10x Genomics Acquires Epinomics, To Launch ATAC-Seq Product

By Allison Proffitt

September 5, 2018 | 10x Genomics has acquired Epinomics, a pioneer in the growing epigenetics space. The acquisition will give 10x Genomics ATAC-seq technology and fundamental IP to accelerate discoveries and further research in epigenomics, paving the way for a new understanding of disease, diagnostics and therapeutics, according to the company.

ATAC-seq is an area 10x has been eyeing. At the AGBT meeting this February, Michael Schnall-Levin, VP Product, R&D and Strategy, made the “first announcement of a commercially-available, single-cell, ATAC-seq assay.” He showed early data and said, “We’re extremely excited about single-cell ATAC-seq because we believe it’s a complimentary data type to single-cell gene expression and we believe it will fundamentally open up additional biology.”

Serge Saxonov, CEO and co-founder of 10x Genomics, told Bio-IT World that 10x has been watching epigenetics, calling it an “incredibly important area.” Saxonov insists, “The right way to do it is at the single-cell level.”

ATAC-seq—Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq)—is a method for mapping chromatin accessibility genome-wide. The method was first published in Nature Methods in 2013 (DOI: 10.1038/nmeth.2688).

“ATAC-seq captures open chromatin sites using a simple two-step protocol with 500–50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution,” the authors wrote in the 2013 paper.

“It creates a very straightforward way of accessing open chromatin,” Saxonov explains. “In a lot of ways, [open chromatin] really defines the programming [of a cell]. The genome is a superset of all the possible things; open chromatin defines what is actually done... To my mind, ATAC-seq gets at precisely that: which areas are open, which ones are closed.”

Three of the paper authors—Howard Chang, professor of Dermatology and Genetics at Stanford University School of Medicine; Will Greenleaf, assistant professor in Genetics at Stanford University School of Medicine; and Paul Giresi—are among those credited with inventing ATAC-seq. The three, plus Fergus Chan, founded Epinomics in 2013.

Epinomics’ patent portfolio includes foundational issued IP relating to ATAC-seq. The company has financial backing from Lightspeed Venture Partners, Felicis Ventures, and Founders Fund. The Epinomics intellectual property enhances and complements 10x Genomics’ existing patent portfolio, 10x said, which covers high throughput single cell applications for ATAC-seq and other epigenetic applications.

Chan, Giresi, and the Epinomics team will join 10x Genomics immediately; the scientific co-founders, Chang and Greenleaf, will join 10x Genomics as scientific advisors.

Stocked Pipeline

Saxonov sees important applications for ATAC-seq and calls it “complimentary” to 10x Genomics’ single cell gene expression product. Immediately, he sees application for the Human Cell Atlas. “But it comes up in just about every area when you look at human health and disease,” he says, listing oncology and immunooncology to start. “Demand from customers has been enormous.”

10x Genomics will immediately integrate Epinomics’ proprietary epigenetic technology into its Chromium Single Cell ATAC Solution, which is expected to launch by the end of this year.

Beta testers are very happy, Saxonov says. “We’ll be sharing more data as the year progresses,” he promises, “but the data look great; the science looks very interesting.”

Epinomics is the first 10x acquisition, but Saxonov promises more. “Our goal is to build a significant company. As a means to that, if we come across great technologies, great companies, great teams, we’ll consider acquisitions,” he says.

10x Genomics was founded in 2012, and had its “first full commercial year” in 2016, after a splashy launch at AGBT in 2015. Since then, the company has been growing “as fast as we can find awesome people and manage the culture,” Saxonov said. In 2017 the company did $71 million in revenue, 150% growth from 2016. The team of about 330 employees is headquartered in Pleasanton, Calif., with staff in Europe and Asia as well. It announced Series D financing earlier this year.

The ATAC-seq product isn’t the only one in the pipeline. Schnall-Levin announced two others in February and Saxonov teased more. “Stay tuned!” he said. “We’ve been moving on a pretty consistent pace of launching new products and new capabilities, always focused on where we see there is potential to make breakthroughs.” He predicts a “slate” of new products for the Chromium platform, all “pretty big advancements.”