bluuebunny/crossref_metadata_2025 huggingface dataset:
MYOD1 c.365G>T, p.L122R Variant Detection by Droplet Digital PCR (ddPCR)
Authors: Lip V , Grimmett L , Diaz C , Cantave J , Yang W , Harris H , Tsai H K , Church A J , Harris M H
Published: October 2021

Introduction/Objective

Rhabomyosarcomas (RMS) are a group of skeletal muscle tumors that include embryonal, alveolar, pleomorphic, spindle cell/sclerosing subtypes (SC/SRMS). Spindle cell RMS occurs in both adult and pediatric populations, and is associated with either more aggressive or better clinical outcomes respectively. A recurrent hotspot variant in MYOD1, p.L122R (NM_002478.4 c.365G>T), has been described in SC/SRMS. The classification of this diagnosis is evolving, with VGLL2 and NCOA2 fusions defining the diagnosis in young children, and MYOD1 p.L122R defining the diagnosis in older children. The MYOD1 p.L122R variant seems to be associated with more aggressive disease, and may be increasingly used in risk stratification with intensification of treatment.

Methods/Case Report

A digital droplet PCR (ddPCR) assay was used to detect the MYOD1 p.L122R in DNA samples with RMS. Patients and controls were coded as positive or negative, and tested for association with clinical features and outcome.

Results (if a Case Study enter NA)

Known-positive cohort of samples was limited by the extreme rarity of this tumor. “Known-positive” status was established by confirmation of the variant with an external clinically-validated assay. The six known positive samples were assessed by ddPCR for the presence of MYOD1 L122R. The L122R variant was detected in all six variants for a sensitivity of 100%. DNA and/or TNA obtained from known wild-type FFPE and frozen material was assessed, for a total of nine unique samples (1 synthetic, 8 patient-derived). All 9 samples were wild- type, with no positive droplets detected, for a specificity of 100%.

Conclusion

Our MYOD1 c.365G>T, p.L122R variant detection by droplet digital PCR (ddPCR) assay is a robust, reproducible, specific and sensitive method to detect the MYOD1 hotspot mutation.
Evaluation of the siemens N Latex free light chain assay and comparison to Binding Site Freelite™ assay
Authors: Lin H
Published: October 2021

Introduction/Objective

The International Myeloma Working Group (IMWG) guidelines include serum free light chain (sFLC) level and κ/λ ratio as excellent indicators of clonality. The Binding Site Freelite ™ was the first FDA approved assay for quantitative measurement of sFLC, the assay was based on a mixture of polyclonal antibodies directed against a variety of FLC epitopes. The Siemens N-Latex assay employs a probe mixture of mouse monoclonal antibodies. Both assays can be run on nephelometers. We assessed the analytical performance of the N-Latex assays and compared it with the Freelite™ assays.

Methods/Case Report

Analytical accuracy, precision, reproducibility and linearity were evaluated according to the regulatory standards. Method comparison was performed with 220 clinical samples for statistic correlation and clinical concordance analysis.

Results (if a Case Study enter NA)

The N-Latex FLC κ and λ assays had coefficient variation of 1-5% with-in run and 3-8% between run precision. Accuracy was verified using assayed controls in the duration of 21 days. Within analytical measuring range, almost perfect linearity was achieved for both κ and λ FLC assays. In comparison study to Freelite™ with 220 clinical samples, good agreement in classification was observed for κ, λ and κ/λ ratio (Cohen’s κ 0.73, 0.82 and 0.87). Pearson correlation analysis showed correlation coefficient value r >0.90 for all the analytes.

Conclusion

The N-Latex FLC assay has good analytical performance, did not exhibit gross antigen excess and can be used in clinical practice. However, it showed markedly lower absolute values for κ/λ ratio compared with Freelite™. Our data demonstrated that although good clinical concordance between N-Latex and Freelite™ FLC assays was achieved, the absolute values from the two assay are not interchangeable. Further studies in modification of the assay-specific diagnostic (involved FLC/non-involved FLC) thresholds for smoldering multiple myeloma (SMM) and multiple myeloma (MM) are needed.
Initial Clinical Laboratory Response to COVID-19: A Qualitative Lookback at a Survey of Medical Laboratory Professionals
Authors: Baker D P , Jones A P , Edwardson K , Nunez-Argote L
Published: October 2021

Introduction/Objective

In this 2020 survey, the co-investigators of this study explored the experiences of medical laboratory professionals (MLPs) and their perceptions of the testing needs of clinical laboratories in the initial response to the COVID-19 pandemic. The responses gathered in this survey highlighted changes in the laboratory workforce and the impact on laboratory operations moving forward.

Methods/Case Report

This cross-sectional, anonymous, web-based survey of MLPs was conducted between April 29, 2020, and May 31, 2020. To recruit participants, ‘invitation to participate’ messages were posted using online forums and social media platforms (i.e. LinkedIn, Twitter). Furthermore, the survey link was shared with professional contacts and laboratory professional groups. The main source of recruitment was the membership of the American Society for Clinical Laboratory Science (ASCLS), which had more than 6,800 active members at the time of the study. Data provided from individuals who provided informed consent was included in the sample. The inclusion criteria for the survey were that participants self-identify as a current employee of a clinical laboratory whose usual employment involved participating in the diagnostic testing and providing of clinical laboratory test results using human specimens. The instrument gathered demographic data about participants and their workplace using 32 closed-ended questions with 8 questions containing branching that allowed for optional open-ended responses. This project was approved by the institutional review board at the University of Kansas Medical Center.

Results (if a Case Study enter NA)

Notably, there was an overall decrease in clinical laboratory testing and overtime work for laboratorians during the first months of the COVID-19 pandemic. Respondents noted a lack of pay increase during the pandemic; however, some received in-kind gifts and messages of support in recognition of their essential work. MLPs reported better (or unchanged) job satisfaction and morale in their respective workplaces.

Conclusion

The response to the testing needs by healthcare facilities and clinical laboratory leadership can influence the job satisfaction of MLPs, perceptions toward their work, and overall morale during the initial phase of the pandemic. Additionally, cost-reducing measures further shaped the perceptions of MLPs while impacting the operational efficiency of clinical laboratories.
Improving the pipeline for pathologists in Botswana
Authors: Kyokunda L , Souda S , Obeng R
Published: October 2021

Introduction/Objective

In the United States, there are approximately 39 pathologists per one million people. In contrast, there is only one pathologist per one million people in sub-Saharan Africa. This shortage of the pathologist workforce significantly impacts the quality of pathology and laboratory services that can be provided in Botswana.

Methods/Case Report

Root cause and SWOT analyses consisting of the major stakeholders including government officials and key leadership figures from the training university and national referral laboratories were conducted to identify areas within the training pipeline that can be improved. The educational structure, core competencies, clinical exposure and hands-on training, as well as retention and additional faculty were some of the areas in the pipeline identified for improvement.

Results (if a Case Study enter NA)

NA

Conclusion

The collaborative training program between Botswana and South Africa were strengthened and additional clinical training sites were incorporated into the training program. The core competencies required of residents were reviewed and additional resources were provided to current residents. The collaboration between Botswana and South Africa for residency and fellowship training was strengthened to include active participation of the head of Pathology at the University of Botswana on the educational curriculum committee. These implemented changes led to the successful advancement of four anatomic pathology residents from the didactic phase to the practical phase of their training. Furthermore, two pathologists were hired to support clinical diagnostics and the education of the pathology residents. In conclusion, a structured review of the educational pipeline and resources that included stakeholders that could effect change led to substantial improvement in the training program and workforce of pathologists in Botswana.
Multi-Health System Comparison of Outpatient Diagnostic Testing for Urinary Tract Infection
Authors: Windham A K , Whitted M , Brimhall B , Clark K , Podichetty A , Shifarraw S
Published: October 2021

Introduction/Objective

Comparisons of diagnostic test utilization for outpatient encounters across multiple health systems are uncommon. Such comparisons are helpful to establish baseline diagnostic testing patterns across health systems.

Methods/Case Report

Using the Vizient Clinical Database, we compared the number of clinical laboratory tests (CPT codes 80000-89999) and imaging studies (CPT codes 70000-79999) per outpatient encounter for patients with urinary tract infection (UTI, N=97,714) or dysuria (N=125,388). We employed primary ICD-10 codes for UTI (N39.0) and dysuria (R30.0, R30.9, R35.0, R39.15) to define each patient group. We measured the aggregate Clinical Resource Intensity Weight (RIW) per outpatient visit to quantify diagnostic resource consumption for each encounter. The RIW is based on the US Centers for Medicare and Medicaid Services (CMS) Ambulatory Payment Classification (APC) weights. CMS assigns an APC weight to each diagnostic test based on the geometric mean cost of each particular test. We compared diagnostic testing at 20 academically affiliated health systems across the United States (2017- 2019) with >500 annual outpatient visits for UTI and dysuria. We also examined two relevant tests: urinalysis (CPT codes 8100, 81001, 81002, 81003, 81005, 81007, and 81015) and basic urine culture (CPT code 87086) testing patterns.

Results (if a Case Study enter NA)

The mean number of laboratory tests was 4.30 tests (range 3.04-5.89) and 3.01 (range 2.41-3.86) for UTI and dysuria patients, respectively. Average laboratory RIW and quantity were moderately correlated with a mean RIW of 0.50 and 0.38 for UTI and dysuria patients, respectively. The mean number of imaging studies for each group was 0.26 (range 0.08-0.46) and 0.05 (range 0.01-0.14), respectively. Average imaging RIW and quantity were more highly correlated with a mean RIW of 0.52 and 0.11 for UTI and dysuria patients, respectively. UTI encounters averaged 0.78 (range 0.38-1.28) urinalysis tests and 0.65 (range 0.39-0.86) urine cultures. Dysuria patient visits averaged 0.77 (range 0.45-1.17) urinalysis tests and 0.58 (range 0.13-0.76) urine cultures.

Conclusion

There are significant differences in diagnostic tests and resource utilization between large health systems for patients with UTI and dysuria. These differences persist with specific test comparisons for urinalysis and urine culture.
Multi-Health System Comparison of Diagnostic Testing in Hospitalized Sepsis Patients
Authors: Brimhall B , Whitted M , Windham A , Podichetty A , Shifarraw S
Published: October 2021

Introduction/Objective

Comparisons of diagnostic testing across multiple health systems over multiple years are uncommon. Such comparisons would quantify variations in test use between health systems.

Methods/Case Report

Using the Vizient Clinical Database, we compared clinical laboratory and imaging utilization for hospitalized adult sepsis patients (N = 69,035) over three years (2017-2019) at 19 large academic-affiliated health systems across the United States. We used Medicare Severity Diagnosis Related Groups (MSDRG), employed by the US Centers for Medicare and Medicaid Services (CMS), and identified sepsis patients (MSDRG triplet 870/871/872). We stratified hospitalized sepsis patients by severity of illness (SOI) into high severity (MSDRG 870), moderate severity (MSDRG 871), and low severity (MSDRG 872) groups. SOI further categorizes patients within a diagnostic group, quantifying the extent of comorbid conditions and complications. We measured hospital length of stay (LOS), number of laboratory tests (CPT codes 80000-89999), and number of imaging studies (CPT codes 70000-79999). We divided the number of laboratory tests and radiology studies by mean hospital LOS (in days) to calculate laboratory tests and imaging studies per hospital day.

Results (if a Case Study enter NA)

Between health systems, lowest and highest values for laboratory and imaging utilization ranged from 50.1 to 141.3 tests per hospitalization and 1.4 to 7.2 studies per hospitalization, respectively. Differences in laboratory tests between health systems persisted after adjusting for SOI with low to high laboratory tests per hospitalization ranging from 127.8 to 405.7, 51.0 to 144.7, and 31.9 to 78.2, for high, moderate, and low SOI groups. Utilization ranges were smaller for imaging studies. After adjusting for hospital LOS, laboratory testing differences between health systems were more pronounced and with low and high laboratory test per day utilization of 6.5 to 24.3, 6.1 to 18.5, and 6.0 to 17.1, for high, moderate, and low SOI groups. Differences in radiology studies were not as pronounced after adjusting for LOS.

Conclusion

There is considerable variation among health systems in laboratory and radiology resource utilization for hospitalized sepsis patients. This variation persists, especially for laboratory testing, after adjusting for SOI and LOS.
Clinical Impact of Bleeding Time and Concordance with Platelet Function Analysis at a Single Academic Institution
Authors: Ly J T , Woo J
Published: October 2021

Introduction/Objective

Bleeding time (BT) was historically used as a screening test to evaluate in vivo primary hemostasis. However, various disadvantages of BT and development of tests such as the platelet function analysis (PFA) contributed towards a discontinuation of its use at many hospitals. As our institution continues to offer BT, we sought to determine the concordance rate of BT with other coagulation tests and its clinical effectiveness.

Methods/Case Report

BT tests from 2014 to 2020 at our institution were evaluated. Results from BT were compared with those from concurrently ordered PFA. A chart review was performed to analyze the effect of BT on patient outcomes, defined as determiningsurgical/medical management or changing the patient’s diagnosis.

Results (if a Case Study enter NA)

From 2014-2020, there were 71 BT orders. There were 22 concurrently ordered PFAs. BT and PFA results were concordant in 14 of 22 instances with 4 of 14 being abnormal while 10 of 14 were normal. In terms of clinical outcomes, after removing five cases from analysis for lack of data, BT had a significant clinical impact in 25 of 66 cases, 20 of 25 determining surgical/medicalmanagement and 5 of 25 changing the patient’s diagnosis. After the release of ASCP’s Choosing Wisely guidance on BT in 2014, the number of BT ordered dropped from 35 in 2014 to 13 in 2015.

Conclusion

At our institution, most BT orders were ordered to assess bleeding risk prior to procedures or to find a cause for bleeding of unknown origin; however, BT affected clinical outcomes in less than half of cases. BT and PFA generally correlated well. Following guidance published by professional groups, including ASCP’s Choosing Wisely, BT utilization saw a decrease.
Secondary sclerosing cholangitis: a lesser known side effect of pembrolizumab therapy
Authors: Taylor C , Reno M , Sharma D
Published: October 2021

Introduction/Objective

Immune check-point inhibitors have increasingly taken hold as mainstays of various cancer treatments, revolutionizing outcomes for individuals diagnosed with terminal malignancy. Hepatotoxicity is reported to occur in 2-10% patients, predominantly manifesting as a mixed cholestatic hepatitis pattern of injury. Cholangitis is a rare immune-mediated adverse event (irAE). We present a case of pembrolizumab-induced secondary sclerosing cholangitis presenting with multiple biliary strictures. Early recognition is crucial as these cases are resistant to treatment with steroids.

Methods/Case Report

82-year-old woman with recurrent, metastatic, high grade urothelial carcinoma status post cystectomy and neoadjuvant chemotherapy, presented with new onset obstructive jaundice (alkaline phosphatase 958 U/L, aspartate aminotransferase of 331 U/L, alanine aminotransferase of 422 U/L, and total bilirubin of 19.8 mg/dL) following two weeks of pembrolizumab therapy. MRCP suggested intrahepatic biliary ductal dilation. ERCP showed multiple strictures involving hepatic bifurcation, left, right and intrahepatic ducts with beaded intrahepatic bile ducts. Liver biopsy showed expanded portal tracts with mixed inflammatory infiltrate, extensive bile duct injury, neutrophilic cholangitis, ductular proliferation, and perivenular cholestasis (10% dropout) concerning for mechanical obstruction. CK7 did not show ductopenia and immunostain IgG4 was negative. All autoimmune work-up was negative. Liver enzymes continued to rise despite multiple therapeutic stents, drains, high-dose corticosteroids, ursodiol and mycophenolate mofetil. The patient died five months later.

Results (if a Case Study enter NA)

NA

Conclusion

Pemrolizumab-induced secondary sclerosing cholangitis is a rare, hence under-recognized, adverse effect of check point inhibitor-mediated hepatotoxicity. It is important to recognize this association, as it has limited benefit from steroid therapy. Our finding of pembrolizumab-related SC adds to the growing body of literature of immune check-point inhibitor-related hepatobiliary injury and calls for further characterization of PD-1/PD-L1 inhibitor SC and its clinical implications.
Cystic angiomatosis of the bone, liver, and spleen
Authors: Fleckenstein J , Milliken John T , Lee J S , Ballentine S J
Published: October 2021

Introduction/Objective

Cystic angiomatosis is a very rare entity characterized by multifocal cystic angiomatous lesions of the skeletal system, occasionally involving visceral organ systems. Clinical presentation and progression are extremely variable. Cases with liver involvement are even rarer, and have been described as invariably fatal. The pathogenesis of this disorder is poorly understood, and no treatments are currently available.

Methods/Case Report

A 24 year old man with history of polysubstance abuse and untreated hepatitis C presented with acute abdominal pain. Imaging revealed hepatosplenomegaly and multiple liver, spleen, and skeletal lesions. Differential diagnoses included metastatic disease, lymphoma, and infection. Apart from known untreated chronic hepatitis C, all infectious, autoimmune and hypercoagulability work-ups were negative. Biopsies of the liver and iliac bone lesions showed areas of benign-appearing vascular proliferation in a background of fibrosis. The vascular endothelial cells were positive for CD34 and CD31 but negative for D2-40. On follow-up approximately eight months later, the patient was asymptomatic.

Results (if a Case Study enter NA)

NA

Conclusion

Liver involvement by cystic angiomatosis is exceedingly rare and has been associated with increased mortality. This case provides an example of a patient with incidentally discovered cystic angiomatosis involving liver, spleen, and bone who remains asymptomatic at follow-up. Additional cases are required to understand the pathophysiology and disease course in this group of patients, and to investigate possible therapeutic targets.
Blood Culture Contamination in a Community Hospital- less than 2% is achievable
Authors: Bedi R , Atkinson J
Published: October 2021

Introduction/Objective

Blood cultures are commonly obtained to evaluate the presence of bacteria or fungal infection in a patient’s bloodstream. The presence of living microorganisms circulating in the bloodstream is of substantial prognostic and diagnostic importance. A positive blood culture indicates a reason for the patient’s illness and provides the etiological agent for antimicrobial therapy. Collection of blood culture is an exact process that requires time, the proper order of draw, and following of correct protocol. The busy Emergency department that requires multiple demands for nurse’s time, turnover of staff, rushing from one task to another can result in the improper collection and false-positive blood cultures. The national benchmark is set at 3% by the American Society of Clinical Microbiology (ASM) and The Clinical and Laboratory Standard Institute (CLSI). False-positive blood culture results in increased length of stay and unnecessary antimicrobial therapy, resulting in an increased cost burden to the hospital of about $5000 per patient.

Methods/Case Report

At our 150-bed community hospital, 26 beds Emergency Department, we have come a long way in reduction of our blood culture contamination rates from upwards of 4% to less than 2%, far lower than the national benchmark.

Results (if a Case Study enter NA)

NA

Conclusion

There are multiple devices available from various manufacturers claiming to reduce blood culture contamination. These devices do reduce blood culture (BC) contamination but at an added cost of the device. The rate of BC can be reduced and less than 3% is achievable by materials available in the laboratory. We have achieved this by providing training to every new staff by demonstration and direct observation, providing everything required for collection in a kit, using proper technique, the inclusion of diversion method that involves the aseptic collection of a clear tube before collecting blood cultures, and following up monthly on any false positive blood cultures.
ABO Blood Groups and COVID-19 Infection
Authors: Petersen J M , Jhala D
Published: October 2021

Introduction/Objective

There exists contradictory evidence in the literature that ABO blood group may have some impact on risk of COVID-19 infection. Some argue that the blood group A may confer a higher susceptibility to infection and thus be overrepresented in those who test positive for COVID-19, though other studies in the literature do not support this. Therefore, we present a regional Veterans Administration Medical Center’s (VAMC) experience early in the pandemic to provide a reference on blood group and risk of testing positive early in the pandemic for a veteran population.

Methods/Case Report

A retrospective review of all positive SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) was performed for all RT-PCR tests collected at a regional VAMC from March 17th, 2020 to May 20th, 2020 was performed to collect ABO blood group information. Patients with no known ABO blood group were excluded.

Results (if a Case Study enter NA)

There were 81 patients who tested positive for SARS-CoV-2 with a known ABO blood group during the study period. This group had an age range of 45 to 99, consisted of 80 males and 1 female, and was racially proportioned at 57 African Americans (70.3%), 2 Asian Americans (2.5%), 1 Hispanic American (1.2%), 20 Caucasian Americans (24.7%), and one of unknown race (1.2%). The blood group distribution among these 81 patients was as follows: 39 were O+ (48.1%), 3 were O- (3.7%), 15 were B+ (18.5%), 3 were AB+ (3.7%), 18 A+ (22.2%), and 3 were A- (3.7%).

Conclusion

Comparison with the known distribution of ABO groups in the general population reveals that the proportion of blood groups of those testing positive are similar. This provides support to the proposition that the ABO type may not predispose significantly to COVID-19 infection.
Evaluation of indeterminate SARS-CoV-2 results with repeat testing on an alternative platform
Authors: Lynn T , Martinez R M
Published: October 2021

Introduction/Objective

Accurate SARS-CoV-2 results are crucial for patient management and infection prevention. Result confidence decreases with low viral load because near the assay’s limit of detection (LOD), test results may alternate between positive and negative, as characterized by Poisson distribution for target analytes at low density. Low positive results may indicate past infection, early infection, a vaccinated individual with low level viral shed, or a false-positive result. EUA methods provide guidance on test interpretation, but laboratories should assess clinical accuracy. The purpose of this study was to assess clinical accuracy of specimens with low positive results.

Methods/Case Report

Respiratory specimens were tested by Cepheid Xpert® Xpress SARS-CoV-2 assay with positive results up to a Ct of 45. A low positive (defined as Ct ≥35), which could not be confirmed by Hologic Aptima® SARS-CoV-2 assay was reported as indeterminate and repeat testing recommended. Repeat testing occurred by Cepheid, Hologic, BioFire, Roche, or Quest assays. Retrospectively, final results were extracted from the LIS (Epic Beaker, Madison, WI, version May 2020) for 5-months (12/1/2020 to 5/31/2021), and chart review performed.

Results (if a Case Study enter NA)

A total of 19,969 tests were performed; 10.4% (n=2,083) were positive, 89% (n=17,728) negative, and 0.79% (n=158) indeterminate. Previous infection (up to 3 months prior) was documented in 18% (n=28) of indeterminate results and defined as true positive. Of remaining indeterminate results, 43% (n=68) had repeat testing as recommended by laboratory; 26% (n=18) were positive and 74% (n=50) were negative. The average number of days between indeterminate and negative result was 7.25 (range 1-38).

Conclusion

Result discordance occurred in < 1% of all samples, excellent agreement. For low positive samples, discordance was higher, as expected. It’s impossible to determine if negative results from the 50 repeat samples were false-positive by Cepheid or false-negative by other methods. In summary, 32% (50/158) of indeterminant samples did not repeat as positive. Overall concordance was high and results fluctuate when low virus is present. In absence of symptoms, we conclude repeat testing is not routinely recommended. Laboratories must recognize that normal variability occurs near assay LOD and must critically assess performance against other methods with similar LODs to fully assess performance of EUA methods.
Next generation sequencing identifies potential PARP inhibitor sensitive mutations
Authors: Humble R , Bossler A
Published: October 2021

Introduction/Objective

Poly ADP-ribose polymerase (PARP) inhibitors are a novel and important drug class targeting homologous recombination DNA repair defects (HRD) and have been approved for use in breast, pancreatic and ovarian cancers. Originally targeted for loss of function mutations in BRCA1 and BRCA2, many other genes are involved in the HRD pathway; Rimar et al detailed 19 DNA repair genes associated with homologous recombination and PARP inhibitor sensitivity. Our 214 gene NGS panel, Iowa Cancer Mutation Profile, includes BRCA1, BRCA2 and 15 other HRD pathway genes. We reviewed cases from the prior 12 months to determine the frequency of HRD7 pathway gene variants in various tumor types with potential PARP inhibitor sensitivity.

Methods/Case Report

Iowa Cancer Mutation Profile NGS test results from June 4, 2020 through May 7, 2021 were reviewed for variants involving ATM, ATR, BAP1, BLM, BRCA1, BRCA2, CDK12, CHEK1, CHEK2, FANCA, FANCC, FANCD2, MRE11A, NBN, PALB2, RAD51c and RAD51d, categorized as pathogenic, likely pathogenic or of unknown significance and had the tumor type identified. Additional chart review for PARP inhibitor therapy was performed in cases of breast, pancreatic, and ovarian cancer.

Results (if a Case Study enter NA)

A total of 599 cases were reviewed with 234 found to have variants in genes with possible PARP inhibitor sensitivity. Of these 2% (n=8) and 11% (n=43) of variants were categorized as pathogenic or likely pathogenic while most (n=334) were categorized as variants of unknown significance. The pathogenic and likely pathogenic variants included mutations in ATM (n=13), BRCA2 (n=12), BAP1 (n=8), FANCA (n=5), BRCA1 (n=4),

NBM (n=3), FANCD2 (n=2), ATR (n=1), CDK12 (n=1), FANCC (n=1), and RAD51d (n=1), and frameshift (n=19) and nonsense (n=19) alterations were most common. Non-small cell lung cancer was the most frequent tumor type identified (n=78). At this time no PARP inhibitors were identified for use in cases of breast (n=9), pancreatic (n=3) and ovarian cancer (n=33).

Conclusion

Review of our institutional results for mutations in HRD pathway genes identified possible PARP inhibitor sensitivity in 8% (46 of 599) of cases during the period of review in a wide variety of tumor types. Our results suggest that variants with possible sensitivity to PARP inhibitor therapy are frequently identified from many tumor types and should be a component of solid tumor mutation profiling.
Semi-automated validation and quantification of CTLA-4 in 90 different Tumor entities using multiple antibodies and artificial intelligence
Authors: Dum D , Blessin N C , Henke T L , Mandelkow T , Bady E , Raedler J , Simon R , Sauter G , Lennartz M , Wilczak W , Burandt E
Published: October 2021

Introduction/Objective

Introduction: CTLA-4 is an inhibitory immune checkpoint receptor and a negative regulator of anti-tumor T-cell function. This study aimed at a comparative analysis of CTLA-4+ entities. cells between different tumor

Methods/Case Report

Methods: To quantify CTLA-4+ cells, 4,582 tumor samples from 90 different tumor entities as well as 608 samples of 76 different normal tissue types were analyzed by immunohistochemistry in a tissue microarray format. Two different antibody clones (MSVA-152R and CAL49) were validated and quantified using a deep learning framework for automated exclusion of unspecific immunostaining.

Results (if a Case Study enter NA)

Results: Comparing both CTLA-4 antibodies revealed a clone dependent unspecific staining pattern in adrenal cortical adenoma (63%) for MSVA-152R and in pheochromocytoma (67%) as well as hepatocellular carcinoma (36%) for CAL49. After automated exclusion of non-specific staining reaction (3.6%), a strong correlation was observed for the densities of CTLA-4+ lymphocytes obtained by both antibodies (r=0.87; p<0.0001). The mean density of CTLA-4+cells was 674±1482 cells/ mm2 and ranged from 71±175 cells/mm2 in leiomyoma to 5916±3826 cells/mm2 in Hodgkin’s lymphoma. Within epithelial tumors, the density of CTLA-4+ lymphocytes were higher in squamous cell (421±467 cells/ mm2) and urothelial carcinomas (419±347 cells/ mm2) than in adenocarcinomas (269±375 cells/ mm2) and renal cell neoplasms (256±269 cells/ mm2). A high CTLA-4+ cell density was linked to low pT category (p<0.0001), absent lymph node metastases (p=0.0354), and PD-L1 expression in tumor cells or inflammatory cells (p<0.0001 each). A high CTLA-4/CD3-ratio was linked to absent lymph node metastases (p=0.0295) and to PD-L1 positivity on immune cells (p<0.0026).

Conclusion

Marked differences exist in the number of CTLA-4+ lymphocytes between tumors. Analyzing two independent antibodies by a deep learning framework can facilitate automated quantification of immunohistochemically analyzed target proteins such as CTLA-4.
Comparison of Abbott COVID-19 testing Platforms for timely results- CMCVAMC experience
Authors: Patel S , Petersen J M , Jhala D
Published: October 2021

Introduction/Objective

COVID-19 is a new disease, caused by the SARS-CoV-2 coronavirus capable of causing severe disease and death. The Alinity-m has a high throughput and random-access features that are not on the Abbott m2000, both of which had been validated and brought into clinical use for high throughput SARS-CoV-2 testing. The additional features of Alinity-m would be expected to improve turnaround time; however, there are no published reports in the English literature comparing the turnaround time between the Abbott m2000 and Alinity-m.

Methods/Case Report

A retrospective quality assurance search for all SARS-CoV-2 tests performed on the Abbott m2000 and Alinity-m (both Chicago IL) between February 1st 2021 to March 1st, 2021, to capture the turnaround time differences for the Abbott m2000 versus the Alinity-m for the month after the Alinity-m was brought into clinical service after validation.

Results (if a Case Study enter NA)

There was a total of 318 tests performed on the Abbott m2000 and 1329 tests performed on the Alinity-m during this time period. The average turnaround time on the Alinity was 6 hours, compared with 11 hours on the Abbott m2000. This difference was statistically significant by the t-test (p-value = <0.01). Both the optimized throughput and random-access features of the Alinity-m contributed significantly to this improvement.

The Alinity-m is capable of producing results within 115 minutes for the first specimen and then 3 minutes for each sequential specimen. On the other hand, the Abbott m2000 must be batched in limited 8-12 hour runs without random access capability. All the results were reported and communicated to the clinical teams, so the timely patient management can be administrated and surveillance of the same can be done in real time.

Conclusion

Alinity M has a significant advantage for a random access as well as improved TAT for detection of SARS-CoV-2, leading to prompt patient care and management.
Extraction-free rapid cycle RT-qPCR and extreme RT-PCR for SARS-CoV-2 virus detection
Authors: Lownik J C , Farrar J S , Way G , Martin R K
Published: October 2021

Introduction/Objective

Since the start of the coronavirus disease 2019 (COVID-19) pandemic, molecular diagnostic testing for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has faced substantial supply chain shortages and noteworthy delays in result reporting after sample collection. Supply chain shortages have been most evident in reagents for RNA extraction and rapid diagnostic testing. In this study, we explored the kinetic limitations of extraction-free rapid cycle RT-qPCR for SARS-CoV-2 virus detection using the commercially available capillary based LightCycler.

Methods/Case Report

We optimized reverse transcription and PCR under extraction-free and rapid thermocycling conditions utilizing hydrolysis probe-based detection methods using a Roche LightCycler.

Results (if a Case Study enter NA)

This protocol improves detection speed while maintaining the sensitivity and specificity of hydrolysis probe-based detection. Percentage agreement between the developed assay and previously tested positive patient samples was 97.6% (n= 40/41) and negative patient samples was 100% (40/40). We further demonstrate that using purified RNA, SARS-CoV-2 testing using extreme RT-PCR and product verification by melting can be completed in less than 3 minutes.

Conclusion

We developed a protocol for sensitive and specific RT-qPCR of SARS-CoV-2 RNA from nasopharyngeal swabs in less than 20 minutes, with minimal hands-on time requirements. Overall, these studies provide a framework for increasing the speed of SARS-CoV-2 and other infectious disease testing.
Intraoperative Assessment of IDH Mutation Status and Tumor Invasioni in Glioma
Authors: Brown H , Chen R , Cooks R , Garcia D , Chaichana K , Quinones-Hinojosa A , Jentoft M , Middlebrooks E
Published: October 2021

Introduction/Objective

Maximizing surgical resection in gliomas, while avoiding compromising non-infiltrated tissue, is associated with survival benefit. Current methodologies are suboptimal in providing rapid, intraoperative molecular characterization of tissue. We address this unmet need by using desorption electrospray ionization mass spectrometry (DESI-MS) for the intraoperative molecular assessment of gliomas.

Methods/Case Report

This prospective study uses intraoperative DESI-MS analysis of fresh tissue to evaluate IDH mutations via 2-hydroxyglutarate intensity and TCP via measurement of N-acetylaspartic acid (NAA) intensity and characteristic lipid profiles in less than three minutes. Blinded review of the tissue smears by a neuropathologist is used to validate IDH mutation status and TCP estimates.

Results (if a Case Study enter NA)

Presently, 529 biopsies from 85 enrolled patients have been collected and analyzed at two institutions. TCP assessment based on NAA intensity in 203 biopsies at the first institution yielded sensitivity, specificity, and accuracy values of 91, 76, and 83%, whereas TCP estimates via characteristic lipid profiles yielded 76, 85, and 81%, respectively. Assessment of IDH mutation status of 71 core biopsies yielded sensitivity, specificity, and accuracy values of 89, 100, and 94%. Ongoing validation of the methodology is being performed at a second institution, where we have collected 282 biopsies from 36 patients. IDH mutation assessment of the first 15 patients indicate 100% sensitivity, specificity, and accuracy.

Conclusion

This study represents the first and largest study using DESI-MS for the intraoperative evaluation of IDH status and TCP measurement in gliomas. Prospectively, we propose to modify our DESI-MS system to allow estimation of IDH mutation status and TCP in surgical cavities without the need for a biopsy by placing a surgical material along the margin and transferring material from the blot to a microscope slide prior to DESI-MS analysis. We envision molecular analysis by DESI-MS as a complementary technique to histopathology capable of providing additional clinical information in near real-time.
Assessment of Comprehensive Mutational Profiling in T-lymphoblastic leukemia/lymphoma (T-ALL/LBL): A Single Center Experience
Authors: Reddy N C , Reddy A C , Reddy K S
Published: October 2021

Introduction/Objective

T-lymphoblastic leukemia/lymphoma (T-ALL/LBL) is a malignancy arising from immature precursor T cells with T-ALL involving bone marrow/blood and T-LBL occurring in the thymus and nodal/extranodal sites. Studies have now revealed >100 recurrently altered genes that are not necessarily disease initiating but can provide diagnostic, prognostic, and predictive information which can then be utilized in personalized therapy.

Methods/Case Report

Next-generation sequencing was performed on DNA and/or RNA extracted from blood/marrow aspirates or tissue at an external CLIA-certified, CAP-accredited laboratory. The hematology panel sequenced DNA of 406 genes, introns of 31 gene rearrangements, and RNA of 265 genes.

This retrospective single-center study highlights salient findings noted in genomic profiles of 15 T-ALL/LBL cases out of 83 total patients with ALL from 2018-2021. While the majority were B-ALL cases, T-ALL accounted for 18%, and all but 1 case were pediatric patients (ages 9-21 years).

Results (if a Case Study enter NA)

In our pediatric cohort (14 patients; 9 males, 5 females), as in literature, NOTCH signaling was most frequently involved with NOTCH1 (50%) and FBXW7 (36%) mutations, followed by those in cell cycle process CDKN2A/2B (36%) and PTEN (28%) mutations. Other mutations: PHF6 (21%), BCOR and TAL1 (14%) each. The prognostic effect of mutations: NOTCH1 favorable, FBXW7 no effect but trend toward favorable when FBXW7 co-occurs with NOTCH1 while PTEN is unfavorable (3 patients had relapses). Some unusual or useful findings: a patient diagnosed initially as AML with aberrant CD3 was re-classified as early T-cell precursor ALL, supported by RELN mutation (occurs in 4% ETP-ALL). The adult with NOTCH1 and BCOR mutations in addition to BCR-ABL1 fusion was diagnosed as having T-ALL blasts with CML. We could not study detailed nuances in mutational profiles of T-ALL vs T-LBL with only 1 case of T-LBL showing FBXW7, PTEN, NF1, RB1, BCOR and NRAS mutations (latter is typically noted in pediatric T-LBL cases).

Conclusion

Clinical molecular testing in our pediatric T-ALL patients revealed gene alterations that provide refinement of diagnosis, prognosis, and risk stratification. It also contributes a useful data set for further analysis and potential use of clinically actionable therapeutic targets in some cases. Longer term follow-up incorporating therapy and outcomes information would be valuable.
Massive Perivillous Fibrin Deposition-A Cause of Recurrent Fetal Demise: A Case Report
Authors: Pandiri M , Kashikar R
Published: October 2021

Introduction/Objective

Massive perivillous fibrin deposition (MPFD) and maternal floor infarction (MFI) are rare placental lesions reported in less than 1% of all pregnancies and have a significant risk of recurrence ranging from 12% to 78%. MPFD/MFI is associated with high rates of adverse perinatal outcomes including preterm delivery, severe intrauterine growth restriction, spontaneous abortion, cystic renal cell dysplasia, fetal metabolic disease with reported mutations in the LCHAD (long-chain 3-hydroxy acyl-CoA-dehydrogenase) gene, neonatal death and long- term neurological impairment.

Methods/Case Report

We report a case of MFPD in a 28-year-old female gravida 3 para 1 with one uncomplicated pregnancy and one therapeutic abortion. The current pregnancy was complicated by abruption resulting in intrauterine fetal demise at 32 weeks of gestation. The placenta was examined. Grossly, the placenta weighed 260 grams (small placenta for the dates) with an eccentrically inserted three vessel umbilical cord and a diffuse, firm pale grey cut surface with focal cystic areas. The histological examination revealed MPFD characterized by extensive transmural perivillous fibrinoid material with encasement of almost entire chorionic villi (transmural type). The villi were viable but fibrotic with focal syncytiotrophoblastic necrosis and focal mild chronic inflammation. The etiology of MPFD is not well understood, but risk factors that have been reported include maternal thrombophilia, coagulopathies, and autoimmune diseases. Given the clinical associations, MFI/MPFD should be reported promptly to the obstetrician and pediatrician. As per the current literature, a combination of thrombolytic therapy (aspirin and heparin), intravenous immunoglobulin and a statin (pravastatin) helps to correct angiogenic/antiangiogenic imbalance which has been thought to be associated with recurrent MFI/MPFD.

Results (if a Case Study enter NA)

N/A

Conclusion

In summary, we present this rare recurring entity of MPFD to emphasize the awareness of this condition and the importance of placental examination in all abortions and fetal abnormalities/demise.
Mature tertiary lymphoid structures in lung adenocarcinoma are associated with better progression free survival
Authors: Obeng R , Parihar V , Alexis D , Behera M , Owonikoko T , Pillai R , Ramalingam S , Sica G , Ahmed R
Published: October 2021

Introduction/Objective

The presence of inducible lymphoid structures known as tertiary lymphoid structures in the tumor microenvironment has been shown to correlate with positive clinical outcome. However, the maturation states of lymphoid aggregates in lung adenocarcinoma are not completely understood.

Methods/Case Report

Seventy tumor samples from 69 patients diagnosed with lung adenocarcinoma (Stages I to III) between 2013 and 2015 were included in the study. The presence and maturation states of the lymphoid structures within the tumors were evaluated by conventional and 26 samples were further analyzed by multiplexed immunohistochemistry of formalin fixed paraffin embedded tissues and then quantified. Mature lymphoid follicles containing germinal centers were identified by the presence of CD21+ and BCL-6+ cells in an organized configuration within tight clusters of T and B cells.

Results (if a Case Study enter NA)

Samples with fully mature lymphoid structures (germinal centers) had larger tumors and higher disease stage. The number of mature lymphoid structures correlated with the total number of lymphoid aggregates present in the tumor microenvironment. Additionally, tumor samples with ≥10 mature lymphoid structures had more primary follicles. While there was no difference in overall survival, progression free survival was significantly longer in patients who had ≥10 mature lymphoid structures in comparison with patients who had <10 mature structures.

Conclusion

In conclusion, a spectrum of lymphoid aggregates in different stages of maturation are present in lung adenocarcinoma. An increase in the number of mature lymphoid structures may be associated with progression free survival in patients with lung adenocarcinoma.
Heterotopic Ossification in Benign and Malignant Renal Neoplasms
Authors: Badeti S , Deb P Q , Heller D , Fitzhugh V , Weiss R
Published: October 2021

Introduction/Objective

Heterotopic bone formation in renal neoplasms is a rare phenomenon. Ossification with or without marrow elements has been reported in both benign and malignant renal tumors. Due to its rarity, the epidemiological and clinical features of this finding are not well-documented. Herein, we have examined heterotopic ossification in renal neoplasms and summarized the epidemiological and clinical features of this entity.

Methods/Case Report

A database search on PubMed, Scopus, and Google Scholar was performed using a combination of proper search terms. Full article texts of all search results were reviewed with reference lists screened for additional articles matching the search criteria. The demographic details of the patients, disease characteristics, treatment, and outcomes were all extracted from full text articles and were summarized in a pre-standardized form. The inclusion criteria were set as any epithelial renal neoplasm with histological evidence of heterotopic ossification. A case of clear cell renal cell carcinoma (CCRCC) with heterotopic ossification diagnosed in our institution is included in the study.

Results (if a Case Study enter NA)

A total of 30 cases were found of renal neoplasms with bone formation. The majority of patients were between the ages of 40 to 60. The male to female ratio was 1:1. The majority (19/30) were histologically diagnosed as CCRCC, the most common subtype of kidney tumor with a few cases diagnosed as chromophobe RCC (4/30), papillary RCC (3/30), and cystic nephroma (2/30). Of the neoplasms reported, tumor size varied from 3.0 cm to 28.8 cm.

Conclusion

Heterotopic ossification of renal neoplasms often presents a diagnostic challenge to the radiologist as other benign conditions such as extramedullary hematopoiesis can be in the differential. The rarity of this phenomenon renders pre-surgical diagnosis difficult. Our study documents this phenomenon to be seen in a variety of renal neoplasms and underscores the necessity to be aware of this rare entity.