Costs of genetic testing: Supporting Brazilian Public Policies for the incorporating of molecular diagnostic technologies

The development of a multiplex recombinase polymerase amplification reaction to detect the most common causative agents of eumycetoma

PURPOSE

Mycetoma is a neglected tropical disease that affects the subcutaneous tissue. The disease can be caused by over 90 different pathogens, including both bacteria (actinomycetoma) and fungi (eumycetoma). While diagnostic tools for eumycetoma causative agents are available, these are generally not well suited for use in endemic regions. This study aims to develop an isothermal based multiplex recombinase polymerase amplification reaction (RPA), that can be integrated in the diagnostic workflow of endemic regions.

METHODS

The RPA was designed targeting the Internal Transcribed Spacer (ITS) region to detect the presence of fungal DNA, and to differentiate between Madurella mycetomatis and Falciformispora senegalensis. The performance of the RPA was evaluated using 71 fungal isolates and five actinomycetes reference isolates. Furthermore, the limit of detection (LOD) was determined for the different probes in singleplex and multiplex.

RESULTS

The ITS probe was positive for all 71 fungal isolates with a mean detection time of 13.1 min. The M. mycetomatis and F. senegalensis probes were only positive for their respective targets, with a mean detection time of 9.3 and 7.6 min, respectively. No cross-reactivity was detected, and a limit of detection of 0.01 ng of fungal DNA was found. The costs of the RPA ranged from €1.56 to €10.03, depending on the workflow.

CONCLUSION

We developed a field-friendly multiplex RPA, that successfully detects fungal DNA and discriminates between M. mycetomatis and F. senegalensis. This tool holds promise for enhancing diagnostic capabilities in eumycetoma endemic regions, paving the way for improved patient management and treatment outcomes.

Operational Feasibility and Performance of mRPA Versus PCR for the Detection of HPV Types 16, 18, and 52 in Clinical Samples: An Exploratory Study

Purpose

This exploratory study investigates the feasibility and performance of multiplex Recombinase Polymerase Amplification (mRPA) compared to conventional Polymerase Chain Reaction (PCR) for the detection and genotyping of high-risk Human Papillomavirus (HPV) types 16, 18, and 52. Current PCR methods are widely used for HPV detection but are limited by the need for complex thermal cycling equipment and lengthy processing times, which restrict their use in low-resource settings. This study aims to evaluate whether mRPA can serve as a faster, simpler, and more accessible alternative for HPV screening in primary healthcare environments.

Methods

A total of 20 clinical samples from cervical swabs were tested using both mRPA and conventional PCR. The samples were preserved in ThinPrep® Specimen Collection fluid and stored at -20°C. mRPA reactions were conducted under isothermal conditions at 39°C for 30 minutes, while conventional PCR followed standard cycling protocols. Sensitivity, specificity, operational efficiency, and feasibility in low-resource settings were assessed and compared between the two methods. The study complies with the Declaration of Helsinki and was approved by the Ethics Committee of Faculty of Medicine, Universitas Indonesia.

Results

The mRPA demonstrated sensitivity and specificity that were lower than PCR, with detection rates of 100% for HPV 16, 80% for HPV 18, and 60% for HPV 52, compared to PCR's 100% across all types. Overall, mRPA achieved an overall sensitivity of 80% and specificity of 100%. However, mRPA significantly reduced the amplification time to 30 minutes and eliminated the need for thermal cyclers, highlighting its potential suitability for primary healthcare settings. The practical implications of mRPA's rapid turnaround time and simplified equipment requirements make it a promising tool for point-of-care applications in resource-limited environments.

Conclusion

The findings suggest that mRPA could serve as a viable alternative to conventional PCR for HPV genotyping, offering advantages in speed and simplicity. Although mRPA's diagnostic performance was lower than PCR, its operational benefits make it particularly suitable for use in resource-limited settings. Future research should focus on further optimization and validation to enhance mRPA's diagnostic accuracy and explore its integration with user-friendly detection platforms.

Cost analyses for malaria molecular diagnosis for research planners in India and beyond

BACKGROUND

Malaria elimination mandates early and accurate diagnosis of infection. Although malaria diagnosis is programmatically dependent on microscopy/RDTs, molecular diagnosis has much better diagnostic accuracy. Higher cost of molecular diagnoses is a recognized challenge for use at the point of care. Because funding is always a recognized constraint, we performed financial cost-analyses of available molecular platforms for better utilization of available budget.

METHODS

Two strategies were applied to deduce the cost per sample. Strategy 1 included recurring components (RC) in minimum pack size, and biologist's time whereas strategy 2 included only RC and non-recurring components and costs are calculated for sample sizes (1-1,000,000) to infer the sample size effect.

RESULTS

Spin column-based manual DNA extraction (US$ 3.93 per sample) is the lowest-cost method, followed by magnetic bead-based automated, semi-automated, and PCI-based manual method. Further, DNA extraction cost per sample via spin column-based manual method and semi-automated method decreases with an increase in sample size up to 10,000. Real-time PCRs are ~ 2-fold more economical than conventional PCR, regardless of sample size.

CONCLUSIONS

This study is the first for malaria to estimate systematic molecular diagnosis financial costs. Kit-based and automated methods may replace conventional DNA extraction and amplification methods for a frugal high-throughput diagnosis.

Integration of IFAST-based nucleic acid extraction and LAMP for on-chip rapid detection of Agroathelia rolfsii in soil

Agroathelia rolfsii (A. rolfsii) is a fungal infection and poses a significant threat to over 500 plant species worldwide. It can reduce crop yields drastically resulting in substantial economic losses. While conventional detection methods like PCR offer high sensitivity and specificity, they require specialized and expensive equipment, limiting their applicability in resource-limited settings and in the field. Herein, we present an integrated workflow with nucleic acid extraction and isothermal amplification in a lab-on-a-chip cartridge based on immiscible filtration assisted by surface tension (IFAST) to detect A. rolfsii fungi in soil for point-of-need application. Our approach enabled both DNA extraction of A. rolfsii from soil and subsequent colorimetric loop-mediated isothermal amplification (LAMP) to be completed on a single chip, termed IFAST-LAMP. LAMP primers targeting ITS region of A. rolfsii were newly designed and tested. Two DNA extraction methods based on silica paramagnetic particles (PMPs) and three LAMP assays were compared. The best-performing assay was selected for on-chip extraction and detection of A. rolfsii from soil samples inoculated with concentrations of 3.75, 0.375 and 0.0375 mg fresh weight per 100-g soil (%FW). The full on-chip workflow was achieved within a 1-h turnaround time. The platform was capable of detecting as low as 3.75 %FW at 2 days after inoculation and down to 0.0375 %FW at 3 days after inoculation. The IFAST-LAMP could be suitable for field-applicability for A. rolfsii detection in low-resource settings.

Cost-Efficient Detection of NTRK1/2/3 Gene Fusions: Single-Center Analysis of 8075 Tumor Samples

The majority of NTRK1, NTRK2, and NTRK3 rearrangements result in increased expression of the kinase portion of the involved gene due to its fusion to an actively transcribed gene partner. Consequently, the analysis of 5'/3'-end expression imbalances is potentially capable of detecting the entire spectrum of NTRK gene fusions. Archival tumor specimens obtained from 8075 patients were subjected to manual dissection of tumor cells, DNA/RNA isolation, and cDNA synthesis. The 5'/3'-end expression imbalances in NTRK genes were analyzed by real-time PCR. Further identification of gene rearrangements was performed by variant-specific PCR for 44 common NTRK fusions, and, whenever necessary, by RNA-based next-generation sequencing (NGS). cDNA of sufficient quality was obtained in 7424/8075 (91.9%) tumors. NTRK rearrangements were detected in 7/6436 (0.1%) lung carcinomas, 11/137 (8.0%) pediatric tumors, and 13/851 (1.5%) adult non-lung malignancies. The highest incidence of NTRK translocations was observed in pediatric sarcomas (7/39, 17.9%). Increased frequency of NTRK fusions was seen in microsatellite-unstable colorectal tumors (6/48, 12.5%), salivary gland carcinomas (5/93, 5.4%), and sarcomas (7/143, 4.9%). None of the 1293 lung carcinomas with driver alterations in EGFR/ALK/ROS1/RET/MET oncogenes had NTRK 5'/3'-end expression imbalances. Variant-specific PCR was performed for 744 tumors with a normal 5'/3'-end expression ratio: there were no rearrangements in 172 EGFR/ALK/ROS1/RET/MET-negative lung cancers and 125 pediatric tumors, while NTRK3 fusions were detected in 2/447 (0.5%) non-lung adult malignancies. In conclusion, this study describes a diagnostic pipeline that can be used as a cost-efficient alternative to conventional methods of NTRK1-3 analysis.

Availability of Genetic Tests in Public Health Services in Brazil: Data from the Brazilian Rare Diseases Network

INTRODUCTION

The Brazilian Policy for Comprehensive Care for People with Rare Diseases (BPCCPRD) was published in 2014, accrediting several reference centers and incorporating many genetic tests for the diagnosis of rare diseases (RDs). The Brazilian Network of Rare Diseases (RARAS) comprises more than 40 institutions that offer diagnosis and treatment for RDs in Brazil. This network includes Reference Services for Rare Diseases (RDRS), Reference Services for Newborn Screening (NSRS), and University Hospitals distributed in all Brazilian regions.

OBJECTIVE

The aim of the study was to map the availability and distribution of the BPCCPRD diagnostic procedures in the Brazilian Unified Health System through RARAS.

METHOD

Data were collected through a questionnaire on the Research Electronic Data Capture platform, with 22 questions regarding the availability of procedures. Thirty-seven coordinators from RARAS participating centers received the questionnaire link for participation by email from August/2020 to March/2021. All participating institutions ethically approved this project.

RESULTS

Of the 37 institutions, 23 (62.16%) offered cytogenetic tests, 20 (54.05%) offered molecular procedures, and 22 (59.46%) offered inborn errors of metabolism diagnostic tests. The Southern blot analysis, enzyme assays on cultured tissue and urinary organic acid tests had the highest outsourcing rate. On the other hand, the procedures most frequently performed on-site were bone marrow karyotype and long-term cultured karyotype. It was observed that 10 of the 37 centers (27%) did not provide access to investigated procedures (on-site or outsourced). The North and Midwest regions stood out in terms of the unavailability of such techniques in at least 40% of the evaluated institutions.

DISCUSSION AND CONCLUSION

This study reveals large discrepancies in the supply of diagnostic procedures in the Brazilian territory. Moreover, there is a broad collaboration between services through the outsourcing of multiple diagnostic techniques to address this issue. Finally, this work corroborates the importance of mapping services for the diagnosis and treatment of individuals with RDs to propose actions for the better supply and distribution of these procedures.

Clinical and genetic characterization and long-term evaluation of individuals with maturity-onset diabetes of the young (MODY): The journey towards appropriate treatment

AIMS

To describe the clinical and genetic characteristics and long-term follow-up of a cohort with maturity-onset diabetes of the young (MODY), and to evaluate how molecular diagnosis impacted on treatment.

METHODS

A large observational, retrospective, cohort study included individuals referred to the University of São Paulo's Monogenic Diabetes Unit between 2011 and 2020. Comprehensive clinical and genetic evaluations were performed.

RESULTS

Overall, 228 individuals (190 GCK-MODY and 38 HNF1A-MODY) were enrolled. Sixty-two different GCK gene mutations (5 novel) and 17 HNF1A gene mutations (2 novel) were found. Data were available on treatment status for 76 index individuals with GCK-MODY. Before molecular diagnosis, nutritional intervention alone was used in 41 cases (53.9%). After molecular diagnosis, this number increased to 72 (94.8%). Glycated haemoglobin (HbA_1c) remained stable over the 6-year follow-up period: 6.5% (47 mmol/mol) at the first and 6.3% (45 mmol/mol) at the final visit (p = 0.056). Prior to molecular diagnosis, 7/21 (33.3%) HNF1A-MODY individuals were using sulfonylurea compared to 17/21 (81%) after testing. After a median of 5 years on sulfonylureas, HbA_1c values improved from 7.5% (58 mmol/mol) to 6.5% (48 mmol/mol) (p = 0.006).

CONCLUSIONS

Molecular diagnosis resulted in appropriate adjustment of treatment in approximately 80% of participants with GCK-MODY or HNF1A-MODY.

Characterization of the adiponectin promoter + Cre recombinase insertion in the Tg(Adipoq-cre)1Evdr mouse by targeted locus amplification and droplet digital PCR

The Tg(Adipoq-cre)1Evdr mouse has become an important tool in adipose tissue biology. However, the exact genomic transgene integration site has not been established. Using Targeted Locus Amplification (TLA) we found the transgene had integrated on mouse chromosome 9 between exons 6 and 7 of Tbx18. We detected transgene-transgene fusion; therefore, we used droplet digital polymerase chain reaction to identify Cre copy number. In two separate experiments, we digested with BAMHI and with HindIII to separate potentially conjoined Cre sequences. We found one copy of intact Cre present in each experiment, indicating transgene-transgene fusion in other parts of the BAC that would not contribute to tissue-specific Cre expression. Cre copy number for Tg(Adipoq-cre)1Evdr mice can be potentially used to identify homozygous mice.

Molecular Identification of Trissolcus japonicus, Parasitoid of the Brown Marmorated Stink Bug, by Species-Specific PCR

The samurai wasp, Trissolcus japonicus (Ashmead), has been proposed as a biocontrol agent against brown marmorated stink bugs (BMSB), due to its ability to parasitize and kill BMSB eggs. However, the wasps' small size makes it challenging for those untrained in morphological identification to determine the wasps' species. To circumvent this problem, a molecular method was created to identify T. japonicus. The method uses species-specific primers, designed in this study, which target the variable region of the mitochondrial Cytochrome Oxidase 1 (CO1) locus. After confirming successful DNA extraction from samples, the PCR amplification using our primers produced 227-bp PCR products for all T. japonicus specimens and no amplification in other microhymenoptera candidates. Additionally, DNA from BMSB-parasitized eggs gave positive PCR amplification, while the control BMSB samples showed no amplification. This indicates that PCR with our primers specifically and sensitively differentiates T. japonicus specimens from other similar wasp species and discriminates between T. japonicus-parasitized and non-parasitized BMSB eggs. Finally, an in silico analysis of CO1 sequences demonstrated that our primers match the sequences of four different haplotypes of T. japonicus, indicating that our diagnostic method could potentially be applied to analyze T. japonicus populations throughout North America, Europe, and parts of Asia.

Are pathogenic BRCA1 mutations associated with parotid mucoepidermoid carcinoma? A case report

OBJECTIVES

To describe a patient with BRCA1 mutation, mucoepidermoid parotid, multiple breasts, and thyroid cancers.

CASE REPORT

A women was diagnosed at 33-years-age with a triple-negative breast cancer (right breast), at 43-years-age with a triple-negative breast cancer in left breast and at 53-years-age with a primary papillary-thyroid carcinoma. At 55-years-age, she was diagnosed with a primary mucoepidermoid carcinoma in right parotid, and concomitantly, her right nipple was affected by Paget's disease and a recurrent carcinoma in right breast (HR + /HER2 = 3 +). At 57-years-age, after the recurrence of a triple-negative breast cancer (left breast), a geneticist evaluated the patient's family history, including one stomach, one non-smoking-related lung, and two smoking-related laryngeal cancers. Genetic testing revealed a BRCA1 mutation (Chr17:41:251.867). The patient's daughter (a non-cancer patient) tested negative for the mutation. Both remain under medical supervision.

CONCLUSIONS

We suggest that BRCA1 mutations are associated with non-breast and non-ovarian cancers such as salivary gland cancer.

Costing Methods as a Means to Measure the Costs of Pharmacogenomics Testing

Clinical implementation of pharmacogenomics and personalized medicine interventions relies on addressing important financial aspects of the delivery of genetic testing to the patients, be it from public or private providers. Details on how to determine the cost items of the genetic testing are often limited. The goal of this study is to present a costing methodology in order to estimate and measure the costs as far as the technical process of pharmacogenomics testing is concerned. Moreover, an overall cost mindset strategy based on the selective genotyping workflow to guide specialized laboratories of interest effectively is provided. We particularly accounted for the resources consumed within the laboratory premises such as cost of reagents for DNA isolation, cost of consumables, cost of personnel, while costs associated with patient recruitment, blood sample collection and maintenance, administration costs in the hospital, and costs of blood sample shipment were not taken into consideration. Our article presents the first-time detailed information on a costing framework for pharmacogenomic testing that could be employed to laboratories involved in routine clinical implementation of pharmacogenomics.

A recombinase polymerase amplification-lateral flow dipstick assay for rapid detection of the quarantine citrus pathogen in China, Phytophthora hibernalis

Phytophthora hibernalis, the causal agent of brown rot of citrus fruit, is an important worldwide pathogen and a quarantine pest in China. Current diagnosis of the disease relies on disease symptoms, pathogen isolation and identification by DNA sequencing. However, symptoms caused by P. hibernalis can be confused with those by other Phytophthora and fungal species. Moreover, pathogen isolation, PCR amplification and sequencing are time-consuming. In this study, a rapid assay including 20-min recombinase polymerase amplification targeting the Ypt1 gene and 5-min visualization using lateral flow dipsticks was developed for detecting P. hibernalis. This assay was able to detect 0.2 ng of P. hibernalis genomic DNA in a 50-µL reaction system. It was specific to P. hibernalis without detection of other tested species including P. citrophthora, P. nicotianae, P. palmivora and P. syringae, four other important citrus pathogens. Using this assay, P. hibernalis was also detected from artificially inoculated orange fruits. Results in this study indicated that this assay has the potential application to detect P. hibernalis at diagnostic laboratories and plant quarantine departments of customs, especially under time- and resource-limited conditions.

Establishing Hematopoietic Stem Cell Transplant Unit in Resource Limited Setting: A Critical Analysis of Indian Council of Medical Research 2017 Guidelines

The scope and application of hematopoietic stem cell transplantation are increasing. With advancement in science and close cooperation of health centers, HSCT units are coming up in new developing and underdeveloped countries. India hosts many HSCT units and often provides financially viable option for HSCT to foreign patients as well. Recently Indian Council of Medical Research (ICMR) issued a guideline about HSCT unit in India. This review article discusses establishment of new HSCT unit in resource limited setting. Subsequent implication of ICMR guideline has been done.

Predictability of BRCA1/2 mutation status in patients with ovarian cancer: How to select women for genetic testing in middle-income countries

OBJECTIVES

To evaluate the accuracy of algorithms for predicting BRCA1/2 germ-line mutation carrier probability, and to identify factors that could improve their performance among Brazilian women with ovarian cancer (OC).

STUDY DESIGN

In this cross-sectional study, we enrolled patients (unselected for family history of cancer) undergoing treatment or follow-up for OC in a single centre in Brazil. Clinical and demographic data, including family history of cancer, were obtained. Blood samples were collected for genetic testing.

MAIN OUTCOME MEASURES

The entire coding sequence of BRCA1 and BRCA2 was evaluated for mutations. Mutation carrier probability was calculated using BOADICEA, BRCAPRO, Myriad and the Manchester score. Sensitivity, specificity, positive and negative predictive values, and area under the receiver operating characteristic curves (AUC) were calculated for each algorithm. Logistic regression was used to detect additional factors associated with BRCA1/2 status, and these were added to the algorithms before recalculating the AUCs.

RESULTS

BRCA1/2 mutations were identified in 19 of the 100 included patients. BOADICEA outperformed other algorithms (sensitivity, 73.7%; specificity, 87.7%; AUC, 0.87, with a threshold of a 10% risk of mutation). Later menarche was associated with the presence of a BRCA1/2 mutation. Although adding age at menarche resulted in a larger AUC for all models, this increase was significant only for the Myriad algorithm.

CONCLUSION

A BOADICEA risk evaluation of 10% or more most accurately predicted BRCA1/2 status, and the inclusion of age at menarche tended to improve the performance of all algorithms. Using these tools could reduce the number of tests, but at the expense of missing a significant proportion of mutation carriers.