Genomics software · Structural variant detection

Spiral Genetics

A Seattle company that spent a decade trying to make cheap short read sequencing see the big mutations everyone else was missing. It was acquired in 2017, bought back by its founder in 2019, and its own accelerator now lists it as inactive.

The worst jigsaw puzzle of your entire life

A sequencing machine does not read your genome end to end. It shatters it and reads the pieces, each about 150 letters long, and hands you billions of fragments with no labels. Almost every pipeline in the world reassembles them by lining them up against a reference genome built mostly from other people.

That works for a single letter changed here or there. It breaks when the difference is large. Adina Mangubat, the company’s co-founder and chief executive, put it to the interviewer Andrew Warner in 2016: “it’s kind of like the worst jigsaw puzzle of your entire life and then you have a box that doesn’t actually match because while it’s human, it’s not actually you.”

The technical version, which she gave GenomeWeb in 2014: align first and “you are biasing everything that you are doing against the reference genome.” If a patient carries a 3,000 letter insertion, whole stretches of it match nothing and vanish from the analysis.

Those vanishing differences are structural variants. Spiral’s bet was that you could find them in ordinary short read data by inverting the usual order of operations.

A psychology major and a molecular biologist

The company started in a classroom. In her senior year at the University of Washington, Mangubat took an entrepreneurship course at the Bothell campus and met Becky Drees, a molecular biologist with an idea for a genetic data analysis company. Their team won the 2009 business plan competition the class ended in, an event called Hell Night. Mangubat, then 22, had a psychology degree and no programming background.

Their first instinct was consumer genetics, which Mangubat later called “not a bad idea at all” before noting that 23andMe already owned it. They turned to analysis software for researchers instead, recruited Jeremy Bruestle as chief technology officer, and incorporated in Delaware in 2009.

The early product was conventional: Spiral Cloud and Spiral Cluster wrapped existing open source tools and ran them faster on rented computers. In March 2013 Draper Fisher Jurvetson led a $3 million round on that story. Mangubat told Chemical and Engineering News the same year that total financing stood at $3.7 million, and offered a forecast that has aged well: “We are headed toward a world where a kid with a laptop can analyze his or her genome.”

The pivot, and the moment it landed

Then the company threw the product away. By late 2014 Spiral had discontinued the platform it had raised money on and rebuilt around a method that reversed the standard pipeline: assemble the reads that do not match the reference first, then map the ones that do. It shipped as Anchored Assembly in spring 2014, with a cancer version called Onco Assembly behind it, at roughly $700 to $800 per whole human genome.

Validation came from Houston. Baylor College of Medicine researchers ran Spiral’s caller against the other tools on the market. William Salerno, a senior staff scientist at its Human Genome Sequencing Center, told GenomeWeb in November 2015: “We really liked Spiral’s method because they had a very high specificity, they didn’t make a lot of false positive calls”. Baylor became a pilot customer for BioGraph, the indexing format Spiral launched that month, which sorted reads by sequence rather than by position on a reference.

Commercially, none of it was enough. Asked in October 2016 what the company earned, Mangubat said: “Our revenue at this point is like in the low hundreds of thousands.”

Sold, then unsold

On January 23, 2017, Omicia, an Oakland company that turned variant data into clinical reports, announced it had acquired Spiral Genetics for an undisclosed sum. The two had been partners since 2013. Most of Spiral’s staff became Omicia’s Seattle office and its secondary analysis division, with Mangubat as general manager. Two months later Omicia renamed itself Fabric Genomics.

It did not hold. Mangubat told Forbes in March 2019 that within a year the combined company had drifted toward analyzing individual patients rather than whole populations, the thing she had started the company to do. She reversed the deal, in what she called an un-acquisition, took the relaunched Spiral through Y Combinator’s Winter 2019 batch, and announced a Microsoft Healthcare partnership. Then the trail goes quiet.

What is proven, and what is still claimed

Read plainly: the science was real and the commercial engine never caught up with it. Spiral’s caller is written into the permanent record of the Genome in a Bottle benchmark, its comparison tool became a standard other people still use, and its method was published openly. Against that sits revenue in the low hundreds of thousands, a flagship benchmark that never cleared peer review, a cancelled trademark, an accelerator entry marked inactive, and a domain squatted by a casino. No shutdown was ever announced. Nothing had to be.

What to watch

• Whether anything revives the BioGraph codebase. It is BSD licensed and public, and the last commit was August 2023.
• Truvari, which came out of this company and is now maintained by its original author.
• Assignment of the patents, which would show where the assets went.
• What Adina Mangubat builds next. She has announced no new venture publicly.

In their words

Spiral Genetics funding profile on HVCFHealthcare Venture Capital Fund

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Sources

1. Public recordForm D and amendments, Spiral Genetics, Inc., CIK 0001555798SEC · 2012 to 2016
2. Public recordTrademark status, SPIRAL GENETICS, registration 4026641USPTO TSDR · Sep 23, 2026
3. Public recordA robust benchmark for detection of germline large deletions and insertionsNature Biotechnology · Nov 2020
4. Public recordLeveraging a WGS compression format to call structural variantsbioRxiv · Apr 25, 2020
5. Public recordChildSeq-RNA, fusion transcripts in childhood sarcomasJ Mol Diagn · May 2014
6. Public recordTruvari: refined structural variant comparisonGenome Biology · Dec 27, 2022
7. Public recordspiralgenetics organization and biograph repositoryGitHub · Sep 23, 2026
8. Public recordY Combinator directory record for Spiral GeneticsY Combinator · Sep 23, 2026
9. IndependentSpiral Genetics Refocuses Business on Structural Variant DetectionGenomeWeb · Nov 7, 2014
10. IndependentSpiral Genetics Launches Large-Scale Query Tech, Kicks Off Pilot With BaylorGenomeWeb · Nov 5, 2015
11. IndependentSeattle’s Spiral Genetics acquired by OmiciaGeekWire, Clare McGrane · Jan 23, 2017
12. IndependentA 32-Year-Old CEO Relaunches Her Genetic Data Mining CompanyForbes, Ellie Kincaid · Mar 15, 2019
13. IndependentC&EN Talks With Adina MangubatChemical & Engineering News · 2013
14. InterviewHow Adina Mangubat built a software company for analyzing DNAMixergy · Oct 21, 2016
15. InterviewSpiral Genetics and its young CEO prepare for fund-raising roundFlynn’s Harp · May 2, 2019
16. CompanyOmicia Acquires Bioinformatics Innovator Spiral GeneticsBusiness Wire · Jan 23, 2017
17. CompanySpiral Genetics websiteInternet Archive · 2020 and 2021