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Coverage of Edico Genome by the media

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Subscribe to Molecular Diagnostics PerkinElmer Builds on Newborn Screening With New Clinical Genomic Testing Services

Sept 12. 2017 | by Julia Karow

…PerkinElmer Genetics has extensively validated its clinical genomics assays on the NovaSeq sequencer using multiple samples, including three different sample types — blood, saliva, and dried blood spot cards — from the same individual, and the platform has been “doing really well,” she said.

The lab also has developed its own bioinformatics pipeline and uses the Edico Genome DRAGEN platform. The team has written its own script for the interpretation, Hegde said, integrating the guidelines from the American College of Medical Genetics and Genomics, and re-analysis and re-interpretation concepts have already been implemented in the system.

Read the whole article here.

Edico & DNAnexus Launch $20, 90 Minute Whole Genome Analysis

Sept 6. 2017 | by Frida Holme

Edico Genome and DNAnexus, Inc. today announced the availability of Edico Genome’s DRAGEN on Amazon Web Service’s EC2 F1/FPGA instances via DNAnexus. For a limited time, the cost to analyse a whole genome at 35X coverage will be $20 and take about an hour and a half, Pieter van Rooyen said.

About a year ago Edico Genome ported the DRAGEN pipeline to Amazon’s FPGA instances, van Rooyen explained. Today the Edico and DNAnexus partnership make the DRAGEN pipeline even more accessible.

“If a customer has data on AWS, they can spin up an F1 instance with our solution it right away,” van Rooyen. “It’s basically an app on the DNAnexus platform.”

Read the full article here.

Tech Nation Radio: The Science of Curiosity

Sept. 2017

“Yes well that’s the thing about a genome a genome is six point four billion DNA letters that’s the equivalent of a book six hundred feet tall, printed with letters eight and half by eleven. And we decode that forty times, and so computationally decoding each of those from an image file and then comparing that to the reference and finding the five million variants that vary in you or I from what’s called normal is a computational challenging. It used to take a supercomputer about twenty four hours. And so we had a forty eight hour process, twenty four hours to decode the genome chemically, and twenty four hours to compute it. And then in partnership with Illumina and with Edico Genome we were able to shorten that to twenty six hours. The actual computational piece we took down to thirty minutes which is staggering to go from twenty four hours to thirty minutes.” – Dr. Stephen Kingsmore, President and CEO of the Rady Children’s Institute for Genomic Medicine

Listen to the full podcast here, starting at 37:00.

Data for Diagnosis: Edico Genome and Congenica to Provide All-in-One Clinical Decision Support Package

May 23, 2017 | By Neil Versel

Technological advances have led to dramatic decreases in the cost of genetic sequencing, ushering in a genomics revolution that aspires to transform medicine. However, developing solutions that can effectively, efficiently, and affordably translate these advances to a clinical setting remains challenging, which is why two genomics companies, Congenica and Edico Genome, have partnered to offer their complementary technologies as an all-in-one solution for data analysis, interpretation, and reporting.

“Both companies are very much driven to deliver these joint solutions in a clinical diagnostic setting,” commented Congenica’s Chief Business Officer, Shikha O’Brien, Ph.D., on the companies’ mutual commitment to bringing genomics-based medicine to fruition through their individual technologies.

Congenica’s cloud-based software platform, Sapientia, enables clinical geneticists to analyze and interpret the gamut of next-generation sequencing data and generate a comprehensive diagnostic report to support clinical decision-making.

The knowledge base underlying Sapientia aggregates data from its users and places it into a knowledge base that can inform future analyses. However, according to O’Brien, “[Sapientia’s] beauty is that it brings all of the information required for variant interpretation together in a single, dynamic interface. All of this information being held together creates an accurate and in depth audit trail to really support the work of our clinical colleagues.”

Referred to as “secondary analysis,” Edico Genome’s hardware-accelerated platform, DRAGEN (Dynamic Read Analysis for Genomics), analyzes raw-read data from sequencing instruments, identifies variants, and outputs a VCF (Variant Call Format) file that Sapientia and other downstream software reads. Unlike other, software-based, secondary analysis platforms, DRAGEN uses a field-programmable gate array (FPGA) processor that facilitates ultra-rapid analysis—without compromising accuracy. This distinctive approach “gives [DRAGEN] an efficiency that is just unachievable in pure software,” commented Gavin Stone, vice president of marketing and development at Edico Genome.


With Edico Investment, Dell VC Arm Bets That WGS Is Ready to Take Off

May 23, 2017 | By Neil Versel

Two weeks ago, sequencing informatics technology developer Edico Genome announced that it had closed on a $22 million Series B funding round led by new investor Dell Technologies Capital, the previously unknown investment arm of computer giant Dell Technologies.

It was the first investment Dell Technologies Capital, formerly known as EMC Ventures, had made in the genomics arena, and was a highlight of the venture capital operation’s big coming-out party: On May 8, it emerged from stealth with a bang, announcing that it had invested in more than 70 startups and was offering up venture capital at the rate of $100 million annually since its unspecified start date

Gregg Adkin, vice president and managing director of Hopkinton, Massachusetts-based Dell Technologies Capital, has been running the operation since 2012, according to his LinkedIn page, so the ex-EMC unit is at least five years old. Dell merged with EMC in September 2016, taking over EMC Ventures in the process.

San Diego-based Edico was one of two companies Dell Technology Capital highlighted at the unveiling, which took place at the annual Dell EMC World user conference in Las Vegas.


The Reconfigurable Future of Healthcare

May 19, 2017 | By Pieter van Rooyen

Data plays a more central role in healthcare than ever before. It won’t be long before every person’s genome is sequenced at birth, with follow-up sequencing done at regular intervals throughout life. Each genomic check-up would produce roughly 180 gigabytes of data that will need to be processed, analyzed, and stored. The promise of using such data is that doctors would be able to intercept diseases before symptoms develop, taking preventative medicine to a whole new level.

Already, whole-genome sequencing is helping to diagnose otherwise-hidden diseases, while machine-learning tools can enhance a doctor’s decision-making by scouring reams of data with speed and accuracy that far surpasses human capabilities. Meanwhile, the advent of wearable sensors is generating an unprecedented amount of additional data, including heart rate, respiration, blood pressure, and other vital signs. No wonder we stand at the threshold of healthcare’s “era of data.”

Big data is at the center of this whirlwind, but putting all this data to good use has been another matter altogether. What we have been missing, until recently, has been ample computing power.

In order to handle the surge of useful health care data—genomic and otherwise— available to us, we must adopt more powerful computing tools than the CPU-based machines that have dominated the computer and server industries for decades. Unless we do so, we will continue to face a data bottleneck that stands in the way of quick answers for healthcare providers and researchers.

Fortunately, an answer exists in a technology that has actually been available for decades —FPGAs, or field-programmable gate arrays—which are now going mainstream. Why now? In the past, programming these chips required significant expertise. Now, however, computing demands have reached a point where the efficiency of an FPGA outweighs programming hurdles. The increased use of FPGAs has in turn lowered costs, further accelerating mass adoption.

Read the full article at

Edico Genome’s Deal with Dell EMC Fits Partnership Strategy

January 4, 2017 | By Bruce V. Bigelow

San Diego’s Edico Genome is now in its fourth year as a startup, and well into the hard slog of striking partnership deals, generating revenue, and building a business.

Founding CEO Pieter van Rooyen started Edico with the idea of developing a specialized processor to accelerate the way genome sequencing data gets processed. Today Edico says it has joined forces with Dell EMC to provide a service that combines Edico’s analytical tools with Dell EMC’s data storage and cloud-based computing capabilities.

The company has grown to almost 50 employees, but Van Rooyen wouldn’t say how much revenue Edico is generating or whether it’s profitable yet. He also wouldn’t talk about financial terms of the Dell EMC deal during a phone call yesterday, but he said the deal with Dell EMC is typical of the kind of partnerships with big tech players that have been key to his strategy from the beginning.

“The issue with a startup is there’s no name recognition,” van Rooyen said. On the other hand, he said, “The genomics space is new, and tech companies see it as a growth area. And we have compelling technology that big tech players see as a big advantage.”

Edico has developed what it calls a “Bio-IT” computer processor for ordering the readout of nucleotides—A, C, T, or G—from the short segments of DNA generated by next-generation sequencing machines so they align with a reference genome. It’s a process that genomics specialists refer to as “mapping,” and determines the sequence of individual genomes.



August 20, 2016 | By Carl Smith

Q&A with Pieter van Rooyen, the Founder and CEO of Edico Genome.

FLG: San Diego is gaining a reputation for being the Genomics Capital of the world, particularly in bringing NGS into the clinic. This is something you’ve had experience in through your work with Dr. Stephen Kingsmore. You had a key role in setting the world record for the fasted genetic diagnosis, but it isn’t just speed for speed’s sake is it? What are the benefits of reducing time?

PVR:  In a critical situation in a Intensive Care Unit (NICU), every second counts and so speed becomes pivotal. Obtaining a genetic diagnosis faster means the right treatment can begin much sooner. In many cases this can mean the difference between life and death. Accelerated data analysis also means research can be done more efficiently, leading to cures for genomic diseases like cancer or Alzheimer’s. In addition, speed translates to massive cost savings in terms of compute resources and storage. For instance, we replace a cluster of 50 or more computers with a single 1U server with DRAGEN. This technology also enables us to reduce storage by a significant margin.

Doctor at Rady’s sets unusual world record

April 25, 2016 | By Marcella Lee

On National DNA Day, Dr. Stephen Kingsmore was honored for his medical breakthrough that will save countless lives, including babies in the neo-natal intensive care unit. Dr. Kingsmore received the Guinness World Record for making the fastest genetic diagnosis. He is able to complete a diagnosis in 26-hours. It’s an amazing accomplishment for the historically pain-staking process of diagnosing a newborn baby with a genetic disorder.

“For the kids right behind us in our care units, those critical hours and days can mean the difference between life and death,” said Dr. Kingsmore.

Read the full article at

Researcher Named Record-Holder for Fastest Genetic Diagnosis

April 25, 2016 | By Alex Philippidis

Stephen Kingsmore, M.D., D.Sc., president and CEO of Rady Children’s Institute for Genomic Medicine at Rady Children’s Hospital-San Diego, now holds the official Guinness World Records® designation for the fastest genetic diagnosis, for the results that he and clinicians published just seven months ago. The feat is being recognized today at a celebration in San Diego to mark National DNA Day. Dr. Kingsmore led a clinician team that studied 35 critically ill infants less than 4 months old. Of those 35, the researchers made a genetic disease diagnosis in 20 of the infants through genome sequencing of the newborns and their parents within 26 hours.

Read the full article at GEN News

Scientists Can Now Sequence a Human’s Genome in 26 Hours

October 5, 2015 | By Danny Lewis

Scientists have figured out how to cut the time it takes to sequence a human genome nearly in half. Researchers from Children’s Mercy Hospital in Kansas City, MO and Edico Genome, a biotech company, have devised a way to sequencing a human genome in just 26 hours. The previous fastest device took about 50 hours to complete and was developed by the same group. In a paper published this week in the journal Genome Medicine, the researchers note that cutting down the time it takes to perform a whole genome sequencing could mean the difference between life and death for some patients.

Read the full article at

Whole Genome Sequencing Time Cut to Just 26 Hours

October 1, 2015 | By Conor Gaffey

Scientists have cut the time required for sequencing a full human genome and getting a diagnosis for any known genetic diseases down to 26 hours. The advance could save the lives of critically ill children.

Read the full article at Newsweek

Genetic Testing in Newborns Gets a Critical Breakthrough

September 29, 2015 | By Alice Park

For the first time, researchers can now sequence the genomes of newborns with mystery conditions in 26 hours

In every neonatal intensive care unit (NICU), about half of the tiny residents are there because they are born prematurely and need help to breathe and get accustomed to their new world outside the womb.

But about third of NICU babies are there because doctors simply don’t know what’s wrong with them. They may have seizures or may not be eating or breathing properly, and nobody knows why.

Fortunately, genetics may be able to help them. With advances in both the depth and speed at which researchers can sequence genomes, newborns can have their DNA analyzed in about 50 hours. But for infants in crisis for whom every minute counts, it may now be possible to unlock their genetic secrets in about 26 hours.

Read the full article at Time

My Déjà vu Moment in Genomics: Why We Need Industry Standards Now

September 29, 2015 | By Pieter van Rooyen

I am a serial entrepreneur who has spent the past couple of decades advancing the front lines of technology in digital healthcare, wireless communications, and semiconductor industries. And I’ve been experiencing a déjà vu moment in genomics.

Back in 1994, when I was designing electrical circuits as part of my doctorate program at the University of Johannesburg, the first smartphone hit the market. It sold for a little over $1,000. Still, that actually seemed like a great deal compared with a decade earlier, when the very first cell phone cost nearly $4,000.

Read the full article at Xconomy

Edico Adds HudsonAlpha to Dragen Client List, Unveils New Pipelines and Product Development Plans

September 10, 2015 | By Uduak Grace Thomas

NEW YORK (GenomeWeb) – Edico Genome has released a new bisulphite sequencing pipeline for its Dragen Bio-IT processor with additional pipelines for microbiome, RNA-seq, and cancer data to follow shortly. The company is also developing a graphical user interface that will offer tools for tasks such as automating data transfer and pipelines on its processor as well as a software development toolkit that will enable customers to install and run their own tools on the company’s processors.

Read the full article at GenomeWeb

As life science converges with big data and redefines biotech, there are more opportunities for engineers and mathematicians to found life science ventures. How difficult is it to make the transition from tech to biotech?

May 28, 2015 | By Pieter van Rooyen

As the worlds of biomedicine, information technology and digital health intersect, numerous opportunities are opening up for new types of biotech startups. Although I trained as an electrical engineer and have built two companies focusing on wireless technology, my latest venture, Edico Genome (La Jolla, CA, USA; Box 1), lies at this intersection of biology and technology. To many in the world of high tech and information technology (IT), the world of biotech ventures and their business models might seem complex and alien. Drawing on my experience moving from wireless technology startups to the world of biotech, I provide here some tips for engineers, mathematicians and others who are thinking about making a similar leap to the world of the bioentrepreneur.

Read the full article at Nature Biotechnology

Intel-Edico partnership aims to break a medical logjam

Intel and start-up Edico are collaborating on technology that could drastically shrink the time between DNA analysis and diagnosis.

April 23, 2015 | By Laura Lorenzetti

Genome sequencing has the potential to enable huge advances in “precision medicine”–genetically tailored treatments for leukemia, cystic fibrosis, and other devastating diseases. A new partnership between Intel Corp. and startup Edico Genome, announced this week, could make the distance between the sequencing and the treatment considerably shorter.

The partnership would pair Edico Genome’s Dragen high-speed DNA sequence analyzer with Intel’s high-powered Xeon processors to accelerate the speed at which genomic sequences can be analyzed. Announcing the partnership this week, the companies estimated that Dragen and Xeon, working together, would be able to analyze a patient’s entire genome in real time. Until recently, it typically took 10 to 20 hours to analyze data from a single genome, and in practice, backlogs and other delays can mean a long wait between sequencing and diagnosis.

Read the full article at Fortune

Edico Genome inks Intel deal

San Diego startup also moves, gets first patent for Dragen processor

April 21, 2015 | By Bradley J. Fikes

Edico Genome, a startup that makes a high-speed DNA sequence analyzer, said Tuesday it has collaborated with Intel Corp. to help its Xeon chips analyze DNA sequence data. Privately held Edico sells the Dragen microprocessor, which greatly reduces the time needed to analyze a human genome.

The San Diego startup has also has moved into a 9,000 square foot office in Torrey Pines, leaving the EvoNexus business incubator . The company now has 28 employees, and plans to add more. The company was founded in 2013 with four employees.

Read the full article at UT San Diego

Top 10 Innovations 2014

The list of the year’s best new products contains both perennial winners and innovative newcomers.

December 1, 2014 | By The Scientist Staff

The Scientist’s annual Top 10 Innovations competition has again turned up some exciting new products that are poised to revolutionize the work of life scientists. Familiar names, such as Illumina and Leica, win again with updates to their sequencing and imaging technologies, while newcomers like Sciencescape, Organovo, and Edico Genome debut with novel products that caught the eyes of our independent, expert judges.

Read the full article at The Scientist

Edico Genome Makes First Sale of NGS Processor

September 4, 2014 | By Laurel Oldach

The year of the thousand-dollar genome just got a little more interesting as Edico Genome, which makes a data processor called the DRAGEN for next generation sequencing (NGS) data, made its first sale to Sequenom, Inc.

According to its designers at Edico, the DRAGEN, short for Dynamic Read Analysis of GENomes, reduces the time to map a complete human genome to reference by sixty-fold. At present the mapping, sorting, deduplication and variant calling that are required to turn 200 GB of raw massively parallel sequences into an interpretable genome takes, by Edico’s estimate, about twenty hours on an industry standard server. The marketing team at Edico Genome likes to compare the task to piecing together a telephone book that’s been put through an industrial shredder. This poses a considerable threat of backlog given that a high-throughput sequencer like Illumina’s HiSeq X Ten can turn out a comparable amount of sequence every thirty minutes.

Read the full article at Bio-IT World

As Genomics Moves to Clinical Domain, Bio-IT Plays Key Role

August 14, 2014 | By Arundhati Parmar

As gene sequencing machines have gotten faster and faster, they are producing ever larger amounts of data that the medical world hopes to mine to link gene variants to specific diseases.

Genomics, which was once the exclusive domain of researchers is moving to the clinical domain thereby making the prospect of personalized medicine not seem that remote. By unlocking the relationship between genetic variation and disease states, drug and diagnostic companies can now race to develop a whole host of tests and medications that can treat individuals more effectively.

Read the full article at MD+DI Online

Edico Genome Draws Greg Lucier among Investors

July 17, 2014 | By Alex Philippidis

A San Diego startup whose technology promises to enable the clinical use of genomics by radically reducing the cost and time of analyzing next-generation sequencing (NGS) data is attractive enough to have drawn Gregory Lucier among investors that have joined to raise $10 million in Series A financing.

Lucier has made his first investment since his days as chairman and CEO of Life Technologies as a member of the investor group behind Edico Genome, which announced the financing today and said it plans to bring to market its Dynamic Read Analysis for Genomics (DRAGEN) Bio-IT Processor this fall.

Read the full article at GEN

To Speed Sequencing, Edico Genome Proposes NGS Processor

April 21, 2014 | By Alison Proffitt

Of sequencing bottlenecks, the most lamented is the analysis pipeline. Edico Genome is developing the DRAGEN Bio-IT Processor, the world’s first Next Generation Sequencing (NGS) bioinformatics ASIC to speed and smooth that process. In alpha testing now, the processor stands to revolutionize genome analysis, Gavin Stone, Edico’s Director of Marketing told Bio-IT World.

Of course, that’s language you’d expect from a director of marketing. But early feedback looks promising. The company’s advisory board boasts Eric Topol, M.D. (Scripps), Charles Cantor, Ph.D. (Sequenom) and Nils Homer, Ph.D. (Broad Institute). Alpha customers are already using the product.

Bio-IT World’s Best of Show judges are eager for a closer look. The product is a finalist in the Best of Show competition and the company will be exhibiting at the Bio-IT World Conference & Expo*.

Read the full article at Bio-IT World

Edico Genome Aims at Data Processing Bottleneck in Whole Genome Sequencing

April 17, 2014 | By Bruce V. Bigelow

With the arrival of next-generation gene sequencing machines like the Illumina (NASDAQ:ILMN) HiSeq X Ten, medicine has been moving to develop new ways of using genomic data to treat patients. Last month, for example, J. Craig Venter unveiled plans to sequence the entire genome of every patient entering the UC San Diego Moores Cancer Center as an initial goal for his latest startup, Human Longevity Inc.

At the same time, though, it’s becoming clear that generating genomic data for thousands of cancer patients involves working with very large numbers—and that means a wave of new opportunities for innovation are emerging as genomics and Big Data come together. One startup moving to catch this wave is Edico Genome, a San Diego startup founded last year to fix a bottleneck in the way the data being generated by the HiSeq X Ten and other next-generation sequencing machines is processed.

Read the full article at Xconomy

Edico Genome Preps for Launch of ASIC Infrastructure for NGS; Touts Low Cost, Speed as Differentiators

April 4, 2014 | By Uduak Grace Thomas

San Diego, Calif.-based Edico Genome is preparing to launch its first product for the bioinformatics market, an application-specific integrated circuit system for next-generation sequence data analysis called the Dragen Wavefront Processor, which consists of a chip loaded with proprietary algorithms for mapping, alignment, sorting, and variant calling.

Edico plans to officially launch Dragen during this year’s Bio-IT World conference to be held in Boston from April 29 to March 1. It is currently testing the system in conjunction with a number of undisclosed sequencing centers.

The company is positioning its appliance as an alternative to large server systems as well cloud infrastructure, which, in the case of the former can be costly to purchase, install, and maintain; and in the case of the latter may not mesh with the privacy requirements of some customers.

Read the full article at GenomeWeb