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Global Supply Chain Issues Catch up to Illumina, Leading to Delayed NGS Projects


NEW YORK – Until recently, Illumina had been able to stay ahead of pandemic-related reagent shortages affecting the entire biotech industry. But since the beginning of the summer, customers have noticed that delivery of certain Illumina next-generation sequencing reagents is being delayed by weeks — or even indefinitely.

"We are mainly seeing delays in receiving NextSeq 2000 kits that we have ordered," said Anoja Perera, director of sequencing and discovery genomics at the Stowers Institute for Medical Research. "We can place new orders but instead of Illumina sending them to us within a few days, we are seeing delays of weeks."

"Given how dependent we are on Illumina, this is painful. On top of that, we still have to pay the service contracts and lease," she said, adding that while her Illumina representative has been responsive, the company has not provided a definitive explanation for the delays.

Other researchers have also seen delays for the P2 sequencing kits for the NextSeq 1000 and 2000 instruments — which include a reagent cartridge, flow cell, and resuspension buffer — as well as some reagents for the iSeq instrument. One customer in Australia said they have recently experienced delays on some NovaSeq consumables, especially unique dual-index plates.

"Usually, Illumina shipments come next day for us," said Jennifer Mosher, lab manager at the Cornell University Institute of Biotechnology. "The last order I placed just says, 'To Be Determined.' They’re not even forecasting, which is alright. The ship dates they were assigning they weren't meeting anyway." Forecasted shipping dates could change several times, she added, only for orders to show up ahead of the most recent updated date.

Mosher speculated that a raw reagent was the rate-limiting factor. "As soon as they get it, they push everything out," she said. "I'll receive multiple orders at once, whether I had ordered them two weeks before or four weeks before."

Illumina generally acknowledged the delays, attributing them to "manufacturing and supplier capacity constraints."

"We are sensitive to how these supply issues impact our customers and fully committed to scaling for their needs, now and into the future, and to address the challenges," Karen Birmingham, Illumina's head of public relations, said in an email. "We have, and will continue to, add additional equipment and staffing to our manufacturing sites, and we're working closely with these suppliers involved while confirming additional sources of supply."

"We anticipate that lead times will improve over the next six weeks and will be substantially back to normal on these products during the month of November," she added.

How Illumina was able to stay ahead of the worldwide phenomenon of strained supply chains and product crunches for so long is unclear. The company did not address a list of specific questions about the supply issues. Since the early days of the pandemic, certain reagents, especially nucleic acid extraction kits and PCR supplies, have been difficult to obtain.

While Illumina's sequencing consumables sales fell in 2020, as many research projects ground to a halt, they have roared back this year. In the first half of this year, Illumina recorded total sequencing consumables revenues of $1.40 billion.

The order delays started around late June or early July, said Peter Schweitzer, genomics facility director at the Cornell Institute of Biotechnology. "For the common kits, we're still having trouble getting them," he said. "For the less-commonly run kits, such as longer read length kits, we seem to be able to get those."

Some customers using these platforms have yet to see delays, though. "So far it has been OK for us," said Chris Mason, a sequencing expert at Weill Cornell Medicine, whose lab has an iSeq. The core lab he uses has a NextSeq 2000, he added, noting that he had not heard of order delays there.

Other sequencing platforms, from Illumina and elsewhere, appear to be unaffected. "We have so far had no problems with reagents for the NextSeq 500," said Lutz Froenicke of the DNA Technologies and Expression Analysis Core at the University of California, Davis. And customers did not report widespread problems obtaining sequencing consumables from other companies, namely Pacific Biosciences and Oxford Nanopore Technologies.

"We have not had any product delivery delays as a result of supply chain pressure," Jen Carroll, director of corporate communications at PacBio, said in an email. "Our team has done a great job and we've been able to work closely with our vendors to secure supply for the next 18 to 24 months." 

Oxford Nanopore did not respond to request for comment.

And though none of the Illumina customers GenomeWeb spoke to have suffered major setbacks, the order delays are causing headaches.

"Luckily for us, we kept the NextSeq 500," Perera said. "Also, we work closely with an academic core lab in the area to process our projects on their NovaSeq. They give us a really great discount and therefore we do not have to absorb significant additional costs due to outsourcing." However, her organization must continue to pay service and leasing fees for an instrument it has limited use of.

Stella Loke, associate research fellow at Deakin University in Australia, said she has had to lend her own lab's stash of NovaSeq consumables to the Deakin Genomics Centre's regional facility "to tide them over."

Marie Adams, genomics core manager at the Van Andel Institute, said in an email that her lab has been experiencing iSeq consumable delays throughout 2021, most often resulting in lead times of a week or more but sometimes in kits arriving weeks or months after the order. "As you can imagine, the latter is more troublesome for our workflow, particularly since we try to keep our kit storage as lean as possible since we're a small core with variable project needs," she said.

"It just slows turnaround time," Mosher said. "Things just sit in the queue ready to go on the sequencer." So far, she hasn't heard of any customers deciding not to send in a project to her core.

"We've rearranged maybe one run," she said. The lab didn't have enough P2 flow cells to run two different sets of samples, but she found a workaround by combining them on a higher-throughput P3 flow cell. The customer agreed and the project went ahead.

Mosher noted that her lab ordered approximately $130,000 worth of reagents from Illumina in August. "Only $20,000 to $30,000 of that is still outstanding," she said, while the rest has been delivered.

Most of the customers experiencing delayed orders praised their Illumina contacts for providing information and advocating for them. "The response from Illumina has been helpful from a procurement standpoint," Adams said. "Our sales representatives have always been responsive, either recommending a different kit — for instance, when the iSeq v2 reagents were more available than the v1 — or attempting to find a kit elsewhere if we really needed one."

Mosher said her sales rep has been "advocating for us, getting us more accurate dates so we can tell our researchers more accurate dates."

And they're grateful that their Illumina supply lines haven't been completely cut off. "Stuff is still flowing in. It's not a dead stop," Schweitzer said. "For some other supply chain issues, like pipette tips, it's a dead stop."