Oxford Nanopore Technologies, London Calling Highlight – CariGenetics.
As proud partners of Oxford Nanopore Technologies, between May 22nd– 24th 2024, Geneyx attended the 10th Anniversary of London Calling. One of the highlights was the plenary session by Dr. Carika Weldon, Founder and CEO of CariGenetics. Dr. Weldon’s Caribbean Breast Cancer Whole Genome Pilot Study aims to identify unique genetic markers for Caribbean women that will allow for more specific predictive screening and earlier intervention.
The motive for this project comes from the disparity between breast cancer rates and deaths between European and non-European populations; 9 of the top 10 countries getting breast cancer are European, but all the top 10 countries dying from breast cancer are non-European. Four in ten of these are Caribbean, with Barbados the highest.
Looking at traditional breast cancer genetic testing methods in the Caribbean, 13% of diagnoses of known genes were not BRCA1 or BRCA2, therefore there is a need to offer broader panel-based testing, including, but extending beyond these genes. Further, as most genetic testing is sent abroad from the Caribbean, the need was identified to repatriate testing. As part of the project, CariGenetics delivered end-to-end testing locally in Bermuda, using Oxford Nanopore Technology, as the first certified ONT Service Lab for PromethION in LATAM & Caribbean region.
In the pilot study, 102 women (18 years and over), with four Caribbean grandparents were recruited into two groups – those who had been diagnosed with breast cancer and those with no diagnoses themselves or in their first-degree relatives. The first aim of the study was to conduct the laboratory testing locally, quicker and cheaper. The second objective was to identify novel variations.
Whole genome sequencing using Oxford Nanopore Technologies human genome protocol, sequenced on the PromethION 24 was performed on these cases, secondary analysis was performed with Claire, Sniffles, and Spectre, and tertiary analysis using the Geneyx Analysis platform.
40% of cases were BRCA1/BRCA2 positive and 60% were not, further emphasizing the need for expanded testing. For the first time in a minority population, variants in DNA mismatch repair genes were identified, which has increased the scope for more therapeutic options.
Repatriation of testing is expected to be economically beneficial, and the unique data set is opening interest from pharmaceutical companies to expand diverse genomic research and therapies in admixed populations.
In the future, Dr. Weldon and her team intend to look more deeply into SV, investigate novel variants and recall for epigenetics using Oxford Nanopore Technologies and Geneyx Analysis.
Dr. Weldon says, ‘This study marks the first step towards a larger Caribbean Genome Project, which has already progressed to looking at prostate cancer in Bermuda and will expand to other Caribbean islands soon. We were thrilled to be working with Geneyx as this tool drastically accelerated the completion of our project, allowing us to give results back to patients in record-breaking time while also allowing for analysis that we could not have imagined doing without this technology.’
Geneyx says ‘We are delighted that CariGenetics has used Geneyx in this novel genomic program; it highlights how the use of Geneyx Analysis in combination with Oxford Nanopore Technologies can be used to advance knowledge. This can ultimately be applied in clinical settings for the benefit of the patient and healthcare professionals managing them, this works even in situations where conventionally it could not be done.
