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Purpose: To assess the clinical and pharmacodynamic activity of dovitinib in a treatment-resistant, molecularly enriched non–muscle-invasive urothelial carcinoma of the bladder (NMIUC) population.Experimental Design: A multi-site pilot phase II trial was conducted. Key eligibility criteria included the following: Bacillus Calmette-Guerin (BCG)-unresponsive NMIUC (>2 prior intravesical regimens) with increased phosphorylated FGFR3 (pFGFR3) expression by centrally analyzed immunohistochemistry (IHC+) or FGFR3 mutations (Mut+) assessed in a CLIA-licensed laboratory. Patients received oral dovitinib 500 mg daily (5 days on/2 days off). The primary endpoint was 6-month TURBT-confirmed complete response (CR) rate.Results: Between 11/2013 and 10/2014, 13 patients enrolled (10 IHC+ Mut−, 3 IHC+ Mut+). Accrual ended prematurely due to cessation of dovitinib clinical development. Demographics included the following: median age 70 years; 85% male; carcinoma in situ (CIS; 3 patients), Ta/T1 (8 patients), and Ta/T1 + CIS (2 patients); median prior regimens 3. Toxicity was frequent with all patients experiencing at least one grade 3–4 event. Six-month CR rate was 8% (0% in IHC+ Mut−; 33% in IHC+ Mut+). The primary endpoint was not met. Pharmacodynamically active (94–5,812 nmol/L) dovitinib concentrations in urothelial tissue were observed in all evaluable patients. Reductions in pFGFR3 IHC staining were observed post-dovitinib treatment.Conclusions: Dovitinib consistently achieved biologically active concentrations within the urothelium and demonstrated pharmacodynamic pFGFR3 inhibition. These results support systemic administration as a viable approach to clinical trials in patients with NMIUC. Long-term dovitinib administration was not feasible due to frequent toxicity. Absent clinical activity suggests that patient selection by pFGFR3 IHC alone does not enrich for response to FGFR3 kinase inhibitors in urothelial carcinoma. Clin Cancer Res; 23(12); 3003–11. ©2016 AACR.

Supplementary Table S3: Baseline Tumor pFGFR3 IHC Intensity

Supplementary Figure Legends

Dermatofibrosarcoma protuberans (DFSP) is a translocation-associated, low-grade sarcoma with fibroblastic differentiation. It is the most common superficial sarcoma, almost exclusively arising within the dermis. In a minority of cases, there is a transition from the conventional morphology to a fibrosarcomatous pattern, known as a fibrosarcomatous DFSP (FS-DFSP). Although a number of different molecular alterations have been described to account for this transformation, it remains poorly understood. Herein we report the first case of a FS-DFSP with a fusion between ERG, an ETS family transcription factor, and MAP3K7CL, a kinase gene rarely observed in fusion gene events.

Next generation sequencing (NGS) has introduced new types of data, such as variant allele frequencies (VAFs), into the workup of acute myeloid leukemias (AML). There is interest in using NGS to prognosticate disease behavior and monitor residual disease, but the attribution of sequencing data entirely to the leukemic clone may be confounded by VAF contribution from background non-leukemic populations and undetected copy number aberrations. Sixty-eight patients with AML were evaluated by a clinically validated gene sequencing panel at our institution from 2015 to 2018. No correlation was found with a direct comparison of blast counts and VAFs in both primary- and secondary-AML (

Malignant melanoma (MM) may display highly variable phenotypic diversity, sometimes associated with loss of immunohistochemical melanocytic markers and acquisition of nonmelanocytic lineage of differentiation. Primary cutaneous MM with rhabdomyosarcomatous differentiation is extremely rare with only 5 reported cases in the literature. To date, a chronological progression of a MM to rhabdomyosarcoma has not been conclusively documented. A 96-year-old man underwent a re-excision of an "atypical fibroxanthoma" of the forearm, which revealed a small lentigo maligna melanoma associated with a dominant dermal high-grade spindle cell nodule admixed with a population of malignant polygonal epithelioid cells. On immunohistochemical studies, the spindle cells were completely negative for all melanocytic markers, whereas a small population of polygonal neoplastic cells at the periphery was positive for Desmin and Myo-D1, supporting early rhabdomyosarcomatous transformation. Several subsequent re-excisions demonstrated merely nodules of malignant pleomorphic epithelioid cells with rhabdomyosarcomatous differentiation and devoid of melanocytic markers. In addition, both rhabdomyosarcomatous component and original MM displayed identical mutations. Therefore, the histologic, immunohistochemical, and molecular findings documented for the first time a chronological progression from an invasive MM to a pleomorphic rhabdomyosarcoma through an intermediate stage of undifferentiated sarcoma/atypical fibroxanthoma. Interestingly, subsequent recurrences of pure rhabdomyosarcomatous component displayed skip lesions/microsatellitosis, marked tumor-infiltrative lymphocytes, and rare junctional nests of rhabdomyosarcomatous cells in the epidermis, histologic features that were not described in primary cutaneous rhabdomyosarcoma and therefore could serve as morphologic clues to the diagnosis of rhabdomyosarcomatous transformation in an MM.

Xanthomas are histiocytic lesions of the skin, soft tissue, and bone and are generally considered to be reactive in nature. When they arise in the bones of the jaw, they are referred to as central xanthomas. New evidence supports the hypothesis that central xanthomas are a separate and distinct entity from their extragnathic counterparts. Noonan syndrome (NS) is an autosomal dominant disorder that has been associated with giant cell lesions, which also commonly occur in the jaw. We present a case of a 15-year-old boy with NS who presented with a radiolucent lesion of the mandible that on excision was found to be a central xanthoma. Although giant cell lesions have been well described in NS, xanthomas of the jaw have not been reported. We will also discuss the entities that must be excluded before making a diagnosis of central xanthoma, as this can affect both treatment and follow-up.

Pulmonary adenofibroma (PAF) is a rare neoplasm that may be related to solitary fibrous tumor (SFT). A subset of PAFs harbor the NAB2-STAT6 fusion that is typical of SFT, but a significant proportion do not. Their distinction is clinically important as SFTs can potentially have an aggressive clinical course, while there has been no report of a PAF behaving in a malignant fashion. We report a case of a 60-year-old male who developed a SFT and PAF in the same lung. The SFT harbored a NAB2-STAT6 fusion, while the PAF did not have any identifiable fusion. This case represents the first instance of a single patient with both of these tumors occurring simultaneously in the same lung.

Isocitrate dehydrogenases 1 and 2 (IDH1/2) are important metabolic enzymes that convert isocitrate to α-ketoglutarate. IDH1/2 mutations are associated with the development of multiple malignancies. In this study, we examine the prevalence and features of non-small cell lung cancers (NSCLC) with IDH1/2 mutations. From May 2013 to March 2017, 800 lung cancer samples were successfully sequenced for somatic mutations on the Ion Torrent PGM with the 50-gene AmpliSeq Cancer Hotspot Panel v2 on the Ion Torrent PGM (318 chip). Variants were identified using the Ion Torrent Variant Caller Plugin and reference genome hg19. Golden Helix's SVS software was used for variant annotation and prediction of significance. Nine samples (1.1%) from 8 patients harbored an IDH1 (3 p.R132C and 2 p.R132L) or IDH2 mutation (p.R140W, p.R172S, and p.R172T). All patients' tumors had adenocarcinoma histology, and all patients had a smoking history. Eighty-eight percent of patients' tumors had a coexisting KRAS mutation and 6 of 8 were diagnosed at greater than 70 years of age. Five patients presented with stage IV disease and 3 with stage I. After comparison to a cohort of KRAS-mutated NSCLC with a history of smoking, IDH-mutated cases were significantly older but presented with similar rates of advanced-stage disease and sex distribution. Additional studies are needed to understand the role of IDH1/2 mutations in the development of NSCLC, but such patients who have poor prognostic indicators (KRAS mutation and advanced stage at presentation) may benefit from IDH1/2-directed therapies.

The tumor suppressor gene TP53 is the most frequently mutated gene in human cancer. It encodes p53, a DNA-binding transcription factor that regulates multiple genes involved in DNA repair, metabolism, cell cycle arrest, apoptosis, and senescence. TP53 is associated with human cancer by mutations that lead to a loss of wild-type p53 function as well as mutations that confer alternate oncogenic functions that enable them to promote invasion, metastasis, proliferation, and cell survival. Identifying the discrete TP53 mutations in tumor cells may help direct therapies that are more effective. In this study, we identified the frequency of individual TP53 mutations in patients with colon adenocarcinoma (48%), non–small cell lung carcinoma (NSCLC) (36%), and glioma/glioblastoma (28%) at our institution using next-generation sequencing. We also identified the occurrence of somatic mutations in numerous actionable genes including BRAF, EGFR, KRAS, IDH1, and PIK3CA that occurred concurrently with these TP53 mutations. Of the 480 tumors examined that contained one or more mutations in the TP53 gene, 219 were colon adenocarcinomas, 215 were NSCLCs, and 46 were gliomas/glioblastomas. Among the patients positive for TP53 mutations diagnosed with colon adenocarcinoma, 50% also showed at least one mutation in pathogenic genes of which 14% were BRAF, 33% were KRAS, and 3% were NRAS. Forty-seven percent of NSCLC patients harboring TP53 mutations also had a mutation in at least one actionable pathogenic variant with the following frequencies: BRAF: 4%, EGFR: 10%, KRAS: 28%, and PIK3CA: 4%. Fifty-two percent of patients diagnosed with glioma/glioblastoma with a positive TP53 mutation had at least one concurrent mutation in a known pathogenic gene of which 9% were CDKN2A, 41% were IDH1, and 11% were PIK3CA.

Presently, the ability to study disease at the most fundamental molecular level has led to a reclassification of human cancers into numerous subtypes that vary in disease progression and response to therapy. Similar to most solid tumors, breast cancer is a heterogeneous disease with considerable variation in histologic and biological features. Triple-negative breast cancer (TNBC) is a subtype of breast cancer in which the estrogen receptor and progesterone receptor are not expressed, and human epidermal growth factor-receptor 2 is not amplified or overexpressed. Data derived from highly complex molecular technologies, such as microarrays and next-generation sequencing, have identified gene expression and somatic mutation profile subsets of TNBC that reflect biological behavior more accurately and may lead to further effective therapeutic targets, better prognosis, and improved outcomes. Herein, we review the genomic findings of TNBC and discuss current efforts in precision medicine as they relate to TNBC.

Matching of actionable tumor mutations with targeted therapy increases response rates and prolongs survival in lung cancer patients. Drug development and trials targeting genetic alterations are expanding rapidly. We describe the role of a Molecular Tumor Board (MTB) in the design of molecularly informed treatment strategies in our lung cancer patient population. Tumor DNA was sequenced using a 50-gene targeted next-generation sequencing panel. Cases were evaluated by a multidisciplinary MTB who suggested a course of treatment based on each patient’s molecular findings. During a three-year period, 21 lung cancer patients were presented at the MTB. All patients lacked common activating EGFR mutations and ALK rearrangements. One patient had Stage IIIb disease; all others were Stage IV; 18 patients had received ≥1 prior line of therapy (range 0–5). Suggestions for treatment with a targeted therapy were made for 19/21 (90.5%) patients, and four patients (21%) underwent treatment with a targeted agent, two as part of a clinical trial. Identified barriers to treatment with targeted therapy included: ineligibility for clinical trials (n ​= ​2), lack of interest in study/distance to travel (n ​= ​2), lack of disease progression (n ​= ​2), poor performance status (n ​= ​5), decision to treat next with immunotherapy (n ​= ​3), and unknown (n ​= ​1). For the majority of lung cancer patients, the MTB provided recommendations based on tumor genetic profiles. Identified barriers to treatment suggest that presentation to the MTB at earlier stages of disease may increase the number of patients eligible for treatment with a genetically informed targeted agent.

Objectives: To describe three methods used to screen for frameshift mutations in exon 9 of the CALR gene. Methods: Genomic DNA from 47 patients was extracted from peripheral blood and bone marrow using the EZ1 DNA Blood Kit (Qiagen, Valencia, CA) and quantified by the Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen, San Diego, CA). After clinical history, cytogenetics, and molecular tests, patients were diagnosed with either clonal or nonclonal hematologic diseases. CALR screening was primarily performed using fragment analysis polymerase chain reaction, then next-generation sequencing and Sanger sequencing. Results: Among the 18 patients diagnosed with clonal diseases, one had acute myeloid leukemia (positive for trisomy 8), and 17 had myeloproliferative neoplasms (MPNs), including chronic myeloid leukemia (CML), essential thrombocythemia (ET), primary myelofibrosis (PMF), and polycythemia vera (PV). Patients with CML were positive for the BCR-ABL1 fusion. Ten patients were positive for JAK2 (PMF, n = 1; ET, n = 2; PV, n = 7), and three were CALR positive (ET, n = 1; PMF, n = 2). Patients diagnosed with a nonclonal disease were negative for JAK2 , BCR-ABL , and CALR mutations. Conclusions: Screening for CALR mutations is essential in BCR-ABL –negative MPNs since it not only provides valuable diagnostic and prognostic information but also identifies potential treatment targets. Since this study describes the importance of screening for known and novel biomarkers, we described in detail three methods that could be easily integrated into a clinical laboratory.

Detection of somatic mutations in non–small cell lung cancers (NSCLCs), especially adenocarcinomas, is important for directing patient care when targeted therapy is available. Here, we present our experience with genotyping NSCLC using the Ion Torrent Personal Genome Machine (PGM) and the AmpliSeq Cancer Hotspot Panel v2. We tested 453 NSCLC samples from 407 individual patients using the 50 gene AmpliSeq Cancer Hotspot Panel v2 from May 2013 to July 2015. Using 10 ng of DNA, up to 11 samples were simultaneously sequenced on the Ion Torrent PGM (316 and 318 chips). We identified variants with the Ion Torrent Variant Caller Plugin, and Golden Helix's SVS software was used for annotation and prediction of the significance of the variants. Three hundred ninety-eight samples were successfully sequenced (12.1% failure rate). In all, 633 variants in 41 genes were detected with a median of 2 (range of 0 to 7) variants per sample. Mutations detected in BRAF, EGFR, ERBB2, KRAS, NRAS, and PIK3CA were considered potentially actionable and were identified in 237 samples, most commonly in KRAS (37.9%), EGFR (11.1%), BRAF (4.8%), and PIK3CA (4.3%). In our patient population, all mutations in EGFR, KRAS, and BRAF were mutually exclusive. The Ion Torrent Ampliseq technology can be utilized on small biopsy and cytology specimens, requires very little input DNA, and can be applied in clinical laboratories for genotyping of NSCLC. This targeted next-generation sequencing approach allows for detection of common and also rare mutations that are clinically actionable in multiple patients simultaneously.

Accurate identification of somatic mutations in formalin-fixed, paraffin-embedded tumor tissue is required for enrollment into clinical trials for many novel targeted therapeutics, including trials requiring EGFR mutation status in non–small-cell lung carcinomas. Central clinical trial laboratories contracted to perform this analysis typically rely on US Food and Drug Administration–approved targeted assays to identify these mutations. We present two cases in which central laboratories inaccurately reported EGFR mutation status because of improper identification and isolation of tumor material and failure to accurately report assay limitations, resulting in enrollment denial. Such cases highlight the need for increased awareness by clinical trials of the limitation of these US Food and Drug Administration–approved assays and the necessity for a mechanism to reevaluate discordant results by alternative laboratory-developed procedures, including clinical next-generation sequencing.

Cholangiocarcinoma is a heterogeneous malignant process, which is further classified into intrahepatic cholangiocarcinoma (ICC) and extrahepatic cholangiocarcinoma (ECC). The poor prognosis of the disease is partly due to the lack of understanding of the disease mechanism. Multiple gene alterations identified by various molecular techniques have been described recently. As a result, multiple targeted therapies for ICC and ECC are being developed. In this study, we identified and compared somatic mutations in ICC and ECC patients using next generation sequencing (NGS) (Ampliseq Cancer Hotspot Panel v2 and Ion Torrent 318v2 chips). Eleven of 16 samples passed internal quality control established for NGS testing. ICC cases (n = 3) showed IDH1 (33.3%) and NRAS (33.3%) mutations. Meanwhile, TP53 (75%), KRAS (50%), and BRAF (12.5%) mutations were identified in ECC cases (n = 8). Our study confirmed the molecular heterogeneity of ICC and ECC using NGS. This information will be important for individual patients as targeted therapies for ICC and ECC become available in the future.

Background. Although genetic profiling of tumors is a potentially powerful tool to predict drug sensitivity and resistance, its routine use has been limited because clinicians are often unfamiliar with interpretation and incorporation of the information into practice. We established a Molecular Tumor Board (MTB) to interpret individual patients’ tumor genetic profiles and provide treatment recommendations. Patients and Methods. DNA from tumor specimens was sequenced in a Clinical Laboratory Improvement Amendments-certified laboratory to identify coding mutations in a 50-gene panel (n = 34) or a 255-gene panel (n = 1). Cases were evaluated by a multidisciplinary MTB that included pathologists, oncologists, hematologists, basic scientists, and genetic counselors. Results. During the first year, 35 cases were evaluated by the MTB, with 32 presented for recommendations on targeted therapies, and 3 referred for potential germline mutations. In 56.3% of cases, MTB recommended treatment with a targeted agent based on evaluation of tumor genetic profile and treatment history. Four patients (12.5%) were subsequently treated with a MTB-recommended targeted therapy; 3 of the 4 patients remain on therapy, 2 of whom experienced clinical benefit lasting >10 months. Conclusion. For the majority of cases evaluated, the MTB was able to provide treatment recommendations based on targetable genetic alterations. The most common reasons that MTB-recommended therapy was not administered stemmed from patient preferences and genetic profiling at either very early or very late stages of disease; lack of drug access was rarely encountered. Increasing awareness of molecular profiling and targeted therapies by both clinicians and patients will improve acceptance and adherence to treatments that could significantly improve outcomes. Implications for Practice: Case evaluation by a multidisciplinary Molecular Tumor Board (MTB) is critical to benefit from individualized genetic data and maximize clinical impact. MTB recommendations shaped treatment options for the majority of cases evaluated. In the few patients treated with MTB-recommended therapy, disease outcomes were positive and support genetically informed treatment.

Summary We report a unique case of a 59-year-old woman diagnosed with a benign phyllodes tumor (PT), which recurred twice in the same location over a 7-year period: first as a malignant PT and then as a malignant PT with coexisting spindle cell metaplastic breast carcinoma (MBC). The MBC was differentiated from the malignant PT by expression of cytokeratins (CKs) AE1/AE3, CK MNF-116, CK 5/6, and p63. Somatic mutation analysis using a next-generation sequencing platform revealed a shared mutation in F-box and WD repeat domain containing 7, a tumor suppressor gene that encodes a ubiquitin ligase–associated protein, in the original benign PT and the first recurrent malignant PT. Chromosomal microarray analysis showed shared genetic gains and losses between the malignant PT and MBC. This case highlights the utility of immunohistochemistry to differentiate malignant PT from spindle cell MBC, describes a novel mutation in PT, and demonstrates a biologic relationship between these 2 entities.

Immunotherapy is emerging as an effective new treatment for many cancers,1 but it has yet to translate into a proven clinical benefit for patients with glioblastoma.2 A purported limitation of applying immunotherapy to gliomas is the tumor-induced impairment of the immune response, especially within the tumor microenvironment.3 Regulatory T cells (Tregs), a subpopulation of CD4+ T cells, characterized by the expression of the unique transcription factor Forkhead box protein 3 (FoxP3), depress immune function. Expression of Helios, a member of the Ikaros transcription factor family, is a marker for thymic or natural Tregs (nTregs).4 Although Tregs share functionality and suppression mechanisms across cancers, an increasing number of reports indicate tumor-specific variability in the proportion of Tregs in peripheral blood and in the tumor microenvironment. There are even reports where elevated numbers of Tregs inversely correlate with patient survival and/or response to immune therapies.5–7 The association between glioblastoma and immunosuppression suggests that accurately assessing immune competency could help to predict survival and identify patients most likely to benefit from immunotherapy. Severe CD4+ lymphopenia early in treatment correlates with shorter survival,8 while extensive lymphocytic infiltration of glioblastoma improves survival.9,10 In patients with glioblastoma, the percentage of Tregs in peripheral blood has been reported to be increased compared with normal controls.11,12 In tumor tissue, the number of Tregs correlates with persistent tumor burden and poor immune antitumor response.13 Several recent studies examining the prognostic implications of Tregs in patients with glioblastoma have reported inconsistent results. Heimberger et al14 and Lohr et al9 found no association between Tregs and prognosis in patients with glioblastoma, while Jacobs et al15 reported a moderate, although not statistically significant, inverse association between tumor Tregs and survival. In contrast, Yue et al16 found a significant association between the density of Tregs infiltrating glioblastoma and poor prognosis. Comparing measurements of Tregs from immunohistochemistry (IHC) and flow cytometry across studies is challenging because there are variations in surface and intracellular markers measured and differences in the parent population used to quantify Treg proportions. In this prospective study, we used epigenetic quantitative (q)PCR, a novel methodology to more accurately measure lymphocyte populations, to determine the association between Tregs measured in tumor tissue and peripheral blood and overall survival (OS) in patients with newly diagnosed glioblastoma.

Advanced stage malignant melanoma often responds poorly to therapy with low survival rates. New therapeutic approaches are based upon a growing understanding of the underlying molecular abnormalities. We demonstrate the feasibility of a next generation sequencing (NGS) assay, which targets hotspots in 50 cancer genes, to assess genotypes that may influence therapeutic selection and response. DNA was extracted from formalin fixed paraffin embedded (FFPE) melanoma specimens to create multiplexed libraries which were sequenced. Of the 121 cases, BRAF mutations were present in 48 cases (40%) and NRAS mutations in 24 cases (20%). We identified other gene variants in 20 BRAF-mutated cases. Additional gene variants were also identified in the 57 BRAF wild-type cases. Four patients harbored different gene mutations at metastatic sites as compared to their primary lesions or metastasis from different sites. Concurrent gene variants may provide additional targets for future therapies and may suggest alternative mechanisms of secondary resistance.

Presently, the ability to study disease at the most fundamental molecular level has led to a reclassification of human cancers into numerous subtypes that vary in disease progression and response to therapy. Similar to most solid tumors, breast cancer is a heterogeneous disease with considerable variation in histologic and biological features. Triple-negative breast cancer (TNBC) is a subtype of breast cancer in which the estrogen receptor and progesterone receptor are not expressed, and human epidermal growth factor-receptor 2 is not amplified or overexpressed. Data derived from highly complex molecular technologies, such as microarrays and next-generation sequencing, have identified gene expression and somatic mutation profile subsets of TNBC that reflect biological behavior more accurately and may lead to further effective therapeutic targets, better prognosis, and improved outcomes. Herein, we review the genomic findings of TNBC and discuss current efforts in precision medicine as they relate to TNBC.

Targeted genomic profiling (TGP) using massively parallel DNA sequencing is becoming the standard methodology in clinical laboratories for detecting somatic variants in solid tumors. The variety of methodologies and sequencing platforms in the marketplace for TGP has resulted in a variety of clinical TGP laboratory developed tests (LDT). The variability of LDTs is a challenge for test-to-test and laboratory-to-laboratory reliability. At the University of Vermont Medical Center (UVMMC), we validated a TGP assay for solid tumors which utilizes DNA hybridization capture and complete exon and selected intron sequencing of 29 clinically actionable genes. The validation samples were run on the Illumina MiSeq platform. Clinical specificity and sensitivity were evaluated by testing samples harboring genomic variants previously identified in CLIA-approved, CAP accredited laboratories with clinically validated molecular assays. The Molecular Laboratory at Dartmouth Hitchcock Medical Center (DHMC) provided 11 FFPE specimens that had been analyzed on AmpliSeq Cancer Hotspot Panel version 2 (CHPv2) and run on the Ion Torrent PGM. A Venn diagram of the gene lists from the two institutions is shown. This provided an excellent opportunity to compare the inter-laboratory reliability using two different target sequencing methods and sequencing platforms. Our data demonstrated an exceptionally high level of concordance with respect to the sensitivity and specificity of the analyses. All clinically-actionable SNV and InDel variant calls in genes covered by both panels (n=17) were identified by both laboratories. This data supports the proposal that distinct gene panel designs and sequencing workflows are capable of making consistent variant calls in solid tumor FFPE-derived samples.

Pancreatic cancer is considered one of the most lethal cancers being the fourth leading cause of cancer deaths in adults in the United States because of the lack of early signs and symptoms and the lack of early detection. Pancreatic ductal adenocarcinoma (PDAC) is the most common histological type among pancreatic cancers, representing 80%–90% of all solid tumors of the pancreas. The majority of PDAC develops from three precursor lesions: pancreatic intraepithelial neoplasia, intraductual papillary mucinous neoplasm and mucinous cystic neoplasm. Although histologic tissue evaluation remains the gold standard for diagnosis, endoscopic ultrasound-guided fine needle aspiration has become the preferred modality for obtaining pathologic confirmation. At Dartmouth-Hitchcock Medical Center (DHMC),we have developed and validated a microRNA (miRNA) panel for patients with pancreatic diseases that can be used in association with the gold standard method for diagnosis. miRNAs have an important role in biological processes, such as apoptosis, metabolism, cell growth and differentiation. In cancer, miRNAs can be classified as either oncogenic or tumor suppressor according to their function in the carcinogenic process. In this study, we describe the expression of many miRNA in benign and malignant pancreatic tissues as well as their clinical significance. For this reason, miRNAs have been considered potential biomarkers of pancreatic diseases that could potentially contribute to an early diagnosis, predict disease progression, accurately monitor disease, contribute to better treatment strategies and reduce mortality by improving disease management.

Background Next-generation sequencing (NGS) assays are highly complex tests that can vary substantially in both their design and intended application. Despite their innumerous advantages, NGS assays present some unique challenges associated with the preanalytical process, library preparation, data analysis, and reporting. According to a number of professional laboratory organization, control materials should be included both during the analytical validation phase and in routine clinical use to guarantee highly accurate results. The SeraseqTM Solid Tumor Mutation Mix AF10 and AF20 control materials consist of 26 biosynthetic DNA constructs in a genomic DNA background, each containing a specific variant or mutation of interest and an internal quality marker at 2 distinct allelic frequencies of 10% and 20%, respectively. The goal of this interlaboratory study was to evaluate the Seraseq AF10 and AF20 control materials by verifying their performance as control materials and by evaluating their ability to measure quality metrics essential to a clinical test. Methods Performance characteristics were assessed within and between 6 CLIA-accredited laboratories and 1 research laboratory. Results Most laboratories detected all 26 mutations of interest; however, some discrepancies involving the internal quality markers were observed. Conclusion This interlaboratory study showed that the Seraseq AF10 and AF20 control materials have high quality, stability, and genomic complexity in variant types that are well suited for assisting in NGS assay analytical validation and monitoring routine clinical applications.

Purpose: To assess the clinical and pharmacodynamic activity of dovitinib in a treatment-resistant, molecularly enriched non–muscle-invasive urothelial carcinoma of the bladder (NMIUC) population. Experimental Design: A multi-site pilot phase II trial was conducted. Key eligibility criteria included the following: Bacillus Calmette-Guerin (BCG)-unresponsive NMIUC (>2 prior intravesical regimens) with increased phosphorylated FGFR3 (pFGFR3) expression by centrally analyzed immunohistochemistry (IHC+) or FGFR3 mutations (Mut+) assessed in a CLIA-licensed laboratory. Patients received oral dovitinib 500 mg daily (5 days on/2 days off). The primary endpoint was 6-month TURBT-confirmed complete response (CR) rate. Results: Between 11/2013 and 10/2014, 13 patients enrolled (10 IHC+ Mut−, 3 IHC+ Mut+). Accrual ended prematurely due to cessation of dovitinib clinical development. Demographics included the following: median age 70 years; 85% male; carcinoma in situ (CIS; 3 patients), Ta/T1 (8 patients), and Ta/T1 + CIS (2 patients); median prior regimens 3. Toxicity was frequent with all patients experiencing at least one grade 3–4 event. Six-month CR rate was 8% (0% in IHC+ Mut−; 33% in IHC+ Mut+). The primary endpoint was not met. Pharmacodynamically active (94–5,812 nmol/L) dovitinib concentrations in urothelial tissue were observed in all evaluable patients. Reductions in pFGFR3 IHC staining were observed post-dovitinib treatment. Conclusions: Dovitinib consistently achieved biologically active concentrations within the urothelium and demonstrated pharmacodynamic pFGFR3 inhibition. These results support systemic administration as a viable approach to clinical trials in patients with NMIUC. Long-term dovitinib administration was not feasible due to frequent toxicity. Absent clinical activity suggests that patient selection by pFGFR3 IHC alone does not enrich for response to FGFR3 kinase inhibitors in urothelial carcinoma. Clin Cancer Res; 23(12); 3003–11. ©2016 AACR.

Background Metastatic breast cancer is a genetically heterogeneous disease and effective therapies for advanced stage disease are limited. Methods In this study, distant metastases of 22 formalin-fixed, paraffin-embedded (FFPE) breast cancer samples were sequenced using the Ion Torrent PGM and the 50 gene AmpliSeq Cancer Hotspot Panel v2 from 10 ng of extracted DNA using 318 chips. Data analysis was performed with the Ion Torrent Variant Caller Plugin (hg19) and Golden Helix's SVS software for annotation and prediction of the significance of the variants. Results All patients were female with a median age of 61 years (range 37–85 years). Metastatic sites included liver (n = 6, 27%), skin (n = 5, 23%), brain (n = 4, 18%), lymph node (n = 3, 14%), lung (n = 2, 9%), retroperitoneum (n = 1, 4.5%), and colon (n = 1, 4.5%). Overall, 28 variants in 11 genes were observed. Five (23%) samples showed no alterations and 17 (77%) showed at least one potentially biologically significant variant (BSV) defined as having FDA-approved drugs or clinical trials evaluating their significance. BSVs included mutations in the following genes: TP53 (n = 8), APC (n = 4), PIK3CA (n = 5), MET (n = 2), ERBB2 (n = 2), AKT1 (n = 1), CDKN2A (n = 1), KRAS (n = 1), and FGFR3 (n = 1). Conclusions Potentially actionable mutations were identified in the majority of breast cancer metastases. Evaluating metastatic breast tumors using a NGS approach provides a better understanding of the mechanisms behind tumor progression and evolution and also identifies additional potentially beneficial therapeutic targets for patient management or eligibility for clinical trials.

Chlamydia causes enteritis in young pigs and calves, and granulomas within intestinal lymphatics. Recently we called attention to the lymphangitis and lymphatic obstruction that occurs in Crohn’s disease. We searched resected tissues from patients for evidence of chlamydia and sera for evidence of previous exposure to chlamydia. Immunohistochemistry and real-time PCR were employed to seek chlamydia in preserved tissues. In the IHC, antibody to C. trachomatis served as primary antibody; in the PCR, primers specific for Chlamydiaceae were employed. Commercial ELISA kits measured anti-chlamydia IgG and IgA against C. trachomatis antigen in sera derived from a population of patients different from that which yielded the tissue specimens. IHC revealed focal positive staining for chlamydia in tissues of 5 of 19 patients. Positive reacting cells occurred within dense inflammation, in sparsely scattered macrophages in the submucosa and subserosa. Tissues from 3 of 22 control subjects were positive. Real-time PCR done on ileal, colonic, and regional lymph node tissues revealed evidence of chlamydia in 3 of 33 patients. Serology for anti-chlamydia IgG revealed 2 positive values in 24 patients, while serology for anti-chlamydia IgA revealed 4 positives among the 24 patients, and 1 positive in the 15 controls. One patient and one control had both elevated IgG and IgA titers. The 4 patients with elevated IgA titers were from a single family of 6 with Crohn’s disease, which had been previously described. Additional consideration needs to be given to the chlamydia species, including those of animal origin, which leave behind little evidence of their previous involvement.

KRAS mutant non-small cell lung cancers (NSCLCs) vary in clinical outcome depending on which specific KRAS mutation is present. Shorter progression free survival has been associated with KRAS variants G12C and G12V. Cell lines with these variants depend to a greater extent on the RAS/RAF/MEK/ERK signaling pathway and become more susceptible to MEK inhibition. Because different KRAS mutations may lead to altered drug sensitivity, we aimed to determine specific KRAS mutation status in a NSCLC patient cohort at our institution. A total of 502 NSCLC samples were screened for somatic mutations using the 50 gene AmpliSeq™ Cancer Hotspot Panel v2 (CHPv2). However only samples positive for variants in the KRAS gene were included in this study. Variants identified in the KRAS genes were curated using publicly available databases. The overall mutation rate in the KRAS gene was 32.7% (164/502). The most common KRAS mutations were G12C (41%), G12V (19%), and G12D (14%) along with less frequent variants. After re-mining our sequencing data, we found that more than a half of our KRAS mutant NSCLC patients could potentially benefit from the addition of a MEK inhibitor such as selumetinib to standard chemotherapeutic agents. Due to mutated KRAS, these patients will likely fail traditional anti-EGFR therapies but be eligible for newer combination therapies.

Accurate identification of somatic mutations in formalin-fixed, paraffin-embedded tumor tissue is required for enrollment into clinical trials for many novel targeted therapeutics, including trials requiring EGFR mutation status in non–small-cell lung carcinomas. Central clinical trial laboratories contracted to perform this analysis typically rely on US Food and Drug Administration–approved targeted assays to identify these mutations. We present two cases in which central laboratories inaccurately reported EGFR mutation status because of improper identification and isolation of tumor material and failure to accurately report assay limitations, resulting in enrollment denial. Such cases highlight the need for increased awareness by clinical trials of the limitation of these US Food and Drug Administration–approved assays and the necessity for a mechanism to reevaluate discordant results by alternative laboratory-developed procedures, including clinical next-generation sequencing.

N-of-1 trials target actionable mutations, yet such approaches do not test genomically-informed therapies in patient tumor models prior to patient treatment. To address this, we developed patient-derived xenograft (PDX) models from fine needle aspiration (FNA) biopsies (FNA-PDX) obtained from primary pancreatic ductal adenocarcinoma (PDAC) at the time of diagnosis. Here, we characterize PDX models established from one primary and two metastatic sites of one patient. We identified an activating KRAS G12R mutation among other mutations in these models. In explant cells derived from these PDX tumor models with a KRAS G12R mutation, treatment with inhibitors of CDKs (including CDK9) reduced phosphorylation of a marker of CDK9 activity (phospho-RNAPII CTD Ser2/5) and reduced viability/growth of explant cells derived from PDAC PDX models. Similarly, a CDK inhibitor reduced phospho-RNAPII CTD Ser2/5, increased apoptosis, and inhibited tumor growth in FNA-PDX and patient-matched metastatic-PDX models. In summary, PDX models can be constructed from FNA biopsies of PDAC which in turn can enable genomic characterization and identification of potential therapies.

Abstract 36 Background: Women in rural Honduras have limited access to cancer education, screening, and care. With village leaders, we piloted breast and cervical cancer screening in El Rosario, Honduras. Our objectives were to improve awareness and access, mitigate barriers, connect community and Honduran providers, and link patients with abnormal findings to cancer treatment. In 2013, health professionals and staff from Norris Cotton Cancer Center at Dartmouth- Hitchcock joined Honduran clinicians and medical students from La Liga Contra el Cáncer for two days of rural cancer screening. Peer educators taught 475 participants from 31 rural communities how to conduct self-breast exams. Of these participants, 238 chose clinical breast exams; 5% were clinically abnormal and 2.9% were referred for services at La Liga with 100% compliance. 34% reported barriers to cervical cancer screening due to distance and lack of transportation. 14.5% tested positive for HPV and 8% were positive for high risk HPV genotypes including 11 of 13 known high risk types. This group has been retested periodically by Pap. The collaborators will return in April 2016 to repeat the study, adding oral and thyroid screening. Genotyping for hrHPV will be onsite with a novel assay for PCR developed at Dartmouth-Hitchcock. Reflex testing with Pap will follow as needed. Follow up will be at La Liga where care is offered for free or at a reduced cost. A similar project for 400 urban factory-workers will also take place in April 2016. Methods: 2-day, multi-modal education and screening outreach run brigade-style combining low-tech primary screening with onsite molecular pathology. Conclusions: Partnerships between local leaders and clinicians are predicted to be essential to project implementation. Targeting populations with education and screening plus building connections to follow up care will provide earlier detection of breast and cervical cancer. We predict that community leadership will be critical to preventing loss to follow-up. AUTHORS' DISCLOSURES OF POTENTIAL CONFLICTS OF INTEREST: Derek S. Stenquist No relationship to disclose Suyapa Bejarano No relationship to disclose Linda S. Kennedy No relationship to disclose Silvia Portillo No relationship to disclose Ana Barrientos No relationship to disclose Suzanne P. Burgos No relationship to disclose Roberto Armando Elvir Zelaya No relationship to disclose Christine Averill No relationship to disclose Emmeline Liu No relationship to disclose Francine de Abreau No relationship to disclose Paul Burchard No relationship to disclose Torrey Gallagher No relationship to disclose Martha Goodrich No relationship to disclose Scottie Eliassen No relationship to disclose Julie Weiss No relationship to disclose Camilo Mandujano No relationship to disclose Jennifer Alford-Teaster No relationship to disclose Gregory J. Tsongalis Research Funding: Illumina, Qiagen, Thermofisher Tracy Onega No relationship to disclose Mary D. Chamberlin No relationship to disclose

Background: Gastric cancer is associated with high morbidity and mortality around the world. In developing countries, patients often present with advanced disease creating a challenge for effective treatment. Next generation sequencing is identifying mutations in more than 50% of gastric cancers in developed countries. Chronic infections and other geographic differences may lead to variations in somatic mutations that could lead to different approaches to treatment. In this pilot study we sought to determine if an overseas collaboration between the University of Rwanda College of Medicine and Health Sciences and the Geisel School of Medicine at Dartmouth was feasible and effective at determining molecular profiles of gastric cancer. Methods: Patients referred for endoscopy at University Teaching Hospital of Kigali, Rwanda were consented to participate prior to the procedure. Biopsy tissues were processed for routine pathologic assessment and those confirmed as gastric adenocarcinoma were included. Formalin-fixed paraffin embedded tissues, H&E stained slides and tissue blocks were transported from Rwanda to New Hampshire, USA by visiting professors participating in the Human Resources for Health Program between May 2015 and July 2016. DNA and RNA from 39 samples were extracted using at least 7 FFPE unstained slides according to AllPrep RNA/DNA FFPE Kit Protocol. Library preparation was performed using 5 ng gDNA using the Pillar NGS SLIMampTM Lung and Colon Hot Spot Panel. Library quanitification was performed using Qubit, and samples with at least 4 nM were normalized, pooled and sequenced on the v3 cartridge on the Illumina's MiSeq system. For data analysis, FASTq files were uploaded to Pillar Biosciences, where sequence alignment, annotation, and variant classification were performed. Results: Eighteen samples had insufficient tissue for nucleic acid extraction. Of the 39 samples processed for sequencing, 17 had low library quantification due to low DNA concentration or poor quality. Mutations were detected in 9/22 samples (41%). One sample contained 3 mutations while the majority of mutated cases had 1-2 mutations identified. A total of 12 mutations were identified: TP53 (4), SMAD4 (2), ERBB4 (2) (S341L and D228N), PTEN (2)(K267RfsTer9 and C136Y), FBXW7 (1) and KRAS (1). Conclusions: Overseas collaboration for next generation sequencing of gastric cancer samples is feasible. Quality control is a common challenge and may improve with larger sized biopsies or tissue blocks. Frequency of mutations is lower than expected. ERBB4 mutations identified are not known to be pathogenic. The PTEN mutations observed are considered pathogenic and this may be a feasible target for therapy. A fusion panel and amplification profiling may be more effective in identifying potential targets for therapeutic trials. Limitations: Small sample size. Panel limited to mutations. Citation Format: Mary D. Chamberlin, Francine B. De Abreu, Torrey L. Gallagher. Next-generation sequencing of gastric cancer samples from Rwanda: a feasibility study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4376. doi:10.1158/1538-7445.AM2017-4376

e20585 Background: Matching of actionable tumor mutations with targeted therapy has been shown to increase response rates and prolong survival in lung cancer patients. Drug development and trials targeting genetic alterations are expanding rapidly. We describe the role of a Molecular Tumor Board (MTB) in the design of molecularly informed treatment strategies in our lung cancer patient population. Methods: DNA from tumor specimens was sequenced to identify coding mutations using a 50-gene targeted next-generation sequencing panel (Ampliseq v2). Cases were evaluated by a multidisciplinary MTB that included medical oncologists, hematologists, molecular and anatomic pathologists, genetic counselors, and basic science researchers who suggested a course of treatment based on the patient’s molecular findings. Results: During a three-year period, 88 patients were presented to the MTB. Of these, 21 patients had lung cancer (23.9%). All patients lacked common (indicated for FDA approved drug) activating EGFR and ALK mutations. One patient was stage IIIb, all others were stage IV; 18 had previously received at least one prior line of therapy (range 0-5). Suggestions for treatment with a targeted therapy were made for 19 of 21 (90.5%) and four patients underwent treatment with a MTB-suggested targeted agent (21.1%); two as part of a clinical trial. One patient received targeted therapy for 27 months before his disease eventually progressed. Barriers to treatment with targeted therapy included: ineligibility for study (n = 2), lack of interest in study/distance to travel (n = 2), lack of disease progression (n = 2), death/hospice enrollment (n = 5), decision to treat with immunotherapy (n = 3), and unknown (n = 1). Conclusions: For the majority of lung cancer patients, the MTB was able to provide suggestions based on targetable genetic alterations. The largest barriers to treatment were death and hospice enrollment indicating that molecular testing and presentation to the MTB at earlier stages of disease may increase the number of patients who ultimately are eligible for treatment with a targeted agent.

BACKGROUND Some epithelial neoplasms of the appendix, including low-grade appendiceal mucinous neoplasm and adenocarcinoma, can result in pseudomyxoma peritonei (PMP). Little is known about the mutational spectra of these tumor types and whether mutations may be of clinical significance with respect to therapeutic selection. In this study, we identified somatic mutations using the Ion Torrent AmpliSeq Cancer Hotspot Panel v2. METHODS Specimens consisted of 3 nonneoplastic retention cysts/mucocele, 15 low-grade mucinous neoplasms (LAMNs), 8 low-grade/well-differentiated mucinous adenocarcinomas with pseudomyxoma peritonei, and 12 adenocarcinomas with/without goblet cell/signet ring cell features. Barcoded libraries were prepared from up to 10 ng of extracted DNA and multiplexed on single 318 chips for sequencing. Data analysis was performed using Golden Helix SVS. Variants that remained after the analysis pipeline were individually interrogated using the Integrative Genomics Viewer. RESULTS A single Janus kinase 3 (JAK3) mutation was detected in the mucocele group. Eight mutations were identified in the V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) and GNAS complex locus (GNAS) genes among LAMN samples. Additional gene mutations were identified in the AKT1 (v-akt murine thymoma viral oncogene homolog 1), APC (adenomatous polyposis coli), JAK3, MET (met proto-oncogene), phosphatidylinositol-4,5-bisphosphate 3-kinase (PIK3CA), RB1 (retinoblastoma 1), STK11 (serine/threonine kinase 11), and tumor protein p53 (TP53) genes. Among the PMPs, 6 mutations were detected in the KRAS gene and also in the GNAS, TP53, and RB1 genes. Appendiceal cancers showed mutations in the APC, ATM (ataxia telangiectasia mutated), KRAS, IDH1 [isocitrate dehydrogenase 1 (NADP+)], NRAS [neuroblastoma RAS viral (v-ras) oncogene homolog], PIK3CA, SMAD4 (SMAD family member 4), and TP53 genes. CONCLUSIONS Our results suggest molecular heterogeneity among epithelial tumors of the appendix. Next generation sequencing efforts have identified mutational spectra in several subtypes of these tumors that may suggest a phenotypic heterogeneity showing mutations that are relevant for targeted therapies.

Background: Somatic mutation analysis is standard of practice for solid tumors in order to identify therapeutic sensitizing and resistance mutations. Our laboratory routinely performed standalone PCR-based methods for mutations in several genes. Rapid discovery and introduction of new therapeutics has demanded additional genomic information for adequate management of the cancer patient. We evaluated a next generation sequencing assay, the Ion Torrent AmpliSeq Cancer Hotspot Panelv2 (CHPv2), capable of identifying multiple somatic mutations in 50 genes in a single assay. Methods: Accuracy, precision, limit of detection, and specificity were evaluated using DNA from well-characterized cell lines, genetically engineered cell lines fixed and embedded in paraffin, and previously tested mutation positive or negative, formalin-fixed, paraffin-embedded (FFPE) tissues. Normal kidney, tonsil and colon FFPE tissues were used as controls. Results: Accuracy studies showed 100% concordance in each patient sample between previous PCR results and the corresponding variants identified using the Ion Torrent panel. Precision studies gave consistent results when libraries were prepared from the same original DNA and were run on multiple 316 chips. The limit of detection was determined to be 5% for single nucleotide variants (SNVs) and 20% for insertions and deletions (indels). Specificity studies using normal FFPE tissue previously tested by PCR methods were also 100%. Conclusions: We have evaluated the performance of the AmpliSeq Cancer Panel Hotspotv2 and show that it is suitable for clinical testing. This next generation sequencing panel has allowed the laboratory to consolidate a broader range of molecular oncology testing to a single platform and single assay.

Background A genetic TA repeat length polymorphism in the UGT1A1 promoter has been shown to affect UDP-glucuronosyltyransferase (UGT1A1) expression levels with significant clinical implications. The presence of 7 TA repeats has been associated with lowered UGT1A1 expression and the mild hyperbilinrubinemia manifested in Gilbert's syndrome. Furthermore, cancer patients carrying this variant exhibit irinotecan-related toxicity and require lower doses of this chemotherapeutic agent compared to patients carrying the 6 TA repeat allele. This polymorphism is very common and, therefore, necessitates the development of reliable means of detecting it in the clinical laboratory to deliver better personalized therapy regimens. Methods We used 45 whole blood samples from patients previously tested with the FDA-approved Invader UGT1A1 assay (Hologic, Madison, WI) to assess extraction method, analytical sensitivity, accuracy and precision of this assay. In addition, cell line controls were used to test for the common and rare alleles of this polymorphism. The assay was based on PCR amplification and capillary electrophoresis for accurate sizing of the TA repeat copy number. Results All samples tested and controls gave the expected results. Conclusions We have developed and validated a simple and sensitive PCR fragment analysis assay for accurately determining TA repeat length in the UGT1A1 promoter. At our medical center, this testing is used primarily for guiding irinotecan dosing decisions for our cancer patients.

e23168Background: Genetic profiling of tumors is quickly increasing as are trials targeting genetic alterations. Furthermore, genetic alterations are a relatively permanent part of a tumor profile,...

This study aimed to evaluate the copy number alteration on 2q24, its association with ACVR1 transcript expression and the prognostic value of these data in head and neck squamous cell carcinomas.Twenty-eight samples of squamous cell carcinoma were evaluated by fluorescence in situ hybridization (FISH) using the probes RP11-546J1 (2q24) and RP11-21P18 (internal control). Significant gains at 2q24 were detected in most cases at frequencies varying from 3 to 35%. ACVR1 gains and amplifications were associated with longer overall survival (P = 0.022). ACVR1 mRNA expression analysis in 78 cases revealed overexpression in 44% (34 of 78) of these tumours, suggesting that gene copy number alterations could be involved in gene overexpression. In laryngeal carcinomas, overexpression of ACVR1 mRNA levels was associated with longer overall survival (P = 0.013). Multivariate analysis revealed that ACVR1 is an independent prognostic marker in laryngeal carcinomas (P = 0.012, hazard ratio = 0.165, 95% confidence interval =0.041-0.668).These findings suggest that copy number alterations at 2q24 can be involved in ACVR1 overexpression, which is associated with longer overall survival in laryngeal carcinomas. To our knowledge, this is the first report indicating the relevance of ACVR1 expression in head and neck cancers.

Somatic mutations in myeloid malignancies correlate with WHO classification, help define genotype/phenotype relationships of clinical relevance, and are an essential part of the diagnostic algorithm. Current methods of detection are timely, costly, and labor intensive, and only assess single genes. The TruSight Myeloid Sequencing Panel (TSMSP) targets 54 genes frequently mutated in myeloid malignancies. This study evaluates the TSMSP. Eight …

s 361 due to limited numbers of laboratories performing this type of testing and lower DNA yields from FFPE tissue. Additionally, use of DNA or tissue samples from other laboratories may not be ideal because of inter-laboratory differences in FFPE DNA extraction methods and tissue processing. Focusing on gliomas and dermatology specimens, we describe a strategy used in our laboratory to validate the OncoScan FFPE Assay Kit (Affymetrix) using specimens from our internal tissue archive. DNA was extracted from 16 glioma and 7 melanocytic lesions using modified protocols of the Gentra Puregene Tissue kit (QIAGEN) or QIAamp FFPE Tissue kit (QIAGEN). Select tissue specimens were extracted using both methods. DNA was subjected to CMA analysis using the OncoScan FFPE Assay kit (Affymetrix) according to the manufacturer’s protocol. CMA results were compared with previous 1p/19q FISH results (gliomas) or a combination of traditional histopathology, immunohistochemistry, and CMA testing in a reference laboratory (dermatopathology). CMA results from all 16 glioma samples were concordant with respect to 1p/19q co-deletion status (6 positive, 10 negative for the co-deletion) with additional concordance for other gains and losses involving chromosomes 1 and 19. All 7 melanocytic lesions were concordant with previous CMA (n Z 2), BAP-1 immunohistochemistry (3p loss; n Z 2), or histopathology (n Z 3). Validation of a Modified OncoScan Protocol for Use in a Clinical Laboratory Christian N. Paxton, Leslie R. Rowe, Sarah T. South ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA Introduction of new procedures into the clinical laboratory always poses potential challenges to the established workflow. In recent years microarray analysis has gained acceptance as a first tier test for detection of copy number changes (CNCs) and loss of heterozygosity (LOH) in the clinical laboratory. Affymetrix recently introduced the OncoScan array for the testing of formalin-fixed paraffin embedded samples. The primary challenge to adopting the OncoScan array into our lab was a difference in hybridization temperatures between the OncoScan and CytoScan arrays, preventing simultaneous hybridization. We also identified additional steps to improve efficiency in the clinical laboratory setting. The modified OncoScan procedure was validated for use in our laboratory. Nineteen samples processed according to the manufacturerrecommended protocol were also processed using our modified protocol. Modifications to the protocol included the elimination of a brief “chill and spin” step, adjustment to the overnight hybridization temperature, and minor reductions in consumables throughout the procedure to reduce material costs. A comparison of 19 paired samples processed using both protocols showed that our modified protocol performs similarly to the manufacturer-recommended protocol, yielding equivalent quality control metrics and calls. In addition, a recent review of over 200 samples shows continued retention of quality control metrics with our modified protocol. Implementation and Routine Clinical Use of the TruSight Myeloid Sequencing Panel in Patients with Myeloid Malignancies Jason D. Peterson, Francine de Abreu, Prabhjot Kaur, Deborah L. Ornstein, Gregory J. Tsongalis Pathology Department, Geisel School of Medicine, Hanover, NH, USA; Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, USA Molecular testing in patients with myeloid diseases has important diagnostic, therapeutic, and prognostic implications. With the addition of next-generation sequencing to routine clinical practice, we have the ability to provide a much more comprehensive screening of clinically actionable mutations. This study describes the data obtained during both the validation process and routine clinical practice. Genomic DNA from 24 patients was extracted from either bone marrow aspirates or peripheral blood. Library preparation was performed using the 54-gene TruSight Myeloid Sequencing Panel according to manufacturer’s recommendations, and sequenced on the Illumina MiSeq System. Base-calling and sequence alignment were performed using the MiSeq Reporter Software, and variants were annotated using VariantStudio v2.1. The average cluster density per run was greater than 1,000 K/mm, and approximately 95.0% of the total bases were Q30. For the validation process, samples with known point mutations in the IDH2, NRAS, FLT3, and JAK2 genes, as well as INDELS in NPM1 and FLT3 genes were included. In the clinical samples, the most commonly identified mutations were present in the SRSF2 (2 samples), ASXL1 (2), STAG2 (2), TP53 (2), CDKN2A (3), and TET2 (5) genes. Isolated mutations were also observed in other genes (EZH2, CEBPA, CSF3R, GATA2, DNMT3A). Of the variants called, 100.0% were covered at >500 , while 92.0% were covered at >1,000 . The detection of mutations associated with myeloid malignancies may lead to an early diagnosis of these diseases, as well as to an appropriate treatment and better clinical outcomes. Evaluation of SNP Genomic Microarray Analysis as an Alternative to FISH Analysis of Pediatric Solid Tumors Anthony Arnoldo , James Stavropoulos , Paul Thorner , Cynthia Hawkins , Gino R. Somers , Mary Shago * Divisions of Genome Diagnostics and Pathology, University of Toronto, Toronto, Ontario; Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, Ontario; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario Central and peripheral nervous system tumors including medulloblastoma, astrocytoma and neuroblastoma are amongst the most common solid tumors in children. Recurrent gains or losses of distinct chromosomal regions are prognostic in these 3 tumors. Currently, we test these loci by FISH analysis, followed by karyotyping if there is sufficient material. We have validated the use of the genomic microarray platform

1550 Background: Genetic profiling of tumors is a powerful approach to predict drug sensitivity and resistance. However, oncologists are often unfamiliar with interpretation of genetic data. We est...

Objective: We have replaced single gene PCR-based methods for the detection of BRAF, KRAS and EGFR variants in routine clinical practice with next generation sequencing assays for the Ion Torrent AmpliSeq Cancer Hotspot Panel v2 (50 genes) and the Illumina TruSeq Amplicon Cancer panel (48 genes). Implementation of these panels requires constant optimization of technical and analytical procedures as reagents and software continue to be developed. In this study we describe somatic mutation findings from our clinical laboratory service. Methods: DNA was extracted from 90 formalin fixed, paraffin embedded tissue specimens that included 50 lung cancer, 24 colon cancer and 16 other cancers. Barcoded libraries were prepared from up to 10ng of extracted DNA and multiplexed on single 318 chips. Data analysis was performed using Golden Helix SVS for the Ion Torrent panel and Variant Studio for the Illumina panel. Variants that remained after the analysis pipeline were individually interrogated using the Integrative Genomics Viewer (IGV). Results: Of the 90 cancer cases sequenced, each panel returned on average 20 variants. Of these, there was 100% concordance between the two panels with respect to the clinically actionable mutations identified. Conclusions: We have implemented next generation sequencing technologies for the detection of somatic mutations in human cancers. Two platforms, the Ion Torrent PGM and the Illumina MiSeq, have been used for the routine analysis of FFPE cancer tissues in a clinical setting with actionable and non-actionable variants reported and archived. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B179. Citation Format: Jason D. Peterson, Francine de Abreu, Torrey L. Gallagher, Paul R. Burchard, Christopher I. Amos, Wendy A. Wells, J. Marc Pipas, Marc S. Ernstoff, Camilo E. Fadul, James R. Rigas, Gregory J. Tsongalis. Targeted next generation sequencing for somatic mutations in human cancer. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B179.

Breast cancer is a complex disease characterized by many morphological, clinical, and molecular features. For many years, breast cancer has been classified according to traditional parameters, such as histological type, grade, tumor size, lymph node involvement and vascular invasion, and biomarkers (eg, estrogen receptor, progesterone receptor, and epidermal growth factor receptor 2), which are used in patient management. With emerging imaging techniques (ie, digital mammography, tomosynthesis, ultrasonography, magnetic resonance imaging, nuclear medicine, and genomic techniques, such as real-time RT-PCR and microarrays), breast cancer diagnostics is going through a significant evolution. Imaging technologies have improved breast cancer diagnosis, survival, and treatment by early detection of primary or metastatic lesions, differentiating benign from malignant lesions and promoting intraoperative surgical guidance and postoperative specimen evaluation. Genomic and transcriptomic technologies make the analysis of gene expression signatures and mutation status possible so that tumors may be classified more accurately with respect to diagnosis and prognosis. The -omic era has also made possible the identification of new biomarkers involved in breast cancer development, survival, and invasion that can be gradually incorporated into clinical testing. These advances in both imaging and genomics contribute to more personalized and predictive patient management. We review the progress made in breast cancer diagnosis and management using these new tools.