Arivarasan Karunamurthy

Evaluation of endobronchial ultrasound‐guided fine‐needle aspirations (EBUS‐FNA): Correlation with adequacy and histologic follow‐up

Endobronchial ultrasound‐guided fine‐needle aspiration (EBUS‐FNA) is a minimally invasive modality for diagnosing mediastinal lesions. When determining adequacy, EBUS‐FNAs are evaluated for diagnostic material or sufficient lymphoid tissue. In this study, the authors evaluated their experience with EBUS‐FNAs and correlated the findings with adequacy and histologic follow‐up.

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines: A Joint Recommendation of the Association for Molecular Pathology and the College of American Pathologists

Bioinformatics pipelines are an integral component of next-generation sequencing (NGS). Processing raw sequence data to detect genomic alterations has significant impact on disease management and patient care. Because of the lack of published guidance, there is currently a high degree of variability in how members of the global molecular genetics and pathology community establish and validate bioinformatics pipelines. Improperly developed, validated, and/or monitored pipelines may generate inaccurate results that may have negative consequences for patient care. To address this unmet need, the Association of Molecular Pathology, with organizational representation from the College of American Pathologists and the American Medical Informatics Association, has developed a set of 17 best practice consensus recommendations for the validation of clinical NGS bioinformatics pipelines. Recommendations include practical guidance for laboratories regarding NGS bioinformatics pipeline design, development, and operation, with additional emphasis on the role of a properly trained and qualified molecular professional to achieve optimal NGS testing quality.

Prevalence and phenotypic correlations of EIF1AX mutations in thyroid nodules

The EIF1AX gene mutations have been recently found in papillary thyroid carcinoma (PTC) and anaplastic thyroid carcinoma (ATC). The prevalence of these mutations in other types of thyroid cancers and benign nodules is unknown. In this study, we analyzed the occurrence of EIF1AX mutations in exons 2, 5, and 6 of the gene in a series of 266 thyroid tumors and hyperplastic nodules by either Sanger or next-generation sequencing (ThyroSeq v.2). In addition, 647 thyroid fine-needle aspiration (FNA) samples with indeterminate cytology were analyzed. Using surgically removed samples, EIF1AX mutations were detected in 3/86 (2.3%) PTC, 1/4 (25%) ATC, 0/53 follicular carcinomas, 0/12 medullary carcinomas, 2/27 (7.4%) follicular adenomas, and 1/80 (1.3%) hyperplastic nodules. Among five mutation-positive FNA samples with surgical follow-up, one nodule was PTC and others were benign follicular adenomas or hyperplastic nodules. Overall, among 33 mutations identified, A113_splice mutation at the intron 5/exon 6 splice site of EIF1AX was the most common. All four carcinomas harbored A113_splice mutation and three of them had one or more coexisting mutations, typically RAS All PTC carrying EIF1AX mutations were encapsulated follicular variants. In summary, this study shows that EIF1AX mutations occur not only in thyroid carcinomas, but also in benign nodules. The most common mutation hotspot is the A113_splice, followed by a cluster of mutations in exon 2. When found in thyroid FNA samples, EIF1AX mutations confer ~20% risk of cancer; the risk is likely to be higher in nodules carrying a A113_splice mutation and when EIF1AX coexists with RAS mutations.

Prevalence and phenotypic characteristics of EIF1AX mutations in thyroid nodules

The EIF1AX gene mutations have been recently found in papillary thyroid carcinoma (PTC) and anaplastic thyroid carcinoma (ATC). The prevalence of these mutations in other types of thyroid cancers and benign nodules is unknown. In this study, we analyzed the occurrence of EIF1AX mutations in exons 2, 5, and 6 of the gene in a series of 266 thyroid tumors and hyperplastic nodules by either Sanger or next-generation sequencing (ThyroSeq v.2). In addition, 647 thyroid fine-needle aspiration (FNA) samples with indeterminate cytology were analyzed. Using surgically removed samples, EIF1AX mutations were detected in 3/86 (2.3%) PTC, 1/4 (25%) ATC, 0/53 follicular carcinomas, 0/12 medullary carcinomas, 2/27 (7.4%) follicular adenomas, and 1/80 (1.3%) hyperplastic nodules. Among five mutation-positive FNA samples with surgical follow-up, one nodule was PTC and others were benign follicular adenomas or hyperplastic nodules. Overall, among 33 mutations identified, A113_splice mutation at the intron 5/exon 6 splice site of EIF1AX was the most common. All four carcinomas harbored A113_splice mutation and three of them had one or more coexisting mutations, typically RAS All PTC carrying EIF1AX mutations were encapsulated follicular variants. In summary, this study shows that EIF1AX mutations occur not only in thyroid carcinomas, but also in benign nodules. The most common mutation hotspot is the A113_splice, followed by a cluster of mutations in exon 2. When found in thyroid FNA samples, EIF1AX mutations confer ~20% risk of cancer; the risk is likely to be higher in nodules carrying a A113_splice mutation and when EIF1AX coexists with RAS mutations.

Multiple Mutations Detected Preoperatively May Predict Aggressive Behavior of Papillary Thyroid Cancer and Guide Management—A Case Report

BACKGROUND Multiple gene mutations in thyroid nodules are rare. The presence of several oncogenic mutations could be associated with aggressive biological behavior of tumors. PATIENT FINDINGS A 60-year-old female presented to her physician after she felt a lump in her neck. On ultrasound, she was found to have a 1.4 cm × 0.8 cm × 1.3 cm nodule in the isthmus and a 0.5 cm × 0.6 cm × 0.6 cm nodule with irregular margins and hypoechogenicity in the right thyroid lobe, warranting fine-needle aspiration (FNA). Cytological examination of the smaller nodule yielded a diagnosis of atypia of undetermined significance (AUS/FLUS, Bethesda Category III). The aspirate was submitted for molecular testing using the next-generation sequencing ThyroSeq(®) v2 panel. The test revealed four distinct mutations: BRAF (p.V600E), TERT (C228T), PIK3CA (p.H1047R), and AKT1 (p.E17K). Presence of multiple oncogenic mutations in the FNA specimen was highly indicative of cancer, and suggestive of a cancer with propensity toward more aggressive biological behavior. Four weeks after the FNA results were available, the patient underwent total thyroidectomy. This was followed by radioactive iodine ablation after the final pathology revealed a 0.5 cm papillary thyroid carcinoma (PTC) with extrathyroidal extension and positive resection margins (pT3 stage). SUMMARY Herein, the first case of four mutations preoperatively detected in a subcentimeter thyroid nodule that was confirmed to be a PTC with aggressive biological behavior is reported. CONCLUSIONS The judicious indication of FNA and use of molecular screening can potentially help in predicting aggressive behavior of small-sized thyroid cancers and in identifying patients who may benefit from early and more extensive therapy.

Lethal Outcomes In Klippel-Trenaunay Syndrome

Klippel-Trenaunay syndrome (KTS) is an uncommon congenital angiodysplasia that manifests in infancy and is characterized by venous and lymphatic malformations of the skin, soft tissue, and bone causing limb hypertrophy. We report 2 patients with long-term KTS who developed lethal complications from uncommon and unusual manifestations. The 1st patient was a female with KTS who at 2 years of age underwent a below-the-knee amputation for a massively hypertrophied and malformed left foot. Two years later she required additional surgical removal of vascular malformations involving her left calf with extension to the groin, pubis, and ipsilateral abdomen. Fifteen years later she underwent splenectomy (400 g) revealing multifocal, cystically dilated vascular channels distorting the splenic architecture and died suddenly of massive intra-abdominal hemorrhage on the 2nd postoperative day. The 2nd patient was a 72-year-old male with long-standing KTS who presented with debilitating chronic penile and scrotal edema. Surgical excision of his lymphedematous scrotal and penile skin revealed a low-grade angiosarcoma arising in the setting of chronic lymphedema. The patient died shortly after surgery from massive hemorrhage due to traumatic rupture of malformed leg vessels. KTS may lead to significant morbidity and mortality, and pathologic consequences from long-term KTS have been rarely reported. These cases illustrate the risk of lethal hemorrhage, organomegaly from protracted vascular malformation, and development of vascular neoplasia associated with chronic lymphedema in KTS.

Surveillance for Recurrent Cancers and Vaginal Epithelial Lesions in Patients With Invasive Cervical Cancer After Hysterectomy

OBJECTIVES To examine whether women who have had a hysterectomy for cervical cancer may be at an increased risk of vaginal epithelial lesions. METHODS We studied 147 patients with invasive cervical carcinoma (76 squamous cell carcinomas [SCCs], 60 adenocarcinomas [ADCs], and 11 adenosquamous cell carcinomas) who were treated by hysterectomy and had vaginal pathologic follow-up for a mean period of 43.3 months. RESULTS Of the patients, 15.0% (22/147) developed vaginal intraepithelial neoplasia (VAIN) or recurrence after hysterectomy, including two recurrent carcinomas and eight high-grade VAINs. More important, these high-grade VAINs or recurrent carcinomas were detected only in patients with cervical SCC within the first two years after hysterectomy but not in patients with cervical ADC. Eleven (23.4%) of 47 patients had at least one positive high-risk human papillomavirus (hrHPV) testing result during the follow-up period, and VAIN was detected in 54.5% (6/11) of patients with an hrHPV-positive result compared with 16.7% (6/36) with an hrHPV-negative result. CONCLUSIONS Our results indicate that women with cervical cancer are at an increased risk of VAIN besides recurrence, and women with cervical SCC are more prone to high-grade VAIN/recurrence, especially within the first two years after hysterectomy. The significantly increased detection rate of VAINs/recurrence in the hrHPV-positive group suggests vaginal cytology and HPV cotesting might be the preferred method for surveillance in these women.

Endobronchial Ultrasound-Transbronchial Needle Aspiration for Lymphoma in Patients With Low Suspicion for Lung Cancer and Mediastinal Lymphadenopathy

BACKGROUND Although the role for endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) for metastatic lung cancer is well described, the usefulness of EBUS-TBNA for diagnosing lymphoma is less well defined. We aimed to determine the diagnostic accuracy for lymphoma of EBUS-TBNA with rapid, on-site evaluation in the evaluation of mediastinal lymphadenopathy in patients with a low-suspicion for lung cancer. METHODS Medical records for all EBUS-TBNA (381 total procedures) from 2007 to 2013 were reviewed, and procedure indication, prior workup, cytologic diagnosis, histologic follow-up, and available ancillary studies were abstracted. Intraoperative rapid on-site evaluation was performed for 170 of 173 patients (98%), and evaluations for 133 (78%) were adequate for diagnosis. RESULTS Of 381 patients, 173 (45.4%) underwent mediastinal tissue sampling to evaluate indeterminate mediastinal lymphadenopathy; 208 patients with known or suspected lung cancer were excluded. EBUS-TBNA provided a definitive diagnosis (predominantly carcinoma and granulomatous inflammation) in 71%. EBUS-TBNA was diagnostic in 8 of 16 patients (50%) where the final diagnosis of lymphoma in 16 was confirmed (9 non-Hodgkin, 6 Hodgkin, and 1 posttransplant lymphoproliferative disorder). EBUS-TBNA was indeterminate in 3 (19%), inadequate in 4 (25%), and falsely negative in 1 (6%). Histologic follow-up was available in 10 patients (63%). When the specimen was adequate for diagnosis, sensitivity for lymphoma was 89%. CONCLUSIONS EBUS-TBNA has high sensitivity and a low false-negative rate for lymphoproliferative disorders when specimens are adequate for analysis and provides alternative diagnoses in most cases, thus reducing the need for mediastinoscopy. Rapid, on-site evaluation was nondiagnostic in approximately 25% of patients; performing EBUS-TBNA in the operating room facilitated conversion to mediastinoscopy and definitive diagnosis in this setting.

Genomic Characterization of a Metastatic Alveolar Rhabdomyosarcoma Case Using FISH Studies and CGH+SNP Microarray Revealing FOXO1-PAX7 Rearrangement with MYCN and MDM2 Amplification and RB1 Region Loss

Rhabdomyosarcomas (RMS) are rare, heterogeneous, soft tissue sarcomas and a common type of childhood malignancy with a distinct histomorphology. At the molecular level, alveolar rhabdomyosarcoma (ARMS), a subtype of RMS, harbors a signature genetic makeup characterized by specific translocations. The type of translocation and associated genetic aberrations correlate with disease progression, hence we used multiple molecular modalities including high-resolution array comparative genomic hybridization to explore the oncogenic gene fusion and associated copy number variations in a case of metastatic ARMS. We describe a case where traditional cytogenetic and molecular methods yielded inconclusive results in detecting the FOXO1 gene rearrangement. However, microarray analysis identified the essential FOXO1-PAX7 aberration and additional submicroscopic genomic alterations, including amplification of MYCN and MDM2 and deletion of RB1.

Aneurysmal fibrous histiocytomas with recurrent rearrangement of the PRKCD gene and LAMTOR1-PRKCD fusions

Aneurysmal fibrous histiocytoma (FH) is an uncommon variant of cutaneous benign fibrous histiocytoma/dermatofibroma1 typically presenting as a solitary, pigmented, up to several centimeters in size nodule on extremities or trunk of middle-aged adults.1,2 Some cases may be clinically concerning for melanoma or vascular neoplasia.1 The local recurrence rate is ~20%, if incompletely excised.1 This article is protected by copyright. All rights reserved.