A companion test from Tempus that uses machine learning to identify solid tumours with an allelic imbalance has secured breakthrough device designation by the US Food and Drug Administration (FDA).

The assay is a companion diagnostic test for Tempus’ already FDA-approved next generation sequencing test xT CDx, which is a 648-gene tissue-based molecular profiling test for solid malignant tumours. The newly designated breakthrough device, called the HLA-LOH assay, uses machine learning models to analyse sequence data produced by xT CDx.

Specifically, it will be used to identify patients with a heterozygous cell that has become homozygous due to an allele being lost in an erroneous genetic event. Loss of heterozygosity (LOH) is recognised as a cause of tumorigenesis, and the assay will look for this chromosome instability in specific human leukocyte antigen (HLA) Class I alleles.

Chicago, US-based Tempus says it has designed the test to increase early diagnosis of patients with solid tumours who make up around 90% of yearly cancer diagnoses. Identifying patients with LOH early on can help expand treatment via targeted therapies.

“HLA-LOH provides a clear molecular distinction between cancer and non-cancer cells and is a potential biomarker for immune therapy resistance. The Tempus HLA-LOH test is intended to measure this biomarker and better understand which patients may respond to new therapies,” said Kate Sasser, PhD, Chief Scientific Officer of Tempus.

“HLA-LOH is of special interest for the application of cell therapy to treat solid tumours, but also has broader potential for other precision medicine approaches in oncology, including in combination with other established biomarkers. The Tempus test is being developed to identify HLA-LOH and may help optimize existing therapies and facilitate the advancement and implementation of novel and transformative treatments.”

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A market model by GlobalData estimates that the NGS global market will reach $64.6m by 2033. According to Cancer Research UK, there could be around half a million new cases of all cancers every year in the UK by 2038-2040.