Present status of microfluidic PCR chip in nucleic acid detection and future perspective

Polymerase chain reaction (PCR) amplifies specific fragment of DNA molecules and has been extensively applied in fields of pathogens and gene mutation detection, food safety and clinical diagnosis which on the other hand, holds the drawbacks of large size instrument, high heat dissipation etc. It has been demonstrated that microfluidics technique coupling with PCR reaction exhibits characteristics of integration, automatization, miniaturization, and portability. Meanwhile, various designed fabrication of microchip could contribute to diverse applications. In this review, we summarized major works about a variety of microfluidic chips equipped with several kinds of PCR techniques (PCR, RT-PCR, mPCR, dPCR) and detection methods like fluorescence, electrochemistry, and electrophoresis detection. The development and application of PCR-based microfluidic chip in pathogen and gene mutation detection, diseases prevention and diagnosis, DNA hybridization and low-volume sample treatment were also discussed. Copyright © 2022 Elsevier B.V.

The utility of using genomic testing on needle core biopsies during the COVID-19 pandemic: Molecular characterization, risk stratification, neoadjuvant outcome, and future implications

Introduction: The COVID-19 pandemic has caused an extraordinary challenge for global health. New guidelines were implemented, including postponing non-essential surgical procedures to conserve resources. In response, the COVID19 Pandemic Breast Cancer Consortium expert opinion suggested the use of core biopsies for genomic testing to help triage patients for surgical vs. systemic treatment. To better understand how expedited genomic results could impact peri-operative care, we performed a pre-operative quality project to assess testing Mammaprint (MP), a 70-gene risk of recurrence assay, and Blueprint (BP), an 80-gene molecular subtyping assay, on core biopsies. Here we report our experience with MP and BP testing on core biopsies, and the correlation between test results and response to neoadjuvant therapy.Design: From April to December 2020, all core biopsies with a breast carcinoma diagnosis from our clinic (300 patients) were routinely sent for MP and BP testing as part of a rapid result program that was initiated to see whether test results could be obtained in time and whether they would lead to more informed pre-operative treatment decisions. Unstained slides were sent for genomic and receptor testing concurrently. When genomic results differed from IHC/FISH results or suggested a different S treatment plan vs. clinical factors alone, we referred to this as "reclassification." For those patients who completed their neoadjuvant chemotherapy, we grouped them by their genomic results and by their conventional IHC/FISH/Clinical classification, and compared the outcome. Results: MP and BP results from core biopsy were available for 96.6% of patients (n=290/300). The average time from biopsy to test results was 10 days, and the average lab turnaround time was 5 days. Results were available for tumor conference discussions 100% of the time. MP and BP re-classified 84 of 300 patients (28%) from conventional IHC/FISH subtyping, and reclassified 42 of 195 patients (22%) of patients from their risk category based on traditional clinical factors (Table-1). Of the 38 patients with available post-neoadjuvant therapy outcome, 13 patients (34%) achieved pathologic complete response (pCR). 16 patients were classified as Her-2 enriched by IHC/FISH of which 9 (56%) achieved pCR. MP/BP aligned with the IHC/FISH Her-2 enriched classification in 11/16 patients, while 5 patients were reclassified to Luminal B by MP/BP. Of the 11 patients with concordant IHC/FISH and MP/BP results, 8 achieved pCR (73%), while one of the 5 cases reclassified to Luminal B achieved pCR (20%). Of the patients who were classified Luminal by IHC (9 patients), one patient achieved pCR (11%), and of the patients classified luminal (A or B) by MP/BP (12 patients) two achieved pCR (16%). Of the IHC-triple negative patients and genomic basal patients, three patients achieved pCR in each group (23% and 20%, respectively). Conclusion: Performing MP/BP tests on core needle biopsies hold a high success rate. Incorporating test results into peri-operative discussions may result in better-informed decisions about treatment planning and timing of surgery versus systemic therapy. A higher rate of pCR was seen in the MP/BP Her-2 enriched group compared to the IHC/FISH Her-2 enriched group. Although this workflow was designed to triage patients during the COVID pandemic, this approach has great potential beyond the pandemic.

Genomic testing on breast cancer core biopsy material is feasible and provides useful treatment information

Background: Genomic profiling assays for invasive breast cancer provide useful predictive and prognostic information and are performed most commonly on surgical resection specimens. Obtaining the molecular profile at the time of initial core needle biopsy is ideal because it could provide information that could significantly alter preoperative decision-making and avoid unnecessary treatments. In January 2020, the breast center began a 3 month pilot program that would reflexively send core biopsy material on all newly diagnosed patients for genomic testing using the MammaPrint (MPT) and BluePrint (BPT) assays regardless of receptor status. The goals were to determine feasibility and examine the impact to patient care. Methods: Breast core biopsy tissue was triaged by an attending pathologist as soon as slides were available. If invasive carcinoma with at least 3 mm in linear extent of tumor with 20% cellularity was identified, materials were immediately sent to Agendia for MPT/BPT testing even before ER/PR/HER2 testing was available to the pathologist. Clinicopathologic information, turn-around time (TAT) and adequacy data were tracked. The impact was discussed regularly at breast tumor board to determine if the results led to altered decision-making that could reduce unnecessary interventions and time to initial treatment. Results: 445 core biopsy specimens were sent for genomic testing. Of those 442, (97%) Syielded genomic results with an average TAT from biopsy to genomic result of 11 calendar days. MPT identified 233 (53%) cases that were low risk and 209 (47%) cases that were high risk. BPT showed that 60 (14%) cases were Basal, 18 (4%) cases were HER2, and 364 (82%) cases were Luminal. Further analysis of the Luminal subgroup demonstrated that 154 (42%) were Luminal A low risk, 78 (21%) were Luminal A Ultralow risk and 132 (36%) were Luminal B High Risk. Analysis by race demonstrated a significantly higher percentage of high risk tumors in African-American women including a higher percentage of basal cancers (26%) as compared to Caucasian women (10%). Of note, 51 patients in the pilot study had additional OncotypeDX (ODX) testing on subsequent surgical resection. There was fair correlation between the assays with the majority of the low risk MPT having low risk ODX scores (<=25) and the high risk MPT having high risk ODX scores (>25), though MPT identified more patients as being high risk. The COVID-19 pandemic altered plans to assess time to treat and treatment interventions as initially intended. However, the knowledge of genomic result enhanced the ability to triage patients, allowing those patients with low risk tumors to begin endocrine therapy and delay surgery. Use of preoperative hormone therapy was considered more often in place of neoadjuvant chemotherapy in patients with low genomic risk ER+/HER2-patients. Because of the continued feedback indicating positive impact, the pilot ultimately was extended to 11 months to allow time for formal implementation. Conclusions: Genomic testing using the MPT/BPT assay on core biopsy samples with at least 3 mm yields results 97% of the time with an average TAT of 11 days from biopsy date to result. The genomic information at the time of initial diagnosis impacted patient care most notably in the ER+ setting. The results led to the immediate implementation of direct reflex testing of all newly diagnosed ER+ and HER2-or IHC 2+ cancers by pathology after the initial pilot phase.

Comparing MammaPrint and BluePrint results between core needle biopsy and surgical resection breast cancer specimens

Goals: The COVID-19 pandemic continues to strain healthcare systems globally. The ESMO COVID-19 adapted recommendations1 advocate for the use of pre-operative/neoadjuvant endocrine therapy as a strategy to defer surgery by 6–12 months in clinical stage I-II breast cancers to prioritize resources for patients that require urgent care. Accurate risk assessment is an integral component of this prioritization process. Adjuvant studies such as MINDACT showed that up to 46% of clinically high risk tumors were classified as genomic Low Risk with MammaPrint, and still have excellent outcomes at 8-yrs with endocrine therapy alone, highlighting the potential for overtreatment if using clinical-risk alone. Here, gene expression results with MammaPrint (MP) and BluePrint (BP) were compared between pre-operative core needle biopsy (CNB) and postoperative surgical resection (SR) specimens to evaluate test performance across specimen type. Methods: 10,574 routine diagnostic samples from outside the US submitted to Agendia between Jan 2017 and Oct 2020 were included in this study.MP and BP testingwere processed according to standard FFPE microarray procedures. MP was used to stratify samples into Ultra LowRisk (UL), LowRisk (LR), and High Risk (HR). BPwas used to classify samples into Basal, Luminal or HER2-type. MP Index (MPI) distribution on BP defined Luminal-type tumors were compared between CNB and SR samples. Comparative “logistics metrics” (avg. turnaround time [TAT] and success rate) were also assessed between these specimen types. Results: 10% of samples were CNB and 90% were SR (Table 1). BP Basal, Luminal and HER2-type distributions were 2%, 97%, and 1% respectively for CNB samples and 1%, 98.6%, and 0.4% respectively for SR samples. Within Luminal-type tumors (majority of the samples), the frequency of UL, LR, and HR results were 14%, 61%, and 39% for CNB, and 13%, 58%, and 42% for SR, respectively. Overall, MP Index distributions were similar between samples tested from CNB vs. SR. Average TAT and success rate % between CNB and SR were similar (Table 2).(Table Presented)Definitions: Turnaround Time (TAT) is calculated from the time a specimen is received at the laboratory to the time a result is available. Success % excludes test failures due to insufficient RNA yield % and sub-optimal RNA quality, and evaluates the total number of specimens that have met the pre-requisite 30% minimum invasive tumor requirement that have a valid result. Conclusion(s): The frequency of each MP risk group as well as the distribution pattern of MP Index were essentially identical between CNB and SR samples, indicating comparable performance regardless of specimen type. With timely TAT and no meaningful difference in MPI distribution between CNB and SR specimens, pre-operative use of MP+BP genomic testing on CNB can be incorporated into the preoperative treatment decision making process. Conflict of Interest: Employee of Agendia, equity/stock ownership interest.