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Australia's Genepath Developing Diagnostic Gene Panels for Newborn Screening, Developmental Delay


SAN FRANCISCO (GenomeWeb) – Australian startup Genepath is developing next-generation sequencing-based diagnostic gene panels, with its first product aimed at newborn screening.

Genepath was launched about four years ago by Glenn Bennett, director of clinical services, and Bennett Shum, laboratory director and managing director, and is predominantly self-funded with several shareholders holding a small stake. The firm runs a lab that is accredited by both Australia's National Association of Testing Authorities and the Royal College of Pathologists of Australia, and currently has seven full-time employees including physicians, clinical geneticists, pathologists, and lab scientists. All had an interest in NGS, Bennett said, and they all previously worked in Australian public hospitals.

"The lab scientists and pathologists realized that NGS wasn't being used to its fullest diagnostic potential in Australia," Bennett said. "That's where myself and clinical geneticists got involved."

The team ultimately decided on newborn screening as a first test because Bennett said that currently not many conditions are screened for, and he and others noticed that they were seeing patients later in life as children or adults with conditions that could be tested for at birth.

In addition, he said, over the last decade, there has been growing evidence that certain genetic syndromes may underlie some cases of sudden infant death, such as inborn errors of metabolism, long QT syndrome, and Brugada syndrome.

Genepath's test sequences 67 genes related to more than 60 genetic conditions. Aside from most of the conditions screened for under the Australian newborn screening program, Genepath's test includes lysosomal storage diseases, such as Gaucher and Pompe disease; metabolic conditions like familial hypercholesterolemia; endocrine conditions like maturity onset diabetes in the young type 2; seizure disorders; and the aforementioned inborn errors of metabolism, long QT syndrome, and Brugada syndrome.

The conditions typically screened for in Australia include cystic fibrosis, congenital hypothyroidism, amino acid disorders like phenylketonuria, and fatty acid oxidation disorders.

Bennett said that while Genepath's test includes most of those disorders, it is not looking to replace standard newborn screening, because some conditions, like congenital hypothyroidism, cannot be tested for with NGS. "The genetics of that condition are not understood," he said. "We see our test as being complementary to current newborn screening and our hope is that eventually both tests would be done."

The conditions included on the test are all ones for which treatments exist, Bennett said, which was key for their inclusion on the panel. And while some conditions are associated with an increased risk of SIDS, Bennett said that there is not currently data on whether diagnosing a condition such as Brugada or inborn errors of metabolism would have a positive impact on SIDS cases. "There's no evidence yet," he said, but it is definitely a question the company would be interested in gathering data on.

Ultimately, Bennett said that Genepath's goal is to develop the cost-effectiveness data necessary to make the test eligible for reimbursement under Australia's Medicare system. At the moment, he said, patients must pay out of pocket and the test costs A$980 (US$727) with a turnaround time of four to six weeks.

Patients interested in the test must request it through their physician. Genepath then sends the patients a sample collection kit, and patients send back a sample from a cheek swab. Genepath performs the DNA extraction and library prep in house and outsources the sequencing to the Australian Genome Research Facility. Genepath then prepares the clinical report that is returned to the physician.

Genepath researchers published a technical validation of the assay in the Journal of Molecular Diagnostics last year, validating it against National Institute of Standards and Technology's whole-genome reference materials.

Bennett said that the study demonstrated the benefit of a targeted approach for this particular application, because the targeted panel was able to detect 5 percent more variants than whole-genome sequencing was on the reference materials.

He said that another reason for using targeted sequencing for this test was to minimize cost as well as false positives, since the goal would be to use the test as a population screen.

Bennett said that the company plans to expand the number of conditions on its newborn screening panel and also is developing an NGS test for developmental delay in children. He said the firm would likely launch that test within the next year. The test would also be based on targeted sequencing and would be geared towards infants and toddlers who have not hit their developmental milestones. Such a test could "help parents avoid a diagnostic odyssey."

He said that although there has been a lot of interest recently in whole-genome and exome sequencing for suspected rare genetic conditions in children, the firm wanted to stick with targeted panels in order to avoid secondary findings and to focus on diagnosing known disorders accurately with as short a turnaround time as possible.

The genomic testing market in Australia is nascent, with few firms offering NGS-based tests. Bennett said that currently no other Australian company offers expanded NGS-based newborn screening, though the Garvan Institute spinout Genome.One does offer diagnostic sequencing for children with undiagnosed genetic disorders. So, when Genepath launches its panel test for developmental delay it would likely compete with that test.