executive Officer
Yeah. So maybe I’ll start with sort of a qualitative view and maybe work our way through that. So, when we talked about sort of the multi-year upgrade opportunity for NovaSeqs, there is this next segment that we are activating starting with the version 1.5 reagents, which is the smaller core labs. They are the ones that are still primarily still using the HiSeqs. And frankly they haven’t had the volume to justify the upgrade because you need volume to see the benefits associated with the consumables drop in cost. So, 1.5 now changes the economics for them. And that’s the segment of the customer base that we’re looking to activate.
In terms of the number of instruments there, maybe I’ll turn it over to you, Sam, to give us some color on that.
Sam Samad — Senior Vice President and Chief Financial Officer
Yeah. Maybe the color, I’ll give Dan and thanks for the question. As we think about the NovaSeq placements, I know we used to give more specificity around this when we first launched NovaSeq and the number of HiSeq customers that we still expect to take on NovaSeq, but we haven’t provided that for some time. But the metric I will give you is for NovaSeq placements year-to-date. We’re still seeing roughly 40%-ish or so coming from new to Illumina customers. So really a great sign around the democratization of sequencing that NovaSeq has done. We’re seeing about an additional 40% or so that’s coming from NovaSeq capacity upgrades. So existing NovaSeq customers that are just upgrading or taking on more capacity. And then, roughly 20% or so from those HiSeq customers that are continuing to transition to NovaSeq.
So that’s still going on. We’re going to continue to see that. The v1.5 upgrade that we talked about will also help catalyze that as well — will drive that as well. So still very encouraging and good room to offset.
Operator
There are no further questions. At this time, I’ll turn it back over to our presenters for any closing remarks.
Juliet Cunningham — Vice President, Investor Relations
Thank you. As a reminder, a replay of this call will be available on our website in the Investor Relations section as well as through the dial-in instructions contained in today’s earnings release. Thank you for joining the call today. This concludes our call and we look forward to updating you on our progress in the fourth quarter.
Operator
[Operator Closing Remarks]