US20120058916A1

US20120058916A1 - Diagnostic methods for liver disorders

Info

Publication number: US20120058916A1
Application number: US13/319,540
Authority: US
Inventors: Eli N. Glezer; Anu Mathew; Martin Stengelin; Mingyue Wang
Original assignee: Meso Scale Technologies LLC
Current assignee: Meso Scale Technologies LLC
Priority date: 2009-05-13
Filing date: 2010-04-29
Publication date: 2012-03-08
Also published as: WO2010132208A3; US20200057070A1; WO2010132208A2; US20170038388A1; US10495643B2

Abstract

The present invention relates to methods of diagnosing a liver disorder in a patient, as well as methods of monitoring the progression of a liver disorder and/or methods of monitoring a treatment protocol of a therapeutic agent or a chemotherapeutic regimen. The invention also relates to assay methods used in connection with the diagnostic methods described herein.

Description

FIELD OF THE INVENTION

This application relates to assay methods, modules and kits for conducting diagnostic assays useful in the detection and treatment of liver disorders.

BACKGROUND OF THE INVENTION

Challenges in the field of oncology include the lack of efficient means for early cancer detection and for specific cancer subtyping. There is a need for new cancer diagnostics that can provide early and specific diagnosis of cancer and enable targeted therapy and prognosis. The need for new diagnostics has been the impetus behind many initiatives targeting the discovery and development of new serum biomarkers for cancer. The hope is that the identification of suitable biomarkers will allow for the development of early cancer detection screening tests and will lead to improved cancer therapy and a reduction in the mortality associated with many cancers.
Alpha-Fetoprotein (AFP is included in the recommended list of biomarkers outlined by the National Academy of Clinical Biochemistry (NACB) in their Practice Guidelines and Recommendations For Use Of Tumor Markers In The Clinic, Liver Cancer (Section 3D) (Lamerz et al., National Academy of Clinical Biochemistry Guidelines for the Use of Tumor Markers in Primary Liver Cancer). The serum concentration of AFP in normal adults is, typically, less than 10 ng/mL. Serum AFP levels above 10 ng/mL may be indicative of cancer or chronic liver diseases, including hepatitis and liver cirrhosis. Levels greater than 400 to 500 ng/mL are considered indicative of human hepatocellular carcinoma (HCC) and may be used to discriminate HCC from chronic benign conditions, particularly if there is a sustained increase in AFP levels over time. However, not all hepatocellular carcinomas secrete AFP (e.g., the Fibrolamellar type do not). Still further, AFP could be elevated in pregnancy, in patients with other tumors of gonadal origin and in some patients with acute or chronic viral hepatitis without a tumor.
CA 125 is a serum biomarker associated primarily with epithelial ovarian cancer. While CA 125 levels are often elevated in liver cancer, it reportedly lacks specificity for HCC, as CA125 levels may also become elevated due to benign liver conditions, the presence of ascites or surgery (Bergmann et al. 1987; Collazos et al. 1992; Devarbhavi et al. 2002; Haglun et al. 1991; Kadayifci et al. 1996, 1997; Elias and Kew 1990; Miralles et al. 2003; Molina et al. 1991; Xiao and Liu, 2003).
CEA and CA 19-9 are serum biomarkers that are most commonly linked with colorectal cancer (CEA) and pancreatic and biliary tract cancer (CA 19-9). Previous studies have not found CEA or CA 19-9 to be significant biomarkers for liver cancer (Fabris et al. 1991; Leandro et al. 1989; Lopez et al. 1997; Maestranzi et al. 1998). There are studies suggesting use of CEA and CA 19-9 as tumor markers of the metastasis of colorectal cancer to the liver (Ishizuka et al. 2001; Lorenz et al. 1989).
Therefore, while the use of AFP as a biomarker for HCC has been documented, the value of CA 125, CEA and CA 19-9, alone or in combination with AFP, has not been recognized in the art. Moreover, the elevation of CEA, CA 19-9, OPN, MMP-9, E-cadherin, and erbB2 in patients with cirrhosis and/or HCC has not been observed to date.

SUMMARY OF THE INVENTION

The present invention provides a method for diagnosing HCC in a patient, wherein the method comprises (a) measuring a level of a first biomarker in a test sample obtained from a patient, wherein the first biomarker is selected from the group consisting of CEA, CA 125, CA 19-9; and (b) diagnosing from the measuring step the presence or absence of HCC in the patient.
The invention also provides a method for monitoring the progression of HCC in a patient diagnosed with HCC, wherein the method comprises (a) measuring the levels of a first biomarker in a plurality of samples obtained, at different times, from the patient, wherein the first biomarker is selected from the group consisting of CEA, CA 125, CA 19-9; and (b) determining from the levels of the first biomarker the progression or efficacy of treatment of the HCC.
The methods of the present invention may also include measuring a level of at least one additional biomarker in the sample and determining from the level of the first biomarker and the level of the at least one additional biomarker the presence or absence of HCC in the patient. Still further, the methods may further include comparing the level of the first biomarker in the sample to a level of the first biomarker in a normal control sample and diagnosing the presence or absence of HCC in the patient based on the comparison.
In addition, the methods may comprise comparing the level of the first biomarker and the at least one additional biomarker in the sample to levels of the first biomarker and the at least one additional biomarker in a normal control sample and diagnosing the presence or absence of HCC in the patient based on that comparison.
The at least one additional biomarker may be selected from the group consisting of AFP, OPN, MMP-9, E-cadherin, erbB2, and combinations thereof. Alternatively, the at least one additional biomarker may be selected from the group consisting of CEA, CA 125 and CA 19-9, provided that the additional biomarker is different from the first biomarker.
The diagnosing step of the instant methods may comprise comparing the level of the first biomarker to a detection cut-off level. Still further, the diagnosing step may comprise comparing the levels of the first biomarker and the at least one additional biomarker in the sample to detection cut-off levels for the biomarkers.
The methods may include determining from the level of the first biomarker the disease progression of HCC. And in one embodiment, the patient has been diagnosed with liver disease, e.g., cirrhosis, fibrosis, hepatitis, alcoholic liver disease, fatty liver disease, and combinations thereof. Moreover, the methods may also include subjecting the patient to an imaging method to evaluate the size, shape and position of the liver and the diagnosing step further comprises evaluating the presence or absence of HCC in the patient based on the results from the imaging method and the measuring step. In one embodiment, the imaging method is an ultrasound.
Still further, the present invention also provides a method for diagnosing cirrhosis in a patient suspected of having cirrhosis, wherein the method comprises (a) measuring a level of a first biomarker in a test sample obtained from a patient, wherein the first biomarker is selected from the group consisting of CEA, CA 125, CA 19-9; and (b) diagnosing from the measuring step the presence or absence of cirrhosis in the patient.
The invention also provides a method for monitoring the progression of cirrhosis in a patient diagnosed with cirrhosis, wherein the method includes (a) measuring the level(s) of a first biomarker in a plurality of samples obtained, at different times, from the patient, wherein the first biomarker is selected from the group consisting of CEA, CA 125, CA 19-9; and (b) determining from the level(s) of the first biomarker the progression or efficacy of treatment of cirrhosis.
The methods of the invention may include measuring a level of at least one additional biomarker in the sample and determining from the level of the first biomarker and the level of the at least one additional biomarker the presence or absence of cirrhosis in said patient. Still further, the methods may also include comparing the level of the first biomarker in the sample to a level of the first biomarker in a normal control sample and diagnosing the presence or absence of cirrhosis in the patient based on the comparison. Moreover, in one embodiment, the methods further comprises comparing the level of the first biomarker and the at least one additional biomarker in the sample to levels of the first biomarker and the at least one additional biomarker in a normal control sample and diagnosing the presence or absence of cirrhosis in the patient based on the comparison. In these embodiments, the at least one additional biomarker may be selected from the group consisting of AFP, CEA, CA 125, CA 19-9, OPN, MMP-9, E-cadherin, erbB2, and combinations thereof. The methods may further comprise determining from the level of the first biomarker the disease progression of cirrhosis.
The levels of the first and the at least one additional biomarker measured in the methods of the present invention may be measured in a multiplexed assay. In one embodiment, the levels of the first and the at least one additional biomarker are measured in a single assay chamber. The assay chamber may be a single well of an assay plate or it may be a cartridge. In addition, the levels may be measured in an immunoassay.
The samples used in the methods of the invention may be blood, serum or plasma. Alternatively, the sample may be biopsy tissue, intestinal mucosa or urine.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 (A-H) shows the concentrations for various biomarkers in serum samples from HCC (♦), cirrhosis (∘), and normal (Δ) patients, with median signal values indicated for each patient group. Each panel in FIG. 1 shows the calculated biomarker concentrations for AFP (Panel A), CA 19-9 (Panel B), CEA (Panel C), CA 125 (Panel D), MMP-9 (Panel E), OPN (Panel F), E-cadherin (Panel G), and erbB2 (Panel H) in HCC (♦), cirrhosis (∘), and normal (Δ) individual samples, with median signal values indicated for each sample group.

FIG. 2 (A-L) shows a two dimensional analysis of biomarker pairs, in which the concentrations of selected biomarker pairs were plotted against each other to determine if a multi-parameter analysis improved the discrimination of HCC cases from controls. The concentrations of selected biomarker pairs were plotted against each other to determine whether the use of two biomarkers improved the ability to distinguish HCC cases from controls. The plots show results for the following biomarker pairs: AFP v. CA19-9 (Panel A), CA19-9 v. CA125 (Panel B), AFP v. CA125 (Panel C), CA19-9 v. MMP-9 (Panel D), AFP v. MMP-9 (Panel E), AFP v, OPN (Panel F), CA 125 v. OPN (Panel G), CA19-9 v. OPN (Panel H), CA125 v. MMP-9 (Panel 1), AFP v. E-cadherin (Panel J), CA19-9 v, ErbB2 (Panel K), and CA19-9 v. E-Cadherin (Panel L).

DETAILED DESCRIPTION OF THE INVENTION

Unless otherwise defined herein, scientific and technical terms used in connection with the present invention shall have the meanings that are commonly understood by those of ordinary skill in the art. Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element.
The applicants have discovered that CEA, CA 125, and CA 19-9 are significantly elevated in sera of HCC patients, as compared to levels from cirrhotic or normal patients. The applicants have also discovered that CEA, CA 125 and CA 19-9 should be as efficient, if not superior, to AFP in diagnosing HCC and distinguishing HCC from cirrhosis. Furthermore, the applicants have discovered that combining the measurement of a marker from the group consisting of AFP, CEA, CA 125 and the measurement of at least one other marker from the same group and/or at least one marker selected from MMP-9, OPN, erbB2, and E-cadherin can detect HCC and/or cirrhosis in patients with a high degree of specificity.
Therefore, in one embodiment, the invention provides a method of diagnosing a cancerous condition in a patient by measuring, in a patient sample, a level of CEA, CA 125, CA 19-9, or combinations thereof and diagnosing the patient for the presence or absence of the cancerous condition. In another embodiment, at least two biomarkers selected from the group consisting of AFP, CEA, CA 125 and CA 19-9 are measured. The at least two markers can be measured in two independent assays conducted on one or more patient samples or the measurements can be conducted in a single multiplexed assay. Specific examples of this embodiment include the measurement, as independent or multiplexed measurements, of AFP and CEA, AFP and CA 125, AFP and CA 19-9 CEA and CA 125, CEA and CA 19-9 or CA 125 and CA 19-9. Additional examples include the independent or multiplexed measurements of AFP, CEA and CA 125; AFP, CA 125 and CA19-9 or CEA, CA 125 and CA 19-9.
The invention also includes a diagnostic method as described above, wherein one or more of AFP, CEA, CA 125 and CA 19-9 are measured, and the level of at least one additional biomarker is also measured (independently or in a multiplexed format) in the sample. Therefore, the levels of the first biomarker and the additional biomarker(s) in the test sample may be used to diagnose a cancerous condition in a patient. In one embodiment, the additional biomarker is selected from OPN, MMP-9, E-cadherin, erbB2, and combinations thereof. Other biomarkers or disease indices are known and may be measured/used in combination with the methods of the present invention, including and not limited to glypican 3, PIVKA II, ER6Q, Vimentin, actin alpha 1 skeletal muscle protein, hMFAP 4, tropomyosin, PTGES 2, amyloid P component, transgelin, calponin 1, homo sapiens p20 protein, 17 kDa myosin light chain, H chain H Igg B12, prolyl 4-hydroxylase, beta subunit methylenetetrahydrofolate dehydrogenase 1, PRO2619, aldehyde dehydrogenase 1, fibrinogen alpha chain preproprotein, fructose-bisphosphate aldolase B, argininosuccinate synthetase, Eefla2, AT P 5 A1, alpha-2 actin, regucalcin, serum albumin, mitochondrial malate dehydrogenase, mitochondrial acetoacetyl-CoA thiolase, Prothrombin, Gamma Glutamyl Transpeptidase, bilirubin, Apolipoprotein A1 (PGA) index, Age platelet (AP) index, Bonacini index, Pohl score, Forms index, Aspartate aminotransferase/Platelets Ratio index (APRI), MP3 (MMP1, PIINP) index, FIB4, FibroIndex and combinations thereof. In one embodiment, one or more cancer biomarkers (as described above) are measured in combination with one or more biomarkers of liver disease (for example, des-gamma carboxyprothrombin (DCP), gamma-glutamyl-carboxylase, lectin-bound AFP, vitamin D binding protein (Ge globulin), and/or liver fatty acid binding protein). In one example of such an embodiment, the combination of cancer markers and liver disease markers allows for better differentiation of liver cancer from non-cancerous liver diseases.
In one embodiment of the present invention, the level of the first biomarker and/or the level of the additional biomarkers in the test sample are compared to the levels of these biomarkers in a corresponding normal control sample. The difference between the normal control sample biomarker levels and that of the test sample may be the basis for diagnosing a cancerous condition in a patient. Alternatively, the level of the first biomarker is compared to a detection cut-off level or range, wherein the first biomarker level above or below the detection cut-off level (or within the detection cut-off range) is indicative of the cancerous condition. In addition, the diagnostic methods of the invention also contemplate comparing the level of the at least one additional biomarker to a detection cut-off level or range, wherein the at least one additional biomarker level above or below the detection cut-off level (or within a detection cut-off range) is indicative of the cancerous condition. Furthermore, the levels of the first and at least one additional marker may both be used to make a determination. For example, i) having a level of at least one of the markers above or below a detection cut-off level (or within a detection cut-off range) for that marker is indicative of the cancerous condition; ii) having the level of two or more (or all) of the markers above or below a detection cut-off level (or within a detection cut-off range) for each of the markers is indicative of the cancerous condition or iii) an algorithm based on the levels of the multiple markers is used to determine if the cancerous condition is present.
In addition, the methods of the present invention may be used in combination with other methods of diagnosing liver disease in a patient. Liver disease includes, e.g. cirrhosis, fibrosis, hepatitis, alcoholic liver disease, fatty liver disease, and combinations thereof. In one embodiment, the patient may also be subjected to one or more diagnostic tools designed to detect liver disease. For example, imaging methods may be used to provide images of the liver to look for tumors and blocked bile ducts and can be used to evaluate liver size and blood flow through the liver. In addition, a liver biopsy may be performed. Imaging methods that may be performed include abdominal ultrasound, computed tomography (CT) scan of the abdomen (including the liver, gallbladder, and spleen), magnetic resonance imaging (MRI) scan of the abdomen, and a liver and spleen scan. Still further, other tests that may be performed include, paracentesis, endoscopy, endoscopic retrograde cholangiopancreatogram, and ammonia testing.
The diagnostic methods of the present invention may be used to diagnose a variety of cancerous conditions, including hepatocellular carcinoma. As used herein, the term “cancer” is intended to mean a class of diseases characterized by the uncontrolled growth of aberrant cells, including all known cancers, and neoplastic conditions, whether characterized as malignant, benign, soft tissue or solid tumor. In one embodiment, the cancerous condition is malignant HCC. HCC is the fifth most common cancer worldwide and the third most common cause of cancer mortality, and is one of the few fastest increasing cancers in the U.S. Treatments for HCC improve survival only in those with early stage HCC. Despite improvements in survival rates for other cancers, the prognosis of HCC is still grim, with 1- and 3-year survival of 33% and 17%, respectively for patients diagnosed in 2002. The dismal prognosis is related to the insensitivities of the current diagnostic tools, alpha-fetoprotein (AFP) and liver ultrasound (US), which prevents detection of early stage HCC when treatment is most effective.
In addition, the diagnostic methods of the present invention may be used to identify cirrhosis. Cirrhosis is a term used to describe scarring of the liver and in advanced cirrhosis, excessive scar tissue inhibits proper liver function. Still further, the biomarkers identified herein may be used to diagnose hepatitis B virus (HBV) infection, hepatitis C virus (HCV) infections. Alternatively, the biomarkers may be used to diagnose fatty liver disease and/or alcoholic liver disease. Fatty liver disease can arise due to chronic alcohol ingestion. The causes of non-alcohol related fatty liver disease are not clearly defined, although risk factors include conditions such as obesity and type 2 diabetes Alcoholic liver disease is an acute form of alcohol-induced liver injury that occurs with the consumption of a large quantity of alcohol over a prolonged period of time. Liver disease may range in severity from asymptomatic derangement of biochemistries to fulminant liver failure and death.
The biomarkers identified by the applicants (i.e., AFP, CEA, CA 125, CA 19-9, OPN, MMP-9, E-cadherin, erbB2, alone or in combination with each other and/or in combination with other markers), may be used to diagnose one or more of these disorders in a patient, to assess the progression of one or more of these disorders in a patient, or to assess the efficacy of a treatment regimen for one or more of these disorders. In one embodiment of the invention, a patient that has been previously diagnosed with liver disease (e.g., cirrhosis, fibrosis, hepatitis, alcoholic liver disease, fatty liver disease, and combinations thereof), is evaluated for progression of that disorder to a cancerous condition. The level(s) of the various biomarkers identified herein may reflect the responsiveness or non-responsiveness of a hepatocellular carcinoma to a given treatment regimen. A response to a therapeutic regimen includes a detectable reduction to some extent of one or more of the symptoms of HCC, including, but not limited to: (1) reduction in the number of cancer cells; (2) reduction in tumor size; (3) inhibition (i.e., slowing to some extent, preferably stopping) of cancer cell infiltration into peripheral organs; (4) inhibition (i.e., slowing to some extent, preferably stopping) of tumor metastasis; (5) inhibition, to some extent, of tumor growth; (6) relieving or reducing to some extent one or more of the symptoms associated with the disorder; and/or (7) increasing, to some extent, the overall survival of a patient relative to that observed for the standard of care for HCC. A response to a therapeutic regimen may also comprise maintenance of a therapeutic benefit, including, but not limited to (1) inhibiting an increase in the number of cancer cells; (2) inhibiting an increase in tumor size; (3) inhibiting cancer cell infiltration into peripheral organs; (4) inhibiting tumor metastases; (5) relieving or reducing to some extent one or more of the symptoms associated with the disorder; and/or (6) inhibiting a recurrence or onset of one or more of the symptoms associated with the disorder.
In addition, the level of a biomarker may be determined at any time point before and/or after initiation of treatment. In one embodiment, the biomarker is used to gauge the efficacy of a therapeutic regimen. Therefore, the method of the present invention may include measuring a baseline level(s) of a biomarker before a therapeutic regimen is initiated, and the method may further comprise comparing the level and the baseline level. Moreover, the method may further comprise measuring an interim level of the biomarker during a therapeutic regimen and the method further comprises comparing the level, the interim level and the baseline level.
Alternatively, the measuring step may comprise measuring a level(s) of a biomarker before a therapeutic regimen is initiated to predict whether a HCC will be responsive or non-responsive to a given therapeutic regimen. The method may further comprise modifying the therapeutic regimen based on the level(s) of a biomarker observed during the measuring step, e.g., increasing or decreasing the dosage, frequency, or route of administration of a therapeutic agent, adding an additional therapeutic agent and/or palliative agent to a treatment regimen, or if the therapeutic regimen includes the administration of two or more therapeutic and/or palliative agents, the treatment regimen may be modified to eliminate one or more of the therapeutic and/or palliative agents used in the combination therapy.
As described herein, the measured levels of one or more biomarkers may be used to detect or monitor cancer (e.g., HCC) and/or to determine the responsiveness of a cancer to a specific treatment regimen. The specific methods/algorithms for using biomarker levels to make these determinations, as described herein, may optionally be implemented by software running on a computer that accepts the biomarker levels as input and returns a report with the determinations to the user. This software may run on a standalone computer or it may be integrated into the software/computing system of the analytical device used to measure the biomarker levels or, alternatively, into a laboratory information management system (LIMS) into which crude or processed analytical data is entered. In one embodiment, biomarkers are measured in a point-of-care clinical device which carries out the appropriate methods/algorithms for detecting, monitoring or determining the responsiveness of a cancer and which reports such determination(s) back to the user.
The assays of the present invention may be conducted by any suitable method. In one embodiment, the measuring step is conducted on a single sample, and it may be conducted in a single assay chamber or assay device, including but not limited to a single well of an assay plate, a single assay cartridge, a single lateral flow device, a single assay tube, etc.
As used herein, the term “sample” is intended to mean any biological fluid, cell, tissue, organ or combinations or portions thereof, which includes or potentially includes a biomarker of a disease of interest. For example, a sample can be a histologic section of a specimen obtained by biopsy, or cells that are placed in or adapted to tissue culture. A sample further can be a subcellular fraction or extract, or a crude or substantially pure nucleic acid molecule or protein preparation. In one embodiment, the samples that are analyzed in the assays of the present invention are blood or blood fractions such as, serum and plasma. Other suitable samples include biopsy tissue, intestinal mucosa and urine. In one embodiment, the level is measured using an immunoassay.
As used herein, a “biomarker” is a substance that is associated with a particular disease. A change in the levels of a biomarker may correlate with the risk or progression of a disease or with the susceptibility of the disease to a given treatment. A biomarker may be useful in the diagnosis of disease risk or the presence of disease in an individual, or to tailor treatments for the disease in an individual (choices of drug treatment or administration regimes). In evaluating potential drug therapies, a biomarker may be used as a surrogate for a natural endpoint such as survival or irreversible morbidity. If a treatment alters a biomarker that has a direct connection to improved health, the biomarker serves as a “surrogate endpoint” for evaluating clinical benefit A sample that is assayed in the diagnostic methods of the present invention may be obtained from any suitable patient, including but not limited to a patient suspected of having cancer, cirrhosis, HBV, HCV or alcoholic liver disease or a patient having a predisposition to one or more of these conditions. The patient may or may not exhibit symptoms associated with one or more of these conditions.
As used herein, the term “level” refers to the amount, concentration, or activity of a biomarker. The term “level” may also refer to the rate of change of the amount, concentration or activity of a biomarker. A level can be represented, for example, by the amount or synthesis rate of messenger RNA (mRNA) encoded by a gene, the amount or synthesis rate of polypeptide corresponding to a given amino acid sequence encoded by a gene, or the amount or synthesis rate of a biochemical form of a biomarker accumulated in a cell, including, for example, the amount of particular post-synthetic modifications of a biomarker such as a polypeptide, nucleic acid or small molecule. The term can be used to refer to an absolute amount of a biomarker in a sample or to a relative amount of the biomarker, including amount or concentration determined under steady-state or non-steady-state conditions. Level may also refer to an assay signal that correlates with the amount, concentration, activity or rate of change of a biomarker. The level of a biomarker can be determined relative to a control marker in a sample.
According to one aspect of the invention, the level(s) of biomarker(s) are measured in samples collected from individuals clinically diagnosed with, suspected of having or at risk of developing HCC. Initial diagnosis may have been carried out using conventional methods, e.g., biopsy or other conventional diagnostic methods. The level(s) of biomarker(s) are also measured in healthy individuals. Specific biomarkers valuable in distinguishing between normal and diseased patients are identified by visual inspection of the data, for example, by visual classification of data plotted on a one-dimensional or multidimensional graph, or by using statistical methods such as characterizing the statistically weighted difference between control individuals and diseased patients and/or by using Receiver Operating Characteristic (ROC) curve analysis. A variety of suitable methods for identifying useful biomarkers and setting detection thresholds/algorithms are known in the art and will be apparent to the skilled artisan.
For example and without limitation, diagnostically valuable biomarkers may be first identified using a statistically weighted difference between control individuals and diseased patients, calculated as
$\frac{D - N}{\sqrt{σ_{D} * σ_{N}}}$
wherein D is the median level of a biomarker in patients diagnosed as having, for example, liver cancer, N is the median (or average) of the control individuals, □_Dis the standard deviation of D and σ_Nis the standard deviation of N. The larger the magnitude, the greater the statistical difference between the diseased and normal populations.
According to one embodiment of the invention, biomarkers resulting in a statistically weighted difference between control individuals and diseased patients of greater than, e.g., 1, 1.5, 2, 2.5 or 3 could be identified as diagnostically valuable markers.
Another method of statistical analysis for identifying biomarkers is the use of z-scores, e.g., as described in Skates et al. (2007) Cancer Epidemiol. Biomarkers Prev. 16(2):334-341.
Another method of statistical analysis that can be useful in the inventive methods of the invention for determining the efficacy of particular candidate analytes, such as particular biomarkers, for acting as diagnostic marker(s) is ROC curve analysis. An ROC curve is a graphical approach to looking at the effect of a cut-off criterion, e.g., a cut-off value for a diagnostic indicator such as an assay signal or the level of an analyte in a sample, on the ability of a diagnostic to correctly identify positive or negative samples or subjects. One axis of the ROC curve is the true positive rate (TPR, i.e., the probability that a true positive sample/subject will be correctly identified as positive, or alternatively, the false negative rate (FNR=1−TPR, the probability that a true positive sample/subject will be incorrectly identified as a negative). The other axis is the true negative rate, i.e., TNR, the probability that a true negative sample will be correctly identified as a negative, or alternatively, the false positive rate (FPR=1−TNR, the probability that a true negative sample will be incorrectly identified as positive). The ROC curve is generated using assay results for a population of samples/subjects by varying the diagnostic cut-off value used to identify samples/subjects as positive or negative and plotting calculated values of TPR or FNR and TNR or FPR for each cut-off value. The area under the ROC curve (referred to herein as the AUC) is one indication of the ability of the diagnostic to separate positive and negative samples/subjects. In one embodiment, a biomarker provides an AUC≧0.7. In another embodiment, a biomarker provides an AUC≧0.8. In another embodiment, a biomarker provides an AUC≧0.9.
Diagnostic indicators analyzed by ROC curve analysis may be a level of an analyte, e.g., a biomarker, or an assay signal. Alternatively, the diagnostic indicator may be a function of multiple measured values, for example, a function of the level/assay signal of a plurality of analytes, e.g., a plurality of biomarkers, or a function that combines the level or assay signal of one or more analytes with a patient's scoring value that is determined based on visual, radiological and/or histological evaluation of a patient. The multi-parameter analysis may provide more accurate diagnosis relative to analysis of a single marker.
Candidates for a multi-analyte panel could be selected by using criteria such as individual analyte ROC areas, median difference between groups normalized by geometric interquartile range (1QR) etc. The objective is to partition the analyte space to improve separation between groups (for example, normal and disease populations) or to minimize the misclassification rate.
One approach is to define a panel response as a weighted combination of individual analytes and then compute an objective function like ROC area, product of sensitivity and specificity, etc. See e.g., WO 2004/058055, as well as US2006/0205012, the disclosures of which are incorporated herein by reference in their entireties.
Biomarker levels may be measured using any of a number of techniques available to the person of ordinary skill in the art, e.g., direct physical measurements (e.g., mass spectrometry) or binding assays (e.g., immunoassays, agglutination assays and immunochromatographic assays). The method may also comprise measuring a signal that results from a chemical reactions, e.g., a change in optical absorbance, a change in fluorescence, the generation of chemiluminescence or electrochemiluminescence, a change in reflectivity, refractive index or light scattering, the accumulation or release of detectable labels from the surface, the oxidation or reduction or redox species, an electrical current or potential, changes in magnetic fields, etc. Suitable detection techniques may detect binding events by measuring the participation of labeled binding reagents through the measurement of the labels via their photoluminescence (e.g., via measurement of fluorescence, time-resolved fluorescence, evanescent wave fluorescence, up-converting phosphors, multi-photon fluorescence, etc.), chemiluminescence, electrochemiluminescence, light scattering, optical absorbance, radioactivity, magnetic fields, enzymatic activity (e.g., by measuring enzyme activity through enzymatic reactions that cause changes in optical absorbance or fluorescence or cause the emission of chemiluminescence). Alternatively, detection techniques may be used that do not require the use of labels, e.g., techniques based on measuring mass (e.g., surface acoustic wave measurements), refractive index (e.g., surface plasmon resonance measurements), or the inherent luminescence of an analyte.
Binding assays for measuring biomarker levels may use solid phase or homogenous formats. Suitable assay methods include sandwich or competitive binding assays. Examples of sandwich immunoassays are described in U.S. Pat. No. 4,168,146 and U.S. Pat. No. 4,366,241, both of which are incorporated herein by reference in their entireties. Examples of competitive immunoassays include those disclosed in U.S. Pat. No. 4,235,601, U.S. Pat. No. 4,442,204 and U.S. Pat. No. 5,208,535, each of which are incorporated herein by reference in their entireties.
Multiple biomarkers may be measured using a multiplexed assay format, e.g., multiplexing through the use of binding reagent arrays, multiplexing using spectral discrimination of labels, multiplexing of flow cytometric analysis of binding assays carried out on particles, e.g., using the Luminex® system. Suitable multiplexing methods include array based binding assays using patterned arrays of immobilized antibodies directed against the biomarkers of interest. Various approaches for conducting multiplexed assays have been described (See e.g., US 20040022677; US 20050052646; US 20030207290; US 20030113713; US 20050142033; and US 20040189311, each of which is incorporated herein by reference in their entireties. One approach to multiplexing binding assays involves the use of patterned arrays of binding reagents, e.g., U.S. Pat. Nos. 5,807,522 and 6,110,426; Delehanty 3-B., Printing functional protein microarrays using piezoelectric capillaries, Methods Mol. Bio. (2004) 278: 135-44; Lue R Y et al., Site-specific immobilization of biotinylated proteins for protein microarray analysis, Methods Mol. Biol. (2004) 278: 85-100; Lovett, Toxicogenomics: Toxicologists Brace for Genomics Revolution, Science (2000) 289: 536-537; Berns A, Cancer: Gene expression in diagnosis, nature (2000), 403, 491-92; Walt, Molecular Biology: Bead-based Fiber-Optic Arrays, Science (2000) 287: 451-52 for more details). Another approach involves the use of binding reagents coated on beads that can be individually identified and interrogated. See e.g., WO 9926067, which describes the use of magnetic particles that vary in size to assay multiple analytes; particles belonging to different distinct size ranges are used to assay different analytes. The particles are designed to be distinguished and individually interrogated by flow cytometry. Vignali has described a multiplex binding assay in which 64 different bead sets of microparticles are employed, each having a uniform and distinct proportion of two dyes (Vignali, D. A A, “Multiplexed Particle-Based Flow Cytometric Assays” J. ImmunoL Meth. (2000) 243: 243-55). A similar approach involving a set of 15 different beads of differing size and fluorescence has been disclosed as useful for simultaneous typing of multiple pneumococcal serotypes (Park, M. K et al., “A Latex Bead-Based Flow Cytometric Immunoassay Capable of Simultaneous Typing of Multiple Pneumococcal Serotypes (Multibead Assay)” Clin. Diag. Lab ImmunoL (2000) 7: 4869). Bishop, JE et al. have described a multiplex sandwich assay for simultaneous quantification of six human cytokines (Bishop, L E. et al., “Simultaneous Quantification of Six Human Cytokines in a Single Sample Using Microparticle-based Flow Cytometric Technology,” Clin. Chem (1999) 45:1693-1694).
A diagnostic test may be conducted in a single assay chamber, such as a single well of an assay plate or an assay chamber that is an assay chamber of a cartridge. The assay modules, e.g., assay plates or cartridges or multi-well assay plates), methods and apparatuses for conducting assay measurements suitable for the present invention are described for example, in US 20040022677; US 20050052646; US 20050142033; US 20040189311, each of which is incorporated herein by reference in their entireties. Assay plates and plate readers are now commercially available (MULTISPOT® and MULTI-ARRAY® plates and SECTOR® instruments, Meso Scale Discovery®, a division of Meso Scale Diagnostics, LLC, Gaithersburg, Md.).
The following non-limiting examples serve to illustrate rather than limit the present invention.

EXAMPLES

Example 1

Measurement of 10 Potential Biomarkers in Serum of HCC, Cirrhotic, and Normal Patients

In order to identify biomarkers useful for diagnosis of HCC, 25 serum samples from patients with primary HCC (Table 1), 25 samples from patients with alcohol-induced or fatty liver disease-induced cirrhosis (Table 2), and 30 samples (serum) from apparently normal individuals were obtained and screened for ten potential biomarkers (AFP, CEA, CA 125, CA 19-9, OPN, MMP-9, E-cadherin, erbB2, EGFR, and eKit) using a multiplexed immunoassay format.

TABLE 1

HCC patient samples with associated treatment
and HCC stage information,
obtained from Bioreclamation, Inc. (5FU refers to 5-Fluorouracil).

	GENDER	AGE (years)	MEDICATIONS	STAGE

FEMALE	46	None	2
FEMALE	49	5FU	2
FEMALE	47	Zometa	3
FEMALE	52	None	2
FEMALE	50	5FU	3
MALE	57	None	2
FEMALE	47	5FU	3
FEMALE	78	Zometa	3
FEMALE	74	Avastin, 5FU	2
FEMALE	66	Gemzar	4
MALE	58	None	2
MALE	63	Zometa	2
FEMALE	38	None	2
FEMALE	48	5FU	3
MALE	57	Gemzar	2
MALE	71	Carboplatin	2
FEMALE	74	Zometa, 5FU	3
FEMALE	62	Avastin,	2
		Carboplatin
FEMALE	77	None	2
MALE	63	Avastin, 5FU	2
FEMALE	65	5FU	3
MALE	67	Zometa	2
FEMALE	58	Gemzar	2
FEMALE	62	None	2
FEMALE	61	Carboplatin	2
		Average age	60
		Median age	61

TABLE 2

Cirrhosis samples obtained from Bioreclamation, Inc

CIRRHOSIS TYPE	GENDER	AGE (years)

ALCOHOL INDUCED	Male	54
ALCOHOL INDUCED	Male	52
ALCOHOL INDUCED	Female	41
ALCOHOL INDUCED	Male	43
ALCOHOL INDUCED	Male	49
ALCOHOL INDUCED	Male		50
ALCOHOL INDUCED	Male	57
ALCOHOL INDUCED	Female	49
ALCOHOL INDUCED	Female	53
ALCOHOL INDUCED	Male	45
ALCOHOL INDUCED	Male	53
ALCOHOL INDUCED	Female	61
ALCOHOL INDUCED	Male	55
FATTY LIVER DISEASE	Female	83
INDUCED
FATTY LIVER DISEASE	Female		50
INDUCED
FATTY LIVER DISEASE	Male	56
INDUCED
FATTY LIVER DISEASE	Male	52
INDUCED
FATTY LIVER DISEASE	Male		60
INDUCED
FATTY LIVER DISEASE	Male	59
INDUCED
FATTY LIVER DISEASE	Male	56
INDUCED
FATTY LIVER DISEASE	Male	72
INDUCED
FATTY LIVER DISEASE	Male	48
INDUCED
FATTY LIVER DISEASE	Female	69
INDUCED
FATTY LIVER DISEASE	Male	65
INDUCED
FATTY LIVER DISEASE	Male	58
INDUCED
	Average age	56
	Median age	54

Each sample in Tables 1 and 2 as well as the normal serum samples were analyzed using a Multi-Spot® 96-well 10-plex Cancer Plate (Mesa Scale Discovery, LLC, Gaithersburg, Md.). Each well of these plates has a 10-plex array of capture antibodies against the 10 target biomarkers (APP, CEA, CA 125, CA 19-9, OPN, MMP-9, E-cadherin, erbB2, EGFR, and cKit). The antibody arrays are printed on integrated carbon ink electrodes to allow for electrochemiluminescence-based detection.
The samples were analyzed using the following assay protocol: The 10-plex Cancer Plate (also supplied by Meso Scale Discovery, LLC), was blocked for 1 hour using a suitable blocking solution (MSD Blocker A, also supplied by Mesa Scale Discovery, LLC), and subsequently washed using a washing buffer (PBS/Tween). Twenty five uL of an assay diluent was added to each well, followed by 25 uL of a five-fold dilution of the sample (diluted in the assay diluent). The plate was incubated with shaking for about 2 hours, and washed. Twenty five uL of a mixture containing labeled detection antibodies against the 10 targets was added to each well and the plate was incubated with shaking for 2 hour. The labels used were electrochemiluminescent Sulfo-TAG™ labels (Mesa Scale Discovery, LLC). The plate was washed, 150 uL of Read Buffer T (Meso Scale Discovery, LLC) was added and the plates were read using a Sector Imager 6000 electrochemiluminescence plate reader (Meso Scale Discovery, LLC). The reader reports assay signals for each array element in relative ECL units. Concentrations (Table 3) were calculated from the ECL values based on calibration curves generated with protein standards. The average and individual concentrations of each analyte for each sample type are plotted in FIG. 1.

TABLE 3

Measured concentrations of AFP, CEA, CA 125, CA 19-9, OPN, MMP-9, E-cadherin, erbB2,
EGFR and cKit in the HCC, cirrhosis, and normal serum samples described above.

AFP

CA 19-9

CA 125

CEA

cKit

E-Cadherin

ErbB2

MMP-9

OPN

EGFR

Sample ID

(ng/ml)

(U/ml)

(ng/ml)

Liver	BRH223908	103	7,188	4,368	471	105	28	13	341	38	117
Cancer	BRH223909	49	3,090	2,100	360	124	32	9	415	23	102
Samples	BRH223910	185	28,853	7,035	675	98	53	16	200	42	117
	BRH223911	64	3,837	2,295	415	118	32	7	615	26	102
	BRH223912	88	8,478	4,078	469	123	29	10	214	32	113
	BRH223913	61	3,953	2,497	342	111	32	9	267	28	107
	BRH223914	143	11,112	6,008	722	106	41	12	193	32	119
	BRH223915	44	3,703	1,712	267	119	29	8	475	14	120
	BRH223916	26	1,547	1,074	165	115	22	7	418	16	146
	BRH223917	52	2,494	2,085	322	98	33	7	764	23	110
	BRH223918	38	2,006	1,480	257	128	46	9	474	12	155
	BRH223919	42	2,168	1,695	246	137	39	7	1,321	20	126
	BRH223920	50	2,366	2,165	288	143	32	7	533	16	123
	BRH223921	29	1,746	1,247	221	125	47	8	617	10	128
	BRH223922	43	2,422	1,731	306	113	37	8	460	16	120
	BRH223923	29	1,756	1,040	187	136	78	8	290	25	108
	BRH223924	22	1,392	830	182	84	18	6	652	10	127
	BRH223925	26	1,489	939	236	89	36	5	299	10	113
	BRH223926	63	3,479	2,335	451	90	43	8	312	13	100
	BRH223927	48	2,482	1,893	440	129	51	7	234	14	135
	BRH223928	44	2,302	1,830	368	112	28	7	291	12	97
	BRH223929	54	3,032	2,304	308	93	29	8	242	15	115
	BRH223930	64	3,421	2,576	439	100	43	8	256	13	127
	BRH223931	40	2,832	1,566	386	93	20	7	1,527	18	98
	BRH223932	2	65	32	3	154	14	5	116	4	130
Cirrhosis	BRH241658	4	146	215	5	87	24	16	222	38	104
Samples	BRH241659	3	168	956	5	101	29	7	66	30	97
	BRH241660	1	609	34	1	213	16	6	929	3	91
	BRH241661	21	334	530	4	106	55	7	76	24	80
	BRH241662	26	363	245	4	112	76	7	135	37	68
	BRH241663	6	207	21	6	95	34	12	799	4	112
	BRH241664	6	194	485	6	102	37	10	437	25	121
	BRH241665	3	312	89	2	131	10	6	199	15	93
	BRH241666	8	51	46	3	103	67	11	63	23	165
	BRH241667	1	1	16	5	111	143	4	1,838	63	143
	BRH241668	2	131	399	4	93	100	5	1,466	49	115
	BRH241669	4	1,259	332	15	118	132	8	54	26	111
	BRH241670	5	171	922	7	101	59	15	110	35	106
	BRH241671	3	209	81	1	162	135	9	13	54	75
	BRH241672	12	468	94	4	174	34	10	215	31	127
	BRH241673	1.767	80	448	4	137	48	6	121	24	108
	BRH241674	23	309	113	3	125	47	9	225	18	141
	BRH241675	37	391	178	6	146	79	8	216	20	117
	BRH241676	24	319	92	4	124	64	6	235	19	111
	BRH241677	44	419	149	5	132	82	7	168	23	79
	BRH241678	27	406	166	4	106	63	7	217	24	94
	BRH241679	5	87	78	4	38	55	4	457	18	111
	BRH241680	5	11	21	4	93	40	6	375	15	109
	BRH241681	21	298	108	4	154	43	8	311	16	121
	BRH241682	9	0.00	11	6	195	51	6	61	24	132
Normal	BRH202043	3	73	11	7	92	27	6	35	5	98
Samples	BRH202044	2	47	6	8	160	42	4	65	2	105
	BRH202045	3	0	9	3	122	23	5	141	1	104
	BRH202046	2	25	6	9	188	29	5	67	1	106
	BRH202047	5	29	6	10	120	18	4	121	1	116
	BRH202048	2	15	46	3	116	29	5	77	4	88
	BRH202049	2	30	8	2	136	11	4	74	3	99
	BRH202050	2	2	8	2	110	16	4	38	13	118
	BRH202051	4	46	13	4	112	25	8	50	4	122
	BRH202052	2	30	19	2	147	18	7	64	2	138
	BRH202053	5	30	12	4	143	28	7	50	8	125
	BRH202054	4	63	18	4	203	16	4	49	3	127
	BRH202055	2	83	22	1	158	27	7	61	2	128
	BRH202056	2	100	6	5	254	21	6	54	6	128
	BRH202057	2	1	13	2	184	22	5	60	12	129
	BRH202058	3	2	18	1	76	16	6	22	4	143
	BRH202059	4	88	14	4	71	10	5	53	2	166
	BRH202060	3	32	14	3	158	30	5	38	3	150
	BRH202061	9	99	157	2	140	33	6	68	3	166
	BRH202062	4	138	23	5	159	31	4	67	2	141
	BRH177512	3	0	11	3	249	27	6	82	8	127
	BRH177513	5	0	6	4	159	26	7	179	4	147
	BRH177514	1	62	19	3	137	22	5	64	4	118
	BRH177515	1	27	6	3	120	25	6	26	21	155
	BRH177516	4	37	18	2	171	20	7	40	4	140
	BRH177517	2	65	5	7	95	16	5	75	5	105
	BRH177518	5	1	5	4	122	57	7	85	6	144
	BRH177519	3	2	17	7	231	57	7	87	18	219
	BRH177520	48	2,348	2,053	241	70	24	6	158	13	67
	BRH177523	4	125	19	5	97	46	6	706	7	181

Example 2

Identification of Biomarkers for Distinguishing Normal, HCC and/or Cirrhotic Patients

The ability of the individual markers AFP, CEA, CA 125, CA 19-9, OPN, MMP-9, E-cadherin, and erbB2 to detect primary HCC and/or cirrhosis is summarized in Table 4 as calculated AUC (area under the curve) values from ROC (Receiver Operating Characteristic) curves. The levels of AFP, CEA, CA 125, and CA 19-9 were found to be significantly elevated in the HCC samples, as compared to levels in the cirrhosis and normal samples. The performance of the CA 125, CA 19-9, and CEA assays were comparable, if not superior, to performance of AFP in distinguishing HCC samples from normal samples, HCC samples from cirrhosis samples, and/or cirrhosis samples from normal samples. The levels of OPN, MMP-9, E-cadherin, and ErbB2 were also significantly altered in the different sample types and also showed utility in distinguishing HCC and cirrhosis samples from normals.

TABLE 4

Area under curve (AUC) values calculated from ROC
curves generated using the data generated for the
MSD Cancer 10-plex assay panel and the HCC, cirrhosis
and normal serum samples (see Example 1).

AUC values from ROC curves

E-			CA	CA		MMP-
cad	erbB2	AFP		125	19-9	CEA	9	OPN

HCC/	0.72	0.85	0.92	0.88	0.95	0.93	0.93	0.89
normal
HCC/	0.16	0.54	0.85	0.92	0.93	0.92	0.67	0.28
cirrhosis
cirrhosis/	0.86	0.78	0.76	0.87	0.81	0.54	0.82	0.91
normal

AUC values are provided for ROC analysis of each biomarker's ability to distinguish HCC samples from normal samples (HCC/normal), HCC samples from cirrhosis samples (HCC/cirrhosis), and cirrhosis samples from normal sample (cirrhosis).

The data for the top four markers, AFP, CA 19-9, CA 125 and CEA, were also used to derive scores of normalized median differences between the three classes of samples, as another means of determining the specificity of the markers in distinguishing the disease states from normals and from each other (Table 5). Scores with a magnitude ≧1 indicate that the biomarker has utility in distinguishing between two classes of samples with increasing scores (e.g., scores with magnitudes ≧2 or ≧3) indicating increasing discriminating ability. According to this analysis approach, CA 19.9 performs almost as well as AFP in both discriminating HCC from cirrhosis and from normals, and CA 125 and CEA perform better than AFP in both categories. CEA had scores >3 for distinguishing HCC from cirrhosis and for distinguishing HCC from normals, indicating that CEA is a highly discriminatory marker for specific detection of HCC cases in patient populations that may potentially include patients with cirrhosis.

TABLE 5

Normalized median difference scores were calculated for each
biomarker as [(D − N))/√(σ_D* σ_N))]
for HCC versus normal (HCC/N), HCC versus cirrhosis (HCC/C),
or cirrhosis versus normal (C/N) samples.

	AFP	CA 19.9	CA 125	CEA

HCC/N	3.6	3.0	4.6	4.5
HCC/C	1.8	1.5	2.6	5.9
C/N	0.7	0.8	1.8	0.3

D = median concentration of biomarker for case sample set,
N = median concentration of biomarker for control sample set (LOG transformed data).
σ_Dand σ_N= standard deviation of concentrations for case or control sets (LOG transformed data), respectively.

Example 3

Using Multi-Parameter Analysis for Distinguishing Normal, HCC and/or Cirrhotic Patients

The levels of AFP, CA 125, CEA, and CA 19-9 in HCC samples were highly correlated to each other, as summarized in Table 6, which tabulates the correlation coefficients for the concentrations of these markers in the HCC samples.

TABLE 6

Correlation coefficients for the observed concentrations of AFP,
CA 19-9, CA 125, and CEA in 25 HCC samples.

AFP	CA 19-9	Ca125	CEA
(ng/ml)	(U/ml)	(U/ml)	(ng/ml)

AFP (ng/ml)	1.0
CA 19-9 (U/ml)	0.9	1.0
Ca125 (U/ml)	1.0	0.9	1.0
CEA (ng/ml)	0.9	0.7	0.9	1.0

Analysis of pairs of markers showed an improved ability to distinguish 1-ICC samples from cirrhosis and normal samples as shown visually in the 2-dimensional plots in FIG. 2 and through the calculated assay sensitivities and specificities presented in Tables 7 and 8. For the calculations of sensitivity and specificity, concentration cut-off values were selected for individual markers based on their ability to separate HCC cases from cirrhotic patients and normal controls. For each individual marker, Tables 7 and 8 provide the selected cut-off values, the sensitivity for HCC detection and the specificity for discriminating against normal patients (Table 7) and cirrhotic patients (Table 8). The tables also provide calculated sensitivity and specificity for pairs of markers determined by using the same cut-off values as for the individual assays, but requiring both markers to be positive for HCC to classify a sample as HCC. The tables demonstrate that, even using this simple algorithm, specificity was substantially increased by combining the listed biomarkers (especially for differentiating HCC and cirrhotic patients) with little or no cost to assay sensitivity. Combinations of these biomarkers should provide superior performance as compared to existing HCC detection modalities.

TABLE 7

Effect of combining results from pairs of biomarkers on the ability to
detect HCC cases and differentiate HCC cases from normal controls.
For assays using individual biomarkers, samples were classified as
HCC positive if they met the cut-off criteria listed next to the individual
biomarker names. For pairs of biomarkers, samples were classified
as HCC positive if the result for both individual biomarkers was HCC
positive. Sensitivity is defined as the percent of HCC samples
correctly classified as HCC. Specificity is defined as percent of
non-HCC (normal) samples correctly classified as non-HCC.

	Sensitivity	Specificity

Performance Using Individual Biomarkers

AFP (>21 ng/ml)	96%	97%
CA125 (>800 U/ml)	96%	97%
CA19-9 (>1350 U/ml)	96%	97%
MMP9 (>190 ng/ml)	96%	97%
E-cadherin (<48 ng/ml)	88%	7%

Performance Using Pairs of Biomarkers

AFP + CA125	96%	97%
MMP9 + CA125	96%	100%
CA19-9 + MMP9	96%	100%
CA125 + E-cadherin	92%	97%
AFP + E-cadherin	84%	97%
AFP + MMP9	96%	100%

TABLE 8

Effect of combining results from pairs of biomarkers on the ability to
detect HCC cases and differentiate HCC cases from cirrhosis cases.
For assays using individual biomarkers, samples were classified as
HCC positive if they met the cut-off criteria listed next to the individual
biomarker names. For pairs of biomarkers, samples were classified
as HCC positive if the result for both individual biomarkers was HCC
positive. Sensitivity is defined as the percent of HCC samples correctly
classified as HCC. Specificity is defined as percent of non-HCC
(cirrhotic) samples correctly classified as non-HCC.

	Sensitivity	Specificity

Performance Using Individual Biomarkers

AFP (>21 ng/ml)	96%	72%
CA125 (>800 U/ml)	96%	92%
CA19-9 (>1350 U/ml)	96%	100%
MMP9 (>190 ng/ml)	96%	40%
E-cadherin (<48 ng/ml)	88%	60%

Performance Using Pairs of Biomarkers

AFP + CA125	96%	100%
MMP9 + CA125	96%	100%
CA125 + E-cadherin	92%	96%
AFP + E-cadherin	84%	96%
AFP + MMP9	96%	84%
AFP + CA125	96%	100%

Various publications and test methods are cited herein, the disclosures of which are incorporated herein by reference in their entireties, In cases where the present specification and a document incorporated by reference and/or referred to herein include conflicting disclosure, and/or inconsistent use of terminology, and/or the incorporated/referenced documents use or define terms differently than they are used or defined in the present specification, the present specification shall control.

Claims

1. A method for diagnosing HCC in a patient, said method comprising

(a) measuring a level of a first biomarker in a test sample obtained from a patient, wherein said first biomarker is selected from the group consisting of CEA, CA 125, CA 19-9; and

(b) diagnosing from said measuring step the presence or absence of HCC in said patient.

2. The method of claim 1 wherein said method further comprises measuring a level of at least one additional biomarker in said sample and determining from said level of said first biomarker and said level of said at least one additional biomarker the presence or absence of HCC in said patient.

3. The method of claim 1 wherein said method further comprises comparing said level of said first biomarker in said sample to a level of said first biomarker in a normal control sample and diagnosing the presence or absence of HCC in said patient based on said comparison.

4. The method of claim 2 wherein said method further comprises comparing said level of said first biomarker and said at least one additional biomarker in said sample to levels of said first biomarker and said at least one additional biomarker in a normal control sample and diagnosing the presence or absence of HCC in said patient based on said comparison.

5. The method of claim 2 wherein said at least one additional biomarker is selected from the group consisting of AFP, OPN, MMP-9, E-cadherin, erbB2, and combinations thereof.

6. The method of claim 2 wherein said at least one additional biomarker is selected from the group consisting of CEA, CA 125 and CA 19-9, provided that said additional biomarker is different from said first biomarker.

7. The method according to claim 1, wherein said diagnosing step comprises comparing said level of said first biomarker to a detection cut-off level.

8. The method according to claim 2, wherein said diagnosing step comprises comparing said levels of said first biomarker and said at least one additional biomarker in said sample to detection cut-off levels for said biomarkers.

9. The method according to claim 1, further comprising determining from said level of said first biomarker the disease progression of HCC.

10. The method according to claim 1, wherein said patient has been diagnosed with liver disease.

11. The method according to claim 10, wherein said liver disease is selected from the group consisting of cirrhosis, fibrosis, hepatitis, alcoholic liver disease, fatty liver disease, and combinations thereof.

12. The method according to claim 1, wherein said method further comprises subjecting said patient to an imaging method to evaluate the size, shape and position of the liver and said diagnosing step further comprises evaluating the presence or absence of HCC in said patient based on the results from said imaging method and said measuring step.

13. The method according to claim 12, wherein said imaging method is an ultrasound.

14. A method for monitoring the progression of HCC in a patient diagnosed with HCC, said method comprising

(a) measuring the levels of a first biomarker in a plurality of samples obtained, at different times, from said patient, wherein said first biomarker is selected from the group consisting of CEA, CA 125, CA 19-9; and

(b) determining from said levels of said first biomarker the progression or efficacy of treatment of the HCC.

15. The method of claim 14, wherein said method further comprises measuring the levels of at least one additional biomarker in said samples and determining from said levels of said first biomarker and said levels of said at least one additional biomarker the progression of HCC in said patient.

16. The method of claim 14, wherein said method further comprises comparing said levels of said first biomarker in said samples to a level of said first biomarker in a normal control sample and determining the progression of HCC in said patient based on said comparison.

17. The method of claim 15, wherein said method further comprises comparing said levels of said first biomarker and said at least one additional biomarker in said samples to levels of said first biomarker and said at least one additional biomarker in a normal control sample and determining the progression of HCC in said patient based on said comparison.

18. The method of claim 15, wherein said at least one additional biomarker is selected from the group consisting of OPN, MMP-9, E-cadherin, erbB2, and combinations thereof.

19. The method of claim 14, wherein said at least one additional biomarker is selected from the group consisting of CEA, CA 125 and CA 19-9, provided that said additional biomarker is different from said first biomarker.

20. The method of claim 14, wherein said determining step comprises comparing said level of said first biomarker to a detection cut-off level.

21. The method of claim 15, wherein said determining step comprises comparing said levels of said first biomarker and said at least one additional biomarker to detection cut-off levels for said biomarkers.

22. The method according to claim 14, wherein said patient has been diagnosed with liver disease.

23. The method according to claim 14, wherein said liver disease is selected from the group consisting of cirrhosis, fibrosis, hepatitis, alcoholic liver disease, fatty liver disease, and combinations thereof.

24. The method according to claim 14, wherein said method further comprises subjecting said patient to an imaging method to evaluate the size, shape and position of the liver and said diagnosing step further comprises evaluating the presence or absence of HCC in said patient based on the results from said imaging method and said measuring step.

25. The method according to claim 24, wherein said imaging method is an ultrasound.

26. The method of claim 1, wherein said measuring step is used to differentiate HCC from non-cancerous liver diseases.

27. The method according to any one of claims 2 and 15, wherein levels of said first and said at least one additional biomarker are measured in a multiplexed assay.

28. The method according to any one of claims 2 and 15, wherein levels of said first and said at least one additional biomarker are measured in a single assay chamber.

29. The method according to claim 28, wherein said assay chamber is a single well of an assay plate.

30. The method according to claim 28, wherein said assay chamber is an assay chamber of a cartridge.

31. The method according to any one of claims 1 and 14, wherein said sample is selected from the group consisting of blood, serum and plasma.

32. The method according to any one of claims 1 and 14, wherein said sample is selected from a group consisting of biopsy tissue, intestinal mucosa and urine.

33. The method according to any one of claims 1 and 14, wherein said level is measured using an immunoassay.

34. The method according to any one of claims 1 and 14, further comprising determining from said level of said first biomarker the disease progression of HCC.

35. A method for diagnosing cirrhosis in a patient suspected of having cirrhosis, said method comprising

(b) diagnosing from said measuring step the presence or absence of cirrhosis in said patient.

36. The method of claim 35, wherein said method further comprises measuring a level of at least one additional biomarker in said sample and determining from said level of said first biomarker and said level of said at least one additional biomarker the presence or absence of cirrhosis in said patient.

37. The method of claim 35, wherein said method further comprises comparing said level of said first biomarker in said sample to a level of said first biomarker in a normal control sample and diagnosing the presence or absence of cirrhosis in said patient based on said comparison.

38. The method of claim 36, wherein said method further comprises comparing said level of said first biomarker and said at least one additional biomarker in said sample to levels of said first biomarker and said at least one additional biomarker in a normal control sample and diagnosing the presence or absence of cirrhosis in said patient based on said comparison.

39. The method of claim 36, wherein said at least one additional biomarker is selected from the group consisting of AFP, CEA, CA 125, CA 19-9, OPN, MMP-9, E-cadherin, erbB2, and combinations thereof.

40. The method according to claim 35, wherein said diagnosing step comprises comparing said level of said first biomarker to a detection cut-off level.

41. The method according to claim 36, wherein said diagnosing step comprises comparing said levels of said first biomarker and said at least one additional biomarker in said sample to detection cut-off levels for said biomarkers.

42. The method according to claim 35, further comprising determining from said level of said first biomarker the disease progression of cirrhosis.

43. A method for monitoring the progression of cirrhosis in a patient diagnosed with cirrhosis, said method comprising

(a) measuring the level(s) of a first biomarker in a plurality of samples obtained, at different times, from said patient, wherein said first biomarker is selected from the group consisting of CEA, CA 125, CA 19-9; and

(b) determining from said level(s) of said first biomarker the progression or efficacy of treatment of cirrhosis.

44. The method of claim 43, wherein said method further comprises measuring the levels of at least one additional biomarker in said samples and determining from said levels of said first biomarker and said levels of said at least one additional biomarker the progression of cirrhosis in said patient.

45. The method of claim 43, wherein said method further comprises comparing said level of said first biomarker in said samples to a level of said first biomarker in a normal control sample and determining the progression of cirrhosis in said patient based on said comparison.

46. The method of claim 44, wherein said method further comprises comparing said levels of said first biomarker and said at least one additional biomarker in said samples to levels of said first biomarker and said at least one additional biomarker in a normal control sample and determining the progression of cirrhosis in said patient based on said comparison.

47. The method of claim 44 wherein said at least one additional biomarker is selected from the group consisting of AFP, CEA, CA 125, CA 19-9, OPN, MMP-9, E-cadherin, erbB2, and combinations thereof.

48. The method of claim 43, wherein said determining step comprises comparing said level of said first biomarker to a detection cut-off level.

49. The method of claim 44, wherein said determining step comprises comparing said levels of said first biomarker and said at least one additional biomarker to detection cut-off levels for said biomarkers.

50. The method according to any one of claims 35 and 43, wherein levels of said first and said at least one additional biomarker are measured in a multiplexed assay.

51. The method according to any one of claims 35 and 43, wherein levels of said first and said at least one additional biomarker are measured in a single assay chamber.

52. The method according to claim 51, wherein said assay chamber is a single well of an assay plate.

53. The method according to claim 51, wherein said assay chamber is a cartridge.

54. The method according to any one of claims 35 and 43, wherein said sample is selected from the group consisting of blood, serum and plasma.

55. The method according to any one of claims 35 and 43, wherein said sample is selected from a group consisting of biopsy tissue, intestinal mucosa and urine.

56. The method according to any one of claims 35 and 43, wherein said level is measured using an immunoassay.

57. The method according to any one of claims 35 and 43, further comprising determining from said level of said first biomarker the disease progression of cirrhosis.