Human Longevity, Inc. plans to overrun BGI

It is already three months as Human Longevity, Inc. was officially announced. The company now has a beautifully designed website and announcements about new executive hires.  The caliber of executives points at the company plans to grow huge and grow fast; thus CIO comes from AstraZeneca, where he was the Vice President, R&D IT responsible for the global IT organization services, analytics and infrastructure supporting drug discovery and development, leading a global team of approximately 300 and was accountable for the more than $120 million R&D IT budget. The company is also building a computing and informatics program and facility in Singapore.

BioIT World was one of the first to write about the company’s launch (for more news check the company’s website):

In a move that would be shocking from almost anyone else, Venter declared that his brand-new company’s sheer sequencing power will be leapfrogging the world’s best-established genomic research centers, such as the Broad Institute.

The company has acquired 20 the latest Illumina’s HiSeq X Ten machines ($1 million a piece), which would allow for sequencing full genomes of 40,000 people a year. For comparison, BGI by the end of 2013 had already sequenced 57,000 individuals. HLI doesn’t even need to compare itself with BGI as it plans to rapidly scale to 100,000 human genomes a year (considering that Illumina is among investors).

Human Longevity will also be characterizing at least some participants’ microbiomes, and, in partnership with Metabolon of North Carolina, their metabolomes, or the constantly changing array of small molecules present in the body. On top of that, said Venter, “we will be importing clinical records of every individual we’re sequencing,” in order to bring on board crucial phenotypic data.

The goal is to integrate this mass of data for new discoveries that can wed individuals’ own genetic variants, the composition of their bacteria, the molecules in their blood, and most importantly, their medical histories. Venter stressed that his aim is to enable predictive and preventative medicine for healthy aging, discovering early warning signs for susceptibility to chronic illnesses like cancer, Alzheimer’s, and heart disease, as well as new interventions tailored to each individual’s distinct profile. “We think this will have a huge impact on changing the cost of medicine,” added Venter.

A longer-term goal is to translate some of this information into stem cell therapies, an application that ties Human Longevity to Venter’s existing company, Synthetic Genomics.

But the goal of this year is sequencing genomes of cancer patients in collaboration with the UCSD Moores Cancer Center.

What exactly the company is going to do with all these data? Do research and publish papers? Yes, and some of principal scientists hired by the company got appointments at Craig Venter Institute. Sell data and the results of analysis? Yes. “Venter and his colleagues also held out the possibility of other commercial products and properties emerging from the company’s basic research.” The company is also actively hiring, and not only computational professionals but clinical and wet lab scientists as well. Here are some more about the company mission from job ads:

HLI will develop the most comprehensive gene-phenotype database in the world, with phenotype information deriving from molecular, physiologic, clinical, microbiome and longitudinal data assays. This database will be mined for biological meaningful patterns that can lead to better diagnostics, therapeutic targets and next-generation cell-replacement therapies.

 

 

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23andMe doesn’t want people to wait around for 10 years for personalized medicine

Human Chromosomes

Eric Topol interviews Anne E. Wojcicki, co-founder and CEO of 23andMe.

Ms. Wojcicki: [We have] 650,000 [genotyped individuals] now. We are by far the largest. It is phenomenal. When you look at some of our papers, and we say that we had 40,000 people with asthma, and 150,000 controls, our numbers are genuinely huge. My inspiration was my father. He’s a particle physicist, and they collect really big data. He used to laugh at clinical trials. He would say, “Three hundred people — what is this?” So my goal was always to get huge numbers to really understand how things work. The price point has dramatically dropped, and that has really spurred the volume.

… everything I see the Obama administration doing is pushing individuals to take more control of their health.

You can already see what the Beijing Genomics Institute is doing. It is the largest in the world. They have massive interest in getting everybody genotyped or sequenced. Saudi Arabia announced plans [to genotype] 100,000 individuals. The United Kingdom is doing 100,000; Scotland has a big program. The rest of the world is moving forward aggressively with this, but we are somewhat stuck. It’s going to happen, and overwhelmingly it is going to improve healthcare. So how do we do that?

Ms. Wojcicki: The way I run the company is to think about if I were sick with a disease; what would I want to happen? If you have a child with sarcoma, you don’t care whether Pfizer or Glaxo or Hopkins or Harvard gets the data. You just want someone to do something with the data. Rather than saying that we are going to monetize and do all of these things, I point the finger at all of the pharma companies and groups who are just sitting on frozen piles of data because they don’t want to do anything with it yet. I want everybody to start to use the data to do something good. Otherwise, for this child with sarcoma, what’s going to happen?

Dr. Topol: When you have a million or even 10 million people, and you can find these rare variants that a lot of other people can’t find, that’s an exciting opportunity. We are going to watch this and follow along with you.

Ms. Wojcicki: That is definitely the direction in which we are going.

See this my post about BGI.

Is Beijing Genomics Institute to establish Chinese dominance in genomics market?

Illumina_Hiseq_2000_sequencers,_BGI_Hong_Kong_sequencing_room

I am well past due to post on the New Yorker’s article about B.G.I. The article is by subscription only, and here I am citing the most interesting parts.

B.G.I., formerly called Beijing Genomics Institute, the world’s largest genetic-research center. With a hundred and seventy-eight machines to sequence the precise order of the billions of chemicals within a molecule of DNA, B.G.I. produces at least a quarter of the world’s genomic data—more than Harvard University, the National Institutes of Health, or any other scientific institution.

the company has already processed the genomes of fifty-seven thousand  (57000) people. B.G.I. also has sequenced many strains of rice, the cucumber, the chickpea, the giant panda, the Arabian camel, the yak, a chicken, and forty types of silkworm.

The company was founded in 9/9/1999 at 9:19 am in Beijing, China. It has now 4000 employees of an average age of 26, is located in Shenzhen nearby to the infamous Foxconn factory, and operates on a $1.58-billion loan from the China Development Bank, including multiple nonprofit and commercial projects, such as DNA sequencing 10000 people from the families with autism in the US and a thousand of obese and healthy people in Denmark. The BGI’s plans include the Million Human Genome Project, the Million Plant and Animal Genomes Project, the Million Microecosystem Genomes Project, and the controversial Cognitive Genomics project, also millet (very drought-tolerant crop) and cassava projects, both holding a big promise for feeding China and Africa.

BGI is the biggest customer of Illumina, which has sold BGI 130 sequencers for half a million dollars each (my guess, that would be HiSeq 2000 and HiSeq 2500; the latest and the most powerful HiSeq X Ten, released in 2014, costs about a million). When in 2013 BGI bought the main Illumina’s competitor Complete Genomics, Jay Flatley, Illumina’s CEO, said: “It is one thing to sell Coke and another to sell the formula for Coke. … when they bought Complete Genomics … they were allowed to … buy the formula.”

The article concludes discussing the Cognitive Genomics project, which goals are to select intelligent high-IQ embryos, to find cure for Alzheimer’s and to map the brain: At some point … people will look back and wonder what all the fuss was about [Chris Chang, a visiting scholar at BGI].”

 

Companies to watch: DNAnexus

DNAnexus

This is an excerpt from the job ad at DNAnexus:

At DNAnexus we are solving the most challenging computer science problems you’re ever likely to see. 
In the last few years, there has been a dramatic development in the world of genomics that has created a huge new opportunity. The price to sequence the full human genome (all of your DNA, not just a sample of it) has fallen to the point were it will soon be affordable for a patient to have multiple samples of their whole genome sequenced to help treat their disease. Want to know what specific gene mutation caused a patient’s cancer? We are building the platform to answer that kind of question. One of the many challenges is the huge amount of data. Think you’ve seen big-data problems? Think again – with each genome comprising 100 GB and months of CPU time to crunch the information, DNA is the next big-data problem, requiring exabytes of storage and parallel workloads distributed across 100,000 servers. We are tackling this by combining web technologies, big-data analytics, and scalable systems on cloud computing infrastructure. 

We are a well-funded start-up backed by Google Ventures, TPG Biotech, and First Round capital. Our founders, Andreas Sundquist, Arend Sidow, Serafim Batzoglou are world-renowned genomics and bioinformatics experts from Stanford University.

We are looking for smart motivated people. Ideal candidates will likely know several of the following technologies: C, C++, Boost, Ruby, Rails, HAML, HTML, CSS, JavaScript, ECMAScript, V8, jQuery, Flash, Flex/ActionScript, Node.js, Python, Perl, PHP, Amazon Web Services (AWS), SQL, MySQL, PostgreSQL, MongoDB, Solr, Sphinx, Hadoop, MapReduce, ZooKeeper, Hive, Pig, Oozie, HDFS, ZFS, MCache. 

And some more about the company from the company’s website:

No proposal is considered too large, as demonstrated through the CHARGE project, a collaboration between Baylor College of Medicine’s Human Genome Sequencing Center (HGSC), DNAnexus, and Amazon Web Services that enabled the largest genomic analysis project to have ever taken place in the cloud. We worked with HGSC to deploy its Mercury variant-calling pipeline on the DNAnexus cloud platform, processing 3,751 whole genomes and 10,940 exomes using 3.3 million core-hours with a peak of 20,800 cores and making Mercury available to 300 researchers participating in the global CHARGE consortium.

Here is the service model and pricing DNAnexus provides, effective May 2014:

DNAnexus_pricing_MAy_2014

 

Big Data, Drugs and Rare Phenotypes

drugs

In the era of Big Data, search for new biologics (therapeutics, such as monoclonal antibodies, recombinant proteins, blood, cells, or tissue components, created via biological processes, rather than chemically synthesized or extracted drugs) and new drug targets not much differ from the search for a terrorist suspect. And if in the latter case, cell phone data are mined; in search for drugs, companies mine rare phenotypes, or individuals, families, groups or communities possessing great self-healing abilities, disease susceptibility, incredible memory, or other extraordinary abilities. Thus, a few dozens of known individuals producing HIV broadly neutralizing antibodies (that are antibodies able to trigger the response of the immune system killing many HIV strains), as their antibodies can be potentially used for HIV therapy; while, still better, the peculiarities of the immune system of those individuals can be deciphered for developing an HIV protective vaccine.

This Forbes’ article discusses three examples of the companies’ approaches at developing drugs via discovering rare phenotypes. The major motivator is a successful (in Phase III trial now) development of lipid-lowering drugs targeting PCSK9, an enzyme discovered from the study of two French families with unusually high cholesterol levels and a strong history of heart disease (when overproduced, PCSK9 increases cholesterol level).

Thus, Amgen acquired deCODE, the Iceland company collected 400,000 blood samples and a large amount of health records. Regeneron partnered with Geisinger Health System to sequence the exome DNA of 100,000 patients (see this article in The New York Times). Belgium-based pharma UCB partnered with Innocentive to crowdsource the search for rare genetic variations associated with extreme phenotypes. The latter overlaps with an approach by PersonalGenomes.org, an online system that matches individuals willing to share their personal health information with researchers seeking such information.

“There are now important opportunities … to collect the dense phenotypic data that, in conjunction with genomic data, biological insight – and yes, muscular,  empirically-driven analytics — will power the medical innovation of the future.” (Forbes)

National Cancer Institute is to create a Cancer Genomics Cloud

Government Health IT reports on the NIH’s National Cancer Institute announcement to set up the cloud infrastructure toward the establishment of a full Cancer Knowledge Commons to enable “democratic access to NCI-generated genomic data”

“Today, researchers often have to mine genomics data from various sources by locating and downloading it — such as the Cancer Genome Atlas, the Cancer Genomics Hub and the International Cancer Genome Consortium — then add their own data and use it all on local hardware.

“This model has been successful for many years,” NCI officials wrote, “but is becoming untenable given the enormous growth of biomedical data since the advent of large-scale scientific programs such as the Cancer Genome Atlas,” which on its own this year is set to generate some 2.5 petabytes, half a petabyte less than the Library of Congress’ digital collection.”

This year, $20M will be spend on awarding contractors to deliver a cloud pilot.

Awards for health Big Data projects

This news from iHealthBits lists seven health-related projects funded by the Knight Foundation. Of 700 applications, only 7 have been awarded, totaled $2.2M. The major winner ($500K) is the Open Humans Network project for PersonalGenomes.org, an online system that matches individuals willing to share their personal health information with researchers seeking such information. Another winner is BW Analytics’ (Principled Strategies, Inc. of San Diego now ?) SafeUseNOW, a prescription drug data analysis tool, which is unfortunately is impossible to glance at as it is not searchable on Google.