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Finding the cause of severe hearing loss in babies is tripled with genomic testing

More babies and children born with severely impaired hearing could have an answer for the underlying cause of their deafness if they are offered comprehensive DNA sequencing, after an Australian-first study showed the test almost tripled the rate of genetic diagnosis.

Researchers say the study shows how genomic sequencing could complement existing newborn hearing screening.

The Melbourne Genomics project provided genomic – DNA – sequencing to more than 100 children with hearing loss in both ears, detected through the Victorian Infant Hearing Screening Program (VIHSP) over a two-year period. Collaborating hospitals were The Royal Children’s Hospital and Monash Health.

More than half the children (56%) received a genetic diagnosis for their hearing loss through genomic testing, which was almost triple the rate achieved through usual methods (21%). For a third of those diagnosed it became clear that no further screening or medical monitoring was required.

Significantly, care changed for 92 per cent of babies who received a genomic finding.

These results from the Melbourne Genomics’ Congenital Deafness project, involving a multi-disciplinary team led by Professor David Amor (University of Melbourne and Murdoch Children’s Research Institute) and Dr Lilian Downie (Murdoch Children’s Research Institute), were published in the European Journal of Human Genetics on December 13.

Prof Amor said there are more than 100 different genetic causes of deafness, which is why a genomics approach – sequencing large amounts at DNA once – is key. He said the study showed the benefits of an early genetic diagnosis for babies with hearing impairment detected at birth. “The high diagnosis rate and medical implications for these children emphasises the need for genomic sequencing to become the gold standard of care,” Prof Amor said.

“Based on our study, we estimate about 50 children born in Victoria each year with congenital deafness would immediately benefit from access to this test. Genomic sequencing will allow these children and their families to get the answers they desperately need to plan for the future.” The test typically costs around $2,000.

The Melbourne Genomics project offered genomic testing to all babies born with deafness during calendar years 2016 and 2017. Children in the study were aged between four weeks to one year old. Almost half (48%) the genetically diagnosed cases were inherited. In these cases, parents are now able to make informed choices regarding their future family planning.

“Victoria has an excellent newborn hearing screening program which tests 98 per cent of newborns,” said Dr Downie, the lead author of the research paper. “Providing genomic sequencing to babies found to have severe hearing impairments would add to this robust service and provide more opportunities for early intervention.”

“More than half of babies diagnosed with deafness at birth will have an underlying genetic cause,” Dr Downie said. “Our research showed the value of providing an answer for families about why their child has a hearing impairment, which cannot be over-estimated.”

Genomic testing uses technology to decode (sequence) large amounts of DNA to find any changes or ‘spelling mistakes’ in the genetic code that are known to cause deafness. While some cases of deafness are isolated, others are syndromic – associated with a condition that may include other complications, such as sight loss.

Dr Downie said there were medical implications for all the children in the study, including a change in care or treatment, or the opportunity to participate in clinical trials to prevent further complications.

In this study, families accessed all the services they needed in a single clinic visit – paediatrics, otolaryngology (ear, nose and throat) and genetic services. This one-stop service enabled a higher rate of diagnoses and streamlined management for both families and the healthcare system, the study found.

“This study has provided a real test-bed for how genomic sequencing could complement newborn hearing screening,” Dr Downie said.

The children in this project were among more than 3,800 patients who received a genomic sequencing test through Melbourne Genomics for 16 medical conditions. Overall results from the program show this type of test can help a wide range of patients, including those with terminal cancer, genetic kidney disease, complex neurological conditions, as well as those at risk of superbugs and even critically ill babies in intensive care.