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.

Spatial metapopulation dynamics with local and global colonization.

We revisit a spatial metapopulation model on continuous space as a stochastic point pattern dynamics. In the model, local patches as points are distributed with a certain spatial configuration and status of each patch changes stochastically between occupied and empty: an occupied patch becomes empty by local extinction and an empty patch becomes occupied both by local and global colonization. We carry out simulation analysis and derive an analytical model in terms of singlet, pair and triplet probabilities that describe the stochastic dynamics. Using a simple closure that approximates triplet probabilities by singlet and pair probabilities, we show that equilibrium singlet and pair probabilities can be analytically derived. The derived equilibrium properties successfully describe simulation results under a certain condition where the range of local colonization and the proportion of global colonization play key roles. Our model is an extension of the classical non-spatial Levins model to a spatially explicit metapopulation model. We appeal the advantage of point pattern approach to study spatial dynamics in general ecology and call for the need to deepen our understanding of mathematical tools to explore point pattern dynamics.

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.

Fragment length profiles of cancer mutations enhance detection of circulating tumor DNA in patients with early-stage hepatocellular carcinoma.

BACKGROUND: Late detection of hepatocellular carcinoma (HCC) results in an overall 5-year survival rate of less than 16%. Liquid biopsy (LB) assays based on detecting circulating tumor DNA (ctDNA) might provide an opportunity to detect HCC early noninvasively. Increasing evidence indicates that ctDNA detection using mutation-based assays is significantly challenged by the abundance of white blood cell-derived mutations, non-tumor tissue-derived somatic mutations in plasma, and the mutational tumor heterogeneity. METHODS: Here, we employed concurrent analysis of cancer-related mutations, and their fragment length profiles to differentiate mutations from different sources. To distinguish persons with HCC (PwHCC) from healthy participants, we built a classification model using three fragmentomic features of ctDNA through deep sequencing of thirteen genes associated with HCC. RESULTS: Our model achieved an area under the curve (AUC) of 0.88, a sensitivity of 89%, and a specificity of 82% in the discovery cohort consisting of 55 PwHCC and 55 healthy participants. In an independent validation cohort of 54 PwHCC and 53 healthy participants, the established model achieved comparable classification performance with an AUC of 0.86 and yielded a sensitivity and specificity of 81%. CONCLUSIONS: Our study provides a rationale for subsequent clinical evaluation of our assay performance in a large-scale prospective study.

Clinical validation of a ctDNA-Based Assay for Multi-Cancer Detection: An Interim Report from a Vietnamese Longitudinal Prospective Cohort Study of 2795 Participants.

The SPOT-MAS assay "Screening for the Presence Of Tumor by Methylation And Size" detects the five most common cancers in Vietnam by evaluating circulating tumor DNA in the blood. Here, we validated its performance in a prospective multi-center clinical trial, K-DETEK. Our analysis of 2795 participants from 14 sites across Vietnam demonstrates its ability to detect cancers in asymptomatic individuals with a positive predictive value of 60%, with 83.3% accuracy in detecting tumor location. We present a case report to support further using SPOT-MAS as a complementary method to achieve early cancer detection and provide the opportunity for early treatment.

Multimodal analysis of ctDNA methylation and fragmentomic profiles enhances detection of nonmetastatic colorectal cancer.

Aims: Early detection of colorectal cancer (CRC) provides substantially better survival rates. This study aimed to develop a blood-based screening assay named SPOT-MAS ('screen for the presence of tumor by DNA methylation and size') for early CRC detection with high accuracy. Methods: Plasma cell-free DNA samples from 159 patients with nonmetastatic CRC and 158 healthy controls were simultaneously analyzed for fragment length and methylation profiles. We then employed a deep neural network with fragment length and methylation signatures to build a classification model. Results: The model achieved an area under the curve of 0.989 and a sensitivity of 96.8% at 97% specificity in detecting CRC. External validation of our model showed comparable performance, with an area under the curve of 0.96. Conclusion: SPOT-MAS based on integration of cancer-specific methylation and fragmentomic signatures could provide high accuracy for early-stage CRC detection.

A novel blood test for early detection of colorectal cancer. Colorectal cancer is a cancer of the colon or rectum, located at the lower end of the digestive tract. The early detection of colorectal cancer can help people with the disease have a higher chance of survival and a better quality of life. Current screening methods can be invasive, cause discomfort or have low accuracy; therefore newer screening methods are needed. In this study we developed a new screening method, called SPOT-MAS, which works by measuring the signals of cancer DNA in the blood. By combining different characteristics of cancer DNA, SPOT-MAS could distinguish blood samples of people with colorectal cancer from those of healthy individuals with high accuracy.

Ultra-Deep Sequencing of Plasma-Circulating DNA for the Detection of Tumor- Derived Mutations in Patients with Nonmetastatic Colorectal Cancer.

Identification of tumor-derived mutation (TDM) in liquid biopsies (LB), especially in early-stage patients, faces several challenges, including low variant-allele frequencies, interference by white blood cell (WBC)-derived mutations (WDM), benign somatic mutations and tumor heterogeneity. Here, we addressed the above-mentioned challenges in a cohort of 50 nonmetastatic colorectal cancer patients, via a workflow involving parallel sequencing of paired WBC- and tumor-gDNA. After excluding potential false positive mutations, we detected at least one TDM in LB of 56% (28/50) of patients, with the majority showing low-patient coverage, except for one TDM mapped to KMT2D that recurred in 30% (15/30) of patients.

Circulating DNA methylation profile improves the accuracy of serum biomarkers for the detection of nonmetastatic hepatocellular carcinoma.

Aim: This study exploited hepatocellular carcinoma (HCC)-specific circulating DNA methylation profiles to improve the accuracy of a current screening assay for HCC patients in high-risk populations. Methods: Differentially methylated regions in cell-free DNA between 58 nonmetastatic HCC and 121 high-risk patients with liver cirrhosis or chronic hepatitis were identified and used to train machine learning classifiers. Results: The model could distinguish HCC from high-risk non-HCC patients in a validation cohort, with an area under the curve of 0.84. Combining these markers with the three serum biomarkers (AFP, lectin-reactive AFP, des-γ-carboxy prothrombin) in a commercial test, µTASWako®, achieved an area under the curve of 0.87 and sensitivity of 68.8% at 95.8% specificity. Conclusion: HCC-specific circulating DNA methylation markers may be added to the available assay to improve the early detection of HCC.

The early detection of liver cancer in high-risk populations can help people with the disease have a higher chance of survival and better quality of life. However, this is still a healthcare challenge. Current commercial blood tests measuring protein signatures in the blood have low accuracy due to increased levels of these proteins being detected in both liver cancer patients and patients with chronic liver diseases. In this study, we identified a set of signatures in DNA released by cancer cells into the bloodstream and used them as biomarkers to distinguish liver cancer patients from high-risk patients. We also demonstrated that adding those signatures to a commercial blood test currently used in clinics could improve the accuracy in detecting liver cancer patients.

Kinetics of Organic Biodegradation and Biogas Production in the Pilot-Scale Moving Bed Biofilm Reactor (MBBR) for Piggery Wastewater Treatment.

In this research, the kinetics of COD biodegradation and biogas production in a moving bed biofilm reactor (MBBR) at pilot scale (10 m3) for piggery wastewater treatment were investigated. Polyethylene (PE) was used as a carrying material, with organic loading rates (OLRs) of 10, 15, and 18 kgCOD/m3 day in accordance to hydraulic retention times (HRTs) of 0.56, 0.37, and 0.3 day. The results showed that a high COD removal efficiency was obtained in the range of 68-78% with the influent COD of 5.2-5.8 g/L at all 3 HRTs. About COD degradation kinetics, in comparison to the first- and second-order kinetics and the Monod model, Stover-Kincannon model showed the best fit with R 2 0.98 and a saturation value constant (K B ) and a maximum utilization rate (U max) of 52.40 g/L day and 82.65 g/L day, respectively. The first- and second-order kinetics with all 3 HRTs and Monod model with the HRT of 0.56 day also obtained high R 2 values. Therefore, these kinetics and models can be further considered to be used for predicting the kinetic characteristics of the MBBR system in piggery wastewater treatment process. The result of a 6-month operation of the MBBR was that biogas production was mostly in the operating period of days 17 to 80, around 0.2 to 0.3 and 0.15-0.20 L/gCODconverted, respectively, and then reduction at an OLR of 18 kgCOD/m3. After the start-up stage, day 35 biogas cumulative volume fluctuated from 20 to 30 m3/day and reached approximately 3500 m3 for 178 days during the whole digestive process. Methane is accounted for about 65-70% of biogas with concentration around 400 mg/L.

Competition or cooperation in transboundary fish stocks management: Insight from a dynamical model.

An idealized system of a shared fish stock associated with different exclusive economic zones (EEZ) is modelled. Parameters were estimated for the case of the small pelagic fisheries shared between Southern Morocco, Mauritania and the Senegambia. Two models of fishing effort distribution were explored. The first one considers independent national fisheries in each EEZ, with a cost per unit of fishing effort that depends on local fishery policy. The second one considers the case of a fully cooperative fishery performed by an international fleet freely moving across the borders. Both models are based on a set of six ordinary differential equations describing the time evolution of the fish biomass and the fishing effort. We take advantage of the two time scales to obtain a reduced model governing the total fish biomass of the system and fishing efforts in each zone. At the fast equilibrium, the fish distribution follows the ideal free distribution according to the carrying capacity in each area. Different equilibria can be reached according to management choices. When fishing fleets are independent and national fishery policies are not harmonized, in the general case, competition leads after a few decades to a scenario where only one fishery remains sustainable. In the case of sub-regional agreement acting on the adjustment of cost per unit of fishing effort in each EEZ, we found that a large number of equilibria exists. In this last case the initial distribution of fishing effort strongly impact the optimal equilibrium that can be reached. Lastly, the country with the highest carrying capacity density may get less landings when collaborating with other countries than if it minimises its fishing costs. The second fully cooperative model shows that a single international fishing fleet moving freely in the fishing areas leads to a sustainable equilibrium. Such findings should foster regional fisheries organizations to get potential new ways for neighbouring fish stock management.

The transfer and decay of maternal antibody against Shigella sonnei in a longitudinal cohort of Vietnamese infants.

BACKGROUND: Shigella sonnei is an emergent and major diarrheal pathogen for which there is currently no vaccine. We aimed to quantify duration of maternal antibody against S. sonnei and investigate transplacental IgG transfer in a birth cohort in southern Vietnam. METHODS AND RESULTS: Over 500-paired maternal/infant plasma samples were evaluated for presence of anti-S. sonnei-O IgG and IgM. Longitudinal plasma samples allowed for the estimation of the median half-life of maternal anti-S. sonnei-O IgG, which was 43 days (95% confidence interval: 41-45 days). Additionally, half of infants lacked a detectable titer by 19 weeks of age. Lower cord titers were associated with greater increases in S. sonnei IgG over the first year of life, and the incidence of S. sonnei seroconversion was estimated to be 4/100 infant years. Maternal IgG titer, the ratio of antibody transfer, the season of birth and gestational age were significantly associated with cord titer. CONCLUSIONS: Maternal anti-S. sonnei-O IgG is efficiently transferred across the placenta and anti-S. sonnei-O maternal IgG declines rapidly after birth and is undetectable after 5 months in the majority of children. Preterm neonates and children born to mothers with low IgG titers have lower cord titers and therefore may be at greater risk of seroconversion in infancy.

Seroprevalence of antibodies against human papillomavirus (HPV) types 16 and 18 in four continents: the International Agency for Research on Cancer HPV Prevalence Surveys.

BACKGROUND: Few human papillomavirus (HPV) seroprevalence studies have been carried out in women from low-resource countries. METHODS: Seroprevalence of antibodies against HPV16 and HPV18 was assessed in 7,074 women ≥15 years of age (median 44 years) from eight world areas. Serum antibodies against HPV16 and HPV18 were tested for using enzyme-linked immunosorbent assay. HPV DNA was assessed using a general primer GP5+/6+-mediated PCR. RESULTS: HPV16 and HPV18 seroprevalence both ranged from <1% (Hanoi, Vietnam) to >or=25% (Nigeria). Of women who were HPV16 or HPV18 DNA-positive, seropositivity for the same type was 39.8% and 23.2%, respectively. Seropositivity for either type was directly associated with markers of sexual behavior. HPV16 and/or 18 (HPV16/18)-seropositive women had an increased risk of having cytologic abnormalities only if they were also HPV DNA-positive. A high international correlation was found between HPV16/18 seroprevalence and overall HPV DNA prevalence (r = 0.81; P = 0.022). However, HPV16/18 seroprevalence was substantially higher than the corresponding DNA prevalence in all study areas (although to different extents) and, contrary to DNA, tended to increase from young to middle age, and then decline or remain fairly constant. In all study areas, the vast majority of the information on the burden of exposure to HPV16/18 derived from serology. CONCLUSIONS: The correlation between HPV DNA and HPV serology was not very good at an individual woman level, but high at a population level. IMPACT: HPV serology is a poor marker of current infection or related lesions, but it can contribute, together with DNA, in evaluating the variations in the burden of HPV infection worldwide.

Determinants of cesarean section in Ho Chi Minh city

Study on 1260 women aged from 19 to 45 years old: 180 cases of elective cesarean section (CS), 360 cases of emergency CS, and 720 cases of vaginal delivery (the control group) at Hung Vuong Hospital in order to evaluate the effects of medical and socioeconomic factors on the decision of CS. Results: economic status didn’t affect on the indication of emergency CS, but the rate of elective CS in women with favorable economic level increased by 3.64 times. Seeking examinations at an obstetric hospital itself may have potential risk of pregnancies, the risk of emergency CS increased 16.99 times and the risk of elective CS raised 5.67 times. In addition, some factors can affect on the decision of CS such as 1st born child, having expected for pregnancy, having request for CS, fetal sex, etc

Surfactant replacement therapy for prevention and treatment of respiratory distress syndrome of preterm infants

During the period between 1999 and 2005, a clinical trial has been conducted at Hung Vuong Hospital to assess the efficacy of surfactant replacement therapy for prevention and treatment of respiratory distress syndrome (RDS) in preterm infants. Results: A total of 83 preterm infants with gestational age from 27 to 33 weeks were recruited, of whom 45 assigned to the prophylactic group and 38 to the rescue group. Percentages of developing or not reassuring RDS were 5.4% and 21.1% in the prophylactic and the rescue group, respectively (p<0.001). However, the difference in neonatal mortality was not statistically significant: 8.9% in the prophylactic in comparison with 15.8% in the rescue group

Prevalence of infections with toxoplasma, rubella, CMV and HSV-2 in cord blood analysis

Cord blood samples were taken from 552 infants for screening TORCH infections by ELISA. Maternal infection was documented by the presence of specific IgG antibody, whereas IgM was used to identify fetal infection. Results: Prevalence of maternal infections with toxoplasma, rubella, CMV and HSV-2 were 17.6%, 73.4%, 99.6% and 40.9%, respectively. Regarding the neonates, no infant presented with congenital toxoplasma, whereas prevalence of neonatal rubella and CMV were 0.2% and 0.5%, respectively, and herpes, 14.7%. No infant, however, was clinical infected

Evaluation of the results of Achilles tendon suture technique with Tcherneiski approach at Hospital 87 from February 2002 to April 2004

Tcherneiski approach in suturing Achilles tendon was applied in 13 patients (11 males, 2 females, ages 20 to 50 years), at Hospital No.87 from February 2002 to April 2004. Results showed that, the cause of breaking tendon: wound 38%, local injury 54% and implicit break 80%. The efficacy of this technique: good 62%, relative good 31%, medium 7% and bad 0%. Advantage of the method is that, in the cases of admission late or broken due to local trauma, the technique of suturing the tendon in 2 phases do often achieved a very good result.

Efficacy of Hoa Long in the prevention of recurrent herpes: A randomized, double-blinded, placebo controlled trial

Women of reproductive age seeking care at the Gynecology Clinic/Hung Vuong Hospital who were HSV-2 (+). Study subjects were randomized to receive either Hoa Long or placebo for oral administration in 12 days, then examined at 1, 3, 6 and 12 months after treatment. Findings: During the first year, 30.6% and 55.6% of the women allocated to HL and GD groups, respectively, had at least one episode of recurrent herpes. In addition, count and proportion of lymphocytes were higher in HL than in GD group. At 3, 6 and 12 months after treatment, CD 4 counts were 806.9, 701.2 and 800.1, respectively, for HL group, compared with 629.2, 584.2 and 629.3, respectively, for GD group. Similarly, CD 8 counts at 3, 6 and 12 months were 771.2, 614.7 and 824.1, respectively, for HL group, compared with 689.1, 489.3 and 596.4, respectively, for GD group. Among HSV-2 (+) women, Hoa Long increases CD 4 and CD 8 counts and reduces the recurrence rate of herpes during the first year after treatment

Human papillomavirus (HPV) prevalence among women in HoChiMinh city

Study on the incidence rate of cervical cancer on 1.122 women aged from 15 to 69 years old were interviewed and had a gynaecological examination in an urban district of HoChiMinh city. HPV DNA detection was performed using a GP5+/6+ primer-mediated PCR enzyme immunoassay. IgG antibodies against herpes simplex virus (HSV-2) were determined in blood samples using an ELISA assay. The results showed that: HPV DNA was detected among 10.9% of women in HoChiMinh city. 28 different HPV types were detected, the most common being HPV 16 (in 14 single and 18 multiple infections), followed by HPV 58, 18 and 56. A peak of HPV DNA detection in women below age 25 was found. Major risk factors for HPV DNA detection in the multivariate analyses were: indicators of sexual habits, most notably the presence of HSV-2 antibodies, nulliparity and the current use of oral contraceptives

Newborn neurological status in Hochiminh City

At HungVương Hospital, 17-48 hours after birth, 58 newborn babies with fetal age of 39,5 weeks in average underwent a neurological examination. Results showed that in comparing with the original British cohort, Vietnamese newborns had got significantly lower scores in 10 out of 25 indicators, including almost relating to truncal tone. Among these studied subjects, the deficiency of long chains fatty acid was unsignificant, while this group of fatty acids was related strictly to the nerve, especially ophtalmic nerve. The relation between transketolase concentration with neurological status was not identified

Human papillomavirus infection among women in South and North Vietnam.

The incidence rate of invasive cervical carcinoma (ICC) is 4-fold higher in Ho Chi Minh City, in the South of Vietnam, than in Hanoi, in the North. Thus, we explored the prevalence of and the risk factors for human papillomavirus (HPV) infection in these 2 areas. A population-based random sample of married women aged 15-69 years were interviewed and had a gynaecological examination in the urban district of Ho Chi Minh City and in a peri-urban district in Hanoi. HPV DNA detection was performed using a GP5+/6+ primer-mediated PCR enzyme immunoassay. A total of 922 women from Ho Chi Minh and 994 from Hanoi, for whom a Pap smear and HPV-status were available, were evaluated. HPV DNA was detected among 10.9% of women in Ho Chi Minh City and 2.0% in Hanoi (age standardized prevalence, world standard population: 10.6% and 2.3%, respectively). In the 2 areas combined, 30 different HPV types were found, the most common being HPV 16 (in 14 single and 18 multiple infections), followed by HPV 58, 18 and 56. A peak of HPV DNA detection in women younger than age 25 was found in Ho Chi Minh City (22.3%) but not in Hanoi. Major risk factors for HPV DNA detection were indicators of sexual habits, most notably the presence of HSV-2 antibodies, nulliparity and the current use of oral contraceptives. Women in Hanoi showed the lowest HPV prevalence ever reported so far, suggesting that HPV has not spread widely in this population. As expected, HPV prevalence in a population seemed to be closely correlated with ICC incidence rates.