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 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.

Purpose To assess the clinical and pharmacodynamic activity of dovitinib in a treatment resistant, molecularly enriched NMIUC population. Experimental Design A multi-site pilot phase 2 trial was conducted. Key eligibility criteria included: 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: median age 70 years; 85% male; CIS (3 pts), Ta/T1 (8 pts), and Ta/T1 + CIS (2 pts); median prior regimens 3. Toxicity was frequent with all patients experiencing at least one grade 3-4 event. 6-month CR rate was 8% (0% in IHC+ Mut−; 33% in IHC+ Mut+). The primary endpoint was not met. Pharmacodynamically active (94-5812 nM) 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 NMIUC patients. 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 UC.

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel member of the coronavirus family that caused the global coronavirus 2019 (COVID-19) pandemic. The prevalence remains largely unknown because of early testing supply shortages. Although it cannot currently be used to determine level of immunity, antibody testing can contribute to epidemiological studies, identify convalescent plasma donors, or satisfy curiosity about previous exposure to the virus. Methods 407 samples collected from hospitalized inpatients with and without a confirmed SARS-CoV-2 infection, 170 remnant clinical specimens collected and frozen prior to the COVID-19 outbreak, and paired serum and plasma samples from 23 convalescent plasma donors were used to determine performance characteristics of the Abbott SARS-CoV-2 IgG and Roche Elecsys Anti-SARS-CoV-2 assays. The sensitivity, specificity, imprecision, interferences, and sample stability were determined. These assays were then used to characterize the antibody response in serial samples from 20 SARS-CoV-2 positive inpatients. Results Both assays exhibited 100% specificity (95% CI; 99.05 – 100.00), giving no positive results in 170 specimens collected before July 2019 and 215 specimens from patients without a confirmed SARS-CoV-2 infection. Differences between platforms were most notable in SARS-CoV-2 positive samples. Roche offered higher sensitivity in convalescent plasma donors at 95.7% (95% CI; 78.1 – 99.9) versus 91.3% (95% CI; 72.0 – 98.9) but Abbott detected antibodies in two immunocompromised patients whereas Roche did not. The Roche and Abbott platforms also exhibited different trends in antibody signal for a subset of patients. Conclusions Both the Abbott and Roche platforms offer excellent specificity but different trends in antibody signal may reflect qualitative differences in the types of antibodies recognized by the two assays. Negative serologic results do not exclude previous SARS-CoV-2 infection.

Despite vaccination efforts, the delta and omicron variants of SARS-CoV-2 have caused global surges of COVID-19. As the COVID-19 pandemic continues, it is important to find new ways of tracking early signs of SARS-CoV-2 outbreaks.

Real-time, reverse transcriptase PCR assays are a pervasive technology used for diagnosis of SARS-CoV-2 infection. These assays produce a cycle threshold value (Ct) corresponding to the first amplification cycle in which reliable amplification is detected. Such Ct values have been used by clinicians and in public health settings to guide treatment, monitor disease progression, assess prognosis, and inform isolation practices. To understanding the risk of reporting out uncalibrated Ct values and potential for instead reporting out calibrated viral load values, we performed a multi-institutional study to benchmark major clinical platforms against a calibrated standard. We found that for any given Ct value, corresponding viral loads varied up to 1000-fold among the different tests. In contrast, when these different assays were calibrated against a common standard and then used to test unknown de-identified specimens at several dilutions, viral load values showed high precision between methods (standard deviation and range of 0.36 and 1.1 log10 genome copies) and high accuracy compared with droplet digital PCR (ddPCR) determinations (difference between mean CDC N2 and Sarbeco E ddPCR determinations and mean determinations by calibrated RT-PCR assays examined in our study of 0.044 log10 genome copies). We, therefore, find strong support for calibration of SARS-CoV-2 RT-PCR tests to allow conversion of cycle thresholds to accurate and precise viral load values that are reproducible across major clinical systems. Implementation of calibrated assays will provide more reliable information for clinical decision making and allow more rigorous interpretation of SARS-CoV-2 laboratory data in clinical and laboratory investigation.

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

CBFβ is the non-DNA binding subunit of the core binding factors, and is required for both the functions of Runx1 in hematopoiesis and Runx2 in osteogenesis. Homozygous disruption of Cbfb results in embryonic lethality at mid-gestation and a severe impairment of fetal liver hematopoiesis, a phenotype similar to Runx1 deficiency. To examine Cbfb requirements at later stages of hematopoiesis, we generated a hypomorphic Cbfb allele (Cbfbrss). Mice homozygous for the Cbfbrss allele have a 4- to 5-fold reduction in CBFβ protein levels, while Cbfbrss/− mice have an 8- to 10-fold reduction in CBFβ concentration. Cbfbrss/rss and Cbfbrss/− mice die at P0 for unknown reasons and display minor defects in bone ossification. Granulocyte and macrophage differentiation at E17.5 is impaired in both Cbfbrss/rss and Cbfbrss/−animals, as evidenced by a 2- to 3- fold decrease in GR1+ and Mac1+ cells. The percentages of Ter119+, B220+, and CD19+ cells are normal. Fetal liver hematopoietic progenitor numbers, as determined by cell surface marker and functional analyses, are increased approximately 2-fold. The most severe defects are in the T cell lineage. Cbfbrss/rss fetuses have reduced thymus cellularity and lower numbers of CD8 SP T cells, consistent with a role for Runx1 and Runx3 in epigenetic CD4 silencing. A further 2-fold reduction in CBFβ levels in Cbfbrss/− fetuses results in an absence of CD4/8 SP and DP cells. These hematopoietic defects were also seen upon transplantation of Cbfbrss/rss and Cbfbrss/− fetal liver cells into congenic Ly5.1/5.2 mice. Our data indicate that the threshold level of CBFβ required for normal hematopoiesis, bone development, and postnatal viability is somewhere between 25%-50% of its normal concentration. The data demonstrate that T cell development is particularly sensitive to CBFβ levels, and both granulocyte and macrophage differentiation require CBFβ. Since the conditional knockout of Runx1 in the adult mouse reported by Ichikawa et al. (Nat Med.10, 299, 2004) did not cause either granulocyte or monocyte/macrophage defects, we hypothesize that Runx2 and/or Runx3 are also required in these lineages. Hemizygosity for CBFB-MYH11, the product of the inv(16), is associated with a more severe phenotype than is seen in the Cbfb rss/− fetuses (Castilla et al. Cell87, 687, 1996). We therefore conclude that the hematopoietic consequences for cells expressing the inv(16) are equivalent to a greater than 10-fold reduction in the level of functional CBFβ.