Development and evaluation of ActSeq: A targeted next-generation sequencing panel for clinical oncology use.

PURPOSE: The demand for high-throughput genetic profiling of somatic mutations in cancer tissues is growing. We sought to establish a targeted next generation sequencing (NGS) panel test for clinical oncology practice. METHODS: Customized probes were designed to capture exonic regions of 141 genes selected for the panel, which was aimed for the detection of clinically actionable genetic variations in cancer, including KRAS, NRAS, BRAF, ALK, ROS1, KIT and EGFR. The size of entire targeted regions is 0.8 Mb. Library preparation used NEBNext Ultra II FS kit coupled with target enrichment. Paired-end sequencing was run on Illumina NextSeq 500 at a read length of 150 nt. A bioinformatics workflow focusing on single nucleotide variant and short insertions and deletions (SNV/indel) discovery was established using open source, in-house and commercial software tools. Standard reference DNA samples were used in testing the sensitivity and precision and limit of detection in variant calling. RESULTS: The general performance of the panel was observed in pilot runs. Average total reads per sample ranged from 30 million to 48 million, 73% ~82% unique reads. All runs had more than 99% average mapping rate. Mean target coverage ranged from 727x to 879x. Depth of coverage at 50x or more reached 87% of targeted region and 60% of targeted region received 500x or more coverage depth. Using OncoSpan HD827 DNA, which bears 144 variants (SNV/indel) from 80 genes that are within the targeted region on the panel, our somatic variant calling pipeline reached 97% sensitivity and 100% precision respectively, with near 48 million reads. High concordance with orthogonal approaches in variant detection was further verified with 7 cancer cell lines and 45 clinical specimens. CONCLUSION: We developed a NGS panel with a focus on clinically actionable gene mutations and validated the performance in library construction, sequencing and variant calling. High concordance with reference materials and orthogonal mutation detection was observed.

EWSR1-WT1 gene fusions in neoplasms other than desmoplastic small round cell tumor: a report of three unusual tumors involving the female genital tract and review of the literature.

Desmoplastic small round cell tumor (DSRCT) is a high-grade round cell sarcoma that typically arises in the abdominopelvic cavity of young males, co-expresses keratins and desmin, and carries a pathognomonic EWSR1-WT1 gene fusion. The EWSR1-WT1 gene fusion is generally considered specific for DSRCT, although there are two reports of this fusion in tumors otherwise lacking features of DSRCT. We report three female genital tract tumors with EWSR1-WT1 fusions but showing morphologic and immunohistochemical features incompatible with DSRCT. The tumors occurred in the uterine cervix, uterine corpus/ovaries, and vagina, respectively, of 46, 30, and 20-year-old women. Two tumors consisted of a sheet-like to fascicular proliferation of relatively uniform spindled to occasionally more epithelioid cells arrayed about thick-walled, hyalinized, and capillary-sized vessels, with distinctive areas of pseudovascular change, and absence of desmoplastic stroma. The third tumor resembled a monomorphic spindle cell sarcoma with necrosis. All had diffuse desmin and variable but more limited keratin expression, two of three expressed smooth muscle actin, and all were negative for h-caldesmon, CD10, estrogen receptor, myogenin, N-terminus WT-1, and S100 protein. One patient received neoadjuvant chemotherapy and radiation therapy followed by resection and is disease-free 42 months after diagnosis. Another patient was managed by resection only and is disease-free 9 months after initial diagnosis. The remaining patient recently underwent resection of multifocal pelvic disease. Comprehensive differential gene expression analysis on two tumors compared to two classic DSRCTs with known EWSR1-WT1 fusions resulted in 1726 genes that were differentially expressed (log2 fold change >2 or < -2) and statistically significant (FDR < 5%). In combination with previous reports, our findings suggest pleiotropy of the EWSR1-WT1 fusion is possible and not limited to DSRCT. Subsets of non-DSRCT EWSR1-WT1 positive tumors may represent discrete entities, but further study is necessary.

Assessment of common somatic mutations of EGFR, KRAS, BRAF, NRAS in pulmonary non-small cell carcinoma using iPLEX® HS, a new highly sensitive assay for the MassARRAY® System.

Increased early detection and personalized therapy for lung cancer have coincided with greater use of minimally invasive sampling techniques such as endobronchial ultrasound-guided biopsy (EBUS), endoscopic ultrasound-guided biopsy (EUS), and navigational biopsy, as well as thin needle core biopsies. As many lung cancer patients have late stage disease and other comorbidities that make open surgical procedures hazardous, the least invasive biopsy technique with the highest potential specimen yield is now the preferred first diagnostic study. However, use of these less invasive procedures generates significant analytical challenges for the laboratory, such as a requirement for robust detection of low level somatic mutations, particularly when the starting sample is very small or demonstrates few intact tumor cells. In this study, we assessed 179 clinical cases of non-small cell lung carcinoma (NSCLC) that had been previously tested for EGFR, KRAS, NRAS, and BRAF mutations using a novel multiplexed analytic approach that reduces wild-type signal and allows for detection of low mutation load approaching 1%, iPLEX® HS panel for the MassARRAY® System (Agena Bioscience, San Diego, CA). This highly sensitive system identified approximately 10% more KRAS, NRAS, EGFR and BRAF mutations than were detected by the original test platform, which had a sensitivity range of 5-10% variant allele frequency (VAF).

Fatal postpartum spontaneous liver rupture: case report and literature review.

Maternal hepatic rupture is a rare complication of pregnancy that can be fatal to both mother and child. This phenomenon is most often associated with preeclampsia/eclampsia and/or HELLP syndrome, which is defined by a collection of clinical features including hemolysis (H), elevated liver enzymes (EL), and a low platelet count (LP). These disease processes are typically identified and treated during pregnancy, often in the last trimester. The described case is unusual in that the decedent had no known history of preeclampsia/eclampsia or HELLP syndrome during this pregnancy, and she died suddenly several days postpartum of liver rupture with massive intraperitoneal hemorrhage following a routine cesarean section delivery and an uneventful hospital course. Similar cases are infrequent in the literature, which is reviewed in this report.

Distribution of human papillomavirus genotypes in invasive squamous carcinoma of the vulva.

Many studies have established a critical role for human papillomavirus (HPV) in the development of anogenital squamous neoplasia. In this report, we show the distribution of 37 high- and low-risk HPV types in 116 cases of invasive squamous vulvar carcinoma. Sections from paraffin-embedded tissue blocks were dissected as necessary to select areas of invasive carcinoma. Clinical and pathologic variables were analyzed using t-tests, univariate odds ratios and logistic regression analysis. Seventy percent of cases were HPV-positive, with an average patient age of 65 years (n=81). HPV-negative cases (n=35) had a higher average age (70 years), but these populations were not statistically different (t=1.65, P=0.10). HPV16 was most common (n=65). Other HPV types were less frequent (HPV33, n=12; HPV45, n=4; HPV52 and 6, each n=3; HPV18, 53 and 62, each n=2). Additional HPV types were identified only once. Multiple infections typically included HPV16 (12/14 cases). Tumors showing low-risk HPV (11 cases) and low-risk HPV only (three cases) were uncommon. Regional node metastasis was documented in 29 of 116 tumors, and 8/9 HPV-positive nodes contained HPV types identical to the primary tumor. Of tumor types, warty carcinoma was most strongly associated with high-risk HPV (odds ratio 4.34, 95% confidence interval 1.32-18.45), particularly high-risk HPVs other than type 16 (odds ratio 9.04, 95% confidence interval 1.60-54.00). Tumors associated with any HPV type (odds ratio 0.40, 95% confidence interval 0.14-1.17), any high-risk type (odds ratio 0.36, 95% confidence interval 0.12-1.08), or type 16 alone (odds ratio 0.34, 95% confidence interval 0.11-1.12) were less likely to metastasize than HPV-negative tumors. Correcting for possible confounding variables, such as patient age and tumor histology, linear logistic regression analysis confirmed this association (high-risk HPV odds ratio 0.28, 95% confidence interval 0.09-0.89).

Detection of the JAK2V617F mutation by asymmetric PCR and melt curve analysis.

The chronic myeloproliferative disorders (CMPDs) are a heterogeneous group of clonal hematopoietic diseases characterized by production of increased numbers of mature leukocytes, erythrocytes, and/or platelets. Clinically these disorders are often insidious in onset, produce nonspecific thrombotic or hemorrhagic complications, and can be easily confused with a variety of benign, reactive conditions. Thus, confirming a CMPD can be difficult as it is often a diagnosis of exclusion. The recently identified JAK2(V617F) mutation is frequently present in the classic CMPDs polycythemia vera, essential thrombocythemia, and chronic idiopathic myelofibrosis. JAK2(V617F) determination has proven to be a useful diagnostic tool in patients with some clinical features suggestive for a CMPD, and may have benefit as a way to monitor known disease. There are several published molecular assays for the JAK2(V617F) target, of variable sensitivity and technical complexity, many of which are not easily replicated in a typical clinical laboratory. We present a robust, sensitive PCR/melt curve assay for the JAK2(V617F) mutation which uses the widely available Roche LightCycler platform, and is thus applicable to many clinical molecular laboratories.