Molecular Testing Research Articles

Molecular Tumor Testing on Colorectal Adenocarcinoma Specimens in a Large Community-Based Healthcare System.

This study aimed to describe the adherence of National Comprehensive Cancer Network guidelines to perform genetic screening for all colorectal cancer (CRC) specimens with molecular tumor testing, eg, immunohistochemical (IHC) testing, in a large community-based healthcare setting. The study also identified trends involving characteristics of CRC, individual reporting physician, and physician location and examined the potential impact of these trends on the performance of molecular tumor testing. This was a retrospective, multi-center study using a centralized pathology database to assess molecular testing on CRC specimens. The primary endpoint was whether tumor testing of a CRC specimen was performed. Secondary endpoints included tumor location within the colon (ie, the right or left side), year of CRC diagnosis, and location of the pathologist within the Advocate Aurora Health (AAH) system. The data were collected from 2016 to 2020. A total of 2469 CRC cases, reviewed by 47 pathologists practicing in five separate hospitals, were identified within the AAH system for the selected five-year time period. IHC testing was performed in 1666 of these specimens (67.5%). There was no statistical difference between CRC sidedness and IHC testing performed (p = 0.9). There were no discernible features or trends for the ordering of IHC testing among different pathologists. Molecular tumor testing for CRC specimens in this large community-based healthcare setting was inconsistent and below the ideal adherence rate of 100%. Secondary findings offered neither explanation nor trends in likelihood to send samples for IHC testing. Education would be beneficial for pathologists and all physicians who care for patients with CRC in community-based health care settings.

Molecular Testing Prevents Overdiagnosis of Epithelioid Hemangioma

Abstract Introduction/Objective Epithelioid hemangiomas (EH) are mostly solitary benign vascular tumors commonly involving the dermal and subcutaneous areas of the head and neck. However, reports of multifocality are increasing, specially in same anatomic region. Some reported cases of EH show morphologic features that may mimic malignant vascular tumors such as hemangioendotheliomas or angiosarcomas. However, there are no reported overlaps in the molecular characteristics of these tumors. We describe a multifocal EH with atypical features, suspicious for angiosarcoma, which needed molecular testing to resolve the diagnosis. Methods/Case Report The patient is a previously healthy 42-year-old male with a 5-month history of multiple growing painless penile nodules. Biopsy of one of the nodules was done. Histologic examination showed multifocal dermal- based ill-circumscribed nodules with interspersed inflammatory infiltrates and focal areas of necrosis. Tumor periphery shows vasoformative growth with intraluminal and extravasated red blood cells. Neoplastic cells were large and ovoid with abundant eosinophilic cytoplasm, large vesicular pleomorphic nuclei and prominent nucleoli. Immunohistochemical stains showed strong expression of ERG, FLI-1, and CD31 and negativity for AE1/AE3, CD34, HHV8 and EMA. The morphologic and immunohistochemical features of the specimen showed significant overlap of two primary differential diagnoses - epithelioid angiosarcoma and epithelioid hemangioma. Ultimately, molecular testing revealed ZFP36-FOSB fusion, confirming the diagnosis of EH. Results (if a Case Study enter NA) NA Conclusion Differentiating benign and malignant epithelioid vascular neoplasms can sometimes be challenging. There can be overlap in terms of architectural variety, presence of necrosis, vasoformation, inflammatory cell components and cytologic features, especially in EH with atypical features and epithelioid angiosarcoma (EA). Both of these tumors show positive immunoreactivity for CD31, CD34, FLI1 and ERG, and negativity for most keratins. Currently, the most reliable way to distinguish each tumor is molecular testing, with EH having FOS/FOSB rearrangements and EA with MYC or FLT4 amplification. Benign and malignant epithelioid vascular tumors can be indistinguishable morphologically and immunohistochemically. Molecular tests can help differentiate these neoplasms to better tailor patient management.

Genotyping for Weak and Partial D Rh Status to Optimize Usage of Limited Blood Supplies

Abstract Introduction The Rh antigen group, expressed on erythrocytes and encoded by highly polymorphic RHD and RHCE genes on chromosome 1 (1p36-p34), is notable in transfusion medicine due to its high polymorphism, strong immunogenicity and ability to cause hemolytic transfusion reactions in patients and hemolytic disease of the fetus and newborn (HDFN). The D antigen specifically contains multiple epitopes with variations that include decreased expression (weak D) or loss of certain epitopes (partial D) which expose patients to risk of alloimmunization depending on the subtype of the Rh(D) antigen. Hence, serologic weak D testing followed by molecular testing is not performed except for donors testing negative for Rh(D) antigen and newborns typing negative for Rh(D) and born to Rh(D) negative mothers. Given the current shortages of blood supplies, understanding patients’ genotypes in the context of weak or partial D-typing and risk of alloimmunization can be essential in the management of increasingly limited supplies of red blood cell (RBC) units. Objective To further characterize patients that initially type negative for Rh(D) but positive for weak D with molecular testing to investigate risk of alloimmunization, retype the Rh(D) and avoid unnecessary use of Rh(D) negative RBC units during critical shortages of RBC units. Methods We collected the results of ABO/Rh(D) typing for patients with negative Rh(D) testing but positive weak D test over a period of four weeks in December 2023 and had D-variant molecular testing performed by a reference laboratory. Initial serologic ABO/Rh(D) was performed in tube followed by weak D testing by indirect Coombs test in tube. Results The total number of patients who initially tested negative for Rh(D) but positive (weak to +4) for weak-D was three patients. Two patients showed a probable genotype of RHD*01W.1 (RHD* weak type 1, 809T>G (V270G)) homozygous which indicated the presence of weak D+ type 1. Patients with weak D+ type 1 can receive Rh(D) positive red cell units, and they are not at risk of alloimmunization and developing anti-D. The third patient showed a probable genotype RHD*DVI type 2 homozygous (lack of Rh(D) exons 4 through 6) and indicated the presence of partial D antigen. Patients with partial D antigen should receive RH(D) negative red cell units as they are at risk of alloimmunization and developing anti-D. Conclusions Although the vast majority of Transfusion Medicine services do not perform the serologic weak D test with reflex to molecular testing, characterizing patients who test negative with initial serologic Rh(D) testing with serologic and molecular D-tests may aid in retyping the Rh(D) of patients during critical shortages, particularly for patients with ABO blood group O.

A Case Report of Congenital Wilms’ Tumor and a Comprehensive Literature Review highlighting the spectrum between Wilms’ Tumor and Nephroblastomata’s

Abstract Introduction/Objective Wilms’ Tumour (WT) represents the most frequently encountered malignant renal neoplasm within pediatric pathology. To delineate the histopathological features of WT with perilobar nephrogenic rests (PLNR) and intralobar nephrogenic rests (ILNR) from nephroblastomatosis, we report a case with literature review to evaluate the clinical implications of WT with or without nephrogenic rests (NR), and nephroblastomatosis. Methods/Case Report Our patient is a 2-week-old neonate with VACTERL, germline mosaic triple X, and stage 1 WT with PLNR and substantial ILNR. The management approach involved radical nephrectomy exclusively. Obtaining a unifying clinical syndrome as well as deciding between WT or nephroblastomatosis was challenging in this case. The molecular testing with VACTERL panel was indeterminate and WT panel revealed DIS3L2 mutation that is indeterminate but likely pathogenic. She has been stable for 12 months and placed on 4-monthly left kidney ultrasound surveillance. Results (if a Case Study enter NA) Our literature review showed that the most common histologic subtype in WT patients without NR (n=59) and with NR (n=33) were classic triphasic (28.8%) and stromal-predominant (39.3%), respectively. WT patients with or without NR, underwent radical nephrectomy followed by adjuvant chemotherapy. Loss of heterozygosity (LOH) in TRIM28 was 4-fold higher in cases with NR. Mortality and relapse rates (12.5%) were higher in non-NR cohort. Conversely, nephroblastomatosis patients (n=14) underwent neoadjuvant chemotherapy, ipsilateral radical nephrectomy, and contralateral nephron-sparing surgery. Nephroblastomatosis patients had higher mortality (22.2%) and relapse rate (30%), with no identifiable mutations on molecular testing. Conclusion WT patients with NR have an earlier diagnosis and lower mortality and relapse rates compared to those without NR. The higher frequency of LOH in TRIM28 in WT patients with NR warrants future exploration to assess its implication in progression free survival. Nephroblastomatosis exhibits higher mortality and relapse rates, emphasizing the importance of reporting nephroblastomatosis in co-existing WT cases.

Clinical Validation and Comparison of Bacterial Vaginosis Detection

Abstract Introduction/Objective Bacterial vaginosis (BV) is considered a top reason for women’s gynecological visits, causing symptoms such as vaginal discharge, foul odor, itching, and burning associated with the alteration of the normal vaginal microbiome. It is often presented as a decrease in Lactobacillus spp. and an increase in anaerobic organisms such as Gardnerella vaginalis and Atopobium vaginae. In response to the demand for more automated and less subjective testing, molecular methods have recently been developed to aid in BV testing. The objectives of this study are to validate and compare the molecular Aptima® Bacterial Vaginosis Assay by Hologic® to the established BV Screen via a Gram stained vaginal smear graded through Nugent scoring at RUSH University Medical Center in Chicago, IL and perform a cost analysis between the testing methods. Methods/Case Report Samples of known BV value were tested on the Panther® instrument to validate the Aptima® Bacterial Vaginosis Assay for accuracy and precision. Clinical samples of vaginal swabs were used to make a Gram stained BV screen for Nugent scoring, then afterwards were placed into Hologic Multitest Aptima® probes for molecular testing on the Panther® instrument. Nugent scoring was performed blind by the molecular test. Molecular results of negative, positive, and invalid were then compared to the Nugent scores: scores of 0-3 for negative/normal vaginal flora, 7-10 for positive BV, and 4-6 for intermediate/altered scores were screened for discrepancy. Results (if a Case Study enter NA) The Aptima® BV Assay tested 52 known samples with 97% accuracy and 100% precision. A total of 80 clinical samples of vaginal swabs used for Gram stained BV screens were run on the Aptima® BV Assay; 61 provided conclusive data for comparative analysis. When compared to the original Nugent scores, the positive percent agreement (PPA) was 77.0% and negative percent agreement (NPA) was 92.9%. Conclusion The Aptima® BV Assay proved to be both accurate and precise in its validation testing. Clinically, it was able to screen for BV in vaginal samples with a good percent agreement to Gram stained BV screens. Further testing of additional clinical samples are to be done to continue analysis. Although the supplies needed to perform a Gram stain cost less than molecular testing, the reimbursement payment for molecular testing is much greater and overall reduces employee time costs for performing the test, making it the more cost effective choice for the laboratory.

Targeted microscopic rare cell retrieval yields sufficient deoxyribonucleic acid for molecular testing in fixed tissue with low tumor fraction

Abstract Introduction/Objective DNA extracted from formalin-fixed paraffin-embedded tissue (FFPE) blocks is often utilized for molecular oncologic testing. Cases with low tumor fraction often fail to obtain adequate tumor for molecular testing. We hypothesized that targeted retrieval of visualized tumor cells from FFPE sections, including those with low tumor fraction, could yield sufficient DNA for molecular testing. Methods/Case Report Unstained sections of various thicknesses were cut from low tumor fraction blocks and visualized by light microscopy and the RareCyte CyteFinder II (Seattle, WA). Microscopic cell retrieval was performed on the RareCyte using 40 µm diameter needles from identified regions of interest. Samples were deparaffinized using Zymo Research (Tustin, CA) solution, and digested and purified using Zymo-Spin Column technology. Sample DNA was quantified with NanoDrop Spectrophotometer (Chino, CA). Results (if a Case Study enter NA) Regions of interest were morphologically identifiable on 4-10 µm thick sections and harder to visualize on 12 µm thick sections. Targeted microscopic cell retrieval was performed with 40 µm diameter needles. Retrieval was performed from 26 to 34 regions of interest per sample and pooled for molecular testing. Samples (n=4) yielded a mean of 81.0 ng of DNA ± 18.4 ng (1.8 ng/µL ± 0.4 ng/µL) and a median of 87.75 ng (1.95 ng/µL). Conclusion Targeted microscopic cell retrieval from low tumor fraction FFPE slides using the RareCyte CyteFinder II can provide sufficient DNA material for molecular testing. Application of this technology has the possibility of recovering sufficient tumor DNA for molecular testing from specimens that may be deemed unsuitable for molecular testing according to current standards. We aim to focus on increasing sample size and completing comprehensive molecular analysis as we continue to expand this work.

Diagnostic workup of triple hit lymphoma by fine needle aspiration

Abstract Introduction/Objective Triple-hit lymphomas (THL) represent a rare and aggressive subset of high-grade B-cell lymphomas characterized by a triad of translocations involving MYC, BCL2, and BCL6. Patients with THL face poor outcomes when treated with the standard diffuse large B-cell lymphoma protocol. Thus, intensified regimens have emerged as a frontline strategy for managing these patients. Therefore, accurate diagnosis and molecular subclassification of these lymphomas are essential for guiding therapeutic decisions for these patients. Here, we report a case study detailing the diagnostic assessment of THL utilizing limited diagnostic material obtained through palpation-guided fine-needle aspiration (FNA). Methods/Case Report A 58-year-old male presented with a rapidly enlarging neck mass, accompanied by worsening dysphagia, pain, and fatigue over the course of two months. Laboratory testing showed leukocytosis and imaging studies revealed a partially necrotic, 7.8 x 9.1 x 9.4 cm right jugular nodal mass. The patient was referred to otolaryngology for further evaluation, where FNA of the mass was performed by the cytopathology team. The aspirate was sent for cytology with cell block and flow cytometry. The Romanowsky stain revealed abundant, large, discohesive cells with prominent nucleoli and scant cytoplasm with an abundance of lymphoglandular bodies in the background. Immunohistochemistry (IHC) on the cell block demonstrated BCL-2, BCL-6, and MYC expression, and a Ki-67 proliferation index >95%. Concurrent flow cytometric analyses showed an aberrant B-cell population expressing CD19, CD20, CD22, CD23 and surface lambda light chain. Further fluorescence in situ hybridization (FISH) analysis performed on the cell block confirmed gene rearrangements in BCL2, BCL6 and MYC, thereby classifying this patient’s disease as THL. Results (if a Case Study enter NA) NA Conclusion Diagnosing THL typically demands sufficient tissue for histology, cytology, flow cytometry, IHC, and molecular testing. Herein, we showcase a notable example where the diagnostic evaluation of THL was accomplished using limited material obtained from FNA. This case highlights the efficacy of conducting comprehensive diagnostic studies even when tissue availability is constrained. Utilizing cytologic samples not only streamlines the diagnostic process but also minimizes the need for patients to undergo additional invasive procedures, thus potentially reducing delays in diagnosis and therapeutic intervention.

ROS1 Translocation Detection in NSCLC: A Comparative Study of PGDx and FISH

Abstract In the United States, lung cancer is the leading cause of cancer-related deaths. In recent decades, the advent of molecularly-targeted therapies in the management of non-small-cell lung cancer (NSCLC) has led to significant improvements in patient outcomes. As such, optimum care depends on timely molecular testing. The mutational spectrum associated with NSCLC, however, is complex and riddled with various point mutations, amplifications, and rearrangements/fusions across multiple genes. Comprehensive testing of NSCLC has historically required multiple testing modalities to detect all clinically-relevant molecular targets. At our institution, a combination of immunohistochemistry, fluorescence in situ hybridization (FISH), and sequencing-based tests are performed on all NSCLCs. Though fragmented, this approach ensures testing for all current targetable genetic alterations is performed. Unfortunately, this style of testing is often incompatible with the limited amount of tumor tissue acquired by biopsy. In 2021, our institution implemented PGDx elio tissue complete (PGDx), introducing redundancy in ROS1 translocation testing, previously assessed by FISH through send-out testing to Mayo Clinic. The objective of this study was to perform a retrospective analysis of our molecular testing experience for NSCLC, with a spotlight on the nuances of ROS1 testing. Since its implementation at our institution, PGDx has been performed on 172 cases of NSCLC. As part of our NSCLC reflex testing agreement, ROS1 translocation FISH testing was also attempted on all cases. Of the 172 cases, one clinically actionable ROS1 translocation was identified by PGDx (0.5%). Interestingly, FISH testing for this case was equivocal. The remaining cases were negative for ROS1 translocations. Notably, FISH failed in six cases (3.5%) due to insufficient tissue. Three additional cases (1.7%) had minimal tumor tissue available for FISH testing (less than 300 cells), providing suboptimal results. Altogether, PGDx was successfully performed on all samples and, in the 166 cases where FISH was successful, there was no discordance between orthogonal tests. This supports the validity and reliability of PGDx in identifying clinically relevant rearrangements/fusions in ROS1. In this study, we demonstrate that PGDx can effectively replace FISH testing for ROS1 translocations in NSCLC. In addition to being technically equivalent to FISH for ROS1 with comparable turnaround times, PGDx adds substantial benefits. Replacing FISH testing with PGDx improves the diagnostic workflow, improves tissue utilization, and eliminates the costs associated with send-out orders. The cost of Mayo ROS1 FISH testing averages $520 per sample and this amount is billed to patient insurance, though reimbursements vary. Further, PGDx can detect the ROS1 gene fusion partners, a feature not possible through routine FISH testing in NSCLC. This added clinical information reduces the ambiguity of equivocal FISH results, exemplified by our study. By implementing this change, our institution will optimize both diagnostic practices and resource utilization in the clinical setting.

Optimization of Turnaround Time and Insufficient Quantity Frequency for Molecular Testing on FFPE Material

Abstract Introduction/Objective With clinical decisions relying progressively more on molecular data extracted from formalin- fixed, paraffin-embedded (FFPE) tissue, it is pivotal to optimize the use of tissue for diagnostic and prognostic purposes. This optimization can be reached by identifying actionable instances that can decrease the turnaround time (TAT) and the rate of “quantity not sufficient” (QNS) results Methods/Case Report From January 2023 to December 2023, the total TAT from the time a molecular study is ordered to its delivery to the molecular lab at LL200A (Tomsich Laboratories), as well as the TAT from the time between the ordering pathologist circling the region of interest to its delivery to LL200A were broken down by subspecialty and site. In addition, the QNS results of Caris genomic profiling were evaluated considering subspecialty and site, amount of material present in the initial sample, and number of levels cut for other ancillary testing from the same material. Results (if a Case Study enter NA) 83% of subspecialties took longer than 48 hours to have material ordered for molecular studies delivered to LL200A. The median TAT for all specialties was 58 hours (average: 71.6 hours). When examining TAT from circling to LL200A, the median time was 19 hours (average: 28.4 hours). Regarding the QNS rate of the Caris assay, most QNS cases were gastrointestinal tract specimens (27%) or specimens obtained from either CT-guided core needle biopsies (30%) or endoscopic biopsies (32%). The longest dimension of QNS cases ranged from 7.5 cm to 0.1 cm (median: 1.3cm)—the average number of slides ordered before Caris ranged from 1 to 52 (median: 12). Conclusion The initial results pointed towards the time from circling to LL200A as one actionable item that could improve the TAT of molecular tests. Possible solutions include enacting a dedicated tumor circling service. In addition, to decrease the rate of Caris QNS results, we propose working together with proceduralists to increase biopsy material yield and to work with pathologists to preserve limited specimens for molecular studies.

PCV ALONE IN GRADE 2 AND GRADE 3 OLIGODENDROGLIOMA – LONG-TERM RESULTS FROM A UK TERTIARY CARE CENTRE

Abstract AIMS Oligodendroglioma is a subgroup of gliomas which affects young adults and has a favourable overall survival (OS) ranging between 31.5 to 56.6.% at 10 years. Standard management of these tumours is maximal safe resection followed by adjuvant radiotherapy and systemic chemotherapy with Procarbazine, Lomustine and Vincristine (PCV), or surveillance where appropriate. PCV alone is an option that helps defer or avoid radiotherapy and its neurocognitive side effects in a selected group of patients. Our retrospective study analyses outcomes with PCV alone in Oligodendroglioma. METHOD We screened patient records between 1999 to 2021 and identified 31 patients who had a histological diagnosis of grade 2/3 oligodendroglioma (with confirmation of 1p19qcodeletion on molecular testing) and received PCV alone after surgery (biopsy/ tumour resection). RESULTS Out of 31 patients, twenty-six patients were grade 2 and five patients were grade 3 oligodendroglioma. Median age was 44 years and male: female was 15:16. Median follow up was 9.5 years. Twenty-five patients (80%) presented with seizures. 80% of patients had tumour resection & twenty four patients received 5 or more cycles of PCV alone as first-line oncological treatment. There was no significant difference in outcomes for grade2/3 tumours. Eighteen patients (58%) had local tumour relapse. Fourteen patients (45%) underwent salvage radiotherapy. Median time to radiotherapy was 7 years. Median OS was 19.4 years and median progression free survival (PFS) was 13.3 years. 9 deaths were reported. CONCLUSION PCV chemotherapy alone is an effective adjuvant treatment option for selected patients with oligodendroglioma, with a favourable PFS and OS shown in our series. Its use may allow deferral of radiotherapy and avoidance of associated neurocognitive side effects which can have a detrimental effect of quality of life for these young patients.

Molecular Profiling and Surgical Outcomes in Indeterminate Thyroid Nodules: Experience from a Tertiary Care Center

Abstract Introduction/Objective This study examines molecular results(MR) and surgical follow-up(SFU) of cytologically- indeterminate thyroid nodules. Methods/Case Report Atypia-of-undetermined significance/suspicious-for-follicular-neoplasm cases that underwent Quest/ThyroSeq molecular testing between 2015-2022 were analyzed for MR, SFU and lymph node metastasis(LNM). Results (if a Case Study enter NA) 417 cases(Quest=192, ThyroSeq=225). 59% had SFU. 43% malignancy rate.SFU for Quest(49%): non-neoplastic(NNP)=20%, neoplastic(NP)=80%. MR in these cases:NRAS=48, HRAS=19, BRAF=15, KRAS=8, RET/PTC=3, PAX8=2. SFU: papillary thyroid carcinoma(PTC)=35, non-invasive-follicular-thyroid- papillary-neoplasm with papillary-like nuclear features(NIFTP)=20, thyroid nodular follicular disease(TFND)=18, follicular adenoma(FA)=10, follicular carcinoma(FC)=5, oncocytic carcinoma(OC)=1, lymphocytic thyroiditis(LT)=1. Surgical-molecular correlation(SMC): PTC in 3/3 RET/PTC-mutated, 14/15 BRAF-mutated cases. 1 TFND was BRAF- positive. RAS-mutated category: NIFTP=20,PTC=18,TFND=17,FA=9, OA=5, FC=5, LT=1. In RAS-mutated PTCs, NRAS was most common(n=13), followed by HRAS(n=4) and KRAS(n=1). 2 PAX8-mutated cases showed FA and OC. 9/41 malignant cases, all PTC, had LNM, MR:BRAF=6, HRAS=2, RET/PTC=1.SFU for ThyroSeq(68%): NN=10%, NNP=90%. MR:NRAS=34, copy number alterations(CNAs)=25, HRAS=14, BRAF=13, KRAS=11, gene expression alterations(GEA)=7, THADA+IGF2BP3=7, CNAs Hurthle cell type(HCT)=6, EIF1AX=6, DICER1=4, PAX8- PPARG fusion=4, CNAs+GEA=3, NTRK3=3, TERT=2, RAS+EIF1AX=2, TERT+CNAs=2, EIF1AX=1, EZH1=1, RET/PTC1 fusion=1, ALK=1, BRAF K601E=1,RAS+TERT=1, RAS+TERT+PTEN+EIF1AX=1, TERT+BRAF=1, TERT+EIF1AX=1,TP53+CNAs=1. SFU:PTC=39, NIFTP=31, OA=21, FA=20, papillary microcarcinoma(PMiC)=13, TFND=10, OC=7, LT=6, FC=5, poorly differentiated carcinoma(PdC)=1.10/13 BRAF-mutated cases were PTC, other 3 PMiC. SFU of RAS-mutated cases(n=59):TFND=6, LT=4, NIFTP=19, FA=8, OA=4, PTC=13, PMiC=2, FC=2. RAS mutations in PTC: KRAS=6, HRAS=4, NRAS=3. SFU of CNAs-HCT: OA=3, OC=2, TFND=1. Infrequently detected mutations with SFU of PTC:RET/PTC(1/1), ALK(1/1), RAS+TERT(1/1), TERT+BRAF(1/1), BRAF K601E(1/1), RAS+EIF1AX(1/2). SFU of RAS+TERT+PTEN+EIF1AX:PdC. 11/65 malignant cases, all PTC had LNM:BRAF=5, KRAS=3, CNAs=1, EIF1AX=1, TERT+BRAF=1. Conclusion Substantial proportion of cases with positive MR underwent surgical resection. BRAF-positive and CNAs- HCT correlated with PTC and oncocytic neoplasms, respectively. BRAF-positive PTCs had a higher incidence of LNM compared to wild-type cases(46% vs.18%).

The Importance of Pathogenesis: A Molecular Investigation on A Solitary Choriocarcinoma Lung Lesion with No Primary Lesion

Abstract Introduction/Objective We present an exceedingly rare case of metastatic choriocarcinoma to the lung with no primary lesion. Notably, this is the only case where STR molecular studies have been conducted. Methods/Case Report A 43-year-old G1P1001 female with no past medical history presents with severe shortness of breath, left-sided back, and chest pain for severe shortness of breath, left sided back and chest pain. Patients pregnancy test was positive with a B-hCG of 17944 u/L. Transvaginal ultrasound was negative for IUP. CTAP showed no masses in the uterine cavity or ovaries. D-dimer was elevated at 623 ng/ml. However, CTA chest was negative for pulmonary emboli but revealed a RLL mass measuring 2.6 x 2.5 cm x 2.9 cm with lobulated areas suspicious for vascular structures and connection to the right pulmonary vein. Patient was treated with a complete right lower lobectomy. An endometrial biopsy was performed and was negative for malignancy with no significant findings. Grossly, the mass was well-circumscribe, hemorrhagic, and necrotic, measuring 3.5 cm. Microscopically, the malignant cells had highly pleomorphic and hyperchromatic nuclei. There were also multiple multinucleated cells and mitotic figures present. Some of the cells had nested architecture leading to us to suspect a pleomorphic lung adenocarcinoma with choriocarcinomatous differentiation. We performed IHC staining that demonstrated strong positivity of AE1/AE3, CK7, hCG and a high Ki-67 index. The neoplastic cells also had focal p63 and p40 positivity. Furthermore, TTF1 and SALL4 were both negative. This staining pattern as well as patient’s clinical history of no gynecological lesion, lead us to favor lung adenocarcinoma with choriocarcinomatous differentiation. However, due to the abundance of syncytiotrophoblastic and trophoblastic cells, metastatic choriocarcinoma could not be ruled out. Therefore, the case was sent out for external consultation and Short Tandem Repeat (STR) molecular testing. Surprisingly, the STR testing results showed some STR of paternal origin indicating a metastatic gestational choriocarcinoma. The patient’s surgery was highly successful and lead to a down trending of b-hCG from 17944 to 1768 after removal. Results (if a Case Study enter NA) NA Conclusion Performing STR testing was pivotal in this case as it revealed the presence of DNA of paternal origin, providing crucial evidence that the tumor was of gestational origin, guiding the diagnosis towards metastatic gestational choriocarcinoma.

Thyroid Lesion with a Novel Concurrent ETV6-NTRK3 Translocation and DICER1 Mutation

Abstract Introduction/Objective Understanding of the behavior of thyroid tumors expand as the basis of their classification gradually move from morphologic to molecular/genetic. The use of molecular methods in detecting mutations in fine needle aspiration (FNA) specimens further helped in tailoring patient management. Here, we describe a case of a thyroid lesion which was diagnosed with atypia of undetermined significance (AUS) on FNA and discovered to have an unreported concurrent mutation pattern. Methods/Case Report The patient is a 26 year-old female with long standing history of prominent anterior neck mass. New onset of neck pain prompted sonographic analysis which revealed a 1.1 cm hypoechoic left thyroid nodule with microcalcification. FNA was done, and was signed out as AUS which initiated molecular genetic testing. The lesion was found to have both ETV6/NTRK3 translocation and DICER1 p.P375R mutation. Existing literature on NTRK3 rearrangements in thyroid tumors confer a >95% risk of malignancy. It is commonly associated with BRAF-negative papillary thyroid carcinomas (PTC) with both in BRAF-like behavior in terms of nodal metastases and extrathyroidal extension. On the other hand, there are no existing literature specifying the malignancy risk of the exact DICER1 mutation identified since it has been linked to follicular neoplasms in general. Furthermore, isolated DICER1 mutations in the thyroid showed RAS-like behavior. Subsequent resection of the thyroid revealed that the tumor is morphologically a PTC, with lymphovascular invasion. Results (if a Case Study enter NA) NA Conclusion Molecular testing in thyroid lesions with morphologically indeterminable features on FNA significantly aided in prognostication of patients and prediction of malignancy risk. In this case with a previously unreported combination of mutations, existing literature helped in describing the probable behavior of the patient’s tumor. Thus, the researchers emphasize the importance of databases of identified mutations in tumors and their associated characteristics such as The Cancer Genomic Atlas (TCGA) and The Catalogue of Somatic Mutations in Cancer (COSMIC).

An Unusual Case of Lymphoplasmacytic Variant of Multiple Myeloma

Abstract Introduction/Objective Multiple myeloma is characterized by unregulated growth of monoclonal plasma cells with overt production of nonfunctional intact immunoglobulins or immunoglobulin chains. Immunohistochemically, the plasma cells are positive for CD138 and CD38, and are rarely positive for CD20 or cyclin D1. CD20 positivity and plasmacytoid morphology in our case pointed towards a lymphoplasmacytic variant of multiple myeloma. The translocation t(11;14) has been detected in this variant, which can explain the positive cyclin D1 immunostaining. The differential diagnosis of this myeloma variant includes lymphoplasmacytic lymphoma. Methods/Case Report We present a case of a 75-year-old female with no significant past medical history who suffered a fall and hesitated to get evaluated until her pain persisted. Initial ER evaluation revealed she had a compression fracture of the T10 and T11 vertebrae with no other abnormality identified. Subsequently, she underwent kyphoplasty, and bone biopsies were performed. The biopsies showed prominent monotonous lymphocytes and some plasmacytoid cell proliferation. Immunostains showed the tumor cells were positive for CD20, Pax-5, Bcl-2, cyclin D1, CD138, and kappa light chain, weakly positive for CD23; and negative for CD5, CD3, CD10, Sox11, and lambda light chain. Based on the morphology and immunoprofile, current findings were considered suggestive of a low-grade B cell lymphoplasmacytic proliferation with cyclin D1 expression. The differential diagnosis includes a lymphoplasmacytic lymphoma or lymphoplasmacytic variant of multiple myeloma. This case was forwarded to a higher-level care facility for consultation and the diagnosis of plasmacytoma, kappa light chain restricted, was rendered. Results (if a Case Study enter NA) NA Conclusion Misdiagnosis of lymphoma can be made in lesions showing classic plasma cells, numerous lymphoplasmacytic cells, and cyclin-D1 positivity on immunohistochemistry if additional testing is not performed. We recommended further testing, including but not limited to bone marrow biopsy, molecular testing, FISH, and genetic testing for a definitive diagnosis.

A Diagnostic Challenge in the Biopsy of a Mammographic Abnormality

Abstract Introduction/Objective Primary breast marginal zone lymphoma (MZL) is an uncommon subtype of extranodal lymphoma, and its diagnosis presents challenges, particularly in distinguishing it from lymphoplasmacytic lymphoma (LPL). MYD88 L265P mutation has been identified in a subset of marginal zone lymphomas, comprising 6-9% of cases. This genetic alteration further complicates the differentiation between MZL and LPL in breast tumors. We present a case highlighting the diagnostic complexities associated with primary breast MZL. Methods/Case Report A 71-year-old female patient underwent mammographic screening, which revealed a suspicious lesion in her left breast. Subsequent PET scan showed a hypermetabolic area consistent with a primary breast lesion. Biopsy histology exhibited a diffuse atypical lymphoid infiltration with varying proportions of neoplastic lymphocytes. Immunohistochemical analysis revealed positivity for CD20, PAX5, BCL2, CD138, MUM1, and negativity for CD3, CD5, Cyclin D1, CD10, CD23, CD34, BCL6, TDT, CD30, GATA3, and CK AE1/3. Additionally, there was lambda light chain restriction, and the Ki67 proliferation rate index was approximately 50%. Fish analysis indicated abnormal BCL6 gene rearrangement. Molecular genetic testing confirmed the presence of MYD88 mutation with c.794T>C p.L265P. Notably, bone marrow biopsy showed no abnormalities, with normal hematopoiesis. Serum electrophoresis and immunofixation detected an IgM monoclonal protein with lambda light chain specificity. Results (if a Case Study enter NA) NA Conclusion The diagnosis of primary breast MZL was favored over LPL due to the absence of common LPL- associated symptoms such as bone marrow involvement. However, the distinction between these entities remains challenging, underscoring the importance of comprehensive diagnostic approaches integrating histopathology, immunohistochemistry, and molecular genetics. Further research is warranted to enhance diagnostic certainty in such cases, particularly as the management of MZL and LPL becomes increasingly specific with the advent of novel therapeutic agents and ongoing clinical trials.

Synchronous endometrial and minor salivary gland carcinomas – role of molecular diagnostics amid lack of clinical suspicion

Abstract Introduction/Objective Synchronous malignancies account for 3-5% of all tumor diagnoses but can be challenging to detect if one or both tumors are rare histologic subtypes and clinical suspicion is lacking. Molecular diagnostics are critical for accurate diagnosis in these difficult cases to guide appropriate patient care. Methods/Case Report We report the case of a 49-year-old female who was diagnosed with a high-grade, mixed- histology endometrial adenocarcinoma a few years back. She was found to have hilar and mediastinal nodal carcinoma of uncertain differentiation a couple of months after her initial diagnosis, clinically labelled as metastatic endometrial carcinoma. Following neoadjuvant chemotherapy, her hysterectomy showed complete pathologic response, and was found to be POLE ultramutated on NGS. Follow-up PET scan in 2023 showed progression of hilar/endobronchial thickening, as well as interval increase in size of mediastinal nodes, again presumed to be endometrial metastases, despite the POLE mutant status. Repeat sampling was performed from both the sites, along with comprehensive molecular profiling. Cytology from the nodes and surgical pathology from the endobronchial lesion showed similar morphology consisting of hyperchromatic basaloid cells in cribriform arrangement with tubular structures containing myxoid stromal material, negative for PAX-8, ER, p40, and TTF1 immunostains, inconsistent with endometrial metastasis. Molecular studies including FISH and NGS showed MYB1::NFIB fusion characteristic of adenoid cystic carcinoma and absence of POLE mutation, definitively refuting the clinically suspected progression of endometrial metastasis. Molecular testing confirmed that the endobronchial tumor and mediastinal nodal involvement were caused by a second primary, distinct from her POLE-ultramutated endometrial carcinoma which disappeared with chemotherapy. Her extended molecular workup also revealed a pathogenic mutation in BRIP1, suggesting a genetic cancer predisposition syndrome requiring referral for genetic counseling. Results (if a Case Study enter NA) NA Conclusion Molecular pathology is an invaluable tool for unravelling diagnostic complexity. Pathologists must integrate cytomorphology, molecular genetics and knowledge of cancer biology to steer the clinical teams towards the best patient care.

Primary Mast Cell Sarcoma of the Maxillary Sinus and Gingiva Mimicking Malignant Neuroendocrine Tumor: A Case Report

Mast cell sarcoma (MCS) is an extremely rare and aggressive malignancy primarily affecting bones, with limited literature associating it with neuroendocrine marker expression. This report presents a rare case of MCS arising in the maxillary sinus and gingiva. A 74-year-old man presented with a progressively enlarging ulcer on the right-sided upper gingiva. Magnetic resonance imaging revealed a 3.4 cm tumor on the floor of the right maxillary sinus. The patient underwent an inferior maxillectomy and right-sided neck dissection. Microscopically, the tumor consisted of monotonous round cells with oval nuclei, vesicular chromatin, inconspicuous nucleoli, and brisk mitoses. A panel of immunohistochemical stains was initially applied to exclude common sinonasal undifferentiated neoplasms, such as sinonasal undifferentiated carcinoma, melanoma, rhabdomyosarcoma, Ewing sarcoma, and lymphoma. The tumor cells showed patchy staining for INSM1 and synaptophysin, but were negative for AE1/AE3, CAM5.2, p40, chromogranin, S100, HMB45, NKX2.2, desmin, CD45 (LCA), CD3, and CD20, with intact INI1 and BRG1 expression. No specific diagnosis could be rendered based on the staining results, leading to consideration of other rare malignancies. Additional staining revealed positivity for CD117, mast cell tryptase, CD13, CD33, CD43, and CD68, confirming the MCS diagnosis. Molecular testing for KIT mutation was negative. Subsequent bone marrow biopsy demonstrated infiltration of atypical mast cells, which led to a diagnosis of mast cell leukemia. Despite high-dose chemotherapy, the patient died three months after the initial diagnosis. The undifferentiated epithelioid morphology and unusual aberrant neuroendocrine marker expression posed significant diagnostic challenges. The major differential diagnoses were discussed in this report.

Evaluation of Loopamp Leishmania detection kit for the diagnosis of cutaneous leishmaniasis in Ethiopia

BackgroundCutaneous leishmaniasis (CL) in Ethiopia and some parts of Kenya is predominantly caused by Leishmania aethiopica. While skin-slit (SS) microscopy is routinely used for CL diagnosis, more sensitive molecular tests are available. The Loopamp™ Leishmania detection kit (Loopamp) is a robust loop-mediated isothermal amplification (LAMP) assay with the potential for implementation in primary healthcare facilities. In this study, we comparatively assessed the diagnostic accuracy of four methods currently used to diagnose CL: Loopamp, kinetoplast DNA (kDNA) PCR, spliced leader RNA (SL-RNA) PCR and SS microscopy.MethodsA study on 122 stored tape disc samples of suspected CL patients was conducted in Gondar, northwestern Ethiopia. Routine SS microscopy results were obtained from all patients. Total nucleic acids were extracted from the tapes and subjected to PCR testing targeting kDNA and SL-RNA, and Loopamp. Diagnostic accuracy was calculated with SS microscopy as a reference test. The limit of detection (LoD) of Loopamp and kDNA PCR were determined for cultured L. aethiopica and Leishmania donovani.ResultsOf the 122 patients, 64 (52.5%) were identified as CL cases based on SS microscopy. Although the PCR tests showed a sensitivity of 95.3% (95% confidence interval [CI] 91.6–99.1), Loopamp only had 48.4% (95% CI 39.6–57.3) sensitivity and 87.9% (95% CI 82.1–93.7) specificity. The LoD of Loopamp for L. donovani was 100-fold lower (20 fg/µl) than that for L. aethiopica (2 pg/µl).ConclusionsThe Loopamp™ Leishmania detection kit is not suitable for the diagnosis of CL in Ethiopia, presumably due to a primer mismatch with the L. aethiopica 18S rRNA target. Further research is needed to develop a simple and sensitive point-of-care test that allows the decentralization of CL diagnosis in Ethiopia.Graphical

Impact of isoniazid monoresistance on overall and vulnerable patient populations in Taiwan

ABSTRACT Isoniazid is an early bactericidal anti-tuberculosis (TB) agent and isoniazid mono-resistance TB is the most prevalent drug-resistant TB worldwide. Concerns exist regarding whether resistance to isoniazid would lead to delayed culture conversion and worst outcomes. From January 2008 to November 2017, adult culture-positive pulmonary TB patients receiving isoniazid, rifampicin, pyrazinamide, and ethambutol were identified through Taiwan Center for Disease Control database and were followed until the end of 2017. Primary outcomes included time to sputum culture conversion (SCC) within two months. Secondary outcomes included death and unfavourable outcomes at the end of 2nd month. A total of 37,193 drug-susceptible and 2,832 isoniazid monoresistant pulmonary TB patients were identified. Compared with no resistance, isoniazid monoresistance was not associated with a delayed SCC (HR: 0.99, 95% CI: 0.94─1.05, p = 0.8145), a higher risk of 2-month mortality (HR: 1.19, 95% CI: 0.92─1.53, p = 0.1884), and unfavourable outcomes at 2nd month (OR: 1.05, 95% CI: 0.97─1.14, p = 0.2427). Isoniazid monoresistance was associated with delayed SCC (HR: 0.90, 95% CI: 0.83─0.98, p = 0.0099) and a higher risk of unfavourable outcomes (OR:1.18, 95% CI: 1.05─1.32, p = 0.0053) in patients aged between 20 and 65, and delayed SCC in patients without underlying comorbidities (HR: 0.90, 95% CI: 0.81─0.98, p = 0.0237). Isoniazid mono-resistant TB had a comparable outcome with drug-susceptible TB at the end of the intensive phase. Healthy, and non-elderly patients were more likely to had culture persistence, raising concerns about disease transmission in these subgroups and warranting early molecular testing for isoniazid resistance.

NANOPORE-BASED INTRA-OPERATIVE CLASSIfiCATION OF CENTRAL NERVOUS SYSTEM TUMOURS IN THE NHS

Abstract AIMS The 2021 WHO classification of CNS tumours necessitates the use of molecular testing in order to reach a confident diagnosis of many tumour types. At present, this is achieved using array-based technology delivered by a centralised model. This approach has inherent delays that mean it is often several weeks before the treating clinical team is informed of diagnosis, delaying the start of adjuvant therapy and causing significant distress for patients. As such, there is an urgent need to rethink this pathway and improve time to diagnosis. Nanopore longread sequencing technology has the potential to enable a paradigm shift in diagnostic and therapeutic pathways, offering rapid, comprehensive molecular diagnosis that can be performed in the intra-operative setting. We aimed to test the hypothesis that intra-operative methylation-based classification can be performed using nanopore sequencing and thereby expediently inform surgical and oncological decision-making. METHOD Oxford Nanopore Technology (ONT) is a native-strand, long-read sequencing platform that can perform copy- number profiling along with parallel single-gene methylation, structural variant, mutational and methylation analyses. Capital and consumable costs are relatively low, and testing can be performed in the local setting on single samples. We have optimised DNA extraction and library preparation for rapid tissue processing. We have developed a robust bioinformatic pipeline which is able to produce intraoperative classification within minutes of sequencing and full molecular profiling after 24 hours. RESULTS We demonstrate the feasibility of using ONT to deliver intra-operative methylation-based classification of CNS tumours in ‘realtime’ within an NHS hospital setting and will discuss the challenges of implementing this testing and the opportunities to inform neuro-oncological practice. CONCLUSION By giving a summary of our novel protocol of rapid DNA extraction, library preparation and bioinformatic analysis, we will show that this approach can revolutionise the diagnosis of brain tumours and has the potential for rapid adoption by non-expert laboratories.