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Partners HealthCare Center's LMM to Introduce Clinical Whole-Genome Sequencing Interpretation Service in 2012


By Julia Karow

This story was originally published June 8.

BOSTON – The Laboratory for Molecular Medicine at the Partners HealthCare Center for Personalized Genetic Medicine is preparing to introduce a clinical whole-genome sequencing test in 2012, initially geared at patients with genetic disorders it cannot diagnose using existing testing panels.

At the Consumer Genetics Conference here last week, Heidi Rehm, director of the LMM, said that while her lab will provide the clinical interpretation services, it will outsource the "technical component" to a CLIA-certified sequencing laboratory. This will be the LMM's first test that it will not run in house, she said.

The lab has not yet decided which sequencing service provider it will use. It has already worked with Illumina's Individual Genome Sequencing service, which runs samples in the company's CLIA laboratory, but it is also considering Complete Genomics, which plans to have its whole-genome sequencing service CLIA-certified in the second half of 2012. The LMM may end up outsourcing whole-genome sequencing to both companies, she said.

Rehm told Clinical Sequencing News that the test will initially be available for patients with genetic conditions for which the lab is already testing, such as cardiomyopathies, hearing loss, and inherited cancer syndromes. The plan is to later offer it for any potentially hereditary disease and, eventually, to offer it to healthy individuals.

The lab also intends to offer the test for analyzing tumor DNA in the future, which has additional challenges regarding sample preparation.

The cost of the test has not been determined yet, mainly because it is difficult to estimate the cost of the data analysis and interpretation, Rehm said, but she hopes that the analysis will initially be under $5,000. The LMM is currently working on automating parts of the analysis, in particular the "data enrichment" that provides a basic annotation of all sequence, and on implementing software filters to help identify candidate disease variants.

Rehm said the lab is still evaluating whether it will outsource components of the bioinformatics pipeline or build everything from scratch, but it is leaning towards initially outsourcing certain components to commercial providers. It has already hired a clinical molecular geneticist, Matthew Lebo, who also has a bioinformatics background, to help the LMM and the center's IT group, led by Sandy Aronson, in developing the CLIA whole-genome interpretation service.

At launch, scheduled for sometime next year, the lab expects to be able to run between one and five whole-genome sequencing tests per month and to scale that number as it automates the analysis. Similar to existing genetic tests, Rehm said she expects the test to be covered by insurance in some cases.

In preparation for the launch, the LMM is currently exploring the test in a clinical research setting and is hoping to sequence its first genome next month. It is currently consenting its first case, a family with several children, some affected and some unaffected by hearing loss, who have tested negative on the lab's current OtoChip hearing loss test.

The test will be one of the first clinical whole-genome sequencing interpretation services to be offered in the US — the Medical College of Wisconsin is currently providing a similar test to diagnose patients with inherited disorders (CSN 3/29/2011).

Have topics you'd like to see covered in In Sequence? Contact the editor at jkarow [at] genomeweb [.] com.

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