Evaluation of Antinuclear Antibody and Subserology Reflex Testing for the Diagnosis of Systemic Autoimmune Rheumatic Disorders in an Academic Teaching Hospital

OBJECTIVE

The aim of this study was to examine appropriate utilization of antinuclear antibody (ANA) screening tests with follow-up subserology tests (reflex testing) for diagnosing systemic autoimmune rheumatic disorder (SARD).

METHODS

We conducted a retrospective chart review of 3003 SARD-test orders at an academic teaching hospital from January to December 2019. Testing patterns were categorized as American College of Rheumatology (ACR)-recommended reflex testing, panel testing, or single subserology testing. We described testing patterns, assessed their diagnostic accuracy, and explored factors associated with reflex testing.

RESULTS

Reflex testing accounted for 79.7% of SARD test-ordering, whereas improper testing (panel or single subserology) accounted for the other 20.3%. Reflex testing was associated with significantly more SARD diagnoses than improper testing (P = .004). Testing patterns were significantly associated with race/ethnicity (P = .008), with reflex testing being less frequent than improper testing in Hispanics and Whites.

CONCLUSION

In summary, one-fifth (20.3%) of testing patterns for suspected SARD did not follow the ACR-recommended guidelines for using reflex testing. Use of reflex testing was associated with an increased frequency of SARD diagnosis.

Increased diagnostic yield from negative whole genome-slice panels using automated reanalysis

We evaluated the diagnostic yield using genome-slice panel reanalysis in the clinical setting using an automated phenotype/gene ranking system. We analyzed whole genome sequencing (WGS) data produced from clinically ordered panels built as bioinformatic slices for 16 clinically diverse, undiagnosed cases referred to the Pediatric Mendelian Genomics Research Center, an NHGRI-funded GREGoR Consortium site. Genome-wide reanalysis was performed using Moon™, a machine-learning-based tool for variant prioritization. In five out of 16 cases, we discovered a potentially clinically significant variant. In four of these cases, the variant was found in a gene not included in the original panel due to phenotypic expansion of a disorder or incomplete initial phenotyping of the patient. In the fifth case, the gene containing the variant was included in the original panel, but being a complex structural rearrangement with intronic breakpoints outside the clinically analyzed regions, it was not initially identified. Automated genome-wide reanalysis of clinical WGS data generated during targeted panels testing yielded a 25% increase in diagnostic findings and a possibly clinically relevant finding in one additional case, underscoring the added value of analyses versus those routinely performed in the clinical setting.

Next-Generation Sequencing Panel Test in Myeloid Neoplasms and Evaluation with the Clinical Results

OBJECTIVE

Myeloid malignancies are heterogeneous disorders due to defective hematopoiesis and myeloid differentiation of hematopoietic stem/progenitor cell. The molecular landscape of the diseases is complex. Molecular alterations are used for classification and evaluation of prognosis and treatment. We aimed to evaluate the advantages of the next-generation sequencing panel testing in myeloid malignancies and clinical outcomes.

MATERIALS AND METHODS

We evaluated the results of 54 patients who underwent next-generation sequenc- ing myeloid panel testing, with fluorescent in situ hybridization (FISH), polymerase chain reaction results and the clinical outcomes. Target genes in the panel were ASXL1, CALR, CBL, CEBPA, CSF3R, DNMT3A, EZH2, FLT3, IDH1, IDH2, JAK2, KIT, KRAS, MPL, NPM1, NRAS, RUNX1, SETBP1, SF3B1, SH2B3, SRSF2, TET2, TP53, U2AF1, and ZRSR2.

RESULTS

Diagnoses were acute myeloid leukemia, essential thrombocytosis, polistemia vera, primary myelo- fibrosis, hypereosinophilic syndrome (HES), chronic myeloid leukemia, myelodysplastic syndromes, chronic myelomonocytic leukemia. Twenty-eight missense, 8 frameshift, 5 stop gain, and 3 in-frame mutations were detected. A double mutation was detected in JAK-2 with next-generation sequencing in the patient who was given a false negative result due to polymerase chain reaction limitation.

CONCLUSION

Screening multiple mutations simultaneously, is time and cost-effective. With the panel test, it is possible to determine the diagnosis, prognosis and targeted treatment options with a single test. Next- generation sequencing myeloid panel tests might be a powerful guide for clinicians.

Clinical utility of target capture-based panel sequencing in hematological malignancies: A multicenter feasibility study

Although next‐generation sequencing‐based panel testing is well practiced in the field of cancer medicine for the identification of target molecules in solid tumors, the clinical utility and clinical issues surrounding panel testing in hematological malignancies have yet to be fully evaluated. We conducted a multicenter prospective clinical sequencing study to verify the feasibility of a panel test for hematological tumors, including acute myeloid leukemia, acute lymphoblastic leukemia, multiple myeloma, and diffuse large B‐cell lymphoma. Out of 96 eligible patients, 79 patients (82%) showed potentially actionable findings, based on the clinical sequencing assays. We identified that genetic alterations with a strong clinical significance were found at a higher frequency in terms of diagnosis (n = 60; 63%) and prognosis (n = 61; 64%) than in terms of therapy (n = 8; 8%). Three patients who harbored a germline mutation in either DDX41 (n = 2) or BRCA2 (n = 1) were provided with genetic counseling. At 6 mo after sequencing, clinical actions based on the diagnostic (n = 5) or prognostic (n = 3) findings were reported, but no patients were enrolled in a clinical trial or received targeted therapies based on the sequencing results. These results suggest that panel testing for hematological malignancies would be feasible given the availability of useful diagnostic and prognostic information. This study is registered with the UMIN Clinical Trial Registry (UMIN000029879, multiple myeloma; UMIN000031343, adult acute myeloid leukemia; UMIN000033144, diffuse large B‐cell lymphoma; and UMIN000034243, childhood leukemia).

Cases and evidence for panel testing in cancer genetics: Is site-specific testing dead?

Historically in cancer genetic counseling, when a pathogenic variant is found which explains the cancers in the family, at risk family members are offered site-specific testing to identify whether or not they have the previously identified pathogenic variant. Factors such as turnaround times, cost, and insurance coverage all made site-specific testing the most appropriate testing option; however, as turnaround times and costs have substantially dropped and the recognition of double heterozygous families and families with nontraditional presentations has increased, the utility of site-specific testing should be questioned. We present four cases where ordering site-specific testing would have missed a clinically relevant pathogenic variant which raises the question of whether or not site-specific testing should be regularly used in cancer genetic testing.

Hereditary cancer testing challenges: assembling the analytical pieces to solve the patient clinical puzzle

Expanded genetic test utilization to guide cancer management has driven the development of larger gene panels and greater diversity in the patient population pursuing testing, resulting in increased identification of atypical or technically challenging genetic findings. To ensure appropriate patient care, it is critical that genetic tests adequately identify and characterize these findings. We describe genetic testing challenges frequently encountered by our laboratory and the methodologies we employ to improve test accuracy for the identification and characterization of atypical genetic findings. While these findings may be individually rare, 15,745 (9%) individuals tested by our laboratory for hereditary cancer risk had an atypical genetic finding, highlighting the importance of employing highly accurate and comprehensive methods in clinical genetic testing.

Application of Panel-Based Tests for Inherited Risk of Cancer

Next-generation or massively parallel sequencing has transformed the landscape of genetic testing for cancer susceptibility. Panel-based genetic tests evaluate multiple genes simultaneously and rapidly. Because these tests are frequently offered in clinical settings, understanding their clinical validity and utility is critical. When evaluating the inherited risk of breast and ovarian cancers, panel-based tests provide incremental benefit compared with BRCA1/2 genetic testing. For inherited risk of other cancers, such as colon cancer and pheochromocytoma-paraganglioma, the clinical utility and yield of panel-based testing are higher; in fact, simultaneous evaluation of multiple genes has been the historical standard for these diseases. Evaluating inherited risk with panel-based testing has recently entered clinical practice for prostate and pancreatic cancers, with potential therapeutic implications. The resulting variants of uncertain significance and mutations with unclear actionability pose challenges to service providers and patients, underscoring the importance of genetic counseling and data-sharing initiatives. This review explores the evolving merits, challenges, and nuances of panel-based testing for cancer susceptibility.

A Pilot Study of Clinical Targeted Next Generation Sequencing for Prostate Cancer: Consequences for Treatment and Genetic Counseling

BACKGROUND

Targeted next generation sequencing (tNGS) is increasingly used in oncology for therapeutic decision-making, but is not yet widely used for prostate cancer. The objective of this study was to determine current clinical utility of tNGS for prostate cancer management.

METHODS

Seven academic genitourinary medical oncologists recruited and consented patients with prostate cancer, largely with unusual clinical and/or pathologic features, from 2013 to 2015. UW-OncoPlex was performed on formalin-fixed, paraffin-embedded (FFPE) primary tumors and/or metastatic biopsies. Results were discussed at a multidisciplinary precision tumor board prior to communicating to patients. FFPE tumor DNA was extracted for tNGS analysis of 194 cancer-associated genes. Results, multidisciplinary discussion, and treatment changes were recorded.

RESULTS

Forty-five patients consented and 42 had reportable results. Findings included mutations in genes frequently observed in prostate cancer. We also found alterations in genes where targeted treatments were available and/or in clinical trials. 4/42 (10%) cases, change in treatment directly resulted from tNGS and multidisciplinary discussion. In 30/42 (71%) cases additional options were available but not pursued and/or were pending. Notably, 10/42 (24%) of patients harbored suspected germline mutations in moderate or high-penetrance cancer risk genes, including BRCA2, TP53, ATM, and CHEK2. One patient's tumor had bi-allelic MSH6 mutation and microsatellite instability. In total, 34/42 (81%) cases resulted in some measure of treatment actionability. Limitations include small size and limited clinical outcomes.

CONCLUSIONS

Targeted NGS tumor sequencing may help guide immediate and future treatment options for men with prostate cancer. A substantial subset had germline mutations in cancer predisposition genes with potential clinical management implications for men and their relatives. Prostate 76:1303-1311, 2016. © 2016 Wiley Periodicals, Inc.

External quality assessment of AFB smear microscopy performances and its associated factors in selected private health facilities in Addis Ababa, Ethiopia

Tuberculosis (TB) is still a public health problem in sub Saharan African countries. In resource-limited settings, TB diagnosis relies on sputum smear microscopy, with low and variable sensitivities, especially in paucibacillary pediatric and HIV-associated TB patients. Tuberculosis microscopy centers have several weaknesses like overworking, insufficiently trained personnel, inconsistent reagent supplies, and poorly maintained equipments; thus, there is a critical need for investments in laboratory infrastructure, capacity building, and quality assurance schemes. The performance of TB microscopy centers in the private health facilities in Addis Ababa is not known so far. The main objective of the study was to assess laboratory performance of acid fast bacilli (AFB) smear microscopy and its associated factors in selected private health facilities in Addis Ababa, Ethiopia. A cross-sectional study was conducted in 33 selected private health facilities of Addis Ababa, Ethiopia comprising 7 hospitals, 2 NGO health centers, 23 higher clinics and 1 diagnostic laboratory that provide AFB smear microscopy services. The study was conducted from January to April 2014. A total of 283 stained sputum smears were randomly collected from participant laboratories for blinded rechecking, 320 panel slides were sent to 32 microscopy centers to evaluate their performance on AFB reading, staining and reporting. Checklists were used to assess quality issues of laboratories. Data were captured, cleaned, and analyzed using SPSS version 16.0; χ(2) tests, kappa statistics were used for comparison purpose. P value < 0.05 considered statistically significant. Among the 32 participant laboratories, 2-scored 100%, 15 scored 80-95% & the remaining 15 scored 50-75% for overall proficiency test performance. There were 10 (3.15%) major errors and 121 (37.8%) minor errors. The sensitivity, specificity, PPV and NPV of panel reading by microscopy centers were 89%, 96%, 96%, and 90% respectively. Out of 283 randomly selected slides for blind rechecking, 11 (3.9%) slides interpreted falsely for AFB, with overall agreement of 97.5%, sensitivity of 88.4% and specificity of 99.3%. In terms of slide quality assessment, 71.6% of AFB slides were graded as good for evenness, cleanness, thickness, size, staining and labeling. The performance score for AFB slide evenness was 56.9% (161 slides) and for labeling quality was 90.8% (257 slides); having significant difference in slide quality (p value < 0.05). On-site evaluation indicated problems in terms of infrastructure, standard operating procedure, reagent quality; equipment maintenance, data management and training issues. Most of the health facilities had poor maintenance scheme for microscope (53.5%) and poor inventory management (25.0%) system. Microscopy centers that scored a proficiency of 75.5%; which is below the acceptable minimum score of 80% and an overall error rate of 3.9% for blinded rechecking needs attention. Moreover, there are gaps identified through on site assessment including poor SOP, reagent quality, equipment maintenance, data management & lack of updated training on AFB microscopy techniques, requiring a concerted effort to alleviate the bottle neck problems and strengthening the public private partnership to control TB.

Hereditary breast cancer: an update on risk assessment and genetic testing in 2015

The last 5 years have brought significant innovation and advancement in the genetics of breast cancer. This clinical opinion aims to summarize and update current approaches to the care of women at risk for a hereditary predisposition to breast cancer. Implications of the BRCA mutation and several other hereditary syndromes will be discussed. Risk assessment and criteria for referral to cancer genetic professionals as well as high-risk screening and prophylactic options will be reviewed. Finally, the newly available genetic cancer panels and implications of mutations in some of these lesser known genes will be discussed. As the field of cancer genetics continues to evolve, the education of medical students, residents, and faculty will be paramount to identify appropriate candidates for genetic counseling and testing in conjunction with cancer genetic professionals.

Use of panel tests in place of single gene tests in the cancer genetics clinic

Improved technology has made it possible to test for mutations within multiple genes simultaneously. It is not clear when these gene 'panels' should be used in the hereditary cancer setting. These analyses were intended to guide panel testing criteria. Offering hereditary panel testing as a first and final, 'single-tier', option was explored. A 'two-tiered' approach, in which panel testing is offered reflexively following stricter criteria, was then applied to the same data. Within our cohort of 105 patients, the single-tier approach was associated with a higher mutation detection rate (6.7% vs 3.8%) and variant of uncertain significance (VUS) rate (0.94 vs 0.23 average per person) compared to a two-tiered approach. Of the VUSs also identified in other patients by another lab, 53% were classified differently between laboratories. Individuals reporting African American race had more VUSs compared to other ancestry groups (p = 0.001). The test cost for a single-tier test was 21% more than a two-tiered approach. Single-tier panel testing was associated with higher mutation and VUS rates, and there is inconsistent classification of the VUS/low penetrant genes between laboratories.

Massively parallel sequencing for diagnosing clinically and genetically heterogeneous disorders

Massively parallel sequencing technology has great potential to identify the precise molecular causes of human disorders, which were once considered difficult to diagnose for either inherited Mendelian or oncological diseases. Besides being a valuable tool for gene discovery, this technology has also gained tremendous momentum in clinical molecular diagnostic laboratories. There are a wide variety of clinical applications recently developed to meet the clinical demands for personalized medicine. This article discusses these up-to-date massively parallel sequencing clinical applications and emphasizes various disorders that can be targeted, as well as some challenges faced in the process of implementing these assays in the clinical setting.