Costs Falling Swiftly for Whole Genome Sequence

Complete Genomics says it is now selling $20,000 sequences to researchers and pharma

CEO SUMMARY: Several companies want to be first to achieve the holy grail in sequencing: an accurate whole human genome sequence produced in an hour for $1,000. Complete Genomics announced earlier this month that it could sequence the full human genome for a materials cost of $4,400 (not including labor and overhead). Another competitor, Illumina, is selling whole genome sequences for $48,000 to private individualsand has customers!

Probably The Fastest-Advancing Field In Genetic Medicine is  whole human genome sequencing. Multiple companies are racing to lower the cost to $1,000 or less for sequencing an individual’s entire genome.

The latest breakthrough was announced by Complete Genomics, Inc., of Mountain View, California. On November 5, 2009, it stated that it was now capable of sequencing whole human genomes for about $4,400 in materials (labor and overhead extra). In September, Complete Genomics disclosed that it was charging $20,000 per genome for orders of eight or more genomes.

For pathologists and laboratory directors, these developments demonstrate the unbridled pace of improvements in the speed, cost, and accuracy of the technology used to sequence whole human genomes. In turn, by lowering the cost to sequence DNA, these developing technologies will give clinical labs and pathology groups new diagnostic tools.

There are many competitors racing to achieve an accurate, whole human genome sequence in less than one hour for $1,000. What motivates these companies and their investors is a widely-held belief that the market for whole human genome sequencing will be huge, once the price for a fast, accurate full sequence falls below $1,000.

With its announcements this month, Complete Genomics is perceived to be the leader in this race—at least for the moment. What distinguishes Complete Genomics from its competitors are two strategies.

First, Complete Genomics is building a service-driven business model. This sets it apart from competitors who expect to generate revenue by selling sequencing systems to researchers, pharmaceutical firms, and biotech companies. (See TDR, October 20, 2008.)

The foundation of this service model is a specialized focus on one task: sequencing the human genome. Daniel MacArthur, in his blog Genetics Future, says that Complete Genomics “aims to create a series of extremely automated sequence factories with a single input (human DNA) and a single output (an accurate and comprehensive list of all of the variants present in that sample’s genome), operating on a massive scale. All of the steps in between will be performed using in-house sequencing technology and analytical software.”

Economies Of Scale

Thus, the goal of this strategy is to apply automation and economies of scale— focused exclusively on human genome sequencing—to achieve cost advantage. The second strategy is to provide the information technology and informatics services that customers need to store, assess, and evaluate the sizeable quantities of data that result from sequencing large numbers of human genomes.

This data warehouse will need to be huge. Complete Genomics is telling the public that it will deliver 100 complete human genomes to customers by the end of this year. In the first half of 2010, it expects to complete 1,000 human genomes. It predicts it will sequence 9,000 human genomes during the second half of 2010.

It seems to be a smart move by Complete Genomics to offer customers the data storage and information processing capability on a contract basis. This enables Complete Genomics to sell a total solution to potential customers. Not only will it sequence the DNA, but it can then immediately help the customer analyze the resulting data, eliminating the need for the customer to spend additional money to create its own extensive computer and software infrastructure.

Of course, a race always needs other competitors, and in the whole genome sequencing arena, there are plenty of firms actively working toward the $1,000 whole human genome sequence. At the moment, many experts consider Illumina, Inc., of San Diego, California, to be the closest competitor to Complete Genomics.

$48,000 Human Genome

Illumina has gotten plenty of publicity. For example, last June, Illumina attracted media attention when it announced that it was charging private individuals $48,000 to run their whole genome sequence.

At least four people have been sequenced by Illumina for this price. They are Jay Flatley, CEO and President of Illumina; Hermann Hauser, Partner at Amadeus Capital Partners Ltd.; Henry Louis “Skip” Gates, Jr., a Professor at Harvard University and Director of the W.E.B. Du Bois Institute of African and African American Research; and his father Henry Louis Gates.

Illumina manufactures and sells second generation sequencing systems. Demand for its systems is strong. Compared to the business strategy of Complete Genomics (total outsourcing for customers of sequencing, data warehousing, and informatics services), Illumina’s strategy is more traditional.

Sells Sequencing Systems

It supports customers who want to buy a sequencing system and use it in their own facilities. These customers gain flexibility, but then face the need to invest in the computing capacity required to work with the data generated by the DNA sequencing systems.

Another company selling whole genome sequences is Knome, Inc., of Cambridge, Massachussetts. In early 2008, when it first launched, Knome and its Chinese partner, Beijing Genomics Institute, would sequence any individual’s genome for $350,000. It has since lowered that price to $98,000.

Knome is also offering different sequencing services to the public. In May 2009, it announced a service priced at $24,500 for individuals and $19,500 per member for families. Knome will sequence the genes and provide a customized analysis of the results. With 20,000 human genes, Knome says it is offering a retail price of less than $1 per gene for sequencing and analysis.

Applied Biosystems, Inc. (ABI), a division of Life Technologies Corporation of Carlsbad, California, is another contender. Its sequencing systems are strong sellers. Its executives predict steady gains in sequencing speed with comparable reductions in cost per base pair sequenced.

454 Life Sciences is a business unit of Roche and is based in Branford, Connecticut. Besides selling its high-throughput DNA sequencing systems, it is also participating in active collaborations with such firms as Eli Lilly and Company and SeqWright.

Another company keeping pace with the race to the $1,000 whole human genome is Helicos BioSciences Corporation of Cambridge, Massachussetts. For third quarter 2009, it reported placing twice the number of its sequencing systems compared to third quarter 2009.

Pacific Biosciences, Inc., of Menlo Park, California, says it will release, in 2010, a high-throughput sequencing system that could enable $100 genome sequencing in 15 minutes in 2013. The company has major support from multiple venture capital companies.

Each of these firms on this short list has declared its intent to achieve a $1,000 whole human genome sequence. Collectively, they represent hundreds of millions of dollars from professional investors. Further, each company has a different technology upon which it is basing its whole genome sequencing systems. This means there is a rather broad range of technologies which may prove viable.

Zeroing In On The Goal

What is notable for the clinical laboratory profession is that the front-runners are declaring that their technology and their sequencing systems will zero in on the $1,000 genome during 2010 or 2011. This is a near-term outcome.

For laboratory managers and pathologists, these developments are a reminder that disruptive technologies are emerging from many sources that are outside the traditional practice of laboratory medicine and pathology. As can be seen with the effort to achieve cheap, fast, and accurate whole human sequencing, success in this endeavor has the potential to overturn or supplant many long-standing technologies common today in the pharmaceutical, laboratory testing, and healthcare industries.

Another aspect of the drive to the $1,000 whole human genome sequence is the importance of information technology (IT) and informatics. Labs working with this data need an IT platform capable of handling the data points generated by the three billion base pairs in a single human genome. It reinforces the need for clinical laboratories and pathology groups to keep current with information technology.
Maybe the greatest surprise that lies ahead is how fast the whole human genome screening market will develop as the cost falls to $1,000 or less. As noted earlier, Complete Genomics is telling Wall Street that it will produce 10,000 whole genome sequences during 2010! This reflects the demand—and the scientific interest—for the knowledge that is currently locked up in the complete human genome.

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Institute for Systems Biology Buys from Complete Genomics

ON NOVEMBER 2, 2009, The Institute for Systems Biology (ISB) announced that it was contracting with Complete Genomics, Inc., to produce 100 whole genome sequences to support an ISB study of Huntington’s Disease.

To study modifiers of the disease presentation and progression, ISB will provide samples to Complete Genomics from individuals affected by Huntington’s Disease, family members, and matched controls.

The Institute for Systems Biology is based in Seattle, Washington, and was co- founded in 2000 by three scientists: Leroy Hood, M.D., Ph.D, an immunologist and technologist; Alan Aderem, Ph.D., an immunologist; and, Ruedi Aebersold, Ph.D., a protein chemist. It is devoted to the study of biological complexity and understanding how biological systems function.

Researchers from ISB are working on diagnostic methods that evaluate multiple metabolic pathways to detect pre-symptomatic and complex diseases. Experts believe that the Institute for Systems Biology will introduce diagnostic technologies that will prove disruptive to the current practice of laboratory medicine.

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