Tissue microarray technology in breast cancer HER2 diagnostics

AI-Assisted High-Throughput Tissue Microarray Workflow

Immunohistochemical (IHC) studies of formalin-fixed paraffin-embedded (FFPE) samples are a gold standard in oncology for tumor characterization, and the identification of prognostic and predictive markers. However, despite the abundance of archived FFPE samples, their research use is limited due to the labor-intensive nature of IHC on large cohorts. This study aimed to create a high-throughput workflow using modern technologies to facilitate IHC biomarker studies on large patient groups. Semiautomatic constructed tissue microarrays (TMAs) were created for two tumor patient cohorts and IHC stained for seven antibodies (ABs). AB expression in the tumor and surrounding stroma was quantified using the AI-supported image analysis software QuPath. The data were correlated with clinicopathological information using an R-script, all results were automatically compiled into formatted reports. By minimizing labor time to 7.7%-compared to whole-slide studies-the established workflow significantly reduced human and material resource consumption. It successfully correlated AB expression with overall patient survival and additional clinicopathological data, providing publication-ready figures and tables. The AI-assisted high-throughput TMA workflow, validated on two patient cohorts, streamlines modern histopathological research by offering cost and time efficiency compared to traditional whole-slide studies. It maintains research quality and preserves patient tissue while significantly reducing material and human resources, making it ideal for high-throughput research centers and collaborations.

Making a Tissue Microarray

Tissue microarray (TMA) is a widely used, high-throughput, cost-effective, and tissue and reagent-conserving method of performing molecular analysis. Multiple donor tissue cores are procured and transferred into a recipient TMA block for simultaneous differential and comparative molecular profiling under theoretically identical performance conditions. Described herein is a discussion of the theory behind the TMA, an overview of the concepts and principles of TMA design and construction, a brief summary of its advantages and disadvantages, and a sample protocol of TMA construction.

Cell adhesion molecule profiles, proliferation activity and p53 expression in advanced epithelial ovarian cancer induced malignant ascites-Correlation of tissue microarray and cytology microarray

INTRODUCTION

Peritoneal dissemination accompanied by ascites formation is common in epithelial ovarian cancer (EOC). Adhesion molecules are crucial in metastatic spread and the latter involves epithelial-mesenchymal transition (EMT). This study aimed at: (1) clarifying whether E-cadherin and β-catenin expression and proliferative activity in metastatic ovarian cancer are inter-related; (2) Identifying possible correlations between cell adhesion molecular expression profiles, the proliferative activity and p53 expression of tumor cells and tumor grade and stage; (3) testing the cytology microarray (CMA) technique in analyzing metastasis formation.

MATERIAL AND METHODS

Both tumorous and ascitic samples from 27 EOC patients were examined by using tissue microarray (TMA) and cytology microarray (CMA), respectively. CMA blocks were constructed using cores from each cell block of the ascitic specimens. Expression of E-cadherin, β-catenin, Ki-67 and p53 was immunohistochemically detected both in TMA and CMA blocks.

RESULTS

E-cadherin expression was higher in ascitic cells than in primary tumor cells (p = .294). β-catenin expression was significantly lower in ascitic cells than in primary tumor cells (p = .006). Expression of Ki-67 was lower and expression of p53 was higher in primary tumors than in ascitic cells, for p53 the difference was significant (p = .001). Both Ki-67 and p53 expression elevated significantly in high-grade primary tumor cells and in ascites cells (p = .039, and p = .004, respectively).

CONCLUSION

Epithelial-mesenchymal transition- mesenchymal-epithelial transition is suggested as the best descriptive term for our IHC observations which accompany increased proliferative activity of ascitic cells. The CMA method is an adequate and reliable method for the analysis of ascitic tumor cells disseminating from ovarian malignancies.

Clinical utility of RT-PCR in assessing HER 2 gene expression versus traditional IHC and FISH in breast cancer patients

BACKGROUND

IHC and FISH are used for categorizing HER 2 status in breast cancer at the protein and DNA level, respectively. HER 2 expression at the RNA level is quantitative, cheaper, easier to standardize and free from interobserver variation.

METHODS

115 consecutive patients were tested by IHC, FISH and RT-PCR (test cohort). Assuming FISH result to be the response variable, ROC curves for RT-PCR ratio were analyzed to label HER 2 negative, equivocal and positive cases as RT-PCR score 1, 2 and 3, respectively. Inter-relationships between RT-PCR, IHC and FISH were defined. 'Clinical benefit' of a test was defined as proportion of patients labeled unequivocally as HER 2 positive or negative. Population for 1 year was simulated constraint to previous reports of HER 2 positivity and IHC category distribution by a meta-analysis of previous studies that evaluated concordance between IHC and FISH to determine HER 2 status (simulation cohort). Four diagnostic pathways in the simulation cohort were defined-(1) initial IHC, followed by FISH (conventional pathway); (2) initial RT-PCR, followed by FISH; (3) initial IHC, followed by RT-PCR and then by FISH; (4) initial RT-PCR, followed by IHC and then by FISH. The clinical benefit of IHC and RT-PCR in the four pathways was analyzed and sensitivity analysis for incremental cost-effectiveness ratio and cost-benefit comapring RT-PCR against IHC, both as first-line tests and among those with IHC score 2 as a reflex second-line test was performed by the Monte Carlo technique.

FINDINGS

115 patients comprised the study population. While none with IHC score of 0 or 1 was FISH positive for HER 2, all cases with IHC score of 3 were FISH positive. 43 cases were assigned IHC score of 2. Thus, 72 patients benefited from the initial IHC testing [clinical benefit 62.6%], with the overall concordance between IHC and FISH being 100% for those with IHC score of 0, 1 and 3 (conclusive IHC categories). For RT-PCR with 100% concordance, 15.7% (115-97 = 18) patients would have benefited from RT-PCR testing if it was used as a first-line test. If RT-PCR would have been used as a second-line test among those with IHC score 2 (n = 43), then only 6 patients would have been assigned a conclusive RT-PCR category (category 1 or 3) translating to a clinical benefit of 14% (6/43) as a second-line test. As a second-line test it had 51% probability to prove more cost-effective than the conventional pathway, provided the cost of RT-PCR was 0.4 times the cost of IHC. Also in a three-step pathway, RT-PCR upfront would have 56% probability of higher cost-benefit provided the cost of RT-PCR was 0.1 times the cost of IHC.

CONCLUSION

RT-PCR results were found to be suboptimal to IHC in terms of discriminative ability and clinical benefit; thus, it is unlikely to replace IHC as a first-line test in the near future.

A meta-analysis on concordance between immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) to detect HER2 gene overexpression in breast cancer

BACKGROUND

We performed this meta-analysis study to evaluate the concordance and discordance between immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) in detecting HER2 alteration in human breast cancer.

METHODS

As a meta-analysis, the present study evaluated the available data from previous studies on the HER2 gene detected by IHC and FISH. To indicate the meta-analysis results, a forest plot was used.

RESULTS

We identified 172 citations, for which our inclusion criteria were met by 18 articles, representing 6629 cases. The overall concordance and discordance rate between IHC staining with score 0/1+ and FISH for detection failure of HER2 expression was 96 and 4 %, respectively. The present study showed that the overall proportion of FISH positive and negative rate for IHC score 2+ for detection of HER2 expression was 36 and 64 %, respectively; and 91 and 9 % for 3+ IHC scores.

CONCLUSION

The results of this study show that IHC score 0/1+ and 3+ cannot be completely considered as negative and positive breast cancer test, respectively. Therefore, we suggest a valid and complementary test, the same as FISH, to explore HER2 expression.

Evaluation of HER2 Gene Status in Breast Cancer Samples with Indeterminate Fluorescence in Situ Hybridization by Quantitative Real-Time PCR

Administration of drugs targeting HER2 (official symbol ERBB2) is an important component of therapy for breast cancer patients with HER2 amplification/overexpression as determined by in situ hybridization (ISH) and immunohistochemistry (IHC). In approximately 5% of breast cancers, ISH assays fail. In these cases, HER2 protein expression is evaluated by IHC alone that may yield false negatives/positives for poor-quality samples. Therefore, we developed a method that was based on quantitative real-time PCR applicable for DNA from formalin-fixed, paraffin-embedded tissue samples. Its limit of detection was determined with breast cancer cell lines and validated with 223 breast cancer patient samples. On the basis of comparisons with fluorescent ISH (FISH) and IHC data, the sensitivity of the new method was 94.2% and 95.1%, its specificity was 100% and 99.1%, and overall concordance between results obtained with the quantitative real-time PCR method and FISH/IHC was 97.6% for both methods. The quantitative real-time PCR method was then used to evaluate the HER2 status of 198 of 3696 breast cancer tissues that yielded indeterminate FISH results. The HER2 copy number was successfully determined in 69.2% of these indeterminate samples. Thus, the DNA-based technique appears to be a specific, sensitive method for determining HER2 copy numbers when the FISH assay fails, which may complement IHC tests.

Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/College of American Pathologists clinical practice guideline update

PURPOSE

To update the American Society of Clinical Oncology (ASCO)/College of American Pathologists (CAP) guideline recommendations for human epidermal growth factor receptor 2 (HER2) testing in breast cancer to improve the accuracy of HER2 testing and its utility as a predictive marker in invasive breast cancer.

METHODS

ASCO/CAP convened an Update Committee that included coauthors of the 2007 guideline to conduct a systematic literature review and update recommendations for optimal HER2 testing.

RESULTS

The Update Committee identified criteria and areas requiring clarification to improve the accuracy of HER2 testing by immunohistochemistry (IHC) or in situ hybridization (ISH). The guideline was reviewed and approved by both organizations.

RECOMMENDATIONS

The Update Committee recommends that HER2 status (HER2 negative or positive) be determined in all patients with invasive (early stage or recurrence) breast cancer on the basis of one or more HER2 test results (negative, equivocal, or positive). Testing criteria define HER2-positive status when (on observing within an area of tumor that amounts to >10% of contiguous and homogeneous tumor cells) there is evidence of protein overexpression (IHC) or gene amplification (HER2 copy number or HER2/CEP17 ratio by ISH based on counting at least 20 cells within the area). If results are equivocal (revised criteria), reflex testing should be performed using an alternative assay (IHC or ISH). Repeat testing should be considered if results seem discordant with other histopathologic findings. Laboratories should demonstrate high concordance with a validated HER2 test on a sufficiently large and representative set of specimens. Testing must be performed in a laboratory accredited by CAP or another accrediting entity. The Update Committee urges providers and health systems to cooperate to ensure the highest quality testing.

Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/College of American Pathologists clinical practice guideline update

PURPOSE

To update the American Society of Clinical Oncology (ASCO)/College of American Pathologists (CAP) guideline recommendations for human epidermal growth factor receptor 2 (HER2) testing in breast cancer to improve the accuracy of HER2 testing and its utility as a predictive marker in invasive breast cancer.

METHODS

ASCO/CAP convened an Update Committee that included coauthors of the 2007 guideline to conduct a systematic literature review and update recommendations for optimal HER2 testing.

RESULTS

The Update Committee identified criteria and areas requiring clarification to improve the accuracy of HER2 testing by immunohistochemistry (IHC) or in situ hybridization (ISH). The guideline was reviewed and approved by both organizations.

RECOMMENDATIONS

The Update Committee recommends that HER2 status (HER2 negative or positive) be determined in all patients with invasive (early stage or recurrence) breast cancer on the basis of one or more HER2 test results (negative, equivocal, or positive). Testing criteria define HER2-positive status when (on observing within an area of tumor that amounts to > 10% of contiguous and homogeneous tumor cells) there is evidence of protein overexpression (IHC) or gene amplification (HER2 copy number or HER2/CEP17 ratio by ISH based on counting at least 20 cells within the area). If results are equivocal (revised criteria), reflex testing should be performed using an alternative assay (IHC or ISH). Repeat testing should be considered if results seem discordant with other histopathologic findings. Laboratories should demonstrate high concordance with a validated HER2 test on a sufficiently large and representative set of specimens. Testing must be performed in a laboratory accredited by CAP or another accrediting entity. The Update Committee urges providers and health systems to cooperate to ensure the highest quality testing. This guideline was developed through a collaboration between the American Society of Clinical Oncology and the College of American Pathologists and has been published jointly by invitation and consent in both Journal of Clinical Oncology and the Archives of Pathology & Laboratory Medicine.

Is it necessary to evaluate nuclei in HER2 FISH evaluation?

A new method that simplifies the evaluation of the traditional HER2 fluorescence in situ hybridization (FISH) evaluation in breast cancer was proposed. HER2 status was evaluated in digital images (DIs) captured from 423 invasive breast cancer stained sections. All centromeric/CEP17 and HER2 gene signals obtained from separated stacked DIs were manually counted on the screen. The global ratios were compared with the traditional FISH evaluation and the immunohistochemical status. The 2 FISH scores were convergent in 96.93% of cases, showing an "almost perfect" agreement with a weighted k of 0.956 (95% confidence interval, 0.928-0.985). The new method evaluates at least 3 times more nuclei than traditional methods and also has an almost perfect agreement with the immunohistochemical scores. The proposed enhanced method substantially improves HER2 FISH assessment in breast cancer biopsy specimens because the evaluation of HER2/CEP17 copy numbers is more representative, easier, and faster than the conventional method.

Construction of a tissue microarray with two millimeters cores of endometrioid endometrial cancer: factors affecting the quality of the recipient block

The tissue microarray (TMA) method currently is not used to render a primary diagnosis of cancer, but its scientific value has been proved in studies of various cancer types. TMA technology still is not used often for uterine tumors, however. We investigated the repeatability of histological diagnosis of endometrioid endometrial cancer (EEC) using conventional histology and TMA using 2 mm cores. We examined EEC tissues from 171 patients. Formalin fixed, paraffin embedded tissue donor blocks from EEC specimens were selected and examined histologically. Duplicate 2 mm tissue cores were inserted into a TMA recipient block. EEC tissues were examined as hematoxylin-eosin stained sections from the TMAs. EEC tissue was identified in the TMAs in 158 cases (92.4%) and not found in 13 cases (7.6%). On the TMA slides, both EEC positive cores were identified in 129 cases (75.4%), but only one core in 29 cases (17.0%). Among 342 biopsies of the donor blocks (each case in duplicate), EEC was found in 287 cases (83.9%) using the TMA: 124/146 (84.9%) with superficial infiltration, 153/178 (86.0%) with deep myometrial infiltration, and 10/18 (55.6%) without myometrial infiltration. We concluded that two 2 mm tissue cores from a biopsy of a donor block inserted into a TMA recipient block were sufficient to diagnose EEC in more than 90% of cases. EEC was identified in the TMAs with similar frequency with respect to superficial and deep myometrial infiltration. Cases without myometrial infiltration were identified less often.

Comparison of in situ hybridization methods for the assessment of HER-2/neu gene amplification status in breast cancer using a tissue microarray

BACKGROUND

This project compared HER-2/neu gene status in breast cancers, as demonstrated by FISH (fluorescent in situ hybridization) and CISH (chromogenic in situ hybridization) and using a tissue microarray (TMA). The study also aimed to show whether the TMA technique could be used in clinical diagnostics, rather than remain a scientific tool.

MATERIALS AND METHODS

A TMA was constructed using 121 breast cancer specimens, 6 cores from each specimen. Demonstration and assessment of HER-2/neu gene status was by FISH (Vysis Path) and CISH (DAKO Duo CISH).

RESULTS

The 121 breast cancer specimens were divided into 3 groups by HER-2 status, as determined by immunohistochemistry. In the HER-2 negative group no amplification was observed in 36 out of 40 cases. 3 cases showed amplification by both methods and one by CISH alone. The equivocal HER-2 group showed no amplification in 30 out of 41 cases and amplification in 9 cases. One case was FISH negative CISH positive and one was discarded. In the HER-2 positive group, amplification was confirmed in 37 of the 40 cases by both methods. 3 cases were unsuitable for assessment.

CONCLUSIONS

This study indicated that CISH is a sensitive alternative to FISH in detecting HER2 gene amplification and may replace FISH in HER2 testing. Good agreement was observed between methods (98.5% - 119 out of 121 cases). Furthermore, as only 4 out of 121 cases were unsuitable for assessment (no signal or missing TMA cores) - it may be feasible to use TMA in diagnostics.

Confirmation of a low HER2 positivity rate of breast carcinomas - limitations of immunohistochemistry and in situ hybridization

Background

Accurate assessment of the human epidermal growth factor receptor 2 (HER2) of invasive breast cancer is essential to treatment decisions since the advent of targeted therapy with the humanized monoclonal antibody trastuzumab and the dual tyrosine kinase inhibitor lapatinib. In the literature, the percentage of HER2-overexpressed/amplified breast carcinomas range from 3% to 30%. The routinely assigned low rate of 9% of HER2-overexpressed breast carcinomas alarmed one of our gynecologists who requested to confirm our HER2 test results.

Methods

A small study of 83 patients with breast carcinoma was designed to reexamine the routinely assessed HER2 status using immunohistochemistry and fluorescence in situ hybridization.

Results

The low rate of 9% of HER2-overexpressed/amplified breast tumors (DIN1C-3, invasive carcinoma) could be confirmed. However, FISH revealed two false positive cases and one false negative case. Moreover a case with an equivocal result in FISH was detected.

Conclusion

The HER2 positivity rate may be as low as 9%. The novel ASCO/CAP criteria for assessing immunohistochemical results in HER 2 testing reduce the false positive rate of HER2. First-line testing with immunohistochemistry may obscure false positive and false negative test results. In heterogeneous carcinomas even fluorescence in situ hybridization may not succeed in a correct evaluation of HER2.

Image analysis as an adjunct to manual HER-2 immunohistochemical review: a diagnostic tool to standardize interpretation

Dobson L, Conway C, Hanley A, Johnson A, Costello S, O’Grady A, Connolly Y, Magee H, O’Shea D, Jeffers M & Kay E (2010) Histopathology57, 27–38 Image analysis as an adjunct to manual HER-2 immunohistochemical review: a diagnostic tool to standardize interpretation

Tissue microarray for routine analysis of breast biomarkers in the clinical laboratory

Tissue microarray analysis (TMA) allows multiple analyses on multiple patients on sections from a single paraffin block. Although it is widely used in research and in quality assurance settings, there are few references to its use in clinical practice. This study evaluated TMA assessment of breast biomarkers using immunohistochemical analysis in a clinical histopathology laboratory. Performance parameters, interobserver variability, and concordance between TMA and whole section results were assessed. The arrays had few lost or noninformative cores. A loss of stain intensity occurred in the arrays compared with the whole sections with some but not all antibodies, highlighting the need to validate the staining protocol for each antibody used on TMA sections. With recommended guidelines for specimen selection and reporting, TMA was found to be an economical replacement for whole section analysis for breast biomarkers.

Analysis of biological prognostic factors using tissue microarrays in neuroblastic tumors

BACKGROUND

Neuroblastic tumors (NT) are pediatric neoplasms with a heterogeneous genetic profile. They present genotypic alterations of prognostic value, the study of which is mandatory in designing therapeutic management. Tissue microarrays (TMA) from paraffin material allow the analysis of a large number of cases with minimal costs. The main purpose of the present study is to analyze specific genetic markers of neuroblastic tumors included in TMAs and determine their prognostic value. We compare the results obtained by different molecular techniques at different substrates to evaluate the feasibility of these assays.

PROCEDURE

One hundred thirty-nine samples were included in four different TMAs. We performed FISH assays to determine the status of MYCN gene, 1p36 region and 17q23 arm. The prognostic value of the genetic markers as well as the statistical correlation among clinical variables and outcome were analyzed by SPSS.

RESULTS

MYCN amplification was detected in 35.3% of the cases, whereas 1p36 deletion and 17q23 gain was observed in 46.8% and 58.3% of the cases, respectively. An adverse prognosis was noted among these patients. Other adverse factors were age (>18 months) as well as high stage of disease (stage 4). Phenotypic signs of differentiation correlated with good outcome.

CONCLUSION

Retrospective studies using paraffin-embedded tissues assembled in TMA are a useful tool for the analysis of prognostic factors in NT.

Significance of Her-2/neu protein over expression in Indian breast cancer patients

BACKGROUND

Racial disparity in presentation and outcome of breast cancer is established but cause is unexplained. Many studies show various molecular markers for racial differences in the prognosis of breast cancer. There is scarcity of data on prognostic significance of HER-2/neu in Indian breast cancer.

AIMS AND OBJECTIVE

To know incidence and prognostic significance of HER-2/neu expression in Indian patients. To correlate HER-2/neu Expression with other prognostic markers and ER/PR Receptor status.

MATERIAL AND METHODS

112 consecutive patients with breast cancer attending the Department of Surgical Oncology from March 1997 to March 2000 were included in this study. The clinical data along with ER/PR status, follow up data and HER-2/neu expression examined by immuno-histochemical method was recorded.

STATISTICAL ANALYSIS

Data was analyzed by univariate and multivariate analysis for all prognostic factors. Significance was calculated by using Chi square test and survival analysis by using Kaplan Meier survival curve.

RESULTS

The median age of 112 patients was 46.56 (±9.55) years. HER-2/neu over expression was present in 46.37%. Significant correlation was found between HER-2/neu over expression and lymph node status, grade of tumor and ER/PR receptor status. Median follow up period of 23 months. There was significant tumour free survival advantage (p < 0.01) and overall survival advantage (p < 0.001) in patients with HER-2/neu negative expression.

CONCLUSION

HER-2/neu oncogene over expression is higher (46.37%) among Indian patients in comparison to 25-30% shown in most western literature. HER-2/neu oncogene over expression significantly correlates with grade, lymph node involvement, ER/PR status and also affects survival.

Tissue microarrays for routine diagnostic assessment of HER2 status in breast carcinoma

The use of tissue microarray (TMA) technology may substantially reduce the costs of routine testing of breast carcinomas for human epidermal growth factor receptor 2 (HER2) status. After a preliminary pilot study comparing the TMA results with those obtained on whole section, which showed an excellent agreement (with kappa values >0.90) for both immunohistochemical and fluorescent in situ hybridization (FISH) method, we introduced the TMA technique in our routine work. A total of 1158 invasive breast carcinomas were submitted for the determination of HER2 status, which was assessed in 74 weekly runs. One hundred twenty-five of 1084 surgical specimens (11.5%) were judged as unsuitable for inclusion into TMAs. In 32 of 959 tumors included in TMAs (3.3%), the respective cores were uninformative, and HER2 status was determined on whole sections. Thus, HER2 status was finally determined on TMA in 927 cases (81.1%). A typical weekly run comprised 1 TMA (consisting, on average, of 13 tumors), 2 whole sections of surgical specimens and 1 whole section of core needle biopsy, and the number of processed slides for each method decreased from 16 to 4 per week. In all, 14.7% of tumors were HER2 positive by FISH. In both TMAs and whole sections, immunohistochemical results were in good agreement with FISH for cases scored as 0/1+ (98% and 97%) and for those scored as 3+ (96% and 87%), whereas concordance was poor in cases scored as 2+ (30% and 13%, respectively).

Tissue microarrays: emerging standard for biomarker validation

With the widespread use of DNA microarrays, hundreds of biomarkers are in need of validation in cohorts of well-annotated clinical samples. Tissue microarrays are emerging as the tool par excellence to rapidly perform DNA, RNA, and especially protein expression analyses on large numbers of clinical samples. Although still somewhat limited by the subjectivity of scoring methods and tissue sample representativeness, TMAs represent an increasingly validated means of understanding the clinical impact of diagnostic-related, prognostic-related, and therapy-related markers. Automated methods are being developed for TMA analysis and cell microarrays and frozen tissue TMAs have been better optimized. More and more biomarker studies are availing themselves of the high-throughput nature of TMAs, recognizing that they are becoming indispensable for rapid translation of laboratory data to the clinic.

New technologies around biomarkers and their interplay with drug development

What conductors are to their orchestras, biomarkers are to their associated technologies. Building fundamental science, supporting early diagnosis of diseases and following their progression, improving efficacy and safety of treatments, optimizing patient selection and adapting dosing of drugs, helping decide which therapy is most appropriate; these are examples of a few contexts in which biomarkers are key players. Technology development can definitely not escape being associated with these steps. In other words, today's biomarkers are the thermometers of tomorrow's therapies. This review provides an overview of recently established platforms as well as new and upcoming technologies for biomarker development in the context of drug development. The roles as well as the pros and cons of different disciplines such as genetics, genomics, proteomics, metabonomics, and assay development will be discussed.

Promises of Biomarkers in Drug Development ? A Reality Check

Biomarkers have been a buzz word in drug development for the last 5 years. But where do we stand now? This perspective article will demonstrate to which extent biomarkers have impacted drug development and the use of drugs. In particular, the different types of biomarkers, their identification, validation and use in different phases of drug development from drug discovery, to approval, to clinical application will be discussed as well as the state-of-the-art biomarker technologies and promising future methods. The high interest in biomarkers has generated the need for development of new technologies and refinement of existing ones. Besides discussing their perspectives of applications, the present article also illustrates the future of biomarker development in terms of qualification for regulatory use and co-development.