A case-controlled validation study of a blood-based seven-gene biomarker panel for colorectal cancer in Malaysia
© Yip et al; licensee BioMed Central Ltd. 2010
Received: 26 August 2010
Accepted: 16 September 2010
Published: 16 September 2010
Colorectal cancer (CRC) screening is key to CRC prevention and mortality reduction, but patient compliance with CRC screening is low. We previously reported a blood-based test for CRC that utilizes a seven-gene panel of biomarkers. The test is currently utilized clinically in North America for CRC risk stratification in the average-risk North American population in order to improve screening compliance and to enhance clinical decision making.
In this study, conducted in Malaysia, we evaluated the seven-gene biomarker panel validated in a North American population using blood samples collected from local patients. The panel employs quantitative RT-PCR (qRT-PCR) to analyze gene expression of the seven biomarkers (ANXA3, CLEC4D, TNFAIP6, LMNB1, PRRG4, VNN1 and IL2RB) that are differentially expressed in CRC patients as compared with controls. Blood samples from 210 patients (99 CRC and 111 controls) were collected, and total blood RNA was isolated and subjected to quantitative RT-PCR and data analysis.
The logistic regression analysis of seven-gene panel has an area under the curve (AUC) of 0.76 (95% confidence interval: 0.70 to 0.82), 77% specificity, 61% sensitivity and 70% accuracy, comparable to the data obtained from the North American investigation of the same biomarker panel.
Our results independently confirm the results of the study conducted in North America and demonstrate the ability of the seven biomarker panel to discriminate CRC from controls in blood samples drawn from a Malaysian population.
Colorectal cancer (CRC) is the second most common cause of cancer mortality among men and women worldwide, with an incidence of approximately 1 million cases per year and more than 500,000 deaths . Although long considered a "western disease", CRC in Asia has been increasing to North American and European levels. In Malaysia, CRC is the second most common cancer in women and has recently overtaken lung cancer to become the most common cancer in men .
Population screening to reduce mortality from CRC has been long and vigorously advocated. However screening uptake remains less than optimal, with screening rates in North America lower than 25% to 50% [3–5]. Low compliance has been explained in part on the uncomfortable and inconvenient nature of current CRC screening tests, which, depending on the test, may require fecal samples, years of commitment, bowel preparation, time off work and may give rise to additional health risks.
We recently published a study, based in a North American population, describing a blood-based, noninvasive risk stratification tool aimed at enhancing compliance and increasing the effectiveness of current CRC screening regimens. In that study we applied blood RNA profiling and quantitative real-time RT-PCR to measure the expression of seven biomarker genes for CRC. We described a logistic regression algorithm which calculates a patient's rank, relative to the average risk population, in order to predict the patient's current risk of having CRC .
The biomarker panel described in that study had a sensitivity of 72% and a specificity of 70%, and was not proposed as a stand-alone test or screening tool. Rather, the panel provides information that was used to develop a risk stratification test for CRC that a clinician can use to triage patients for invasive and scarce technologies such as colonoscopy. An editorial accompanying the report describes the work as a "conceptually novel approach" that is "potentially a substantial step ahead in cancer screening technologies" .
In this report we tested this seven-gene biomarker panel in a Malaysian population. The Malaysian population differs from the North American in two important respects. First, the Malaysian population comprises different ethnic groups, each with different susceptibilities to CRC: Chinese Malaysians have the highest incidence rates of CRC, with an Age Standardized Rate (ASR) of 21.4 per 100,000; Indian Malaysians have an ASR of 11.3 per 100,000; and ethnic Malays have the lowest ASR of 9.5 per 100,000 . Furthermore, CRC in Asian populations are more likely to be flat or depressed (non-polypoid) cancers or to arise de novo . This presentation differs from western populations in which most colorectal cancers arise from precursor adenomatous polyps, which may take 10-12 years to progress to malignant cancer . The specific differences in incidence between Asian groups and in the localization and distinct type of precursor lesions in the Asian populations suggest genetic variables .
Thus in our current study, our objective is to validate in a genetically and racially diverse Malaysian population our North American findings that a seven gene biomarker panel can differentiate colorectal cancer from controls.
Blood samples were taken from patients referred to colonoscopy clinics in Lam Wah Ee Hospital, Penang, Malaysia, over a two-year period from August 2007 to November 2009. Patients meeting defined inclusion and exclusion criteria for the study were enrolled. Patients provided a blood sample prior to endoscopy, and anonymous clinical data was collected from each subject. Informed consent was obtained as approved by the institutions' Research Ethics Board and Joint Ethics Committee. All subjects were 21 years or older, and subjects with known, blood-borne infectious diseases (e.g. HIV, HCV) were excluded.
Isolation of Whole Blood RNA
All blood specimens were collected prior to colonoscopy using PAXgene™tubes (PreAnalytix) and processed according to the PAXgene Blood RNA Kit protocol. Blood specimens for RNA isolation and downstream testing were kept refrigerated after collection and during transportation to GeneNews (Malaysia) Laboratory, a Standards Malaysia ISO-17025 accredited laboratory at Mount Miriam Cancer Hospital in Penang. RNA quality was assessed using Agilent 2100 Bioanalyzer RNA 6000 Nano Kit (Agilent Technologies). RNA quantity was determined by absorbance at 260 nm in a DU800 Spectrophotometer (Beckman-Coulter). The acceptance criteria for the RNA samples are: RIN ≥ 7.0; rRNA ratio ≥ 1.0 and a validated Agilent Bioanalyzer scan.
Quantitative Reverse-Transcriptase Polymerase Chain Reaction
Quantitative reverse-transcriptase real-time RT-PCR reaction procedures for the seven gene biomarkers (ANXA3, CLEC4D, TNFAIP6, LMNB1, PRRG4, VNN1 and the duplex partner or reference gene, IL2RB) have been described previously . Briefly, one microgram of RNA was reverse-transcribed into single-stranded complementary DNA (cDNA) using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems) in 1X RT reaction. For qPCR, 20 ng cDNA was mixed with QuantiTect® Probe PCR Master Mix (Qiagen) and Taqman® dual-labeled probe and primers corresponding to the gene-of-interest and reference gene, IL2RB, in a 25 μL reaction volume. PCR amplification was performed using a 7500 Real-Time PCR System (Applied Biosystems).
Up to 4 samples - each sample run in duplicate - can be analyzed on a single plate. Water was added to the outer wells to ensure proper temperature equilibrium. No-template controls (NTC) containing water and master mix were added to column 12 to check for possible reagent or test contamination. Column 2 and column 11 were designated for pooled blood RNA (PBR) samples for monitoring the performance of both RT and qPCR steps. PBR was prepared from blood RNA isolated from specimens collected from volunteers. Wells from row 2 to row 7 were designated for the corresponding six biomarkers, ANXA3, CLEC4D, TNFAIP6, LMNB1, PRRG4 and VNN1. IL2RB served as the reference gene for the six biomarkers.
Blood Specimen Collection and RNA Sample Quality Statistics
Gender and Age Distribution in the Study Samples
31 - 50
51 - 70
71 - 90
Total Sample No.
Racial/Ethnic Composition of North American and Malaysian Samples
Expression of Gene Biomarkers in North American and Malaysian Samples
Comparison on Logistic Regression Analyses between North American and Malaysian Samples.
P = 0.5
P = 0.5
P = 0.5
Area under ROC Curve
(0.74 - 0.85)
(0.76 - 0.84)
(0.70 - 0.82)
P < 0.0001
P < 0.0001
P < 0.0001
Current CRC screening programmes are complex, with multiple options. Despite efforts to establish mass population screening for CRC, screening tests remain problematic and compliance remains suboptimal .
Ideally, a screening procedure should be a simple and inexpensive test with a sensitivity of about 95% and a specificity about 90%. Fecal Occult Blood Tests (FOBT) are the most common tests for CRC screening, with sensitivities of about 64.3% and 81.8%, respectively for gFOBT (guaiac-based fecal occult blood test) and FIT (fecal immuno-chemical test) . The effectiveness of fecal screening, however, requires patient compliance with testing over many years, and the majority of cases identified by occult blood testing are false-positives, which subjects patients to unnecessary further investigations . Colonoscopy is considered the gold standard for CRC diagnosis, and is more likely to identify lesions than any other screening test. However, colonoscopy requires patient sedation, vigorous bowel preparation and carries a higher risk of complications than does other tests.
In light of the difficulties of screening, clinical practice guidelines for CRC population screening were recently updated , and it was concluded that "ideally, screening should be supported in a programmatic fashion that begins with risk stratification and the results from an initial test and continues through proper follow-up based on findings." Our recently introduced blood-based biomarker panel test for colorectal cancer addresses this need for risk-stratification. We showed that whole-blood gene expression profiling can stratify individuals according to their current risk of having CRC . The blood-based seven-gene biomarker panel test benefits patients who wish to have information about their CRC risk status prior to considering current screening procedures. (Such patients may be uncomfortable with current screening procedures due to fear of health risks, discomfort, cultural, personal or other reasons)
The blood-based test employs receiver operator characteristic (ROC) curve analysis of the expression of six genes of interest relative to a reference gene. Continuous biomarker outputs are estimated; thus a threshold can be set to achieve a combination of sensitivity and specificity that best fits the intended use of the test. By contrast, current CRC tests such as gFOBT, FIT, fecal DNA test, are discrete, yielding yes-or-no information.
On the basis of the biomarker test, patients can be stratified by their current risk of CRC. Our calculations showed that by using our test it is possible to stratify the average risk population and select those patients with an elevated risk for CRC of 2 times or higher, such that 51% of the cancers can be found by performing colonoscopy on only 12% of the population. This is equivalent to a four-fold increase in detection rates, and can substantially increase healthcare efficiency and the use of scarce resources such as colonoscopy .
In this study, we independently confirm that a seven-gene biomarker panel validated in a North American population is also applicable for current CRC risk stratification in a Malaysian population. The extension of the North American findings lends considerable independent validity to the blood-based CRC test, supporting the clinically utility of the risk stratification approach across different ethnicities.
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