06 April 2020

Researchers have announced a blood test which is able to detect more than 50 types of cancer, including types of lymphoma and myeloma, and identify in which tissue the cancer originated – often before symptoms show.

The test was found to have a 0.7% false positive rate for cancer detection and was able to predict the tissue in which the cancer originated in 96% of samples, with accuracy of 93%.

However, more research is needed to improve the test’s ability to pick up early stage cancers.

The research team, led by US Oncology Research in Texas, USA, analysed gene methylation in cell‑free DNA (cfDNA) found in blood samples. Gene methylation usually controls gene expression, and abnormal methylation patterns and the resulting changes in gene expression can contribute to tumour growth.

The blood test targeted approximately one million of the 30 million methylation sites in the human genome. In earlier research an algorithm was developed to predict the presence of cancer and the type of cancer based on the patterns of methylation in the cfDNA shed by tumours.

Dr Michael Seiden, senior author from US Oncology Research, said: “Our earlier research showed that the methylation approach outperformed both whole genome and targeted sequencing in the detection of multiple deadly cancer types across all clinical stages, and in identifying the tissue of origin. It also allowed us to identify the most informative regions of the genome, which are now targeted by the refined methylation test that is reported in this paper.”

The study involved the analysis of blood samples donated by 6,689 North American participants, of whom 2482 patients had previously untreated cancer and 4207 had no cancer.

They were divided into a training set and a validation set and of these, 4316 participants were available for analysis, of whom 3052 in the training set (1531 with cancer, 1521 without cancer) and 1264 in the validation set (654 with cancer and 610 without cancer).

The blood samples were analysed to identify methylation changes and to classify the samples as cancer or non-cancer, and to identify the tissue of origin. The research team say performance was consistent in both the training and validation sets, with a false positive rate of 0.7% in the validation set.

There was also consistency in correctly identifying when cancer was present between the two sets. In 12 types of cancer – anal, bladder, bowel, oesophageal, stomach, head and neck, liver and bile duct, lung, ovarian and pancreatic cancers, lymphoma, and plasma cell neoplasms – the true positive rate (sensitivity) was 67.3% across clinical stages I, II and III.

The true positive rate was 43.9% for all cancer types in the study across the three clinical stages.

Detection also improved with each cancer stage. In the 12 pre-specified cancers, the true positive rate was 39% in stage I, 69% in stage II, 83% in stage III and 92% in stage IV. In more than 50 cancer types, the corresponding rates were 18%, 43%, 81% and 93%, respectively.

The test was also consistent between the training and validation sets in its ability to identify the tissue where cancer had originated, with an accuracy of 93% in the validation set.

Dr Seiden said: “These data support the ability of this targeted methylation test to meet what we believe are the fundamental requirements for a multi-cancer early detection blood test that could be used for population-level screening: the ability to detect multiple deadly cancer types with a single test that has a very low false positive rate, and the ability to identify where in the body the cancer is located with high accuracy to help healthcare providers to direct next steps for diagnosis and care.”

Source: Liu MC, Oxnard GR, Klein EA, Swanton C, Seiden MV, on behalf of the CCGA Consortium (2020) “Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA”, Annals of Oncology, doi: 10.1016/j.annonc.2020.02.011

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