Performance of non-formalin fixed paraffin embedded samples in hybrid capture and amplicon next-generation sequencing panels

BACKGROUND

Genomic profiling using next-generation sequencing (NGS) is fundamental for driving prognostic and therapy in cancer. Formalin-fixed paraffin embedded (FFPE) tissue is the widely used material, whereas non-FFPE may represent an alternative. However, studies comparing the NGS performance of non-FFPE materials to FFPE are still lacking in the literature. The objective of this study was to characterize in non-FFPE preparations the nucleic acid yield and NGS performance on both a capture-based and an amplicon-based NGS platform. NGS quality metrics obtained from non-FFPE preparations were compared to FFPE.

METHODS

We analyzed the cellularity and nucleic acid yield in 111 tumors from non-FFPE preparations. In addition, comprehensive hybrid capture panel sequencing metrics obtained from DNA and RNA libraries were compared between independent non-FFPE and FFPE samples. A paired comparison between non-FFPE and FFPE samples was performed to analyze concordance in mutant allele detection using an amplicon panel.

RESULTS

The mean target coverage from DNA libraries was 2× higher in non-FFPE samples than in FFPE. The detection of exogenous DNA was 2.5× higher in non-FFPE than in FFPE. Conversely, a lower performance was observed in non-FFPE RNA libraries in comparison to FFPE DNA libraries with no impact in minimum standard cutoffs. The variant allele detection in non-FFPE was found to be comparable to that of FFPE tumor samples in matched samples.

CONCLUSIONS

Non-FFPE was demonstrated to be a suitable material for DNA and RNA library preparations using a comprehensive NGS panel. This is the first study reporting library quality metrics according to the TSO500 analysis pipeline.

Cytological features of chordoid glioma: A case report with summary of prior published cases

Chordoid glioma is an uncommon low-grade glioma and is a CNS WHO grade 2 tumour in the current WHO 2021 classification. Predominantly it is seen in the third ventricle and in young adults. Although the histological features of chordoid glioma are well documented, there is sparse literature describing its cytological features. Here we describe the squash cytological features of a case of chordoid glioma along with summary of prior published cases. The smears tend to be quite cellular, the cells show mild pleomorphism, anisonucleosis, and absent mitotic activity. The background shows a distinctive bluish myxoid stroma. It can be mistaken for high grade glioma on squash cytology.

Cytopathology of glioneuronal and neuronal tumours with histological correlations

Glioneuronal and neuronal tumours constitute a diverse group of tumours that feature neuronal differentiation. In mixed glioneuronal tumours, a glial component is present in addition to the neuronal component. With a few exceptions (eg diffuse leptomeningeal glioneuronal tumour) they are well-circumscribed and slow-growing tumours, which is why their prognosis is intrinsically favourable after gross total resection. Rendering an intraoperative diagnosis of glioneuronal/neuronal tumour is therefore important-neurosurgeons should remove them to prevent the persistence of clinical symptoms and/or recurrence. In this context, cytopathological examination can be especially useful for assessing cellular details when frozen section artefacts render poor-quality preparations, as is the case for this group of tumours, which are frequently mistaken for infiltrating gliomas (eg diffuse astrocytoma infiltrating grey matter, oligodendroglioma) on frozen section slides. The aim of this article is to review the cytomorphological features of glioneuronal and neuronal tumours according to the 2021 World Health Organization classification of central nervous system tumours, 5th edition. Additionally, since interpretation in intraoperative cytology relies on intuiting tissue patterns from cytology preparations, representative histological figures of all discussed entities have been included. Clues for specific diagnoses and the primary diagnostic problems encountered during intraoperative procedures are also discussed.

Squash Cytology Diagnosing Plasmacytoma of Frontal Bone as First Presentation of Nonsecretory Multiple Myeloma

Plasmacytoma of bone is one of the criteria for diagnosing plasma cell myeloma (multiple myeloma). A plasmacytoma involving a frontal bone is unusual, with only few being reported so far. Also, when typical clinical presentation is absent, diagnosis is usually not suspected clinicoradiologically. We report a rare case of frontal bone plasmacytoma presenting as a lump over the forehead, the squash cytology of which gave the diagnosis of neoplastic etiology. Thus, squash cytology helped in early and definitive diagnosis in this patient, hastening meticulous diagnostic investigations and appropriate management. With full workup, the final diagnosis of a nonsecretory multiple myeloma was made.

Cytological Features in Pilomyxoid Astrocytoma: A Case Report with Summary of Prior Published Cases

Pilomyxoid astrocytoma is a subtype of pilocytic astrocytoma described as grade 1 tumour in the WHO classification of CNS tumors, 2022. It occurs preferentially in the hypothalamic region in infants. Although the histological features of pilomyxoid astrocytomas are well documented, there is sparse literature available on the cytological findings of the same. Here we describe the squash cytological features of a case of pilomyxoid astrocytoma along with a summary of prior published cases. The smears of this tumour tend to be more cellular with piloid cells arranged in an angiocentric pattern without Rosenthal fibres or eosinophilic granular bodies. The background can have blue myxoid substance.

Comparison of Frozen Section and Squash Cytology as Intra-Operative Diagnostic Tool in Pediatric CNS Tumors

BACKGROUND

Pediatric central nervous system (CNS) tumors have a different histological spectrum as compared to adults with the infantile group having even more varied and distinct histological profiles. Intra-operative diagnosis is especially important as it guides the neurosurgeon to tailor an approach which is best suited for a particular case. The aim of the study was to evaluate the diagnostic accuracy, sensitivity, specificity, positive predictive value, negative predictive value of frozen section (FS) and squash cytology and to find out the degree of correlation (kappa value) between the two procedures.

MATERIALS AND METHODS

A prospective study was conducted on 55 pediatric patients with clinicoradiologically diagnosed CNS lesions for a period of 2.5 years. Intra-operative squash smears and FS were made and stained with hematoxylin and eosin stain. Diagnosis made subsequently on paraffin embedded sections was taken as the gold standard.

RESULTS

Although the specificity (90%) and positive predictive value (96%) were comparable between the two procedures, sensitivity (91.4%) and negative predictive value (75%) of FS was more as compared to squash cytology. Both the diagnostic modalities showed substantial agreement (k = 0.728).

CONCLUSION

Even though the histological spectrum of pediatric CNS tumors is more varied than adults, FS gives a reasonable intra-operative diagnosis and better results when compared to squash alone.

Scoring system for intraoperative diagnosis of intracranial schwannoma by squash cytology

OBJECTIVE

To assess the utility of a newly developed squash cytology (SC)-based scoring system for accurate intraoperative diagnosis of schwannoma.

METHODS

We first compared SC-based and frozen section (FS) diagnoses with final pathological diagnoses of schwannoma (16 cases), meningioma (39 cases) and low-grade astrocytoma (16 cases). Then, by logistic regression modeling, we identified features of SC preparations that were independently predictive of schwannoma. To develop a diagnostic scoring system, we assigned one point to each feature, and performed receiver operating characteristic analysis to determine the score cut-off value that was most discriminatory for differentiating schwannoma from the other tumour types. We then compared accuracy, sensitivity, and specificity of diagnosis before and after the application of the scoring system.

RESULTS

Overall diagnostic concordance rates for SC and FS were almost the same, at 73.2% (52/71) and 77.5% (55/71 cases), respectively. Of the 16 SC features entered into the analysis, the following nine were found to independently predict schwannoma, and were thus incorporated into the scoring system: smooth cluster margins, few or no isolated tumour cells, fibrillary stroma, spindle-shaped nuclei, parallel arrangement of stroma, parallel arrangement of nuclei, presence of anisonucleosis, absence of nucleoli, and hemosiderin deposition. A cut-off score of four items yielded the best sensitivity, specificity and predictive values for prediction of schwannoma. Use of the scoring system improved accuracy of intraoperative diagnosis from 80.3% to 94.4%, sensitivity from 56.2% to 93.8%, and specificity from 87.3% to 94.5%.

CONCLUSION

Our proposed SC-based scoring system will increase accuracy of intraoperative diagnosis of schwannoma vs non-schwannoma tumours.

Role of intra-operative squash cytology in rosette-forming glio-neuronal tumor of the fourth ventricle; A case report

Rosette-forming glioneuronal tumor (RGNT) of the 4^th ventricle is a newly described WHO grade I brain tumor included in recent WHO classification of CNS tumors. It is a biphasic tumor thought to originate from pluripotent progenitor cells of subependymal plate. Intra-operative diagnosis plays an important role, as complete surgical excision is the treatment of choice. We are reporting a case of RGNT in a 19 years-old young male emphasizing the intra-operative pathological pointers and their role in accurate diagnosis for the suitable surgical intervention.

Intraoperative Imprint-squash Methods in Central Nervous System Tumors

Objectives:

Central nervous system (CNS) tumors constitute 1.3% of all cancers in adults and are the seventh leading cause of death in developed countries. CNS tumors are very soft and have a gelatin-like texture. Smear technique is a very simple and fast method for the diagnosis of brain tumors.

Methods:

In this study, we evaluated the imprint and squash cytology of 100 cases sent to the pathology clinic. The sections of the paraffin blocks were prepared after the operation in the neurosurgery clinic of the SBU Hamidiye Şişli Efal Training and Research Hospital. The accuracy rate was 90% in the differential diagnosis of malignant tumors from the benign ones.

Conclusion:

Cytological samples were taken from 100 cases of intracranial tumors that were operated in the neurosurgery clinic of Şişli Etfal Hospital, and the paraffin sections prepared from the biopsy materials were examined. The cases with misdiagnosis were usually differentiated from solid-hard tumors, epithelial-grade cystic structures, and medulloblastoma localized in the posterior fossa, medulloblastoma and ependymoma. However, this method has been found to be very convenient in practice due to its ease technically, low cost and equipment savings.

Squash cytology of a case of medulloblastoma with myogenic differentiation

Medulloblastoma with myogenic differentiation is not a distinct entity but a pattern of differentiation seen in <1% of medulloblastomas. Although squash cytology of medulloblastoma is well described, there are no reports available describing squash cytomorphology of this unusual variant of medulloblastoma. Intraoperative squash smears on a 2-year-old girl with a midline posterior fossa space occupying lesion revealed features of an embryonal tumor composed of small, round, and blue cells. In addition, it had several large, round, eosinophilic rhabomyoblasts, and a few strap cells scattered among the sea of small blue cells. Subsequent histology showed features of a medulloblastoma, classic type with myogenic differentiation. Molecular subtyping, based on immunohistochemistry alone, was in keeping with a non-Wnt/non-SHH activated type. Here we describe the squash cytomorphological details of a case of medulloblastoma with myogenic differentiation, along with its cytological differentials.

Intraoperative squash cytology provides a qualitative intraoperative diagnosis for cases in which frozen section yields a diagnosis of equivocal brain tumour

OBJECTIVE

We assessed whether intraoperative squash cytology could provide surgeons with a qualitative diagnosis of brain lesions when frozen section diagnosis is equivocal.

METHODS

The study included 51 lesions that were diagnosed intraoperatively as equivocal brain tumour on the basis of frozen section. We retrospectively classified the lesions into five groups according to the final histopathological diagnoses (I: malignant lymphomas; II: diffuse astrocytic and oligodendroglia tumours; III: pituitary adenomas, IV: metastatic carcinomas; V: others). We assessed the squash cytology features of Groups I-IV and of the specific lesion types, and compared features among the groups.

RESULTS

The four groups differed in a range of salient cytomorphological features: lymphoglandular bodies in Group I (eight of nine cases), cytoplasmic fibrillary processes in Group II (six of eight cases), low-grade nuclear atypia in Group III (seven of seven cases), and large nuclei (approximately 80 μm² ) and nuclear crush artefacts in Group IV (seven of nine cases).

CONCLUSION

Findings of lymphoglandular bodies on intraoperative squash cytology can be considered characteristic of malignant lymphomas, while cytoplasmic fibrillary processes indicate diffuse astrocytic and oligodendroglial tumours. We conclude that squash cytology could yield a qualitative intraoperative diagnosis in over 25% of cases for which frozen section yields a diagnosis of equivocal brain tumour.

Intraoperative Squash Smear in Central Nervous System Tumors and Its Correlation with Histopathology: 1 Year Study at a Tertiary Care Centre

Background:

Intraoperative squash smear cytology is a simple and reliable technique for rapid intraoperative diagnosis of neurosurgical specimens. The study was designed to assess the accuracy of intraoperative squash smear in the diagnosis of central nervous system (CNS) space-occupying lesions.

Materials and Methods:

One hundred and fifty cases of CNS space-occupying lesion were studied in a period of 15 months. Smears were prepared from the biopsy sample obtained at the time of operation and were stained with rapid hematoxylin and eosin method.

Results:

One hundred and forty-one cases showed complete correlation with histopathology, two cases showed partial correlation, and seven cases were discrepant. The overall diagnostic accuracy was found to be 94%.

Conclusion:

Intraoperative squash smear thus provides diagnosis with fair accuracy in brain tumors and is of great value in intraoperative consultation.

Papillary Ependymoma of the Spinal Cord: A Case Report with Summary of Prior Published Cases

Papillary ependymoma is a rare variant of ependymoma. It has been included in Grade II tumors of updated 2016 WHO classification of central nervous system tumors. Only a handful of cases of spinal papillary ependymomas have been reported so far. The differential diagnoses include choroid plexus papilloma, papillary meningioma, metastatic carcinoma, and papillary tumor of the pineal region. Here, we take the opportunity of reporting a rare case of spinal papillary ependymoma along with its squash cytological features and a summary of prior published cases.

Utility of intraoperative squash cytology in diagnosis of paediatric central nervous system lesions

BACKGROUND

Role of squash cytology in intraoperative diagnosis of central nervous system lesions has been well established. Intraoperative diagnosis is especially important in paediatric CNS lesions as decision regarding gross total resection or near total resection or subtotal resection is crucial and radiotherapy and chemotherapy are best avoided in this age group. The aim of this study was to evaluate the utility of squash cytology of CNS lesions in paediatric age group and to assess its diagnostic accuracy, sensitivity, specificity, positive predictive value and negative predictive value.

MATERIALS AND METHODS

A prospective study was conducted on 42 paediatric patients with clinico-radiologically diagnosed CNS lesions. Intraoperative squash smears were stained with haematoxylin and eosin (H&E) stain. Diagnosis made subsequently on paraffin sections was taken as gold standard.

RESULTS

The overall diagnostic accuracy of intraoperative squash cytology of CNS lesions in paediatric age group was 73.80%. The sensitivity, specificity, positive predictive value and negative predictive value of this modality were 92.31%, 87.50%, 96.00% and 77.78%, respectively.

CONCLUSIONS

The spectrum of CNS lesions in paediatric age group is different from that in adults. Though the sensitivity and specificity of squash cytology in paediatric tumours are less than that of adults, it is an important tool for intraoperative diagnosis that guides regarding the extent of resection.

Role of Squash Cytology in Intraoperative Diagnosis of Spinal Lesions

Background:

Squash cytology for intra operative diagnosis of central nervous system (CNS) tumors is an immensely important modality. Though its role in brain lesions is unquestionable and has been proven in a number of studies, its utility for spinal lesions is still a grey zone.

Aims:

To assess the diagnostic accuracy of squash preparation in spinal lesions and its statistical significance (sensitivity, specificity, positive predictive value, negative predictive value) following histological confirmation.

Materials and Methods:

A total of 57 cases of spinal tumors were taken. May-Grunewald-Giemsa staining (MGG) and Hematoxylin-Eosin (H&E) were done in each one of them. Rest of the tissue was processed for histological diagnosis and results were compared.

Results:

In our study, histology was taken as the gold standard. By comparing the results, squash preparation had sensitivity of 95.75%, specificity 80.0%, positive predictive value (PPV)95.74%, and negative predictive value (NPV) 80.80%. Schwannoma was found to be the most prevalent tumor in the spine (17/57) in our study, followed by meningioma (13/57). Diagnostic accuracy for schwannoma was fairly high i.e. 92.3%, followed by meningioma (82.35%). Highest diagnostic accuracy was documented in intradural, extramedullary compartment.

Conclusion:

Inspite of having pitfalls and various limitations in case of spinal lesions, squash preparation is a rapid and easy method with fairly high diagnostic accuracy. So it can be reliably used as an intraoperative diagnostic tool in spinal lesions.

Rhabdoid Meningioma of Brain - A Rare Aggressive Tumor

Rhabdoid meningioma is a rare aggressive variant of meningioma, regarded as WHO Grade III type. Histologically and cytologically, it is distinctive type having abundant eosinophilic cytoplasm, cytoplasmic inclusion with eccentrically placed vesicular nuclei and prominent nucleoli. High recurrence rate and poor outcome are important features. Here, we are presenting a rare case of rhabdoid meningioma found in a recurrent meningioma of the posterior fossa in a middle-aged female. We emphasized the squash cytology and histology finding of the rare neoplasm.

Clear-cell meningioma: Intraoperative diagnosis by squash cytology: Case report and review of the literature

Clear-cell meningioma (CCM), an unusual subset of meningioma has prominent, clear-cell morphology. It is a wolf in sheep's clothing characterized by benign histologic attributes, but tendency for recurrence (61%) and metastasis. Therefore, WHO has classified it as grade II meningioma. Fine-needle aspiration cytology diagnosis is simple, rapid, cost-effective and reliable procedure primarily aimed at preoperative diagnosis of advanced and metastatic extracranial tumor. Preoperative and/or intraoperative cytodiagnosis of CCM demand expertise in the evaluation of cytology smears. However in case of intra operative evaluation of squash smears there is a time constraint and a very small tissue material obtained by stereotactic biopsy are available for interpretation. Knowledge of clinical features including age, anatomical locations, neuroimaging findings and cytomorphologic features, are prerequisites for arriving at definitive cytodiagnosis. We describe intra operative squash cytology of CCM in a 16-year-old female, located in cerebello-pontine angle. The diagnosis of CCM offered on squash cytology was subsequently confirmed on histopathology and immunohistochemistry. It typically showed pattern less sheets and groups of polyhedral, clear cells with monomorphic, round nuclei having a bland chromatin and inconspicuous nucleoli. Separation of CCM from other tumors having clear -cell morphology and variants of meningioma is important because of its high recurrence rate and mortality.

Evaluation of Intraoperative Cytological Smears for Diagnosis of Brain Tumors with Special Reference to Immunohistochemistry

Context:

Brain tumors are heterogeneous group of benign and malignant tumors of glial, meningeal, neuronal, embryonal, and lymphoid origin. Rapid intraoperative diagnosis of the nature of the tumor helps the surgeon to plan the extent of surgery and modify it accordingly.

Aims:

(1) To establish the validity and reliability of squash cytology in the intraoperative diagnosis of brain tumors. (2) To correlate with histopathological report and immunohistochemistry (IHC) profile.

Settings and Design:

Prospective, observational study.

Subjects and Methods:

prospective, observational study was conducted in the Department of Pathology in collaboration with the Department of Neurosurgery of a tertiary care hospital. One hundred and seven patients with symptomatic or radiologically detected brain tumors were included in the study. Intraoperative squash smears were stained with hematoxylin and eosin and rapid papanicolaou stain. Cytological diagnosis was recorded and communicated to the surgeon. Cytological findings were corroborated with histological findings subsequently. GFAP, Ki-67, and ER-PR IHC were used as additional markers.

Statistical Analysis Used:

Software used in statistical analysis of our study was MedCalc version 11.6 (Mariakerke, Belgium: MedCalc Software 2011).

Results:

A total of 107 cases were included in the study. Meningioma was the most common lesion. Overall sensitivity in our study to diagnose benign and malignant tumors was 94.7% and the specificity is 97.6% with positive and negative predictive value of 94.7% and 97.6%, respectively. Diagnostic accuracy was highest in pituitary adenoma.

Conclusions:

The combination of meticulous evaluation of clinical, radiological, and cytological findings helps in accurate and rapid diagnosis of brain tumors.

Squash cytology of tanycytic ependymoma: A report of two cases

Tanycytic ependymoma is a rare variant of ependymoma which has a predilection for the spinal cord. It is a WHO grade II tumour with favourable outcome. Although squash cytology of ependymoma is well described, there is sparse literature available on squash cytomorphology of tanycytic variant. Here we present two cases of squash cytology of tanycytic ependymoma. In the first case the diagnosis of tanycytic ependymoma was considered. However, in the second case a diagnosis of usual ependymoma was offered. Subsequently histopathology confirmed tanycytic nature in both the cases. In this article we discuss the squash cytological features of tanycytic ependymoma along with its differential diagnosis. Diagn. Cytopathol. 2017;45:270-273. © 2016 Wiley Periodicals, Inc.

Intraoperative cytology of central neurocytoma mimicking oligodendroglioma

Central neurocytomas (CNs) are uncommon tumors of the central nervous system. These tumors have a predilection for the lateral ventricles of young adults and are known to display characteristic neuroimaging and histomorphologic features. Typically, CNs are associated with a favorable outcome, although cases with more aggressive clinical course with recurrences are not unknown. Most descriptions of this tumor are available in the form of isolated histopathology-based case reports and small series. Cytology-based publications of CN are rare. Here, we report a case of CN in a 22-year-old girl. Intra-operative squash cytology and subsequent histopathology of the tumor simulated an oligodendroglioma and a clear cell ependydoma. Final confirmation was obtained on immunohistochemistry. This paper discusses the salient cytological, histomorphological and immunohistochemical features of CN that are useful in distinguishing from its mimickers.