Abstract 1386: Clinical research results for a NGS-based kit for targeted detection of clinically relevant gene rearrangements in lung tumor samples

In recent years, advances in next-generation sequencing (NGS) technologies have enabled faster and cheaper methods for uncovering the genetic basis of disease. For cancer, NGS based screening for known tumor subtypes may inform diagnosis and allow the clinician to tailor a specific therapeutic approach in the future. Here, we present the testing results of one such NGS based kit used to detect specific chromosomal translocations in retrospective non-small cell lung cancer (NSCLC) samples by targeting specific breakpoints in known fusion transcripts.

The included panel tested consists of a single primer pool containing amplicon designs to simultaneously screen for over 75 specific rearrangements involving the receptor tyrosine kinase (RTK) genes ALK, RET and ROS1 as well as NTRK1. The panel was compatible with formalin-fixed paraffin-embedded (FFPE) lung tumor research samples and achieved high-sensitivity down to 10 ng of RNA input. In addition, amplicon assays designed at the 5’ and 3’ ends the RTK genes provide non-specific evidence that a translocation exists in a sample by comparing expression imbalance between the two ends.

Testing was carried out at three external clinical research laboratories. In addition to positive and negative control samples, each site contributed FFPE lung tumor research samples for which ALK fusion status was known prior to NGS library preparation carried out using the Ion AmpliSeq™ workflow. For site-specific samples (n = 144, 16 samples per sequencing run), high concordance, sensitivity and specificity were measured at 97.2%, 90.5% and 98.4%, respectively.

Citation Format: Jeoffrey J. Schageman, José Luis Costa, Orla Sheils, John E. Glassco, David Chi, Jon Sherlock, John Bishop, Rosella P. Petraroli, Kelli S. Bramlett. Clinical research results for a NGS-based kit for targeted detection of clinically relevant gene rearrangements in lung tumor samples. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1386.

Pleural fluid metastases of myoepithelial carcinoma: A case report and review of the literature

Myoepithelial carcinoma (MECA) is one of the rarest salivary gland neoplasms, which may either arise de novo or develop within a preexisting pleomorphic adenoma or benign myoepithelioma. The tumor occurs mainly in the parotid gland followed by minor salivary glands and other body sites. As a result of their morphologic heterogeneity, they can be confused easily with many tumors. Awareness of their unique cytoarchitectural patterns and immunohistochemical profile is crucial for accurate identification. Herein, we report a rare case of a 51-year-old female patient with MECA of the maxillary sinus that metastasized to the pleural fluid. To the best of our knowledge, this is the first case of pleural fluid involvement by MECA reported in the literature.

Gun-shot injuries in UK military casualties - Features associated with wound severity

INTRODUCTION

Surgical treatment of high-energy gun-shot wounds (GSWs) to the extremities is challenging. Recent surgical doctrine states that wound tracts from high-energy GSWs should be laid open, however the experience from previous conflicts suggests that some of these injuries can be managed more conservatively. The aim of this study is to firstly characterise the GSW injuries sustained by UK forces, and secondly test the hypothesis that the likely severity of GSWs can be predicted by features of the wound.

METHODS

The UK Military trauma registry was searched for cases injured by GSW in the five years between 01 January 2009 and 31 December 2013: only UK personnel were included. Clinical notes and radiographs were then reviewed. Features associated with energy transfer in extremity wounds in survivors were further examined with number of wound debridements used as a surrogate marker of wound severity.

RESULTS

There were 450 cases who met the inclusion criteria. 96 (21%) were fatally injured, with 354 (79%) surviving their injuries. Casualties in the fatality group had a median New Injury Severity Score (NISS) of 75 (IQR 75-75), while the median NISS of the survivors was 12 (IQR 4-48) with 10 survivors having a NISS of 75. In survivors the limbs were most commonly injured (56%). 'Through and through' wounds, where the bullet passes intact through the body, were strongly associated with less requirement for debridement (p<0.0001). When a bullet fragmented there was a significant association with a requirement for a greater number of wound debridements (p=0.0002), as there was if a bullet fractured a bone (p=0.0006).

CONCLUSIONS

More complex wounds, as indicated by the requirement for repeated debridements, are associated with injuries where the bullet does not pass straight through the body, or where a bone is fractured. Gunshot wounds should be assessed according to the likely energy transferred, extremity wounds without features of high energy transfer do not require extensive exploration.

Salivary acinic cell carcinoma: reappraisal and update

Epidemiologic and clinicopathologic features, therapeutic strategies, and prognosis for acinic cell carcinoma of the major and minor salivary glands are critically reviewed. We explore histopathologic, histochemical, electron microscopic and immunohistochemical aspects and discuss histologic grading, histogenesis, animal models, and genetic events. In the context of possible diagnostic difficulties, the relationship to mammary analog secretory carcinoma is probed and a classification is suggested. Areas of controversy or uncertainty, which may benefit from further investigations, are also highlighted.

A prospective longitudinal study of growth and pubertal progress in adolescents with inflammatory bowel disease

BACKGROUND

Puberty and growth may be affected in inflammatory bowel disease (IBD) but the extent is unclear.

METHODS

We performed a prospective study over 12 months in 63 adolescents (Crohn's disease, CD, n = 45; ulcerative colitis/IBD unclassified, UC, n = 18) with a median age of 13.4 years (range 10-16.6). Assessment included anthropometry, biochemical markers of growth and puberty and an assessment of quality of life by IMPACT-III.

RESULTS

Compared to the normal population, boys with CD were shorter, with a median height SDS (HtSDS) of -0.13 (-2.52 to 1.58; p < 0.05). In addition, the study cohort had a lower median IGF-1 SDS of -0.29 (-4.53 to 2.96; p = 0.008) and a higher median IGFBP3 SDS of 0.45 (-3.15 to 2.55; p = 0.002). Over the study period, the median Ht velocity (HV) was 5 cm/year (0.2-8.7) and the change in HtSDS was 0.06 (-0.48 to 0.57). The median difference between the chronological and bone age was 0.3 years (-2.5 to 3.0) and pubertal examination was not delayed. In the whole group, the erythrocyte sedimentation rate (ESR) showed an inverse association with HV (r = -0.29; p = 0.025) and IGF-1:IGFBP3 (r = -0.34; p = 0.016). The score in the body image domain, IMPACT-III, was inversely associated with HtSDS (r = -0.31; p = 0.03).

CONCLUSION

Despite no evidence of pubertal delay, adolescents with IBD display growth retardation which may be associated with raised ESR, adverse quality of life measures and an abnormality of IGF-1 bioavailability.

Triptans disrupt brain networks and promote stress-induced CSD-like responses in cortical and subcortical areas

A number of drugs, including triptans, promote migraine chronification in susceptible individuals. In rats, a period of triptan administration over 7 days can produce "latent sensitization" (14 days after discontinuation of drug) demonstrated as enhanced sensitivity to presumed migraine triggers such as environmental stress and lowered threshold for electrically induced cortical spreading depression (CSD). Here we have used fMRI to evaluate the early changes in brain networks at day 7 of sumatriptan administration that may induce latent sensitization as well as the potential response to stress. After continuous infusion of sumatriptan, rats were scanned to measure changes in resting state networks and the response to bright light environmental stress. Rats receiving sumatriptan, but not saline infusion, showed significant differences in default mode, autonomic, basal ganglia, salience, and sensorimotor networks. Bright light stress produced CSD-like responses in sumatriptan-treated but not control rats. Our data show the first brain-related changes in a rat model of medication overuse headache and suggest that this approach could be used to evaluate the multiple brain networks involved that may promote this condition.

Demonstration of equivalence of a generic glatiramer acetate (Glatopa™)

Glatiramer acetate (GA) has been available under the brand name Copaxone® for nearly two decades. Recently, the US Food and Drug Administration (FDA) approved the first generic GA, Glatopa™, as fully substitutable for all indications for which Copaxone 20mg is approved; Glatopa also represents the first FDA-approved "AP-rated," substitutable generic for treating patients with MS. Glatiramer acetate is a complex mixture of polypeptides and, consequently, its characterization presented challenges not generally encountered in drug development. Despite its complexity, and without requiring any clinical data, approval was accomplished through an Abbreviated New Drug Application in which equivalence to Copaxone was evaluated across four criteria: starting materials and basic chemistry; structural signatures for polymerization, depolymerization, and purification; physicochemical properties; and biological and immunological properties. This article describes the rigorous overall scientific approach used to successfully establish equivalence between Glatopa and Copaxone, and presents key representative data from several of the comprehensive sets of physicochemical (structural) and biological (functional) assays that were conducted.

Sinonasal melanoma arising from conjunctival primary acquired melanosis

A 66-year-old woman was treated with excision and cryotherapy for recurrent primary acquired melanosis (PAM) with atypia of the right conjunctiva. Four years later, she developed a melanoma of the ipsilateral inferior turbinate and nasolacrimal duct. She was treated with right medial maxillectomy and postoperative radiation therapy. This is the first reported case of conjunctival PAM resulting in delayed progression to melanoma in the nasolacrimal duct and sinonasal cavity.

Medium-term outcomes following limb salvage for severe open tibia fracture are similar to trans-tibial amputation

Extremity injuries define the surgical burden of recent conflicts. Current literature is inconclusive when assessing the merits of limb salvage over amputation. The aim of this study was to determine medium term functional outcomes in military casualties undergoing limb salvage for severe open tibia fractures, and compare them to equivalent outcomes for unilateral trans-tibial amputees. Cases of severe open diaphyseal tibia fractures sustained in combat between 2006 and 2010, as described in a previously published series, were contacted. Consenting individuals conducted a brief telephone interview and were asked to complete a SF-36 questionnaire. These results were compared to a similar cohort of 18 military patients who sustained a unilateral trans-tibial amputation between 2004 and 2010. Forty-nine patients with 57 severe open tibia fractures met the inclusion criteria. Telephone follow-up and SF-36 questionnaire data was available for 30 patients (61%). The median follow-up was 4 years (49 months, IQR 39-63). Ten of the 30 patients required revision surgery, three of which involved conversion from initial fixation to a circular frame for non- or mal-union. Twenty-two of the 30 patients (73%) recovered sufficiently to complete an age-standardised basic military fitness test. The median physical component score of SF-36 in the limb salvage group was 46 (IQR 35-54) which was similar to the trans-tibial amputation cohort (p=0.3057, Mann-Whitney). Similarly there was no difference in mental component scores between the limb salvage and amputation groups (p=0.1595, Mann-Whitney). There was no significant difference in the proportion of patients in either the amputation or limb salvage group reporting pain (p=0.1157, Fisher's exact test) or with respect to SF-36 physical pain scores (p=0.5258, Mann-Whitney). This study demonstrates that medium term outcomes for military patients are similar following trans-tibial amputation or limb salvage following combat trauma.

Competing causes of death and medical comorbidities among patients with human papillomavirus-positive vs human papillomavirus-negative oropharyngeal carcinoma and impact on adherence to radiotherapy

IMPORTANCE

Survival of patients with head and neck cancer can be affected by competing causes of mortality, as well as comorbidities that result in radiation treatment interruptions.

OBJECTIVE

To discern how differences in preexisting medical and psychosocial comorbidities potentially influence adherence to radiation therapy according to human papillomavirus (HPV) status.

DESIGN, SETTING, AND PARTICIPANTS

Retrospective analysis at a comprehensive cancer center of 162 consecutive patients with locally advanced squamous cell carcinoma of the oropharynx treated with primary chemoradiation (n = 95) or primary surgery followed by adjuvant radiation (n = 67). Immunostaining for p16 was used to determine HPV status.

MAIN OUTCOMES AND MEASURES

Difference in alcohol, tobacco, and marijuana use was compared between patients with HPV-positive and HPV-negative tumors, as well as the prevalence of the following comorbidities: diabetes mellitus, chronic obstructive pulmonary disease (COPD), anxiety disorder, and major depression. The number of total missed treatment days was analyzed as both a continuous and categorical variable.

RESULTS

Rates of self-reported heavy alcohol use (47% vs 16%; P = .02) and any marijuana use (47% vs 23%; P = .003) were significantly higher among HPV-negative patients. Fifty-four percent of HPV-positive patients self-identified as never smokers, compared with only 12% of HPV-negative patients (P < .001). HPV-negative patients had more missed treatment days (mean, 2.8 vs 1.7 days; P = .02), as well as an increased rate of at least 5 missed days (24% vs 10%; P = .04), and higher prevalences of COPD (12% vs 7%; P = .37) and anxiety disorder (12% vs 6%; P = .35).

CONCLUSIONS AND RELEVANCE

Pronounced differences exist in lifestyle habits between patients with HPV-negative and HPV-positive oropharyngeal cancer at diagnosis. These differences, as well as those of medical and psychosocial burden, may contribute to observed discrepancies in treatment adherence and need to be considered in outcomes reporting and clinical trial design.

Managing inflammatory bowel disease in adolescent patients

Increasing numbers of adolescents are being diagnosed with Crohn's disease or ulcerative colitis, the two main subtypes of inflammatory bowel disease. These young people face many short- and long-term challenges; one or more medical therapies may be required indefinitely; their disease may have great impact, in terms of their schooling and social activities. However, the management of adolescents with one of these incurable conditions needs to encompass more than just medical therapies. Growth, pubertal development, schooling, transition, adherence, and psychological well-being are all important aspects. A multidisciplinary team setting, catering to these components of care, is required to ensure optimal outcomes in adolescents with inflammatory bowel disease.

The complexity of obesity in U.K. adolescents: relationships with quantity and type of technology, sleep duration and quality, academic performance and aspiration

BACKGROUND

Contemporary technology and multiple device use may link to increased body mass index (BMI). The sleep-obesity relationship is inconsistent in adolescents. Sleep duration and quality may have crucial connections to obesity development, particularly in adolescents where sleep alterations are common. Elevated BMI in adolescents may influence academic performance and aspiration, but data are limited.

OBJECTIVES

The objectives of this study was to assess the linear associations between BMI z-score and (i) quantity/type of technology used; (ii) sleep quantity/quality and (iii) academic performance/aspiration.

METHODS

Consenting adolescents (n = 624; 64.9% girls, aged 11-18 years) were recruited. The Schools Sleep Habits Survey and Technology Use Questionnaire were administered. Objective measures of height/weight were obtained.

RESULTS

Quantity of technology was positively associated with BMI z-score β = 0.10, P < 0.01. Those who always engaged in video gaming had significantly higher BMI z-score vs. never-users, β = 1.00, P < 0.001. Weekday sleep duration and sleep onset latency were related to BMI z-score, β = -0.24, P < 0.001 and β = 0.01, P < 0.001, respectively. An inverse linear association was observed between BMI z-score and academic performance, β = -0.68, P < 0.001.

CONCLUSIONS

If confirmed prospectively, reducing bedtime use of technology and improving sleep hygiene in adolescents could be an achievable intervention for attenuating obesity with potentially positive effects on academic performance.

Early trends in landcover change and forest fragmentation due to shale-gas development in Pennsylvania: a potential outcome for the Northcentral Appalachians

Worldwide shale-gas development has the potential to cause substantial landscape disturbance. The northeastern U.S., specifically the Allegheny Plateau in Pennsylvania, West Virginia, Ohio, and Kentucky, is experiencing rapid exploration. Using Pennsylvania as a proxy for regional development across the Plateau, we examine land cover change due to shale-gas exploration, with emphasis on forest fragmentation. Pennsylvania's shale-gas development is greatest on private land, and is dominated by pads with 1-2 wells; less than 10 % of pads have five wells or more. Approximately 45-62 % of pads occur on agricultural land and 38-54 % in forest land (many in core forest on private land). Development of permits granted as of June 3, 2011, would convert at least 644-1072 ha of agricultural land and 536-894 ha of forest land. Agricultural land conversion suggests that drilling is somewhat competing with food production. Accounting for existing pads and development of all permits would result in at least 649 km of new road, which, along with pipelines, would fragment forest cover. The Susquehanna River basin (feeding the Chesapeake Bay), is most developed, with 885 pads (26 % in core forest); permit data suggests the basin will experience continued heavy development. The intensity of core forest disturbance, where many headwater streams occur, suggests that such streams should become a focus of aquatic monitoring. Given the intense development on private lands, we believe a regional strategy is needed to help guide infrastructure development, so that habitat loss, farmland conversion, and the risk to waterways are better managed.

Impact of inflammatory bowel disease on pubertal growth

BACKGROUND

Puberty is thought to be commonly affected in adolescents with inflammatory bowel disease (IBD).

AIMS

To determine the impact of Crohn's disease (CD) and ulcerative colitis (UC) on the pubertal growth spurt.

METHODS

Retrospective study of 30 boys with CD (CD-M), 11 girls with CD (CD-F), 14 boys with UC (UC-M) and 12 girls with UC (UC-F). Pubertal growth was assessed by calculating peak height velocity SDS (PHV SDS), height SDS at diagnosis (Ht(Diag)) and height SDS at PHV (Ht(PHV)) and age at PHV (Age(PHV)). Systemic markers of disease activity were also collected.

RESULTS

Altered parameters of pubertal growth were observed in the CD groups compared to the normal population: in the CD-M group, median Ht(Diag) was -0.56 (p = 0.001) and median Age(PHV) was 14.45 years (p = 0.004), and in the CD-F group, median Ht(Diag) was -1.14 (p = 0.007) and Ht(PHV) was -0.79 (p = 0.039). Individually, 8/30 CD-M cases had one or more parameter affected: 2 boys had Ht(Diag )<-2, 3 boys had Ht(PHV) <-2, 2 boys had an Age(PHV) >2 years above population mean, and 2 boys had a PHV SDS <-2. In the whole group, Age(PHV) showed an association with erythrocyte sedimentation rate (r = 0.4; p = 0.005) and an inverse association with BMI (r = 0.4; p = 0.001).

CONCLUSION

Disorders of pubertal growth are more likely to occur in CD and, particularly, in boys.

Evaluating the use of metabolite measurement in children receiving treatment with a thiopurine

BACKGROUND

Clinical response to thiopurine medication is related to the concentration of its metabolites. Proxy measures are traditionally used to assess dose adequacy. We present our experience of using tioguanine (previously known/formerly referred to as thioguanine) metabolite measurements in paediatric patients and evaluate their effect on clinical practice.

AIMS

To report our experience of using tioguanine metabolite measurements in paediatric patients and to evaluate their effects on clinical practice.

METHODS

The 6-tioguanine nucleotide (6-TGN) and 6-methylmercaptopurine (6-MMP) were measured in children prescribed thiopurine medication for at least 3 months. Data were collected on thiopurine methyl transferase (TPMT) genotype, drug dose, laboratory indices and management changes. Therapeutic 6-TGN levels were defined as 235-400 pmol/8 × 10(8) RBCs. Seventy individuals (30 males) with a median age of 15 years. Underlying diagnoses were 'IBD' (68/70) and two cases of eosinophilic colitis. Sixty-three were treated with azathioprine and seven with mercaptopurine. A total of 103 separate measurements were made.

RESULTS

On initial measurement, 68% of patients had 6-TGN levels outside therapeutic levels despite standard thiopurine dosing. Initial 6-TGN levels were significantly higher in patients with TPMT mutations. Toxicity occurred in seven cases. The 6-TGN levels were significantly higher in those with signs of marrow toxicity. The 6-TGN level correlated with WBC, leukocyte count, mean corpuscular volume (MCV) and ΔMCV; however, the ability of each of these to predict therapeutic 6-TGN levels was poor. After initial measurement, management was changed in 25/70 cases (36%).

CONCLUSIONS

6-TGN levels were therapeutic in a minority of those patients who were tested. Proxy measures perform poorly in predicting therapeutic 6-TGN levels. Measuring thiopurine metabolites is useful for dosage adjustment in children, and for the detection of potential toxicity.