Integrated genomic analysis using chromosomal microarray, fluorescence in situ hybridization and mate pair analyses: Characterization of a cryptic t(9;22)(p24.1;q11.2)/BCR-JAK2 in myeloid/lymphoid neoplasm with eosinophilia.

The 2016 World Health Organization entity 'Myeloid/lymphoid neoplasms with eosinophilia and rearrangement of PDGFRA, PDGFRB or FGFR1, or with PCM1-JAK2' encompasses a group of rare neoplasms that result from the formation of a fusion gene that leads to expression of an aberrant tyrosine kinase. This entity also contains variant JAK2 fusion partners, and detection of this defining event can be facilitated by various cytogenetic and molecular methods. Cryptic rearrangements of 9p24/JAK2 can be particularly challenging to identify. We describe the use of chromosomal microarray analysis (CMA), fluorescence in situ hybridization (FISH) with a probe for JAK2, and genomic mate pair analysis to describe a complex karyotype with a t(9;22) that produced a functional BCR-JAK2 fusion, leading to the appropriate diagnosis for the patient. This case highlights the importance of using an integrated genomic approach to fully define complex aberrations to assign proper diagnoses.

Molecular profiling of vitreous fluid by massively parallel sequencing: a case series.

INTRODUCTION: In cases of suspected intraocular malignancy, vitreous may be the preferred pathologic sample; however, cellularity may be insufficient for definitive cytopathological diagnosis. Ancillary methodology to study vitreous fluid aspiration for mutational analysis may assist in treatment decisions. MATERIALS AND METHODS: Three individual patient vitreous humor samples were received in the laboratory for mutation testing. The samples were collected during standard of care and analyzed for routine cytopathology. In each case, cytopathology was inconclusive and mutational analyses to support diagnostic suspicions were clinically requested. Based on the clinically and pathologically suspected diagnoses, an appropriate massively parallel sequencing assay previously validated for clinical use was performed using DNA extracted from vitreous samples that had previously undergone various processing. Nucleic acid yield was assessed by fluorometric or spectrophotometric methods, with yield ranging from 2.7 to 86.5 ng. Library preparations were performed using standard laboratory protocols. RESULTS: Two of the cases were suspicious for melanoma and a 50-gene solid tumor panel was performed. The third case was worrisome for vitreoretinal lymphoma and a 49-gene myeloid panel was performed. CONCLUSIONS: In all cases, the molecular profiling assisted with the clinical assessment and/or management of each patient.

Three-year review of gene sequencing analyses of pulmonary non-small cell lung cancers obtained by fine-needle aspiration or surgical biopsy: mutation and failure rates.

INTRODUCTION: Mutational analysis is becoming the standard of diagnostic workup. Sufficient amounts of and quality tumor tissue can be challenging when faced with a small biopsy or biopsy by fine-needle aspiration (FNA). MATERIALS AND METHODS: We reviewed the failures of FNA and surgical biopsy to yield sequencing data and causes thereof over a 3-year period. We executed a search of the laboratory information system for requests to perform our targeted 50-gene assay by massively parallel sequencing on surgical biopsies and FNAs and compared the results. RESULTS: Three failure causes were assigned: insufficient tissue as defined by the pathologist, failure to meet quality control indicating library preparation or sequencing failure, and failure of pre-qualifying step for DNA integrity. A total of 327 of 354 cases were successfully sequenced (92%), including 151 FNA cases and 203 biopsies, with 16 (10.6%) and 11 (5.4%) failures, respectively. The Fisher's exact test two-tailed P-value equals 0.050381, making the difference between FNA and biopsy not statistically significant. Insufficient tissue, quality control failure, and DNA integrity were identified as the cause of the failure in 10 (62%), 3 (19%), and 3 (19%) FNA biopsies, and in 5 (45.5%), 1 (9%), and 5 (45.5%) surgical biopsies. The most common cause of failure of FNA was insufficient tissue. For surgical biopsies, DNA integrity and insufficient tissue were equally as likely to be implicated. Both FNA and surgical biopsy have a low failure rate overall without statistical significance between them. CONCLUSIONS: Although surgical biopsy is considered the gold standard, these findings support FNA as an equal modality.

Myeloid sarcoma identified on liquid-based cervical cytology samples: A report of two cases.

The purpose of the Papanicolaou (Pap) smear is to detect primary squamous lesions of the uterine cervix. Although most successful at detection of squamous lesions, the Pap may also detect metastatic carcinomas, sarcomas, and melanomas. We report two rare cases of myeloid sarcoma (MS) of the uterine cervix identified on screening Pap smears with concurrent confirmatory cervical biopsies. The purpose of our study is to identify and report cytologic features of MS on Pap smears utilizing a liquid-based ThinPrep method, which has not been previously documented in literature. Two Pap smears were identified from the pathology laboratory information system, both with positive cervical biopsy findings of MS. Both women, age 40 and 39, presented with ureteral obstruction, hydronephrosis, and past medical histories significant for acute myeloid leukemia (AML). On imaging, cervical masses were identified, and subsequent work-up with Pap smears and biopsies were performed. Cytologic examination of the ThinPrep Pap smears were negative for squamous intraepithelial lesion. Atypical hematologic cells were seen in the background with irregular nuclear contours, increased nuclear to cytoplasmic ratios, variably prominent nucleoli, and variable amounts of agranular cytoplasm. The biopsy confirmed these findings to represent MS. MS is defined as a tumor mass of myeloblasts or immature myeloid cells occurring in an extramedullary site. This rarely involves the female genital tract, about 50 reported cases. Although very rare, MSs in the setting of a history of AML are able to be identified on liquid-based ThinPrep smears.