Metasin-an intra-operative RT-qPCR assay to detect metastatic breast cancer in sentinel lymph nodes

Ultra-rapid somatic variant detection via real-time targeted amplicon sequencing

Molecular markers are essential for cancer diagnosis, clinical trial enrollment, and some surgical decision making, motivating ultra-rapid, intraoperative variant detection. Sequencing-based detection is considered the gold standard approach, but typically takes hours to perform due to time-consuming DNA extraction, targeted amplification, and library preparation times. In this work, we present a proof-of-principle approach for sub-1 hour targeted variant detection using real-time DNA sequencers. By modifying existing protocols, optimizing for diagnostic time-to-result, we demonstrate confirmation of a hot-spot mutation from tumor tissue in ~52 minutes. To further reduce time, we explore rapid, targeted Loop-mediated Isothermal Amplification (LAMP) and design a bioinformatics tool-LAMPrey-to process sequenced LAMP product. LAMPrey's concatemer aware alignment algorithm is designed to maximize recovery of diagnostically relevant information leading to a more rapid detection versus standard read alignment approaches. Using LAMPrey, we demonstrate confirmation of a hot-spot mutation (250x support) from tumor tissue in less than 30 minutes.

RT-qPCR Detection of SARS-CoV-2: No Need for a Dedicated Reverse Transcription Step

Reverse transcription of RNA coupled to amplification of the resulting cDNA by the polymerase chain reaction (RT-PCR) is one of the principal molecular technologies in use today, with applications across all areas of science and medicine. In its real-time, fluorescence-based usage (RT-qPCR), it has long been a core technology driving the accurate, rapid and sensitive laboratory diagnosis of infectious diseases. However, RT-qPCR protocols have changed little over the past 30 years, with the RT step constituting a significant percentage of the time taken to complete a typical RT-qPCR assay. When applied to research investigations, reverse transcription has been evaluated by criteria such as maximum yield, length of transcription, fidelity, and faithful representation of an RNA pool. Crucially, however, these are of less relevance in a diagnostic RT-PCR test, where speed and sensitivity are the prime RT imperatives, with specificity contributed by the PCR component. We propose a paradigm shift that omits the requirement for a separate high-temperature RT step at the beginning of an RT-qPCR assay. This is achieved by means of an innovative protocol that incorporates suitable reagents with a revised primer and amplicon design and we demonstrate a proof of principle that incorporates the RT step as part of the PCR assay setup at room temperature. Use of this modification as part of a diagnostic assay will of course require additional characterisation, validation and optimisation of the PCR step. Combining this revision with our previous development of fast qPCR protocols allows completion of a 40 cycle RT-qPCR run on a suitable commercial instrument in approximately 15 min. Even faster times, in combination with extreme PCR procedures, can be achieved.

Intra-operative assessment of sentinel lymph nodes for breast cancer surgery: An update

Lymph node (LN) involvement is the strongest prognostic factor in operable breast cancer (BC). Therefore, accurate assessment of LN status is essential for management of BC patients. The introduction of sentinel LN approach reduced the need for extensive axillary surgery to achieve accurate staging. However, positive sentinel LN as determined on postoperative histological examination often leads to a second axillary operation to ensure an accurate staging and that positive non-sentinel LNs are removed. Although preoperative assessment of LN has improved significantly, its accuracy remains insufficient to avoid further axillary surgery and is not sufficient to predict the status of the LN. Therefore, intraoperative evaluation of the sentinel LN to determine the need for completing lymph node dissection in case of metastasis can provide an important approach to guide BC management decision making. This article reviews the techniques available and under development for intraoperative detection of sentinel LN metastasis in BC surgery. The key features of each technique are described in detail, emphasising the benefits offered by label-free optical techniques: minimal sample preparation, high spatial resolution, and immediate on-site implementation. Optical techniques have the potential to provide a cost-effective and accurate intraoperative platform for the assessment of SLN within the operating theatre.

High-Frequency Ultrasonic Forceps for the In Vivo Detection of Cancer During Breast-Conserving Surgery

A major aim in the surgical management of soft tissue cancers is to detect and remove all cancerous tissues while ensuring noncancerous tissue remains intact. Breast-conserving surgery provides a prime illustration of this aim, since remaining cancer in breast margins results in multiple surgeries, while removal of too much unaffected tissue often has undesirable cosmetic effects. Similarly, resection of benign lymph nodes during sentinel lymph node biopsy can cause deleterious health outcomes. The objective of this study was to create an intraoperative, in vivo device to address these challenges. Instant diagnostic information generated by this device could allow surgeons to precisely and completely remove all malignant tissue during the first surgery. Surgical forceps based on Martin forceps were instrumented at the tips with high-frequency ultrasonic transducers composed of polyvinylidene difluoride, a thickness-sensing rotary potentiometer at the base, and a spring to provide the appropriate restoring force. Transducer wires within the forceps were connected to an external high-frequency pulser-receiver, activating the forceps' transmitting transducer at 50 MHz and amplifying through-transmission signals from the receiving transducer. The forceps were tested with tissue-mimicking agarose phantoms embedded with 58–550 μm polyethylene microspheres to simulate various stages of cancer progression and to provide a range of measurement values. Results were compared with measurements from standard 50 MHz immersion transducers. The results showed that the forceps displayed similar sensitivity for attenuation and increased accuracy for wave speed. The forceps could also be extended to endoscopes and laparoscopes.

Detection of mammagloblin by RT-PCR as a biomarker for lymph node metastasis in breast cancer patients: A systematic review and meta-analysis

Background

This meta-analysis presents evidence regarding the diagnostic accuracy of mammaglobin detected using the RT-PCR technique, related to the presence of sentinel node metastasis in breast cancer patients.

Methods

The following databases were consulted: Cochrane, Lilacs, Scielo, Hinary, PubMed, Elsevier, Embase, ProQuest, the Universidad del Rosario´s Centro de Recursos Para el Aprendizaje y la Investigación (CRAI-UR) [Resource Center for Learning and Research], and the Google Scholar search engine. The quality of the studies was assessed using the QUADAS-2 and CASpe tools. The selected studies presented the necessary data to calculate diagnostic validity index of mammaglobin detection using RT-PCR, compared with the reference standard test. Global values for the sensitivity, specificity, positive predictive value, negative predictive value, probability ratios, diagnostic ORs, and summary ROC curves of this meta-analysis were obtained using the Meta-DiSc 1.4 program.

Results

Initially, 731 articles were obtained; but only 25 were included in the meta-analysis. Sensitivity was 84% (95% CI: 83% - 86%), and specificity was 92% (95% CI: 91% - 93%). Positive and negative predictive values were 9.26 (95% CI: 6.47–13.26) and 0.17 (95% CI: 0.13–0.23), respectively. The diagnostic OR was 66.34 (95% CI: 42.52–103.52). The predictive area under the sROC curve was 94.78 (Q = 0.8876).

Conclusions

The evaluated diagnostic index showed that the expression of the mammaglobin biomarker has diagnostic prediction for detecting lymph node metastasis in breast cancer patients, when analyzed using RT-PCR, although more than 50% heterogeneity was found.

Clinical significance of MSKCC nomogram on guiding the application of touch imprint cytology and frozen section in intraoperative assessment of breast sentinel lymph nodes

The widely practiced intra-operative methods for rapid evaluation and detection of sentinel lymph node (SLN) status include frozen section (FS) and touch imprint cytology (TIC). This study optimized the use of TIC and FS in the intra-operative detection of breast SLNs based on the Memorial Sloan Kettering Cancer Center (MSKCC) nomogram. Three hundred forty-two SLNs were removed from 79 patients. SLN metastatic probability was assessed by the MSKCC nomogram. The SLNs underwent intra-operative TIC and FS, as well as routine post-operative paraffin sections (RPSs). The relationships between TIC, FS, and SLN metastatic probability were analyzed. Overall, TIC was more sensitive than FS (92.31% vs. 76.92%), while TIC specificity was inferior to FS specificity (84.85% vs. 100%). In addition, the best cut-off value for TIC based on the MSKCC nomogram was inferior to the best FS cut-off value (22.5% vs. 34.5%). All patients with a MSKCC value <22.5% in the present study were negative based on FS and RPS, while the true-negative and false-positive rates for TIC were 92.5% and 7.5%, respectively. Thus, early breast cancer patients, based on a MSKCC value <22.5%, can safely avoid FS, but should have TIC performed intra-operatively. Patients with a MSKCC value >22.5% should have TIC and FS to determine the size of metastases, whether or not to proceed with axillary lymph node dissection, and to avoid easily missed metastases.

Evaluation of the Metasin assay for intraoperative assessment of sentinel lymph node metastases in breast cancer

AIMS

Sentinel lymph node (SLN) biopsy is the preferred surgical technique for staging the axilla in clinically node-negative breast cancer. Accurate intraoperative staging allows for the immediate performance of an axillary clearance in node-positive patients. We assessed the Metasin assay for the intraoperative analysis of SLNs in a prospective evaluation of 250 consecutive patients undergoing intraoperative SLN analysis at the Breast Unit, University Hospital, Southampton, UK.

METHODS

Metasin uses a quantitative reverse transcription PCR to detect two markers of metastasis: cytokeratin 19 (CK19) an epithelial marker and mammaglobin (MGB) a breast specific marker. Metasin results were compared with the results from routine paraffin block histopathology.

RESULTS

Metasin was robust, with a failure rate of <1%, and demonstrated excellent accuracy and reproducibility. The average turnaround time for the Metasin assay was 42 min, the largest variable being the number of nodes assayed. A total of 533 SLNs were evaluated with 75 patients testing positive for MGB and/or CK19. Based on the analysis of individual SLNs, the overall concordance between Metasin and histology was 92.3% (sensitivity 88.7%, specificity 92.9%). When adjusted for tissue allocation bias, the concordance was 93.8% (sensitivity 89.8%, specificity 94.6%). In this evaluation, 57/250 patients (23%) proceeded to axillary clearance based on Metasin results and were considered spared a second operative procedure.

CONCLUSIONS

Metasin has proven to be an accurate, reproducible and reliable laboratory test. The analysis time is acceptable for intraoperative use, and in comparison to routine histology demonstrates acceptable concordance, sensitivity and specificity.

A multicentre validation of Metasin: a molecular assay for the intraoperative assessment of sentinel lymph nodes from breast cancer patients

AIMS

Treatment strategies for breast cancer continue to evolve. No uniformity exists in the UK for the management of node-positive breast cancer patients. Most centres continue to use conventional histopathology of sampled sentinel lymph nodes (SLNs), which requires delayed axillary clearance in up to 25% of patients. Some use touch imprint cytology or frozen section for intraoperative testing, although both have inherent sensitivity issues. An intraoperative molecular diagnostic approach helps to overcome some of these limitations. The aim of this study was to assess the clinical effectiveness of Metasin, a molecular method for the intraoperative evaluation of SLNs.

METHODS AND RESULTS

RNA from 3296 lymph nodes from 1836 patients undergoing SLN assessment was analysed with Metasin. Alternate slices of tissue were examined in parallel by histology. Cases deemed to be discordant were analysed by protein gel electrophoresis. There was concordance between Metasin and histology in 94.1% of cases, with a sensitivity of 92% [95% confidence interval (CI) 88-94%] and a specificity of 97% (95% CI 95-97%). Positive and negative predictive values were 88% and 98%, respectively. Over half of the discordant cases (4.4%) were ascribed to tissue allocation bias (TAB).

CONCLUSIONS

Clinical validation of the Metasin assay suggests that it is sufficiently sensitive and specific to make it fit for purpose in the intraoperative setting.

A systematic review and economic evaluation of intraoperative tests [RD-100i one-step nucleic acid amplification (OSNA) system and Metasin test] for detecting sentinel lymph node metastases in breast cancer

BACKGROUND

In breast cancer patients, sentinel lymph node biopsy is carried out at the same time as the removal of the primary tumour to postoperatively test with histopathology for regional metastases in the sentinel lymph node. Those patients with positive test results are then operated on 2-4 weeks after primary surgery to remove the lymph nodes from the axilla (axillary lymph node dissection, ALND). New molecular tests RD-100i [one-step nucleic acid amplification (OSNA); based on messenger RNA amplification to identify the cytokeratin-19 (CK19) gene marker] (Sysmex, Norderstedt, Germany) and Metasin (using the CK19 and mammaglobin gene markers) (Cellular Pathology, Princess Alexandra Hospital NHS Trust, Harlow, UK) are intended to provide an intraoperative diagnosis, thereby avoiding the need for postoperative histopathology and, in positive cases, a second operation for ALND.

OBJECTIVE

To evaluate the clinical effectiveness and cost-effectiveness of using OSNA and Metasin in the NHS in England for the intraoperative diagnosis of sentinel lymph nodes metastases, compared with postoperative histopathology, the current standard.

DATA SOURCES

Electronic databases including MEDLINE, MEDLINE In-Process & Other Non-Indexed Citations, EMBASE, The Cochrane Library and the Health Economic Evaluations Database as well as clinical trial registries, grey literature and conference proceedings were searched up to July 2012.

REVIEW METHODS

A systematic review of the evidence was carried out using standard methods. Single-gate studies were used to estimate the accuracy of OSNA with histopathology as the reference standard. The cost-effectiveness analysis adapted an existing simulation model of the long-term costs and health implications of early breast cancer diagnostic outcomes. The model accounted for the costs of an extended first operation with intraoperative testing, the loss of health-related quality of life (disutility) from waiting for postoperative test results, disutility and costs of a second operation, and long-term costs and disutility from lymphoedema related to ALND, adjuvant therapy, locoregional recurrence and metastatic recurrence.

RESULTS

A total of 724 references were identified in the searches, of which 17 studies assessing test accuracy were included in the review, 15 on OSNA and two on Metasin. Both Metasin studies were unpublished. OSNA sensitivity of 84.5% [95% confidence interval (CI) 74.7% to 91.0%] and specificity of 91.8% (95% CI 87.8% to 94.6%) for patient nodal status were estimated in a meta-analysis of five studies [unadjusted for tissue allocation bias (TAB)]. At these values and a 20% node-positive rate, OSNA resulted in lifetime discounted cost-savings of £498 and a quality-adjusted life-year (QALY) loss of 0.048 relative to histopathology, that is, £4324 saved per QALY lost. The most favourable plausible scenario for OSNA in terms of the node-positive rate (range 10-40%), diagnostic accuracy values (91.3% sensitivity and 94.2% specificity, from three reports that adjusted for TAB), the costs of histopathology, OSNA and second surgery, and long-term costs and utilities resulted in a maximum saving per QALY lost of £10,500; OSNA sensitivity and specificity would need to be ≥ 95% for this figure to be ≥ £20,000.

LIMITATIONS

There is limited evidence on the diagnostic test accuracy of intraoperative tests. The quality of information on costs of resource utilisation during the diagnostic pathway is low and no evidence exists on the disutility of waiting for a second surgery. No comparative studies exist that report clinical outcomes of intraoperative diagnostic tests. These knowledge gaps have more influence on the decision than current uncertainty in the performance of postoperative histopathology in standard practice.

CONCLUSIONS

One-step nucleic acid amplification is not cost-effective for the intraoperative diagnosis of sentinel lymph node metastases. OSNA is less accurate than histopathology and the consequent loss of health benefits in this patient group is not compensated for by health gains elsewhere in the health system that may be obtained with the cost-savings made. The evidence on Metasin is insufficient to evaluate its cost-effectiveness.

STUDY REGISTRATION

This study is registered as PROSPERO CRD42012002889.

FUNDING

The National Institute for Health Research Health Technology Assessment programme.