Genomics tools · Synthetic long read sequencing
Loop Genomics
A San Jose startup that turned short read sequencers into long read machines by stamping one barcode into many places inside a single DNA molecule. Element Biosciences bought it in 2022, shipped it as Element LoopSeq, and has since dropped it from the catalog.
Copy the barcode, then copy it again
Take one long strand of DNA. Tag it with a unique molecular identifier. Then, using enzymes the company never named, copy and paste that tag into many positions along the strand. Amplify, run it on an Illumina machine, then gather every short read carrying the same tag and assemble them into one long read.
The order of operations was the point. “An important part is that all amplification is always done post barcoding,” founder Tuval Ben-Yehezkel told GenomeWeb in April 2018. “So, you get long-read sequencing, but also molecule counting.”
No new instrument. A lab that owned a sequencer bought reagents instead.
The gap it aimed at
Short read sequencers are cheap, accurate and everywhere, and they read a few hundred bases at a time. Plenty of biology needs thousands: which mutations sit on the same chromosome, which messenger RNA isoform a cell made, which bacterial strain is present. Long read platforms from Pacific Biosciences and Oxford Nanopore answered that at a higher price and, for years, a higher error rate.
Illumina had already tried the synthetic route and let it lapse, buying Moleculo in 2012 and selling the result as TruSeq Synthetic Long Reads. The analyst Keith Robison later filed that attempt alongside Loop’s: “Illumina’s failed productization of the Moleculo technology as TruSeq Synthetic Long Reads is another.”
The market was also under legal siege. In November 2018 Illumina agreed to buy PacBio for about $1.2 billion. The FTC sued to block it, the UK regulator found competition concerns, and on January 2, 2020 the deal died, with Illumina paying a $98 million fee. The FTC put Illumina’s share of sequencing hardware near 80 percent. Loop’s pitch, that its customers already owned the winning instrument, let it stand beside that machine rather than in front of it.
One founder, four labs, one filing
Ben-Yehezkel earned his doctorate at the Weizmann Institute of Science and helped start Synvaccine. A 2021 Twist Bioscience webinar page dates the handover: “In 2016, he transitioned to Loop Genomics, developing the first fully generic synthetic long-read DNA sequencing platform.” He told GenomeWeb the technology drew on work at Stanford, Michigan State, A*STAR and the Weizmann Institute, and that the founders had “consolidated all those different lines of research and IP” to launch in 2015.
The public record keeps a different name. The corporate entity is MetaBiotech Corp, incorporated in Delaware in 2015 at 5941 Optical Court in San Jose. Three published patent families are assigned to Metabiotech Corporation, the earliest claiming priority to November 21, 2014, and its one SEC filing lists a single related person: Ben-Yehezkel. The LOOP GENOMICS trademark, filed under the Metabiotech name in 2017, was abandoned in September 2019 after a final refusal.
Kits, then a raid on Sanger
LoopSeq Complete for 16S and 18S ribosomal RNA reached the market in 2018, when the company had ten employees. On November 1, 2018 Loop announced an $8 million Series A led by Khosla Ventures, with Fusion Fund, DN Capital, Y Combinator, WSGR and Wisemont Capital. A transcriptome kit followed in March 2019 at $70 a sample, service at $299, with Geisinger, Cancer Research UK, Vancouver Prostate Centre and UFL named as early adopters.
August 2020 brought the most pointed product: LoopSeq Solo prepared up to 6,000 clonal isolates at once, aimed at the Sanger sequencing microbiology labs still ran. “That’s prohibitively expensive and it’s preventing people from scaling their projects,” Ben-Yehezkel said of the old way. By then Loop had distributors in eleven countries and, he told GenomeWeb, “is not actively fundraising now as it is comfortable with its cash runway.”
Absorbed, shipped, then quietly gone
On February 7, 2022 Element Biosciences announced it had closed its acquisition of Loop Genomics. Terms were not disclosed, and it was Element’s first acquisition since its 2017 founding. Ben-Yehezkel joined as Senior Director, Applications. Element had closed a $276 million Series C the previous June and had not yet shipped a sequencer.
Five weeks later Element launched the AVITI benchtop system at $289,000. “And with the recent Loop Genomics acquisition, we will offer both short and long-read capabilities on a single platform,” chief executive Molly He said. In November 2022 the Element LoopSeq kits for AVITI arrived with read lengths up to 5 kilobases, and Element called itself “the first company to own a general purpose long-read technology that runs on its native short-read sequencer.”
As of September 23, 2026, Element’s sitemap lists fourteen product pages and none is LoopSeq. The LoopSeq services page and FAQ, both captured in 2023, return 404. The current AVITI page describes Cloudbreak, Elevate and Adept workflows and does not mention long reads.
What is proven, and what is still claimed
| Evidence | What the record shows | Source type |
|---|---|---|
| Accuracy, vendor co-authored | Microbiome, June 2021: a per-base error rate of 0.005% for full-length reads, holding to 6 kilobases; two of five authors were Loop employees. Communications Biology, April 2021: 99.4% isoform accuracy and 0.01% per-base error, with three Loop authors. | Public record |
| Marketing claim | The LoopSeq services page advertised “40x lower error when compared to Illumina library prep, 7,500x lower error when compared to PacBio.” No published study found here reports the 7,500x comparison. | Beyond the record |
| Independent comparison | Microbiology Spectrum, February 2022: South China Agricultural University with BGI authors ran V4, LoopSeq and PacBio 16S side by side and reported improved accuracy and lower cost respectively. | Independent |
| Independent limitation | Frontiers in Microbiology, January 2025, on Guaymas Basin sediments: “chimeras were prevalent in sequences as affiliated with the thermophilic Candidatus Desulfofervidus and Thermodesulfobacterium.” | Independent |
| Use in trial data | Am J Respir Crit Care Med, August 2025, reanalyzing ORBIT-3 and ORBIT-4: “Baseline sputum from the trials were analyzed by 16S rRNA sequencing (LoopSeq) (n = 377).” | Public record |
| Patents and mark | US10233490B2, assigned to Metabiotech Corporation, granted March 19, 2019, inventor James A. Stapleton. Element filed a PCT under the same title in June 2023 with the same inventor. | Public record |
| Regulatory and grants | No FDA 510(k) or PMA records, no trials sponsored by the company, no NIH or NSF awards to Loop Genomics or MetaBiotech Corp. | Not found |
Read plainly: the accuracy claims were real and published, but the two headline papers were vendor co-authored, and the sharpest marketing number, 7,500 fold against PacBio, never appeared in a study. Independent labs used the kits and mostly liked them, with one group flagging chimeras. The technology was good enough to buy and to ship. Four years after the AVITI launch, the brand is gone.
What to watch
- Whether Element revives the LoopSeq name, folds the chemistry into another workflow, or lets it lapse the way Illumina let TruSeq Synthetic Long Reads lapse.
- Element’s patent continuations. A 2023 PCT filing carries the same title and inventor as the 2015 Metabiotech patent.
- Any Element registration statement, which would be the first document obliged to say what Loop Genomics cost.
In their words
“So, you get long-read sequencing, but also molecule counting.”
Tuval Ben-Yehezkel, CEO and founder, GenomeWeb, April 2018 · Independent
“We’ve learned so much from our customers about what they need to use long-reads for, and we are building our new kits and services tailored to those specifications and to meet those needs leveraging our platform.”
Tuval Ben-Yehezkel, on the Series A, GenomeWeb, November 2018 · Independent
“That’s prohibitively expensive and it’s preventing people from scaling their projects.”
Tuval Ben-Yehezkel on per-sample Sanger workflows, GenomeWeb, August 2020 · Independent
“It’s allowing us a faster and more reliable access to the isolates that we’re providing to our customers.”
Crystal Emery, application scientist, General Automation Lab Technologies, GenomeWeb, 2020 · Customer
“Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies.”
Callahan et al., Microbiome, 2021, with two Loop Genomics co-authors · Peer reviewed
“Loop Genomics has successfully commercialized innovative products that bring long-read resolution to short-read platforms in a wide variety of genetic analysis applications.”
Molly He, CEO and co-founder, Element Biosciences, February 2022 · Acquirer release
“Element’s new sequencer, now armed with long-read capabilities, is positioned to disrupt the genomics space.”
Tuval Ben-Yehezkel, acquisition release, February 2022 · Acquirer release
“LoopSeq, now owned by Element Biosciences, is an example though alas the molecular details haven’t been disclosed.”
Keith Robison, Omics! Omics!, October 2022 · Independent
Related companies
Sources
- Public recordForm D, MetaBiotech Corp, CIK 0001731460
- Public recordUS10233490B2, assignee Metabiotech Corporation
- Public recordLOOP GENOMICS trademark, serial 87583090
- Public recordUltra-accurate microbial amplicon sequencing with synthetic long reads
- Public recordTargeted transcriptome analysis using synthetic long read sequencing
- Public recordIllumina and Pacific Biosciences announce termination of merger agreement
- IndependentWaterlogging and soybean rhizosphere bacteria using V4, LoopSeq and PacBio 16S
- IndependentComplex bacterial diversity of Guaymas Basin hydrothermal sediments
- IndependentEndotypes of Pseudomonas aeruginosa infection in bronchiectasis
- IndependentLoop Genomics enters synthetic long-read sequencing market
- IndependentLoop Genomics closes $8M Series A round
- IndependentLoop Genomics seeks slice of Sanger market
- IndependentElement Biosciences acquires Loop Genomics
- IndependentIllumina roadmap part 2: Infinity becomes Illumina Complete Long Reads
- CompanyLoop Genomics expands kit and service offerings
- CompanyElement LoopSeq long-read sequencing services page
- CompanyElement Biosciences closes acquisition of Loop Genomics
- CompanyElement introduces new Element LoopSeq kits for AVITI
- PartnerTwist Biopharma and LoopSeq webinar page with founder bio
Profile researched and written by Healthcare Discovery. Last updated September 29, 2026.
