Ultrasensitive and affordable assay for early detection of primary liver cancer using plasma cell‐free DNA fragmentomics

Abstract

Background and Aims: Early detection of primary liver cancer (PLC), including HCC, intrahepatic cholangiocarcinoma (ICC), and combined HCC-ICC (cHCC-ICC), is essential for patients' survival. This study aims to develop an accurate and affordable method for PLC early detection and differentiating ICC from HCC using plasma cell-free DNA (cfDNA) fragmentomic profiles. Approach and Results: Whole-genome sequencings (WGS) were performed using plasma cfDNA samples from 192 patients with PLC (159 HCC, 26 ICC, 7 cHCC-ICC) and 170 noncancer controls (including 53 liver cirrhosis [LC] or HBV-positive) enrolled in the training cohort. An ensembled stacked model for PLC detection was constructed using the training cohort. The model performance was assessed in an independent test cohort (189 patients with PLC [157 HCC, 26 ICC, 6 cHCC-ICC], 164 noncancer controls [including 51 LC/HBV]). Our model showed excellent performance for cancer detection in the test cohort (AUC: 0.995, 96.8% sensitivity at 98.8% specificity). It showed excellent sensitivities in detecting early-stage PLC (I: 95.9%, II: 97.9%), small tumors (≤3 cm: 98.2%), and HCC (96.2%) or ICC (100%). The AUC for distinguishing PLC from LC/HBV reached 0.985 (96.8% specificity at 96.

Noninvasive cancer detection by extracting and integrating multi-modal data from whole-methylome sequencing of plasma cell-free DNA

“…The copyright holder for this preprint (which this version posted July 5, 2022. ; https://doi.org/10.1101/2022.07.04.498641 doi: bioRxiv preprint Indeed, across the genome of plasma samples from example colorectal cancer patients, we observed pronounced correlation between FSI and copy number in CNA-positive genomic regions in agreement with other reports (15,24,25); meanwhile we noticed strong anti-correlation between methylation and copy number in these regions (Figure 3). Second, we noticed consistent cancer detection performance between the training and the test cohort with both the base models of individual biomarkers and the integrative THEMIS model (Figure 4 Localizing the origin of cancer-like signal is a crucial component of blood-based multi-cancer detection test to provide guidance on the follow-up diagnostic workup.…”

“…For example, large-scale methylation changes are characteristic of most types of tumors (20)(21)(22) and analysis of hypomethylated segments of the plasma genome shows diagnostic value for hepatocellular carcinoma (23). Similarly, fragment sizes of plasma cfDNA among cancer patients show more variability than healthy individuals and exhibit position-specific patterns, allowing for the employment of genome-wide fragmentation profiling for multi-cancer detection (15,(24)(25)(26). Another fragmentomic marker is the composition of the 4-mer fragment end motifs whose frequencies are revealed to be perturbed in cancer patients (27).…”

Circulating cell-free DNA for cancer early detection

“… 83 Notably, the cfDNA fragmentation profile sequenced by WGS was also leveraged to detect early-stage HCC. 86 This model showed excellent sensitivities of 95.9% and 97.9% in distinguishing stage I and stage II liver cancer from non-cancers including chronic hepatitis B, liver cirrhosis, and healthy controls at a 98.8% specificity, 86 showing the potential of cfDNA fragmentation in the early detection of HCC.…”

Improved anti-hepatocellular carcinoma effect by enhanced Co-delivery of Tim-3 siRNA and sorafenib via multiple pH triggered drug-eluting nanoparticles

“…Hepatocellular Carcinoma (HCC) is one of the most common malignant cancers in clinical practice [ 1 , 2 ]. Due to the insidious onset of HCC, most patients are in the middle or late stage of the disease when they are diagnosed, thus missing the optimal period of surgical resection [ [3] , [4] , [5] , [6] ]. In addition, the remission rates of radiotherapy and chemotherapy for intermediate and advanced HCC are also very low [ 7 ].…”