New tool to detect structural variants enhances value of whole genome sequencing

Genome.One researchers have developed a new tool to detect unbalanced structural variants including Copy Number Variants (CNVs) through whole genome sequencing (WGS), giving promise for increased diagnoses of complex genetic disorders.

Principal Scientist Ben Lundie said the ClinSV analysis pipeline applied as part of WGS lowers the minimum size limit for detecting these types of variants, resulting in higher resolution and greater sensitivity than currently used technologies including microarray.

Principal Scientist Ben Lundie: CNV analysis increases diagnostic yield of whole genome sequencing

He presented a poster at the European Society for Human Genetics (ESHG) annual conference in Milan, Italy, this week, outlining preliminary findings of a study of previous WGS cases with no diagnostic result, in which the new analysis was used to identify disease-causing CNVs.

CNVs are a type of structural variant involving alterations in the number of copies of specific regions of DNA, which can either be deleted or duplicated, and which are associated with many rare genetic diseases.

Analysis of 30 previously negative WGS cases revealed two diagnostic CNVs, one clinically significant incidental finding and one variant of uncertain significance. In one of the cases, the test revealed a CNV associated with autosomal recessive spastic paraplegia.

“Genome-wide CNV analysis has wider breadth and higher resolution than any other test available and increases the diagnostic yield of WGS," Mr Lundie said. “It is particularly relevant to those patients with previous uninformative genome and exome testing.”

Long-term utility of WGS

Genome.One Chief Medical Officer Professor Leslie Burnett also presented a poster at the Milan conference highlighting the long-term clinical value of WGS, with the addition of new analytical techniques such as the CNV analysis.

The newly developed CNV analysis could boost diagnoses by about 10%, providing the greatest single improvement in diagnostic yield to date, he said. Genome.One’s CNV analysis has been clinically validated and is awaiting official NATA accreditation.

 “This illustrates the long-term utility of WGS: as newer analytical techniques are progressively developed, they can be added retrospectively during re-analysis of WGS data,” Dr Burnett said.

Telehealth genetic counselling

Meanwhile, another poster presented by Genome.One Head of Clinical Services Mary-Anne Young at the European Meeting on Psychological Aspects of Genetics (EMPAG), being held concurrently in Milan, showed that a telehealth model of genetic counselling was an acceptable and effective way to reduce barriers to treatment.

Ms Young outlined research conducted with Peter MacCallum Cancer Centre evaluating a telephone genetic counselling service for women with recurrent high-grade ovarian cancer, aimed at facilitating BRCA 1/2 testing. 

Most women were satisfied with the telephone counselling service and it overcame geographical barriers to enable access to genetics services, and to ensure BRCA1/2 testing was facilitated expediently to inform treatment.

The findings come after Genome.One launched new phone and telehealth options for genetic counselling for patients undergoing genomic and genetic testing, through its newly opened genomics clinic.

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