Liquid Biopsy Enables Early Cancer Detection in Li-Fraumeni Syndrome Patients

This aggressive clinical surveillance for early tumor detection is associated with improved survival, but is disruptive to quality of life. For some cancers, conventional screening methods may not be entirely effective. Detection and analysis of circulating tumor DNA (ctDNA) has seen a variety of uses in sporadic cancer including the detection of stages I and II cancers but has not been explored for hereditary cancer syndromes such as LFS.

A team of medical scientists led those at the Princess Margaret Cancer Center (Toronto, ON, Canada) collected more than150 plasma samples from more than 100 LFS patients. The cohort includes both pediatric and adult patients. Each plasma sample underwent shallow genome sequencing (sGS, 1×), cell-free methylated DNA immunoprecipitation (cfMeDIP, 60M clusters), and targeted panel sequencing (20,000×), given sufficient DNA. To date, 53 targeted panel, 96 sGS, and 96 cfMeDIP samples have been sequenced.

The team reported that the known germline TP53 variants were identified in 49/53 samples which included exon-level deletions and non-canonical splicing mutations. Using an error suppression method (ConsensusCruncher) and a variant calling pipeline, somatic TP53 mutations were identified in 3/15 cancer positive and 4/38 cancer negative samples.

Somatic copy number alterations and tumor fraction were predicted using ichorCNA (Broad Institute, Cambridge, MA, USA). Positive predicted tumor fractions were detected in 30/96 samples (12/18 cancer positive). In several cancer positive cases where no somatic TP53 mutation was found, ichorCNA was able to detect copy number alterations and predict positive tumour fraction. The investigators used sGS, and also evaluated DNA fragmentation as previous studies have highlighted the shorter length of ctDNA. On a global scale, they observed an increased proportion of short DNA fragments in LFS samples, regardless of cancer status, and an even greater increase in cancer positive LFS samples compared to non-LFS healthy controls. On a genome-wide scale, LFS patients also consistently exhibited abnormal fragmentation profiles compared to non-LFS healthy controls.

Derek Wong, PhD, a postdoctoral fellow and a senior author of the study, said, “Li-Fraumeni is a good proving ground for the “cfDNA in hereditary and high-risk malignancies" (CHARM) consortium due to the overall high risk of developing a variety of cancer types and multiple cancers over the patients' lifetime. The most common cancers include breast, brain, bone, adrenal, and soft tissue sarcoma, and despite our advances in treatment and understanding of these cancers, early detection is often the best prognostic indicator for survival.”

The authors concluded that their approach demonstrated that each individual assay, while sensitive, is not comprehensive. However, in synthesis, targeted panel sequencing, sGS, and cfMeDIP are capable of accurately and sensitively detecting ctDNA. Their method presents a novel approach to the management of patients with LFS that is both comprehensive, non-invasive, and sensitive. The study was presented at the American College of Medical Genetics and Genomics annual meeting, held March 22-26, 2022 in Nashville TN, USA.

Related Links:
Princess Margaret Cancer Center 
Broad Institute