Skip to main content
Premium Trial:

Request an Annual Quote

Harvard-Partners Transfers Cardio Tests to Affy Platform to Cut Cost, Turnaround Time

This article has been corrected to more accurately reflect the content of the HCM CardioChip.
Researchers at Harvard Medical School – Partners HealthCare Center for Genetics and Genomics in Boston have decided to move a genetic test for cardiovascular diseases from Applied Biosystems’ sequencing platform to the Affymetrix GeneChip platform.
Last month, HPCGG’s Laboratory for Molecular Medicine began offering a test for hypertrophic cardiomyopathy based on an Affy-manufactured resequencing array. The test, called the HCM CardioChip, can detect mutations in 11 genes associated with the disease, which can cause heart failure, exercise intolerance, and chest pain. Harvard-Partners signed a contract-array manufacturing deal with Affymetrix in July (see BAN 7/24/2007).


Raju Kucherlapati, the scientific director at HPCGG, said the center originally offered the HCM diagnostic using the Applied Biosystems 3730 Genetic Analyzer sequencer, but decided to migrate the test to the GeneChip platform to reduce the amount of time it takes to report results back to customers and to halve the cost of the test.
He wrote in an e-mail to BioArray News last week that the HCM test originally cost “about $6,500 based on capillary sequencing and we now offer the new test for $3,000.” The time required to complete the testing has also been cut from around 10 weeks to 5 weeks.
HPCGG is also planning to move other cardiovascular diagnostics developed on the AB 3730 to the Affy platform over the next 12 months in order to increase their affordability and accessibility, Kucherlapati said.
Harvard-Partners has access to the patents for genes used in HPCGG’s CardioChip and these patents have also been licensed to one other company, Correlagen Diagnostics, which offers sequencing-based HCM testing.
Kucherlapati said that the HCM CardioChip differs from some other array-based tests in the market because it is based on resequencing arrays that detect the presence of gene mutations, rather than a particular gene expression profile that is associated with a disease. Other array-based diagnostic tests on the market, such as Agendia’s MammaPrint test for breast cancer recurrence, use gene expression signatures.
“HCM mutations in any one of 11 different genes can cause disease and it is necessary to sequence all of the genes to find out,” Kucherlapati said. “Until recently, that was done by sequencing using the ABI 3730 machines. We developed the Affy chip to reduce the cost and reduce the time that it takes to get the results.”
The HCM CardioChip is currently offered to patients as a homebrew assay in the Laboratory for Molecular Medicine under guidelines established by the Clinical Laboratory Improvement Acts. Approximately one in 500 people are thought to suffer from HCM, which can lead to sudden cardiac death.

“This test is based on resequencing DNA, not looking for expression profiles.”

The center is not only recommending the test for patients exhibiting symptoms of HCM, but also relatives who may carry the mutations associated with risk for the disease. A positive test result will enable HPCGG to refer patients to a cardiology center that can help them to better manage their HCM, according to the center’s website.


Kucherlapati wrote that reimbursement for the $3,000 test is not an issue. “Any physician in this country or another country can order the test for their patients,” he wrote.  “Clients have to provide a payment mechanism, [and] we have people that help the patients with their reimbursement issues,” he added.
Heidi Rehm, an associate molecular geneticist at HPCGG, told BioArray News this week that there are array-based CPT codes for HCM CardioChip, and that generally institutions order the test from HPCGG on behalf of patients and in turn bill third-party insurers.
She added that HPCGG offers a service to other patients that helps them navigate the reimbursement process and in some cases get up to 80 percent of their testing costs reimbursed.
Future Tests
According to Rehm, HPCGG will move other tests that it currently offers using ABI’s 3730 sequencer to the Affy platform later this year.
Such tests include an assay that can detect mutations related to dilated cardiomyopathy, a primary disorder of the myocardium that is characterized by left ventricle enlargement and the most common reason for heart failure and transplant.
Rehm said that a DCM CardioChip is in development and that it will contain more genes than are offered in the sequencing-based test. “The number of genes will increase significantly. We currently offer 10 genes and we may expand up to 20,” she said.
Rehm said another chip is in development that will combine tests for diseases related to the raf/MAP kinase pathway, including Noonan syndrome, CFC syndrome, and Costello syndrome — all congenital conditions that affect many parts of the body. And an additional chip tests for many genes involved in hearing loss and Usher syndrome.
HPCGG offers sequencing-based tests for mutations associated with other cardiovascular diseases such as arrhythmogenic right ventricular dysplasia or cardiomyopathy.
Rehm said that if platform “continues to be robust”, HPCGG will continue to offer other tests on it. She added that it is more likely that these tests will be for diseases with genetic heterogeneity or diseases that are caused by multiple mutations in different genes, rather than mutations in only one gene, like cystic fibrosis.
In cases where the disease is caused mostly by mutations in one gene, HPCGG will continue to offer testing on the 3730 sequencer rather than on Affy arrays, Rehm said.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.