My Weblog on Bioinformatics, Genome Science and Next Generation Sequencing
Friday, 11 March 2016
Ambry to share aggregated anonymous data from 10,000+ human exomes.
Firms are starting to be more open with the data they have collected for the benefit of mankind. But do watch out for the fine print. there's a disclaimer that although the data is 'free to download and use, the company retains copyright.'
By Andrew Pollack
Posted March 08, 2016
GENETIC TEST FIRM TO MAKE CUSTOMERS’ DATA PUBLICLY AVAILABLE
In an unusual move, a leading genetic testing company is making genetic information from the people it has tested publicly available, a move the company says could make a large trove of data available to researchers looking for genes linked to various diseases.
The company, Ambry Genetics, is expected to announce on Tuesday that it will put information from 10,000 of its customers into a database called AmbryShare.
“We’re going to discover a lot of new diagnostic targets and a lot of new drug targets,” Aaron Elliott, interim chief scientific officer at Ambry, which is based in Southern California, said in an interview. “With our volume, we can pull out a significant number of genes just by the sheer number we are looking at.”
The 10,000 people all have or have had breast or ovarian cancer and were tested by Ambry to see if they have genetic variants that increase the risk of those diseases. Ambry returned to the samples from those customers and, at its own expense, sequenced their exomes — the roughly 1.5 percent of a person’s genome that contains the recipes for the proteins produced by the body.
Since proteins perform most of the functions in the body, sequencing just that part of the genome provides considerable information, and is less expensive than sequencing the entire genome.
AmbryShare will not contain the actual exome of each person, because that would pose a risk to patient privacy. Rather it will contain aggregated data on the genetic variants.
For example, a researcher could look up how frequently a particular mutation occurs among the 10,000 people. Ones that occur frequently in these 10,000 patients, but not among healthy people, could raise the risk of developing those cancers.
Specialists welcomed Ambry’s move, but some said it was unclear how useful the information will be. The Exome Aggregation Consortium, an academic collaboration based at the Broad Institute of M.I.T. and Harvard, already has a similar publicly available database containing information from more than 60,000 exomes.
“It is not clear to me that 10,000 exomes changes the game much,” said David B. Goldstein, professor of genetics at Columbia University.
Ambry said its data would be from people with the diseases it tests for, like epilepsy and intellectual development problems, while the Broad database covers a more general population. Ambry said it hoped to add data from as many as 200,000 customers a year to the database.
The Ambry customers whose data is being used were not told specifically about this project. But in ordering tests they consent to having their samples used for research.
Various labs, including Ambry, have been pooling information on which mutations in certain known breast cancer risk genes are harmful or not. AmbryShare is different — aimed more at novel discoveries of genes linked to diseases.
Data can be valuable to drug companies. The consumer genetics company 23andMe sells access to data from its testing to drug makers and uses that data to develop drugs itself.
Charles Dunlop, founder and chief executive of Ambry, said he was approached by drug companies, but decided to make the company’s data freely available to expedite research.
“I’ve got Stage 4 cancer myself,” he said, referring to advanced prostate cancer that is in remission. “I don’t want to wait an extra day.”
He said Ambry had spent $20 million on the project. Ambry is privately held and majority-owned by Mr. Dunlop and his family, insulating it somewhat from shareholder pressure.
Correction: March 10, 2016
An earlier version of this article described incorrectly the step that Ambry is taking with its customers’ data. It is making the data publicly available; it is not putting the data in the public domain. While the data is free to download and use, the company retains copyright.