Whole genome sequencing as a ticket to cancer treatment in the Netherlands: Are inequalities in access to molecular diagnostics unfair?

Whole genome sequencing (WGS) of a tumour may sometimes reveal additional potential targets for medical treatment. Practice variation in the use of WGS is therefore a source of unequal access to targeted therapies and, as a consequence, of disparities in health outcomes. Moreover, this may even be more significant if patients seek access to WGS by paying a relatively limited amount of money out of pocket, and sometimes effectively buy themselves a ticket to (very) expensive publicly funded treatments. Should resulting unequal access to WGS be considered unfair? Drawing from current practice in the Dutch healthcare system, known as egalitarian, we argue that differences in employment of WGS between hospitals are the consequence of the fact that medical innovation and its subsequent uptake inevitably takes time. Consequently, temporal inequalities in access can be deemed acceptable, or at least tolerated, because and insofar as, ultimately, all patients benefit. However, we argue against allowing a practice of out-of-pocket payments for WGS in publicly funded healthcare systems, for four reasons: because allowing private spending favours patients with higher socio-economic status significantly more than practice variation between hospitals does, may lead to displacement of publicly funded health care, does not help to ultimately benefit all, and may undermine the solidaristic ethos essential for egalitarian healthcare systems.

Assessment of biological organ age using molecular pathology in pre-transplant kidney biopsies.

Organ shortage is a major challenge in kidney transplantation but the use of older donors, often with co-morbidities, is hampered by inconsistent outcomes. Methods of accurately stratifying marginal donor organs by clinical and histological assessment are lacking. To better understand organ variability, we profiled the transcriptomes of 271 kidneys from deceased donors at retrieval. Following correction for biopsy composition, we assessed molecular pathways that associated with delayed, and sub-optimal one-year graft function. Analysis of cortical biopsies identified an adaptive immune gene-rich module that significantly associated with increasing age and worse outcomes. Cellular deconvolution using human kidney reference single cell transcriptomes confirmed an increase in kidney-specific B and T cell signatures, as well as kidney macrophage, myofibroblast and fibroblast gene sets in this module. Surprisingly, innate immune pathway and neutrophil gene signature enrichment was associated with better outcomes. Thus, our work uncovers cellular molecular features of pathological organ ageing, identifiable at kidney retrieval, with translational potential.

High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment.

A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.

Breast cancer molecular diagnostics in Rwanda: a cost-minimization study of immunohistochemistry versus a novel GeneXpert® mRNA expression assay.

Objective: To compare the financial and time cost of breast cancer biomarker analysis by immunohistochemistry with that by the Xpert® STRAT4 assay. Methods: We estimated costs (personnel, location, consumables and indirect) and time involved in breast cancer diagnosis at the Butaro Cancer Centre of Excellence, Rwanda, using time-driven activity-based costing. We performed a cost-minimization analysis to compare the cost of biomarker analysis for estrogen receptor, progesterone receptor and human epidermal growth factor receptor-2 status with immunohistochemistry versus STRAT4. We performed sensitivity analyses by altering laboratory-specific parameters for the two methods. Findings: We estimated that breast cancer diagnosis in Rwanda costs 138.29 United States dollars (US$) per patient when conducting biomarker analysis by immunohistochemistry. At a realistic immunohistochemistry antibody utilization efficiency of 70%, biomarker analysis comprises 48.7% (US$ 67.33) of diagnostic costs and takes 33 min. We determined that biomarker analysis with STRAT4 yields a reduction in diagnosis cost of US$ 7.33 (10.9%; 7.33/67.33), and in pathologist and technician time of 20 min (60.6%; 20/33), per patient. Our sensitivity analysis revealed that no cost savings would be made in laboratories with antibody utilization efficiencies over 90%, or where only estrogen and/or progesterone receptor status are assessed; however, such operational efficiencies are unlikely, and more laboratories are pursuing human epidermal growth factor receptor-2 analysis as targeted therapies become increasingly available. Conclusion: Breast cancer biomarker analysis with STRAT4 has the potential to reduce the required human and capital resources in sub-Saharan African laboratories, leading to improved treatment selection and better clinical outcomes.

Informing variant assessment using structured evidence from prior classifications (PS1, PM5, and PVS1 sequence variant interpretation criteria).

PURPOSE: This study aimed to explore whether evidence of pathogenicity from prior variant classifications in ClinVar could be used to inform variant interpretation using the American College of Medical Genetics and Genomics/Association for Molecular Pathology clinical guidelines. METHODS: We identified distinct single-nucleotide variants (SNVs) that are either similar in location or in functional consequence to pathogenic variants in ClinVar and analyzed evidence in support of pathogenicity using 3 interpretation criteria. RESULTS: Thousands of variants, including many in clinically actionable disease genes (American College of Medical Genetics and Genomics secondary findings v3.0), have evidence of pathogenicity from existing variant classifications, accounting for 2.5% of nonsynonymous SNVs within ClinVar. Notably, there are many variants with uncertain or conflicting classifications that cause the same amino acid substitution as other pathogenic variants (PS1, N = 323), variants that are predicted to cause different amino acid substitutions in the same codon as pathogenic variants (PM5, N = 7692), and loss-of-function variants that are present in genes in which many loss-of-function variants are classified as pathogenic (PVS1, N = 3635). Most of these variants have similar computational predictions of pathogenicity and splicing effect as their associated pathogenic variants. CONCLUSION: Broadly, for >1.4 million SNVs exome wide, information from previously classified variants could be used to provide evidence of pathogenicity. We have developed a pipeline to identify variants meeting these criteria that may inform interpretation efforts.

The Molecular Microscope Diagnostic System: Assessment of Rejection and Injury in Heart Transplant Biopsies.

This review describes the development of the Molecular Microscope Diagnostic System (MMDx) for heart transplant endomyocardial biopsies (EMBs). MMDx-Heart uses microarrays to measure biopsy-based gene expression and ensembles of machine learning algorithms to interpret the results and compare each new biopsy to a large reference set of earlier biopsies. MMDx assesses T cell-mediated rejection (TCMR), antibody-mediated rejection (AMR), recent parenchymal injury, and atrophy-fibrosis, continually "learning" from new biopsies. Rejection-associated transcripts mapped in kidney transplants and experimental systems were used to identify TCMR, AMR, and recent injury-induced inflammation. Rejection and injury emerged as gradients of intensity, rather than binary classes. AMR was one-third donor-specific antibody (DSA)-negative, and many EMBs first considered to have no rejection displayed minor AMR-like changes, with increased probability of DSA positivity and subtle inflammation. Rejection-associated transcript-based algorithms now classify EMBs as "Normal," "Minor AMR changes," "AMR," "possible AMR," "TCMR," "possible TCMR," and "recent injury." Additionally, MMDx uses injury-associated transcript sets to assess the degree of parenchymal injury and atrophy-fibrosis in every biopsy and study the effect of rejection on the parenchyma. TCMR directly injures the parenchyma whereas AMR usually induces microcirculation stress but relatively little initial parenchymal damage, although slowly inducing parenchymal atrophy-fibrosis. Function (left ventricular ejection fraction) and short-term risk of failure are strongly determined by parenchymal injury. These discoveries can guide molecular diagnostic applications, either as a central MMDx system or adapted to other platforms. MMDx can also help calibrate noninvasive blood-based biomarkers to avoid unnecessary biopsies and monitor response to therapy.

Toward a More Just System of Care in Molecular Pathology.

Policy Points American health care policy must be critically assessed to establish the role it plays in sustaining and alleviating the health disparities that currently exist in molecular genetic testing. It is critical to understand the economic and sociocultural influences that drive patients to undergo or forgo molecular testing, especially in marginalized patient populations. A multipronged solution with actions necessary from multiple stakeholders is required to reduce the cost of health care, rebalance regional disparities, encourage physician engagement, reduce data bias, and earn patients' trust. CONTEXT: The health status of a population is greatly influenced by both biological processes and external factors. For years, minority and low socioeconomic patient populations have faced worse outcomes and poorer health in the United States. Experts have worked extensively to understand the issues and find solutions to alleviate this disproportionate burden of disease. As a result, there have been some improvements and successes, but wide gaps still exist. Diagnostic molecular genetic testing and so-called personalized medicine are just now being integrated into the current American health care system. The way in which these tests are integrated can either exacerbate or reduce health disparities. METHODS: We provide case scenarios-loosely based on real-life patients-so that nonexperts can see the impacts of complex policy decisions and unintentional biases in technology without needing to understand all the intricacies. We use data to explain these findings from an extensive literature search examining both peer-reviewed and gray literature. FINDINGS: Access to diagnostic molecular genetic testing is not equitable or sufficient, owing to at least five major factors: (1) cost to the patient, (2) location, (3) lack of provider buy-in, (4) data-set bias, and (5) lack of public trust. CONCLUSIONS: Molecular genetic pathology can be made more equitable with the concerted efforts of multiple stakeholders. Confronting the five major factors identified here may help us usher in a new era of precision medicine without its discriminatory counterpart.

Optimizing Vaginitis Diagnosis to Reduce Health Care Costs in Nonpregnant Women Utilizing Molecular Diagnostics.

Vaginitis is a common condition that affects women of reproductive age. Early and accurate diagnosis and identification of the causative agents (ie, fungi, protozoa, bacterial species, etc.) help to avoid incorrect treatment and subsequent visits that add costs and therapies, which increase overall health care utilization. A prior study by Kong et al presented a cost analysis demonstrating that women who received a nucleic acid amplification test (NAAT) on the day of their vaginitis diagnosis had significantly lower 12-month follow-up costs than women who received a direct probe (DP) test or women who received clinical evaluation without the use of a molecular test. This prior analysis included pregnant women, which may have influenced the findings. The objective of this analysis is to determine whether the exclusion of pregnant women from the study cohort impacts the previously observed NAAT cost-savings results. The current analysis adds evidence that nonpregnant women diagnosed with NAAT at their initial visit have significantly lower 12-month overall health care costs than women evaluated through DP or other clinical methods. This is an update to an article titled "Diagnostic Testing of Vaginitis: Improving the Value of Care," which was published on August 16, 2021 and is available at https://doi.org/10.1089/pop.2021.0143.

Alignment of Fellowship Training with Practice Patterns for Molecular Pathologists: A Report of the Association for Molecular Pathology Training and Education Committee.

In the two decades since Accreditation Council for Graduate Medical Education-accredited Molecular Genetic Pathology fellowships began, the field of clinical molecular pathology has evolved considerably. The American Board of Pathology gathered data from board-certified molecular genetic pathologists assessing the alignment of skills and knowledge gained during fellowship with current needs on the job. The Association of Molecular Pathology conducted a parallel survey of program directors, and included questions on how various topics were taught during fellowship, as well as ranking their importance. Both surveys showed that most training aligned well with the practice needs of former trainees. Genomic profiling of tumors by next-generation sequencing, bioinformatics, laboratory management, and regulatory issues were topics thought to require increased emphasis in training. Topics related to clinical genetics and microbiology were deemed less important by those in practice, perhaps reflecting the increasing subspecialization of molecular pathologists. Program directors still viewed these topics as important to provide foundational knowledge. Parentage, identity, and human leukocyte antigen testing were less important to both survey audiences. These data may be helpful in guiding future adjustments to the Molecular Genetic Pathology curriculum and Accreditation Council for Graduate Medical Education program requirements.

An Educational Assessment of Evidence Used for Variant Classification: A Report of the Association for Molecular Pathology.

The Association for Molecular Pathology Variant Interpretation Testing Among Laboratories (VITAL) Working Group convened to evaluate the Standards and Guidelines for the Interpretation of Sequence Variants implementation into clinical practice, identify problematic classification rules, and define implementation challenges. Variants and associated clinical information were provided to volunteer respondents. Participant variant classifications were compared with intended consensus-derived classifications of the Working Group. The 24 variant challenges received 1379 responses; 1119 agreed with the intended response (81%; 95% CI, 79% to 83%). Agreement ranged from 44% to 100%, with 16 challenges (67%; 47% to 82%) reaching consensus (≥80% agreement). Participant classifications were also compared to a calculated interpretation of the ACMG Guidelines using the participant-reported criteria as input. The 24 variant challenges had 1368 responses with specific evidence provided and 1121 (82%; 80% to 84%) agreed with the calculated interpretation. Agreement for challenges ranged from 63% to 98%; 15 (63%; 43% to 79%) reaching consensus. Among 81 individual participants, 32 (40%; 30% to 50%) reached agreement with at least 80% of the intended classifications and 42 (52%; 41% to 62%) with the calculated classifications. This study demonstrated that although variant classification remains challenging, published guidelines are being utilized and adapted to improve variant calling consensus. This study identified situations where clarifications are warranted and provides a model for competency assessment.

Enhancing Molecular and Cytogenetic Fellow Education With an Integrative Hematopathology/Molecular Genetic Pathology Joint Conference.

OBJECTIVES: To overcome the challenges associated with molecular and cytogenetic (MG) education in hematopathology (HP), a monthly joint HP/MG conference with specific curricular goals was established and evaluated by the participants. METHODS: All cases from the HP/MG conference over 56 months were reviewed. To assess the educational impact, a survey was distributed to current/former HP/molecular genetic pathology fellows and faculty. RESULTS: During the study period, a total of 252 cases covering MG testing considered important for HP fellowship training were presented. The 100 most recent cases since 2018 discussed findings of diagnostic (85%), prognostic (40%), or therapeutic (10%) importance. A broad range of technologies were discussed such as karyotyping, cytogenetic fluorescence in situ hybridization studies, microarrays, polymerase chain reaction-based tests, next-generation sequencing, and Sanger sequencing. Twenty-three (95.8%) of 24 survey respondents agreed that the conference achieved all of its goals, and all agreed it was worth implementing. CONCLUSIONS: This educationally based HP/MG conference supplements existing rotations, didactic presentations, and consensus case conferences and enhances MG education in HP without excessive time commitment or need for extensive in-house MG testing. It also contributes to enhancing HP knowledge among the MG faculty and fellows.

Contamination Assessment for Cancer Next-Generation Sequencing.

CONTEXT.­: The presence of allogeneic contamination impacts clinical reporting in cancer next-generation sequencing specimens. Although consensus guidelines recommend the identification of contaminating DNA as a part of quality control, implementation of contamination assessment methods in clinical molecular diagnostic laboratories has not been reported in the literature. OBJECTIVE.­: To develop and implement a method to assess allogeneic contamination in clinical cancer next-generation sequencing specimens. DESIGN.­: We describe a method to detect contamination based on the evaluation of single-nucleotide polymorphic sites from tumor-only specimens. We validate this method and apply it to a large cohort of cancer sequencing specimens. RESULTS.­: Identification of specimen contamination was validated via in silico and in vitro mixtures, and reference range and reproducibility were established in a panel of normal specimens. The algorithm accurately detects an episode of systemic contamination due to reagent impurity. We prospectively applied this algorithm across 7571 clinical cancer specimens from a targeted next-generation sequencing panel, in which 262 specimens (3.5%) were predicted to be affected by greater than 5% contamination. CONCLUSIONS.­: Allogeneic contamination can be inferred from intrinsic cancer next-generation sequencing data without paired normal sequencing. The adoption of this approach can be useful as a quality control measure for laboratories performing clinical next-generation sequencing.

Comparative pathology, molecular pathogenicity, immunological features, and genetic characterization of three highly pathogenic human coronaviruses (MERS-CoV, SARS-CoV, and SARS-CoV-2).

The last two decades have witnessed the emergence of three deadly coronaviruses (CoVs) in humans: severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There are still no reliable and efficient therapeutics to manage the devastating consequences of these CoVs. Of these, SARS-CoV-2, the cause of the currently ongoing coronavirus disease 2019 (COVID-19) pandemic, has posed great global health concerns. The COVID-19 pandemic has resulted in an unprecedented crisis with devastating socio-economic and health impacts worldwide. This highlights the fact that CoVs continue to evolve and have the genetic flexibility to become highly pathogenic in humans and other mammals. SARS-CoV-2 carries a high genetic homology to the previously identified CoV (SARS-CoV), and the immunological and pathogenic characteristics of SARS-CoV-2, SARS-CoV, and MERS contain key similarities and differences that can guide therapy and management. This review presents salient and updated information on comparative pathology, molecular pathogenicity, immunological features, and genetic characterization of SARS-CoV, MERS-CoV, and SARS-CoV-2; this can help in the design of more effective vaccines and therapeutics for countering these pathogenic CoVs.

Detección de SARS-CoV-2 en contactos estrechos asintomáticos de casos confirmados por diagnóstico molecular, provincia de Buenos Aires, Argentina / Detection of SARS-CoV-2 in asymptomatic close contacts of cases confirmed by molecular diagnosis, Buenos Aires province, Argentina

Resumen La detección de SARS-CoV-2 y su implicancia en el diagnóstico de COVID-19 han sido muy debatidas en la pandemia. El objetivo de este estudio fue evaluar el costo/beneficio de la detección de SARS-CoV-2 en contactos estrechos asintomáticos (CE) mediante el uso de distintas pruebas de diagnóstico molecular. Se estudiaron 51 CE de personas con diagnóstico de SARS-CoV-2 confirmado por RTqPCR, clasificadas por el umbral de ciclos (Ct) (<20, entre 20 y 30 y >30) en hospitales públicos de la provincia de Buenos Aires. Del total de contactos estudiados el 15,7% resultó confirmado para SARS-CoV-2; no hubo contactos positivos de casos con Ct>30. La cantidad de contactos positivos de casos con Ct<20 fue significativamente mayor que la de casos con Ct>20. Las muestras con Ct<20 se asociaron a una carga viral estimada de entre uno a cuatro órdenes de magnitud de diferencia con los rangos de Ct>20. Un 13,7% de contactos positivos fueron casos con Ct<20. De las muestras positivas confirmadas por PCR, correspondientes a la semana epidemiológica 1 de 2021 (SE1), sólo un 19,35% correspondían a muestras con Ct<20 y un 50,7% con Ct entre 20 y 30. Estos datos muestran un incremento de sólo un 3,7% de casos detectados. El esfuerzo por parte del sistema de salud pública para esta estrategia, con bajo poder predictivo, puede tener un efecto negativo para el cumplimiento del aislamiento de los contactos y podría generar una demora en los resultados de los casos sospechosos, sin aportar significativamente en el control de la pandemia.

Abstract The detection of SARS-CoV-2 and its implication in the diagnosis of COVID-19 have been highly debated in the pandemic. The objective of this study was to evaluate the cost/benefit of detecting SARS-CoV-2 in asymptomatic close contacts (CC) using different molecular diagnostic tests. A total of 51 CC of people with a diagnosis of SARS-CoV-2 confirmed by RTqPCR, classified by the cycle threshold (Ct) (<20, between 20 and 30 and >30), were studied in public hospitals in the Province of Buenos Aires. Of the total contacts studied, 15.7% were confirmed for SARS-CoV-2; there were no positive contacts of cases with Ct>30 positive. The number of positive contacts of cases with Ct<20 was significantly higher than that of cases with Ct>20. Samples with Ct<20 were associated with an estimated viral load of one to four orders of magnitude difference with Ct ranges >20. A total of 13.7% of positive close contacts were from cases with Ct<20. When studying positive samples with confirmed diagnosis by PCR, corresponding to 1 epidemiological week of 2021 (EW1), only 19.35% corresponded to samples with Ct<20 and 50.7% with Ct between 20 and 30. From these data it is shown that with the CC test only 3.7% of the cases were detected. The effort by the public health system for this strategy, with low predictive power, may have a negative effect on the fulfillment of the isolation of contacts and could generate a delay in the results of suspected cases, without contributing significantly to controlling the pandemic.

Resumo A detecção do SARS-CoV-2 e seu envolvimento no diagnóstico da COVID-19 têm sido muito discutidos durante a pandemia. O objetivo desse estudo foi avaliar a relação custo/benefício na detecção de SARSCoV- 2 em casos de contatos próximos assintomático (CP), por meio do uso de diferentes testes de diagnóstico molecular. Foram estudados 51 casos de CP de pessoas com diagnóstico de SARS-CoV-2 confirmado pelo RTqPCR, sendo classificados pelo limiar de ciclos (Ct) (<20, entre 20 e 30 e >30), em hospitais públicos da província de Buenos Aires. Do total de contatos estudados, 15,7% foram confirmados para SARS-CoV-2, não houve contatos positivos de casos com Ct>30. O número de contatos positivos de casos com Ct<20, foi significativamente maior que os casos com Ct>20. As amostras com Ct<20 foram associadas a uma carga viral estimada de uma a quatro ordens de magnitude de diferença com os intervalos de Ct>20. Dos casos positivos, 13,7% foram com Ct<20. Das amostras positivas confirmadas por PCR, correspondentes à semana epidemiológica 1 de 2021 (SE1), apenas 19,35% correspondiam a amostras com Ct>20 e 50,7% com Ct entre 20 e 30. Esses dados mostram incremento de apenas 3,7% de casos detectados. O esforço por parte do sistema de saúde pública para essa estratégia, com baixo poder preditivo, pode ter um efeito negativo no cumprimento do isolamento dos contatos e poderia gerar uma demora nos resultados dos casos suspeitos, sem contribuir significativamente para o controle da pandemia.

Yield and costs of molecular diagnostics on thyroid cytology slides in the Netherlands, adapting the Bethesda classification.

OBJECTIVE: To evaluate our institutional experience with molecular diagnostics (MD) on thyroid cytology smears, evaluate the costs and describe MD guided clinical management of indeterminate Bethesda III/V thyroid nodules. METHODS: We performed a retrospective review of 164 Bethesda III or V thyroid cytopathology reports subjected to MD from 2013 to 2020, that altered Bethesda classification or management. MD consisted of mutation and gene fusion analysis by next-generation sequencing (NGS) of morphologically analysed and selected cytological slides. Findings were modelled to nationwide data on Bethesda incidences from 'the Dutch Pathology Registry' PALGA, and costs were estimated. RESULTS: 82 of 164 cases received an upgrade in Bethesda class. Twenty cases changed from Bethesda III to IV/V, 62 from Bethesda III or V to VI, and 72 remained unaltered. We estimate net savings with implementing MD, by preventing 454 repeat cytology and 326 (diagnostic) hemithyroidectomies, to be at least 2 million Euro annually in the Netherlands. Per Bethesda III and V patient, net savings would be about 100 Euro and 4100 Euro, respectively. CONCLUSION: NGS-based MD on nucleic acids extracted directly from cytology slides is a feasible and cost saving tool for personalized management in indeterminate Bethesda III/V thyroid cytology. Based on the interpretation of our retrospective data, we assume that this approach results in less disease burden for the patient, reduced surgical interventions and complication risks, reduced sick leave, among others. Further evaluation of structural implementation of the presented approach in routine thyroid Bethesda III/V cytology in a prospective setting is warranted.

A Curriculum for Genomic Education of Molecular Genetic Pathology Fellows: A Report of the Association for Molecular Pathology Training and Education Committee.

Molecular genetic pathology (MGP) is a subspecialty of pathology and medical genetics and genomics. Genomic testing, which is defined as that which generates large data sets and interrogates large segments of the genome in a single assay, is increasingly recognized as essential for optimal patient care through precision medicine. The most common genomic testing technologies in clinical laboratories are next-generation sequencing and microarray. It is essential to train in these methods and to consider the data generated in the context of the diagnosis, medical history, and other clinical findings of individual patients. Accordingly, updating the MGP fellowship curriculum to include genomics is timely, important, and challenging. At the completion of training, an MGP fellow should be capable of independently interpreting and signing out results of a wide range of genomic assays and, given the appropriate context and institutional support, of developing and validating new assays in compliance with applicable regulations. The Genomics Task Force of the MGP Program Directors, a working group of the Association for Molecular Pathology Training and Education Committee, has developed a genomics curriculum framework and recommendations specific to the MGP fellowship. These recommendations are presented for consideration and implementation by MGP fellowship programs with the understanding that MGP programs exist in a diversity of clinical practice environments with a spectrum of available resources.

Quantitative assessment of HER2 gene amplification of breast cancer using droplet digital PCR.

We previously reported the usefulness of droplet digital polymerase chain reaction (ddPCR) for the assessment of Human epithelial growth factor receptor 2 (HER2) gene amplification in breast cancer using formalin-fixed and paraffin-embedded sections. In our previous study, we combined HER2/CEP17 ratio (HER2 gene signals to chromosome 17 signals) with ddPCR and tumor content ratio (TCR) of each sample and determined the HER2 status by adopting a two-dimensional chart. This "ddPCR-TCR method" showed a high concordance with conventional HER2 status. In this study, we updated our method to assess the HER2 status of breast cancer in a more quantitative manner. We combined obtained data of the ddPCR ratio [Rx ] and TCR [x]; we calculated "(Rx - 1)/x + 1" for 41 samples with primary breast cancer and named the value led by this formula as "eHER2 (estimated HER2/CEP17 ratio of a tumor cell)". eHER2 was equivalent to conventional in situ hybridization (ISH) HER2/CEP17 ratio in most cases. eHER2 and ISH ratio showed a strong correlation (Spearman rank correlation ρ = 0.70, p < 0.0001). The obtained results indicated that eHER2 is a potential tool for HER2 status diagnosis in breast cancer.

Mitigating Future Respiratory Virus Pandemics: New Threats and Approaches to Consider.

Despite many recent efforts to predict and control emerging infectious disease threats to humans, we failed to anticipate the zoonotic viruses which led to pandemics in 2009 and 2020. The morbidity, mortality, and economic costs of these pandemics have been staggering. We desperately need a more targeted, cost-efficient, and sustainable strategy to detect and mitigate future zoonotic respiratory virus threats. Evidence suggests that the transition from an animal virus to a human pathogen is incremental and requires a considerable number of spillover events and considerable time before a pandemic variant emerges. This evolutionary view argues for the refocusing of public health resources on novel respiratory virus surveillance at human-animal interfaces in geographical hotspots for emerging infectious diseases. Where human-animal interface surveillance is not possible, a secondary high-yield, cost-efficient strategy is to conduct novel respiratory virus surveillance among pneumonia patients in these same hotspots. When novel pathogens are discovered, they must be quickly assessed for their human risk and, if indicated, mitigation strategies initiated. In this review, we discuss the most common respiratory virus threats, current efforts at early emerging pathogen detection, and propose and defend new molecular pathogen discovery strategies with the goal of preempting future pandemics.

Whole exome sequencing in molecular diagnostics of cancer decreases over time: evidence from a cost analysis in the French setting.

OBJECTIVES: Although high-throughput sequencing is revolutionising medicine, data on the actual cost of whole exome sequencing (WES) applications are needed. We aimed at assessing the cost of WES at a French cancer institute in 2015 and 2018. METHODS: Actual costs of WES application in oncology research were determined using both micro-costing and gross-costing for the years 2015 and 2018, before and after the acquisition of a new sequencer. The entire workflow process of a WES test was tracked, and the number and unit price of each resource were identified at the most detailed level, from library preparation to bioinformatics analyses. In addition, we conducted an ad hoc analysis of the bioinformatics storage costs of data issued from WES analyses. RESULTS: The cost of WES has decreased substantially, from €1921 per sample (i.e. cost of €3842 per patient) in 2015 to €804 per sample (i.e. cost of €1,608 per patient) in 2018, representing a decrease of 58%. In the meantime, the cost of bioinformatics storage has increased from €19,836 to €200,711. CONCLUSION: This study suggests that WES cost has decreased significantly in recent years. WES has become affordable, even though clinical utility and efficiency still need to be confirmed.