Ontology engineering

news feature© 2010 Nature America, Inc. All rights reserved.The HER2 testing conundrumProblems in interpreting diagnostic tests for HER2 may becompromising patient access to effective treatments. As newversions of therapies targeting HER2 work their way throughclinical trials, will the situation get even murkier? Malorye Allisoninvestigates.A recent study from the University of California,San Francisco, reveals that one in five HER2tests gives the wrong answer 1 . Furthermore, thearticle, which reviews the medical literature,reports that as many as two-thirds of breastcancer patients who should be tested for HER2are not, and consequently a significant fractionof women treated with Genentech’s Herceptin(trastuzumab) have never been tested for HER2overexpression.The health benefit provider Wellpoint,of Indianapolis, might dispute that finding.According to Genentech staff scientist MarkSliwkowski, the insurer has data showing that98% of its breast cancer patients are tested.However, doctors differ in their views on testingbefore prescribing Herceptin. “Some doctorsdon’t know how to interpret test results,Table 1 Selected HER2 testsCompanyLocationBiogenexSan Ramon, CaliforniaDakoGlostrup, DenmarkDakoGenomic HealthInvitrogenCarlsbad, CaliforniaMonogram BiosciencesSiemens Healthcare DiagnosticsErlangen, GermanyVentana-RocheTucsonVentana-RocheVysis (Abbott)Name of testStatusInSite HER2/neu CB11FDA approvedHER2 FISH pharmDx KitFDA approvedHercepTestFDA approvedOncotype DXCLIA validatedSPOT-Light HER2 CISH KitFDA approvedHERmark Breast Cancer AssayCLIA-validatedHER2/neu ELISAFDA approvedthey prefer just to prescribe it and assess thepatient’s progress,” says Michael Liebman ofthe patient stratification company StrategicMedicine of Kennett Square, Pennsylvania.More than a decade after the drug receivedUS Food and Drug Administration (FDA)approval, the personalized medicine paradigmclearly has holes. Many experts are frustratedand troubled by the state of HER2 testing, especiallyas new opportunities for tests are on thehorizon. And as trials testing Herceptin at earlierstages and in combination with other drugscontinue, experts are starting to wonder whatbesides HER2 overexpression might be influencingan individual’s response to the drug.These questions promise to not only spur thedevelopment of a range of new tests to guidebreast cancer therapy but also fundamentallyInform HER2 Silver in situ HybridizationApproved in Europe and elsewhere but notby FDAPathway anti-HER2/neu (Clone CB11)FDA approvedPathVysion HER2 DNA Probe KitFDA approvedCLIA, Clinical Laboratory Improvement Amendment; ELISA, enzyme-linked immunosorbent assay.change understanding of this disease, lead tonew treatments and potentially have an impacton treatment of other cancers.Testing tempestPersonalized medicine proponents point toHerceptin as a paradigm changer: the monoclonalantibody targeting HER2 (also referredto as HER2/neu and ERBB2) evens the playingfield for breast cancer patients overexpressingHER2, whose tumors are typically more aggressive.But testing was problematic from thestart, due to either sloppy execution or complextumor biology. “Giving Herceptin earlyimproves outcome so dramatically that it is anabsolute tragedy to miss patients who shouldbe getting it,” says Jeffrey Ross, from AlbanyMedical College in Albany, New York, whohelped develop a fluorescent in situ hybridization(FISH) HER2 test marketed by DownersGrove, Illinois–based Vysis (Table 1). FISH testsare currently considered the gold standard.As more data become available and theHER2 story evolves, it’s becoming clear thatsome pieces don’t fit together quite as wellas they might. For example, patients whosetumors have progressed on the drug, sometimesrespond to Herceptin when it is givenlater with chemotherapy. Furthermore, fewerthan 50% of HER2-positive metastatic breastTechnologyImmunohistochemistry assay using a monoclonal antibody directed against the internaldomain of HER2/neu available either in automated or manual formatsFISH assay to determine HER2 gene amplification in formalin-fixed, paraffin-embeddedbreast cancer specimens. Gene amplification is determined from the ratio between thenumber of signals from the hybridization of the HER2 gene probe and the number ofsignals from the hybridization of the reference chromosome 17 probe (green signals)Semi-quantitative immunohistochemistry assay for determination of HER2 proteinoverexpression in breast cancer tissues routinely processed for histological evaluationRT PCR–based assay analyzes the expression of a panel of 21 genes, among themHER2. Oncotype DX predicts disease recurrence and assesses benefit from certaintypes of chemotherapyChromogenic in situ hybridization (CISH) using a DNA probe. Quantifiable results arevisualized under a standard brightfield microscope.Proximity-based assay, which provides direct quantitative measurements of HER2total protein and HER2 homodimer levelsSandwich enzyme immunoassay using mouse monoclonal for capture and a differentbiotinylated mouse monoclonal antibody for the detection of human HER2/neu protein.Detection is by direct chemiluminescence. Protein is quantified by spectrophotometryFully automated silver in situ hybridization assay for HER2 and chromosome 17detection. Chromogenic signals are detected through the use of silver depositiontechnology. Results and morphological significance can be interpreted using conventionalbrightfield microscopySemiquantitative immunohistochemistry assay using a monoclonal antibody for thedetection of c-erbB-2 (HER2) antigen using Ventana’s family of automated instrumentplatformsFluorescence in situ hybridization (FISH) assay to determine HER2 amplification,using LSI HER2 probe, which spans HER2, and CEP 17 probe, which hybridizes tothe alpha satellite DNA located at the centromere of chromosomenature biotechnology volume 28 number 2 february 2010 117