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Principal Investigator: SARASWATI SUKUMAR
Organization: JOHNS HOPKINS UNIVERSITY
Fiscal Year: 2024
Award: $544,861
Funding agency: National Cancer Institute
ABSTRACT
Colorectal cancer (CRC) is diagnosed at advanced stages in many low- and middle-income countries (LMICs).
The lack of knowledge of CRC signs and symptoms by patients and community health practitioners frequently
leads to delayed presentation with Stage 3-4 disease. This initial delay, paired with limited colonoscopy facilities,
leads to prolonged diagnostic delays. The result is a 5-year mortality rate in LMIC up to 5 times higher than that
in USA. An innovative solution to this problem could be an affordable, easily deployable, “point of care” molecular
test to identify and prioritize patients likely to have a malignancy for expedited colonoscopy and pathology review
leading to better outcomes. Continuing our established collaboration with our industrial partner, Cepheid, we
propose to build on our strong published data on hypermethylated markers in CRC to develop an affordable, <3-
hour, automated CRC-methylation detection blood test that analyzes a panel of five hypermethylated genes in
cell free DNA from 1 ml of plasma. The proposed innovations could lead to a single-cartridge assay for quick
CRC detection with a 3-fold reduction in cost. In Aim 1a, we will optimize a cartridge-less bisulfite DNA
conversion method for plasma and test its efficiency in Patient Set 1 plasma (N= 20 malignant, 20 normal). In
Aim 1b we will select one optimal 5-marker panel out of 20 CRC markers using DNA from FFPE samples from
the U.S and Nigeria (N= 30 malignant, 30 benign), and one optimal “pan” set will be confirmed in plasma using
U.S Patient Set 2 and Nigeria Set 3 (N=35 malignant, 35 benign). In Aim 1c, we will evaluate analytical
performance of the CRC-MD assay. Intra-assay reproducibility will be assessed on multiple aliquots of U.S
Patient Set 4 plasma (N=35 malignant, 35 benign). Inter-operator reproducibility will be determined using
replicate aliquots of plasma from Patient Set 4 (N= 35 malignant, 35 benign). The goal of Aim 2a is to technically
validate the CRC-MD assay using prospectively collected samples in Nigeria. We will first select a threshold in
a Training set of plasma from Patient Set 4 (N=90 malignant, 90 benign) to optimally balance sensitivity and
specificity, and validate performance of the selected threshold in a Test set of plasma from Patient Set 5 (N= 90
malignant, 90 benign). Accuracy (sensitivity, specificity, and positive- and negative-predictive value) of CRC-
MD-based diagnosis to distinguish benign versus malignant disease will be measured using histopathological
diagnosis of the lesion as the gold standard. Lastly, in Aim 2b, to determine whether the performance of the
CRC-MD assay is altered by select patient characteristics, we will test its clinical accuracy among specific patient
subgroups classified by age, sex, BMI, and tumor characteristics. Our prior success in developing automated
cell-based/liquid biopsy assays with Cepheid has established the path ensuring an accurate and reliable test.
This intervention could be cost saving by hastening colonoscopy for those who need it urgently, thus expediting
detection and treatment of CRC in LMICs. This will save thousands of lives yearly. This study will also facilitate
further development of the CRC-MD assay moving toward future commercialization and access globally.
Terms: <2019 novel corona virus><2019 novel coronavirus><2019-nCoV><Actins><Affect><Africa><African><Age><Aliquot><Asia><Assay><Attention><BMI><BMI percentile><BMI z-score><Benign><Bioassay><Biological Assay><Blood Plasma><Blood Tests><Body Tissues><Body mass index><Breast Cancer Detection><Breast cancer screening><Breast screening><COVID-19 virus><COVID19 virus><CRC screening><Cancers><Cell Body><Cells><Cessation of life><Characteristics><Classification><Clinical><Clinical Research><Clinical Study><CoV-2><CoV2><Collaborations><Colonoscopy><Colorectal Cancer><Communicable Diseases><Community Health><Cost Savings><DNA><DNA Methylation><DNA Modification><DNA Modification Process><Data><Death><Death Rate><Deoxyribonucleic Acid><Detection><Development><Diagnosis><Diagnostic><Diagnostic Findings><Disease><Disorder><Early Diagnosis><Ensure><Equilibrium><Future><Genes><Goals><Hematologic Tests><Hematological Tests><Hematology Testing><Hour><Hypermethylation><Industrialization><Infectious Disease Pathway><Infectious Diseases><Infectious Disorder><Infrastructure><Intervention><Intervention Strategies><Knowledge><LMIC><Laboratories><Lead><Lesion><Low-resource area><Low-resource community><Low-resource environment><Low-resource region><Low-resource setting><MSKCC><Malignant><Malignant - descriptor><Malignant Neoplasms><Malignant Tumor><Manuals><Measures><Memorial Sloan-Kettering Cancer Center><Methods><Methylation><Modification><Molecular><Nigeria><Oncology Group><Outcome><Pathology><Patient Care><Patient Care Delivery><Patient Selection><Patients><Pb element><Performance><Persons><Plasma><Plasma Serum><Predictive Value><Prospective Studies><Publishing><Quetelet index><Reproducibility><Research><Research Resources><Resource-constrained area><Resource-constrained community><Resource-constrained environment><Resource-constrained region><Resource-constrained setting><Resource-limited area><Resource-limited community><Resource-limited environment><Resource-limited region><Resource-limited setting><Resource-poor area><Resource-poor community><Resource-poor environment><Resource-poor region><Resource-poor setting><Resources><Reticuloendothelial System, Serum, Plasma><SARS corona virus 2><SARS-CO-V2><SARS-COVID-2><SARS-CoV-2><SARS-CoV2><SARS-associated corona virus 2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related corona virus 2><SARS-related coronavirus 2><SARSCoV2><Sampling><Sensitivity and Specificity><Severe Acute Respiratory Coronavirus 2><Severe Acute Respiratory Distress Syndrome CoV 2><Severe Acute Respiratory Distress Syndrome Corona Virus 2><Severe Acute Respiratory Distress Syndrome Coronavirus 2><Severe Acute Respiratory Syndrome CoV 2><Severe Acute Respiratory Syndrome-associated coronavirus 2><Severe Acute Respiratory Syndrome-related coronavirus 2><Severe acute respiratory syndrome associated corona virus 2><Severe acute respiratory syndrome coronavirus 2><Severe acute respiratory syndrome related corona virus 2><Signs and Symptoms><Specificity><System><Systematics><Technology><Testing><Tissues><Training><Triage><Tumor Subtype><Validation><Wuhan coronavirus><ages><balance><balance function><biomarker array><biomarker panel><bisulfite><cancer biomarkers><cancer markers><care for patients><care of patients><caring for patients><cell free DNA><cell free circulating DNA><clinical practice><colon cancer patients><colorectal cancer detection><colorectal cancer early detection><colorectal cancer patients><colorectal cancer screening><colorectal cancer therapy><colorectal cancer treatment><commercialization><community-based health><coronavirus disease 2019 virus><coronavirus disease-19 virus><cost><detect colorectal cancer><detection assay><developmental><diagnostic tool><early detection><financial toxicity><flu><hCoV19><heavy metal Pb><heavy metal lead><hydrogen sulfite><hydrosulfite><improved><industrial partnership><industry partner><industry partnership><innovate><innovation><innovative><interventional strategy><liquid biopsy><low and middle-income countries><malignancy><mammary cancer detection><mammary screening><marker panel><methylation biomarker><methylation marker><mortality rate><mortality ratio><nCoV2><neoplasm/cancer><patient subclass><patient subcluster><patient subgroups><patient subpopulations><patient subsets><patient subtypes><point of care><point of care testing><product development><programs><prospective><prototype><rapid detection><rapid diagnosis><sex><success><tumor><under served area><under served geographic area><under served location><under served region><underserved area><underserved geographic area><underserved location><underserved region><validations>