Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localization

Despite their promise, circulating tumor DNA (ctDNA)-based assays for multi-cancer early detection face challenges in test performance, due mostly to the limited abundance of ctDNA and its inherent variability. To address these challenges, published assays to date demanded a very high-depth sequencing, resulting in an elevated price of test. Herein, we developed a multimodal assay called SPOT-MAS (screening for the presence of tumor by methylation and size) to simultaneously profile methylomics, fragmentomics, copy number, and end motifs in a single workflow using targeted and shallow genome-wide sequencing (~0.55×) of cell-free DNA. We applied SPOT-MAS to 738 non-metastatic patients with breast, colorectal, gastric, lung, and liver cancer, and 1550 healthy controls. We then employed machine learning to extract multiple cancer and tissue-specific signatures for detecting and locating cancer. SPOT-MAS successfully detected the five cancer types with a sensitivity of 72.4% at 97.0% specificity. The sensitivities for detecting early-stage cancers were 73.9% and 62.3% for stages I and II, respectively, increasing to 88.3% for non-metastatic stage IIIA. For tumor-of-origin, our assay achieved an accuracy of 0.7. Our study demonstrates comparable performance to other ctDNA-based assays while requiring significantly lower sequencing depth, making it economically feasible for population-wide screening.

Multimodal analysis of genome-wide methylation, copy number aberrations, and end motif signatures enhances detection of early-stage breast cancer

Introduction

Breast cancer causes the most cancer-related death in women and is the costliest cancer in the US regarding medical service and prescription drug expenses. Breast cancer screening is recommended by health authorities in the US, but current screening efforts are often compromised by high false positive rates. Liquid biopsy based on circulating tumor DNA (ctDNA) has emerged as a potential approach to screen for cancer. However, the detection of breast cancer, particularly in early stages, is challenging due to the low amount of ctDNA and heterogeneity of molecular subtypes.

Methods

Here, we employed a multimodal approach, namely Screen for the Presence of Tumor by DNA Methylation and Size (SPOT-MAS), to simultaneously analyze multiple signatures of cell free DNA (cfDNA) in plasma samples of 239 nonmetastatic breast cancer patients and 278 healthy subjects.

Results

We identified distinct profiles of genome-wide methylation changes (GWM), copy number alterations (CNA), and 4-nucleotide oligomer (4-mer) end motifs (EM) in cfDNA of breast cancer patients. We further used all three signatures to construct a multi-featured machine learning model and showed that the combination model outperformed base models built from individual features, achieving an AUC of 0.91 (95% CI: 0.87-0.95), a sensitivity of 65% at 96% specificity.

Discussion

Our findings showed that a multimodal liquid biopsy assay based on analysis of cfDNA methylation, CNA and EM could enhance the accuracy for the detection of early- stage breast cancer.

The ecology of health care in a Belgian area

INTRODUCTION

Focusing on the monthly prevalence of health problems and recourse to different levels of care of the population is an interesting approach to demonstrate the respective roles of different levels of health care. In the present study, the ecology of health care was studied in the region of Liège, Belgium.

METHOD

A survey questioning people about their health problems was conducted in 2009 in two communes of the province of Liège. For each health problem, 'health care' was defined as contact with any qualified care provider. For each consultation, three elements were recorded: the profession of the health care provider; the place where the care was provided and the kind of health care received.

RESULTS

A total of 537 people were interviewed. The monthly prevalence of people who experienced a health problem during the previous month was 85.1%. The monthly prevalence of people who turned to a health care provider at least once during the month was 62.2%. The proportion of people turning to doctors, primarily local doctors, for a simple consultation was important (49.2%).

DISCUSSION

Our results are highly comparable with those of other studies. Recourse to a doctor is high (49%), which probably reflects the broad accessibility of health care in Belgium and maybe its overuse. Additional questions on the current and future organisation of the Belgian health care system are debated.

Embryonic chicken gizzard: immunolocalization of collagen and smooth muscle myosin

Antibodies to chicken gizzard myosin and to chicken skin collagen type I allow the myofibrillar and connective tissue development in the embryonic chicken gizzard to be followed. Fibroblasts are assumed to synthesize collagen prior to the onset of smooth muscle cell development in the muscle primordium (day 5); they are presumably also responsible for collagen synthesis close to the presumptive lamina propria and in the developing tubular glands (day 14 to 17). From day 6 to 8, myosin and collagen are colocalized intracellularly, and from day 9 onward collagen fibers start to appear extracellularly, eventually forming the trellis-like connective tissue septa that give the rhomboid profile found in the adult muscle. The close association of collagen and myosin in early development suggests that the muscle cells themselves produce and export collagen.

Cancerization of eccrine sweat ducts in Bowen's disease as studied by light microscopy, DNA spectrophotometry and immunohistochemistry

This study assesses the incidence, histogenesis, and significance of eccrine sweat duct involvement in Bowen's disease (BD). In a review of 96 cases of BD, four showed eccrine duct involvement on hematoxylin and eosin-stained histologic sections. One case was analyzed for deoxyribonucleic acid (DNA) ploidy by using computerized image analysis on Feulgen-stained slides. Sections were also stained immunohistochemically, using antibodies to carcinoembryonic antigen (CEA), gross cystic disease fluid protein (GCDFP), and S-100 protein, and for cytokeratins (CAM 5.2, AE 1/3). Our results showed that, in BD, (a) the eccrine sweat ducts can be extensively involved by atypical cells, (b) the atypical eccrine duct cells had an aneuploid DNA pattern, and (c) the atypical eccrine duct cells were negative for CEA, GCDFP, and S-100 protein but were positive for cytokeratins. We conclude that (a) the frequency of eccrine duct involvement in BD is relatively low (approximately 4 to 9%), (b) the aneuploid DNA pattern makes a benign squamous metaplasia unlikely, (c) the immunohistochemical results exclude coincidental Paget's disease or carcinoma of eccrine sweat glands, (d) the involvement of eccrine sweat ducts may represent a direct extension of the neoplastic epidermal keratinocytes, and (e) this process may have practical implications in the recurrence of superficially treated cases of BD.