Urinary Androgens Provide Additional Evidence Related to Metabolism and Are Correlated With Serum Androgens in Girls

Context

Androgen levels are generally measured in serum samples, but urine may be a more feasible option, especially in children, as it is a noninvasive alternative.

Objective

To assess the correlations of 10 urinary androgen metabolites with 4 serum androgens [dehydroepiandrosterone-sulfate (DHEA-S), androstenedione, and total and free testosterone] and assess if their correlations differ by participant characteristics.

Methods

Our study consisted of 44 girls, ages 6-13, who participated in the New York site of the LEGACY Girls Study and had both serum and urine samples collected at the same visit. We performed Pearson's correlation coefficient tests between 4 serum and 10 individual urinary metabolite measures and their sum. We examined the influence of participant characteristics on the magnitude and direction of the correlations.

Results

The summed urinary metabolite measures had the highest correlation with free testosterone in serum (global sum, r = 0.83) and correlated least with DHEA-S in serum (global sum, r = 0.64). The correlation between individual urinary metabolites and serum androgens ranged from 0.08 to 0.84.Two 11-oxygenated urinary metabolites (5α-androstane-3α-ol-11,17-dione5β-androstane-3α,11β-diol-17-one) were weakly correlated with all serum androgens. Participant age, weight, height, waist:hip ratio, and pubic hair growth stage changed the correlations between urinary and serum androgens measures between 10% and 213%.

Conclusion

The sum of urinary androgen metabolites was a good marker of circulating androstenedione, testosterone, and free testosterone. Individual urinary metabolites provide additional information about the metabolic processes of disease development compared to the antecedent serum androgens.

Nutritional intake when cycling under racing and training conditions in professional male cyclists with type 1 diabetes

This study sought to detail and compare the in-ride nutritional practices of a group of professional cyclists with type 1 diabetes (T1D) under training and racing conditions. We observed seven male professional road cyclists with T1D (Age: 28 ± 4 years, HbA_1c: 6.4 ± 0.4% [46 ± 4 mmol.mol^-1], VO_2max: 73.9 ± 4.3 ml.kg ^-1.min^-1) during pre-season training and during a Union Cycliste Internationale multi-stage road cycling race (Tour of Slovenia). In-ride nutritional, interstitial glucose, and performance variables were quantified and compared between the two events.    The in-ride energy intake was similar between training and racing conditions     (p = 0.909), with carbohydrates being the major source of fuel in both events during exercise at a rate of 41.9 ± 6.8 g.h^-1 and 45.4 ± 15.5 g.h^-1 (p = 0.548), respectively. Protein consumption was higher during training (2.6 ± 0.6 g.h^-1) than race rides (1.9 ± 0.9 g.h^-1; p = 0.051).   A similar amount of time was spent within the euglycaemic range (≥70-≤180 mg.dL^-1): training 77.1 ± 32.8% vs racing 73.4 ± 3.9%; p = 0.818. These data provide new information on the in-ride nutritional intake in professional cyclists with T1D during different stages of the competitive season.

A phase 2 trial of buparlisib in patients with platinum-resistant metastatic urothelial carcinoma

BACKGROUND

The phosphatidyl 3-inositol kinase (PI3K)/Akt/mechanistic target of rapamycin (mTOR) pathway frequently is activated in patients with urothelial carcinoma (UC). In the current study, the authors performed a phase 2 study evaluating the efficacy of the pan-isoform class I PI3K inhibitor buparlisib in patients with platinum-refractory metastatic UC.

METHODS

Two cohorts were recruited: an initial genetically unselected cohort and a subsequent expansion cohort of patients with PI3K/Akt/mTOR pathway-altered tumors. The primary endpoint was the 2-month progression-free survival rate. A rate of ≥80% was considered promising using a Simon 2-stage minimax design. Secondary endpoints included safety and correlation of markers of PI3K pathway activation with outcome.

RESULTS

Six of 13 evaluable patients within the initial cohort demonstrated stable disease and 1 demonstrated a partial response, which was below the cutoff of 9 patients required to proceed to stage 2. Three of the patients with stable disease and the patient with a partial response harbored somatic TSC1 alterations. Four patients subsequently were recruited onto an expansion cohort: 3 patients with TSC1 alterations and 1 patient with a PIK3CA-activating mutation. No patient achieved disease control at 8 weeks and accrual was halted. Of the 19 patients evaluable for toxicity, 17 demonstrated treatment-related toxicities, 2 of whom had to discontinue therapy.

CONCLUSIONS

Buparlisib was found to demonstrate modest activity in patients with metastatic UC whose tumors harbored TSC1 loss of function alterations; however, this was not a robust predictor of response to buparlisib. The pattern of genetic coalterations likely influences drug sensitivity. Given the modest clinical activity and substantial toxicity of buparlisib, future trials of PI3K inhibitors in patients with UC should focus on isoform-selective PI3K inhibitors in genomically selected patients.

LAY SUMMARY

The phosphatidyl 3-inositol kinase (PI3K)/Akt/mechanistic target of rapamycin (mTOR) signaling pathway frequently is upregulated in patients with metastatic urothelial carcinoma (UC). This trial explored buparlisib, an inhibitor of the pathway, in patients with heavily pretreated metastatic UC. Although the drug was found to have modest efficacy, with 6 patients experiencing stable disease and 1 patient achieving a partial response at 8 weeks on therapy, significant side effects also were observed. Patients with specific genetic alterations responded to treatment. Further studies of PI3K pathway inhibition are warranted using newer agents that have superior toxicity profiles and are more selective inhibitors of the pathway.

The repertoire of genetic alterations in salivary duct carcinoma including a novel HNRNPH3-ALK rearrangement

Salivary duct carcinoma (SDC) is a rare, aggressive malignancy with limited treatment options and poor outcome. Twenty-nine primary resected SDC, including 15 SDC de novo (SDCDN), and 14 SDC ex pleomorphic adenoma (SDCXPA) were subjected to the massive parallel sequencing assay (MSK-IMPACT) targeting 287 to 468 cancer-related genes. TP53 was the most frequently altered gene (69%). TP53 mutations and ERBB2 amplification were more frequent in SDCXPA than in SDCDN (P = .0007 and P = .01, respectively). Potentially targetable mutations were detected in 79% (23/29) of SDC involving ERBB2 (31%), PIK3CA (28%), HRAS (21%), ALK (7%) and BRAF (3%), and 22% (5/23) of those cases harbored possible primary resistance mutations involving CCNE1, NF1 and PTEN. A novel HNRNPH3-ALK rearrangement was found in one SDCDN. In another case, EML4-ALK fusion detected in the primary tumor was associated with ALK G1202R secondary resistance mutation in the post-treatment metastasis. A germline analysis of the DNA repair genes revealed a case with a pathogenic BRCA1 E23fs germline variant. SDCDN and SDCXPA are genetically distinct. Although the majority of SDC may be amenable to molecular targeted therapy, concurrent possible resistance mutations may be found in a significant minority of cases. A broad genomic profiling is necessary to ensure detection of rare but clinically actionable somatic alterations in SDC.

The genetic landscape of endometrial clear cell carcinomas

Clear cell carcinoma of the endometrium is a rare type of endometrial cancer that is generally associated with an aggressive clinical behaviour. Here, we sought to define the repertoire of somatic genetic alterations in endometrial clear cell carcinomas (ECCs), and whether ECCs could be classified into the molecular subtypes described for endometrial endometrioid and serous carcinomas. We performed a rigorous histopathological review, immunohistochemical analysis and massively parallel sequencing targeting 300 cancer-related genes of 32 pure ECCs. Eleven (34%), seven (22%) and six (19%) ECCs showed abnormal expression patterns for p53, ARID1A, and at least one DNA mismatch repair (MMR) protein, respectively. Targeted sequencing data were obtained from 30 of the 32 ECCs included in this study, and these revealed that two ECCs (7%) were ultramutated and harboured mutations affecting the exonuclease domain of POLE. In POLE wild-type ECCs, TP53 (46%), PIK3CA (36%), PPP2R1A (36%), FBXW7 (25%), ARID1A (21%), PIK3R1 (18%) and SPOP (18%) were the genes most commonly affected by mutations; 18% and 11% harboured CCNE1 and ERBB2 amplifications, respectively, and 11% showed DAXX homozygous deletions. ECCs less frequently harboured mutations affecting CTNNB1 and PTEN but more frequently harboured PPP2R1A and TP53 mutations than non-POLE endometrioid carcinomas from The Cancer Genome Atlas (TCGA). Compared to endometrial serous carcinomas (TCGA), ECCs less frequently harboured TP53 mutations. When a surrogate model for the molecular-based TCGA classification was used, all molecular subtypes previously identified in endometrial endometrioid and serous carcinomas were present in the ECCs studied, including POLE, MMR-deficient, copy-number high (serous-like)/p53 abnormal, and copy-number low (endometrioid)/p53 wild-type, which were significantly associated with disease-free survival in univariate analysis. These findings demonstrate that ECCs constitute a histologically and genetically heterogeneous group of tumours with varying outcomes. Furthermore, our data suggest that the classification of ECCs as being generally 'high-grade' or 'type II' tumours may not be warranted. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Next-generation sequencing of urine specimens: A novel platform for genomic analysis in patients with non-muscle-invasive urothelial carcinoma treated with bacille Calmette-Guérin

BACKGROUND

Biopsies from patients with high-risk (HR) non-muscle-invasive urothelial carcinoma (NMIUC), especially flat urothelial carcinoma in situ, frequently contain scant diagnostic material or denuded mucosa only, and this precludes further extensive genomic analysis. This study evaluated the use of next-generation sequencing (NGS) analysis of urine cytology material from patients with HR NMIUC in an attempt to identify genetic alterations that might correlate with clinical features and responses to bacille Calmette-Guérin (BCG) treatment.

METHODS

Forty-one cytology slides from patients with HR NMIUC treated with intravesical BCG were selected for this study. Histological confirmation was available for all cases. The specimens were subjected to NGS analysis with a customized targeted exome capture assay composed of 341 genes.

RESULTS

In this cohort, genomic alterations were successfully identified in all cytology samples. Mutations were detected down to a 2% allele frequency and chromosomal rearrangements including copy number alterations and gene fusions were identified. The most frequently altered genes included telomerase reverse transcriptase (TERT), tumor protein 53 (TP53), Erb-B2 receptor tyrosine kinase 2 (ERBB2), and chromatin remodeling genes such as lysine demethylase 6A (KDM6A) and AT-rich interaction domain 1A (ARID1A). For patients with matched tumor tissue, cytology specimens revealed all mutations detected in tissue as well as additional mutations, and this suggested that urine might more effectively capture the full genetic heterogeneity of disease than an individual cystectomy. Alterations in multiple genes correlated with clinical and histopathological features, including responses to BCG treatment, flat architecture versus papillary architecture, and smoking history.

CONCLUSIONS

Urine specimens can replace tissue as a substrate for NGS analysis of HR NMIUC. Several genomic alterations identified in urine specimens might be associated with histological features and clinical characteristics. Cancer Cytopathol 2017;125:416-26. © 2017 American Cancer Society.

Genomic characterization of response to chemoradiation in urothelial bladder cancer

BACKGROUND

The authors characterized the genetic landscape of chemoradiation-treated urothelial carcinoma of the bladder (UCB) with the objective of identifying potential correlates of response.

METHODS

Primary tumors with (n = 8) or without (n = 40) matched recurrent tumors from 48 patients who had non-metastatic, high-grade UCB and received treatment primarily with chemoradiation were analyzed using a next-generation sequencing assay enriched for cancer-related and canonical DNA damage response (DDR) genes. Protein expression of meiotic recombination 11 homolog (MRE11), a previously suggested biomarker, was assessed in 44 patients. Recurrent tumors were compared with primary tumors, and the clinical impact of likely deleterious DDR gene alterations was evaluated.

RESULTS

The profile of alterations approximated that of prior UCB cohorts. Within 5 pairs of matched primary-recurrent tumors, a median of 92% of somatic mutations were shared. A median 33% of mutations were shared between 3 matched bladder-metastasis pairs. Of 26 patients (54%) who had DDR gene alterations, 12 (25%) harbored likely deleterious alterations. In multivariable analysis, these patients displayed a trend toward reduced bladder recurrence (hazard ratio, 0.32; P = .070) or any recurrence (hazard ratio, 0.37; P = .070). The most common of these alterations, ERCC2 (excision repair cross-complementation group 2) mutations, were associated with significantly lower 2-year metastatic recurrence (0% vs 43%; log-rank P = .044). No impact of MRE11 protein expression on outcome was detected.

CONCLUSIONS

A similar mutation profile between primary and recurrent tumors suggests that pre-existing, resistant clonal populations represent the primary mechanism of chemoradiation treatment failure. Deleterious DDR genetic alterations, particularly recurrent alterations in ERCC2, may be associated with improved chemoradiation outcomes in patients with UCB. A small sample size necessitates independent validation of these observations. Cancer 2016;122:3715-23. © 2016 American Cancer Society.

Frequent somatic CDH1 loss-of-function mutations in plasmacytoid variant bladder cancer

Plasmacytoid bladder cancer is an aggressive histologic variant with a high risk of disease-specific mortality. Using whole-exome and targeted sequencing, we find that truncating somatic alterations in the CDH1 gene occur in 84% of plasmacytoid carcinomas and are specific to this histologic variant. Consistent with the aggressive clinical behavior of plasmacytoid carcinomas, which frequently recur locally, CRISPR/Cas9-mediated knockout of CDH1 in bladder cancer cells enhanced cell migration.

Genomic Biomarkers for the Prediction of Stage and Prognosis of Upper Tract Urothelial Carcinoma

PURPOSE

Genomic characterization of radical nephroureterectomy specimens in patients with upper tract urothelial carcinoma may allow for thoughtful integration of systemic and targeted therapies. We sought to determine whether genomic alterations in upper tract urothelial carcinoma are associated with adverse pathological and clinical outcomes.

MATERIALS AND METHODS

Next generation exon capture sequencing of 300 cancer associated genes was performed in 83 patients with upper tract urothelial carcinoma. Genomic alterations were assessed individually and also grouped into core signal transduction pathways or canonical cell functions for association with clinicopathological outcomes. Binary outcomes, including grade (high vs low), T stage (pTa/T1/T2 vs pT3/T4) and organ confined status (pT2 or less and N0/Nx vs greater than pT2 or N+) were assessed with the Kruskal-Wallis and Fisher exact tests as appropriate. Associations between alterations and survival were estimated using the Kaplan-Meier method and Cox regression.

RESULTS

Of the 24 most commonly altered genes in 9 pathways TP53/MDM2 alterations and FGFR3 mutations were the only 2 alterations uniformly associated with high grade, advanced stage, nonorgan confined disease, and recurrence-free and cancer specific survival. TP53/MDM2 alterations were associated with adverse clinicopathological outcomes whereas FGFR3 mutations were associated with favorable outcomes. We created a risk score using TP53/MDM2 and FGFR3 status that was able to discriminate between adverse pathological and clinical outcomes, including in the subset of patients with high grade disease. The study is limited by small numbers and lack of validation.

CONCLUSIONS

Our data indicate that specific genomic alterations in radical nephroureterectomy specimens correlate with tumor grade, stage and cancer specific survival outcomes.

Targeted exome sequencing profiles genetic alterations in leiomyosarcoma

Leiomyosarcoma (LMS) belongs to the class of genetically complex sarcomas and shows numerous, often non-recurrent chromosomal imbalances and aberrations. We investigated a group of LMS using NGS platform to identify recurrent genetic abnormalities and possible therapeutic targets. Targeted exome sequencing of 230 cancer-associated genes was performed on 35 primary soft tissue and visceral (extra-uterine) LMS. Sequence data were analyzed to identify single nucleotide variants, small insertions/deletions (indels), and copy number alterations. Key alterations were further investigated using FISH assay. The study group included patients with median age of 64 years and median tumor size of 7 cm. The primary sites included retroperitoneal/intra-abdominal, extremity, truncal, and visceral. Thirty-one tumors were high grade LMS, while four were low grade. Losses of chromosomal regions involving key tumor suppressor genes PTEN (10q), RB1 (13q), CDH1 (16q), and TP53 (17p) were the most frequent genetic events. Gains mainly involved chromosome regions 17p11.2 (MYOCD) and 15q25-26 (IGF1R). The most frequent mutations were identified in the TP53 gene in 13 of 35 (37%) cases. FISH analysis showed amplification of the myocardin (MYOCD) gene in 5 of 25 (20%) cases analyzed. None of the four low grade LMS showed losses or mutations of PTEN or TP53 genes. Genetic complexity is the hallmark of LMS with losses of important tumor suppressor genes being a common feature. MYOCD, a key gene associated with smooth muscle differentiation, is amplified in a subset of both retroperitoneal and extremity LMS. Further studies are necessary to investigate the significance of gains/amplifications in the development of these tumors.

Alternative transcription initiation leads to expression of a novel ALK isoform in cancer

Activation of oncogenes by mechanisms other than genetic aberrations such as mutations, translocations, or amplifications is largely undefined. Here we report a novel isoform of the anaplastic lymphoma kinase (ALK) that is expressed in ∼11% of melanomas and sporadically in other human cancer types, but not in normal tissues. The novel ALK transcript initiates from a de novo alternative transcription initiation (ATI) site in ALK intron 19, and was termed ALK(ATI). In ALK(ATI)-expressing tumours, the ATI site is enriched for H3K4me3 and RNA polymerase II, chromatin marks characteristic of active transcription initiation sites. ALK(ATI) is expressed from both ALK alleles, and no recurrent genetic aberrations are found at the ALK locus, indicating that the transcriptional activation is independent of genetic aberrations at the ALK locus. The ALK(ATI) transcript encodes three proteins with molecular weights of 61.1, 60.8 and 58.7 kilodaltons, consisting primarily of the intracellular tyrosine kinase domain. ALK(ATI) stimulates multiple oncogenic signalling pathways, drives growth-factor-independent cell proliferation in vitro, and promotes tumorigenesis in vivo in mouse models. ALK inhibitors can suppress the kinase activity of ALK(ATI), suggesting that patients with ALK(ATI)-expressing tumours may benefit from ALK inhibitors. Our findings suggest a novel mechanism of oncogene activation in cancer through de novo alternative transcription initiation.

Genomic Characterization of Upper Tract Urothelial Carcinoma

BACKGROUND

Despite a similar histologic appearance, upper tract urothelial carcinoma (UTUC) and urothelial carcinoma of the bladder (UCB) tumors have distinct epidemiologic and clinicopathologic differences.

OBJECTIVE

To investigate whether the differences between UTUC and UCB result from intrinsic biological diversity.

DESIGN, SETTING, AND PARTICIPANTS

Tumor and germline DNA from patients with UTUC (n=83) and UCB (n=102) were analyzed using a custom next-generation sequencing assay to identify somatic mutations and copy number alterations in 300 cancer-associated genes.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

We described co-mutation patterns and copy number alterations in UTUC. We also compared mutation frequencies in high-grade UTUC (n=59) and high-grade UCB (n=102).

RESULTS AND LIMITATIONS

Comparison of high-grade UTUC and UCB revealed significant differences in the prevalence of somatic alterations. Genes altered more commonly in high-grade UTUC included FGFR3 (35.6% vs 21.6%; p=0.065), HRAS (13.6% vs 1.0%; p=0.001), and CDKN2B (15.3% vs 3.9%; p=0.016). Genes less frequently mutated in high-grade UTUC included TP53 (25.4% vs 57.8%; p<0.001), RB1 (0.0% vs 18.6%; p<0.001), and ARID1A (13.6% vs 27.5%; p=0.050). Because our assay was restricted to genomic alterations in a targeted panel, rare mutations and epigenetic changes were not analyzed.

CONCLUSIONS

High-grade UTUC tumors display a spectrum of genetic alterations similar to high-grade UCB. However, there were significant differences in the prevalence of several recurrently mutated genes including HRAS, TP53, and RB1. As relevant targeted inhibitors are being developed and tested, these results may have important implications for the site-specific management of patients with urothelial carcinoma.

PATIENT SUMMARY

Comparison of next-generation sequencing of upper tract urothelial carcinoma (UTUC) with urothelial bladder cancer identified that similar mutations were present in both cancer types but at different frequencies, indicating a potential need for unique management strategies. UTUC tumors were found to have a high rate of mutations that could be targeted with novel therapies.

Cutaneous squamous and neuroendocrine carcinoma: genetically and immunohistochemically different from Merkel cell carcinoma

Cutaneous neuroendocrine (Merkel cell) carcinoma most often arises de novo in the background of a clonally integrated virus, the Merkel cell polyomavirus, and is notable for positive expression of retinoblastoma 1 (RB1) protein and low expression of p53 compared with the rare Merkel cell polyomavirus-negative Merkel cell carcinomas. Combined squamous and Merkel cell tumors are consistently negative for Merkel cell polyomavirus. Little is known about their immunophenotypic or molecular profile. Herein, we studied 10 combined cutaneous squamous cell and neuroendocrine carcinomas for immunohistochemical expression of p53, retinoblastoma 1 protein, neurofilament, p63, and cytokeratin 20 (CK20). We compared mutation profiles of five combined Merkel cell carcinomas and seven 'pure' Merkel cell carcinomas using targeted next-generation sequencing. Combined tumors were from the head, trunk, and leg of Caucasian males and one female aged 52-89. All cases were highly p53- and p63-positive and neurofilament-negative in the squamous component, whereas RB1-negative in both components. Eight out of 10 were p53-positive, 3/10 p63-positive, and 3/10 focally neurofilament-positive in the neuroendocrine component. Six out of 10 were CK20-positive in any part. By next-generation sequencing, combined tumors were highly mutated, with an average of 48 mutations per megabase compared with pure tumors, which showed 1.25 mutations per megabase. RB1 and p53 mutations were identified in all five combined tumors. Combined tumors represent an immunophenotypically and genetically distinct variant of primary cutaneous neuroendocrine carcinomas, notable for a highly mutated genetic profile, significant p53 expression and/or mutation, absent RB1 expression in the context of increased RB1 mutation, and minimal neurofilament expression.

Abstract 602: Deleterious alterations in DNA damage response genes are associated with improved outcome in muscle-invasive bladder cancer patients treated with radiation-based bladder preservation

Purpose: Radiotherapy (RT)-based bladder preservation is an alternative to perioperative chemotherapy and radical cystectomy (RC) for selected patients with muscle-invasive bladder cancer (MIBC). Recent data suggest that somatic DNA damage response (DDR) alterations are associated with improved outcome in MIBC patients receiving RC +/- perioperative chemotherapy. Improved understanding of the influence of DDR genetics on response to RT-based bladder preservation may aid patient selection.

Methods: We performed deep, targeted capture sequencing of primary bladder tumors and paired/pooled normal specimens from 48 RT treated MIBC patients with a DDR gene-enriched panel. To test whether correlations of DDR alterations with outcomes were specific to a RT cohort, we also assessed a subset of these DDR genes that were sequenced in a previously published series of 89 patients who received RC +/- neoadjuvant platinum-based chemotherapy. Specimens were re-reviewed to confirm urothelial histology. Deleterious alterations were defined as somatic nonsense, frameshift, or splice site mutations, or missense mutations at or near functionally significant residues validated in the literature.

Results: In the RT cohort, median RT dose was 66 Gy, and chemotherapy use was neoadjuvant and concurrent (46%), concurrent only (48%), or none (6%). Visibly complete TURBT was achieved in 71% of patients. Median surviving follow up was 28 months. There were 30 progression events (crude rate 63%), comprised of 22 metastases (crude 46%) and 24 local in-bladder recurrences (crude 50%). While 30 (63%) patients had alterations in DDR genes, only 13 (27%) patients had deleterious DDR alterations, specifically in ATM (2), BRCA1 (1), BRIP1 (1), ERCC2 (6), FANCD2 (1), and PALB2 (1). On multivariable Cox proportional hazards analysis, the presence of a deleterious DDR alteration was associated significantly with lower relapse risk (HR 0.28, 95% CI 0.08-0.95; p = 0.041), as well as with a trend towards lower risk for metastasis (HR 0.32, 95% CI 0.10-1.11; p = 0.07) and any disease progression (HR 0.35, 95% CI 0.12-1.03; p = 0.06). In the RC cohort, neoadjuvant chemotherapy was given in 39% of patients, and deleterious DDR gene alterations were noted only in 8% of the patients. On 2-sided log-rank testing, such alterations conferred a non-significant trend for improved recurrence-free survival (p = 0.20) and disease-specific survival (p = 0.10). 

Conclusion: Deleterious somatic alterations in DDR genes were associated with significantly improved outcomes in bladder cancer patients undergoing RT-based therapy and with a trend for improved outcomes in those treated with RC +/- platinum chemotherapy. Further research is warranted to validate these findings on an independent RT-treated dataset and to clarify the relationship in a larger chemotherapy-treated RC cohort.

Citation Format: Neil B. Desai, Gopa Iyer, Eugene K. Cha, Sasinya N. Scott, Joseph Hreiki, John P. Sfakianos, Philip Kim, Aditya Bagroida, Bernard H. Bochner, Jonathan E. Rosenberg, Dean F. Bajorin, Michael F. Berger, Marisa A. Kollmeier, Hikmat Al-Ahmadie, David B. Solit. Deleterious alterations in DNA damage response genes are associated with improved outcome in muscle-invasive bladder cancer patients treated with radiation-based bladder preservation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 602. doi:10.1158/1538-7445.AM2015-602

Abstract LB-174: Examining the genomic differences between upper and lower tract urothelial carcinomas

Background

Urothelial carcinomas are capable of arising at multiple sites within the urinary tract. About 90% of cases originate in the urinary bladder (lower tract) and about 10% of cases emerge in the pelvis or ureter (upper tract). While these sites have similar histologic appearances, there are differences in their epidemiologic, clinical and pathologic characteristics, suggesting they may represent two distinct diseases. Previous studies have observed a more aggressive disease from patients with upper tract urothelial carcinoma (UTUC) versus patients with urothelial carcinoma of the bladder (UCB). Our aim was to examine whether the clinicopathological differences between upper and lower tract urothelial tumors are the result of differences in their scope of somatic genetic alterations.

Methods

Tumors and matched germline DNA from 59 patients with high-grade UTUC and 102 patients with high-grade UCB were extracted. The genomic profiles of these patients were analyzed and compared using a custom hybridization capture-based sequencing assay to identify point mutations, small insertions, deletions and copy number alterations of 230 cancer-associated genes.

Results

Average next-generation sequencing coverage for high-grade UTUC (674x) and UCB (762x) tumors. The comparison between the high-grade UTUC and UCB tumors identified significant differences in the prevalence of somatic alterations between these cohorts. Alterations in oncogene HRAS (13.6% UTUC vs. 1.0% UCB, p = 0.001) were more common in high-grade UTUC. Another oncogene FGFR3 (35.6% UTUC vs. 21.6% UCB, p = 0.065) was not significantly different between the UTUC and UCB cohorts. Genes identified as significantly less frequently altered in UTUC compared to UCB tumors included tumor suppressor genes TP53 (25.4% vs. 57.8%, p&lt;0.001), RB1 (0.0% vs. 18.6%, p&lt;0.001), and ARID1A (13.6% vs. 27.5%, p = 0.05).

Conclusions

While the genes with somatic alterations in upper and lower tract urothelial tumors were similar, we did identify significant differences in the prevalence of several recurrently altered genes including TP53, RB1, HRAS and ARID1A between UTUC and UCB cohorts. These findings may account for the divergence in clinical outcomes observed between these two disease sites and the high prevalence of actionable genomic targets may assist in the development of novel therapeutic approaches for these diseases.

Citation Format: Sasinya N. Scott, John P. Sfakianos, Eugene K. Cha, Gopa Iyer, Emily C. Zabor, Philip H. Kim, A. A. Hakimi, Irina Ostrovnaya, Ricardo Ramirez, Aphrothiti J. Hanrahan, Neil Desai, Qinghu Ren, Arony Sun, Jonathan E. Rosenberg, Guido Dalbagni, Dean F. Bajorin, Michael F. Berger, Bernard H. Bochner, Hikmat Al-Ahmadie, David B. Solit, Jonathan A. Coleman. Examining the genomic differences between upper and lower tract urothelial carcinomas. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-174. doi:10.1158/1538-7445.AM2015-LB-174

GNAS and KRAS Mutations Define Separate Progression Pathways in Intraductal Papillary Mucinous Neoplasm-Associated Carcinoma

BACKGROUND

Intraductal papillary mucinous neoplasms (IPMN) are being increasingly recognized as important precursors to pancreatic adenocarcinoma. Elucidation of the genetic changes underlying IPMN carcinogenesis may improve the diagnosis and management of IPMN. We sought to determine whether different histologic subtypes of IPMN would exhibit different frequencies of specific genetic mutations.

STUDY DESIGN

Patients with resected IPMN-associated invasive carcinoma (IPMN-INV) between 1997 and 2012 were reviewed. Areas of carcinoma, high-grade dysplasia, and low-grade dysplasia were micro-dissected from each pathologic specimen. Targeted, massively parallel sequencing was then performed on a panel of 275 genes (including KRAS, GNAS, and RNF43).

RESULTS

Thirty-eight patients with resected IPMN-INV and sufficient tissue for micro-dissection were identified. Median follow-up was 2.6 years. Mutations in GNAS were more prevalent in colloid-type IPMN-INV than tubular-type IPMN-INV (89% vs 32% respectively; p = 0.0003). Conversely, KRAS mutations were more prevalent in tubular-type than colloid-type IPMN-INV (89% vs 52%, respectively; p = 0.01). For noninvasive IPMN subtypes, GNAS mutations were more prevalent in intestinal (74%) compared with pancreatobiliary (31%) and gastric (50%) subtypes (p = 0.02). The presence of these mutations did not vary according to the degree of dysplasia (GNAS: invasive 61%, high-grade 59%, low-grade 53%; KRAS: invasive 71%, high-grade 62%, low-grade 74%), suggesting that mutations in these genes occur early in IPMN carcinogenesis.

CONCLUSIONS

Colloid carcinoma associated with IPMN and its intestinal-type preinvasive precursor are associated with high frequencies of GNAS mutations. The mutation profile of tubular carcinoma resembles that of conventional pancreatic adenocarcinoma. Preoperative determination of mutational status may assist with clinical treatment decisions.

Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology

The identification of specific genetic alterations as key oncogenic drivers and the development of targeted therapies are together transforming clinical oncology and creating a pressing need for increased breadth and throughput of clinical genotyping. Next-generation sequencing assays allow the efficient and unbiased detection of clinically actionable mutations. To enable precision oncology in patients with solid tumors, we developed Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT), a hybridization capture-based next-generation sequencing assay for targeted deep sequencing of all exons and selected introns of 341 key cancer genes in formalin-fixed, paraffin-embedded tumors. Barcoded libraries from patient-matched tumor and normal samples were captured, sequenced, and subjected to a custom analysis pipeline to identify somatic mutations. Sensitivity, specificity, reproducibility of MSK-IMPACT were assessed through extensive analytical validation. We tested 284 tumor samples with previously known point mutations and insertions/deletions in 47 exons of 19 cancer genes. All known variants were accurately detected, and there was high reproducibility of inter- and intrarun replicates. The detection limit for low-frequency variants was approximately 2% for hotspot mutations and 5% for nonhotspot mutations. Copy number alterations and structural rearrangements were also reliably detected. MSK-IMPACT profiles oncogenic DNA alterations in clinical solid tumor samples with high accuracy and sensitivity. Paired analysis of tumors and patient-matched normal samples enables unambiguous detection of somatic mutations to guide treatment decisions.

Phase 2 study of the pan-isoform PI3 kinase inhibitor BKM120 in metastatic urothelial carcinoma patients

324

Background: PI3 kinase (PI3K) pathway alterations are found in 39% of urothelial carcinoma (UC) (TCGA). Prior reports have shown significant responses in metastatic UC patients (pts) whose tumors harbor PI3K pathway alterations treated with mTOR inhibitors, providing a rationale to investigate BKM120 in mUC. Methods: This phase II study enrolled mUC pts progressing on platinum-based chemotherapy (up to 4 prior agents). The primary and secondary endpoints were proportion of pts progression-free at 2 months and response rate (RR) by Response Criteria in Solid Tumors (RECIST) v1.1, respectively. A Simon 2-stage design was used to discriminate between a 2 month PFS rate of <60% (at which point the trial would be halted) vs. >80%. Pts received 100 mg drug once daily. To identify predictors of response/resistance to BKM120, targeted exon capture sequencing was performed to define the mutation status of PIK3CA, PTEN, AKT1, TSC1, and additional genes within tumors from all treated pts. Results: 13 of 15 enrolled pts were eligible for the primary endpoint. Median age was 65 (53-82). Pts had received an average of 3 agents (2-4) before enrollment. The median progression-free survival (PFS) was 2.77 months (95% CI: 1.83-3.71) with 6 pts displaying stable disease (SD) and 1 partial response (PR) at 2 months (PFS rate 54%). Sequencing identified 2 pts with PIK3CA mutations (E542K, H1047R) who experienced progression as best RECIST response. Tumor from the pt with a 16 month PR harbored a TSC1 R500* nonsense mutation. 1 pt with SD lasting 3.7 months had a TSC1 L330fs truncation. Conclusions: While BKM120 therapy did not display a significant improvement in 2-month PFS rate compared to standard chemotherapy in the second-line setting, 2 pts, one with a durable PR and one with SD, had tumors with inactivating mutations in TSC1. Based upon these results, an expansion cohort is accruing in which select mUC pts whose tumors harbor PI3K pathway alterations receive BKM120. Clinical trial information: NCT01551030.

Clonality of bladder tumors following radical nephroureterectomy: Against the field defect hypothesis

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Background: Urothelial carcinoma is characterized by multifocal and metachronous tumors. To explain this phenomenon, two hypotheses have been proposed: the ‘field defect’ hypothesis - urothelial cells are primed to undergo transformation by exposure to carcinogens, and the clonal, or ‘single progenitor cell,’ hypothesis - tumors arise from intraluminal seeding of transformed cells. Methods: To examine their clonal relationships, we compared the genomic profiles of primary upper tract urothelial carcinoma (UTUC) tumors and metachronous bladder tumors (intravesical recurrences) in patients treated with radical nephroureterectomy (RNU) and subsequent transurethral resection. Specimens were analyzed using a next-generation, targeted sequencing assay designed to identify point mutations, indels, and copy number alterations in 341 cancer-associated genes. Results: We analyzed 16 primary UTUC tumors and 41 intravesical recurrences in patients treated with RNU. The median number of intravesical recurrences per patient was 2 (range 1-7) and the interval from RNU to intravesical recurrence ranged from 3.5 months to 129 months. With an average sequencing coverage of 516x, we found strong evidence delineating the clonal relationship between primary UTUC tumors and subsequent bladder tumors. The majority of somatic mutations present in the primary UTUC tumors (median=7, range 4-39) were detected in all subsequent bladder tumors (128/146, 88%). In an illustrative case, one patient followed with periodic cystoscopy/cytology who had been NED for 5.5 years then developed 7 bladder tumors over the next 44 months, each with the identical mutation profile (8 mutations) as the primary tumor. Conclusions: We demonstrate that bladder tumors following RNU represent true intravesical recurrences, with almost all tumors sharing the same somatic mutation profile as the primary UTUC tumor. This has important implications for surgical techniques to minimize the risk of intraluminal seeding, the delivery of intravesical therapy following RNU, and the development of strategies employing systemic chemotherapy or targeted agents.

Comprehensive mutation profiling by next-generation sequencing of effusion fluids from patients with high-grade serous ovarian carcinoma

BACKGROUND

Mutation analysis for personalized treatment has become increasingly important in the management of different types of cancer. The advent of new DNA extraction protocols and sequencing platforms with reduced DNA input requirements might allow the use of cytology specimens for high-throughput mutation analysis. In this study, the authors evaluated the use of effusion fluid for next-generation sequencing-based, multigene mutation profiling.

METHODS

Four specimens from each of 5 patients who had at least stage III, high-grade serous ovarian carcinoma were selected: effusion fluid; frozen tumor; formalin-fixed, paraffin embedded tumor; and matched normal blood. Frozen tumors from each patient were previously characterized by The Cancer Genomic Atlas (TCGA). DNA was extracted from all specimens and was sequenced using a custom hybridization capture-based assay. Genomic alterations were compared among all specimens from each patient as well as with mutations reported in TCGA for the same tumors.

RESULTS

In total, 17 distinct somatic mutations were identified in the cohort. Ten of 17 mutations were reported in TCGA and were called in all 3 malignant specimens procured from the patients. Of the remaining 7 mutations, 2 were called in all 3 specimens, and the other 5 were sample-specific. Two mutations were detected only in the cytology specimens. Copy number profiles were concordant among the tumors analyzed.

CONCLUSIONS

Cytology specimens represent suitable material for high-throughput sequencing, because all mutations described by TCGA were independently identified in the effusion fluid. Differences in mutations detected in samples procured from the same patient may reflect tumor heterogeneity.

Abstract LB-91: SMARCA4 mutations in small cell carcinoma of the ovary

Background: Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare, highly aggressive form of ovarian cancer primarily diagnosed in young women. The molecular basis of this disease is unknown, and there are limited therapeutic options. The tissue of origin remains speculative, and SCCOHT is still categorized as a miscellaneous tumor by the World Health Organization.

Methods: We performed target capture and massively parallel DNA sequencing to a mean depth 442x across 279 key cancer-associated genes in 12 SCCOHT samples. All mutations were validated using orthogonal techniques and their somatic nature was determined by sequencing matched germline DNA. Mutation expression and the consequence of splice site variants were determined through RNA sequencing. Protein expression was determined through immunoblotting and immunohistochemistry. Functional significance was determined through in vitro manipulation using over-expression and knockdown constructs.

Results: All 12 patients (median age 26.5 yrs; range 18-42 yrs) had inactivating bi-allelic variants in the chromatin regulator SMARCA4, including splice site, nonsense, and frameshift mutations or exon deletions. One patient had a germline mutation with somatic loss of the wild-type allele. All mutations were detected in RNA transcripts, and splice site variants resulted in transcribed introns. Immunoblotting and immunohistochemistry confirmed loss of SMARCA4 protein expression in 7 of 9 cases with mutations and available tissue. SMARCA4 somatic mutations were more common in SCCOHT than other solid tumors found in The Cancer Genome Atlas (p &lt; 2.22 x 10-16). Ectopic re-introduction of SMARCA4 resulted in a dose-dependent suppression of cell growth and an expected increase in p21. Stable depletion of SMARCA4 using lentiviral expressed short hairpin RNA led to an increase in cell growth as measured by an XTT proliferation assay.

Conclusions: SMARCA4 SWI/SNF chromatin-remodeling complex mutations were uniformly identified in all SCCOHT examined. The SCCOHT tumors had few other mutations in the panel of sequenced genes. The inactivating mutations are infrequently mutated in other solid tumors and are consistent with the characteristics of a tumor suppressor. Most of the identified mutations reside within the known helicase catalytic domains of SMARCA4, suggesting a role in tumorigenesis. One case contained a germline mutation, which is consistent with prior reports suggesting a hereditary component to this disease. These data suggest that canonical mutations in SMARCA4 are an important therapeutic target for further investigation.

Citation Format: Petar Jelinic, Jennifer Mueller, Narciso Olvera, Fanny Dao, Sasinya N. Scott, Ronak Shah, JianJiong Gao, Nikolaus Schultz, Mithat Gonen, Robert A. Soslow, Michael F. Berger, Douglas A. Levine. SMARCA4 mutations in small cell carcinoma of the ovary. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-91. doi:10.1158/1538-7445.AM2014-LB-91

Abstract 3419: Frequency and function of ERBB3 mutations in bladder cancer

Deregulation of the HER family of receptor tyrosine kinases has been widely implicated in cancer initiation and progression. Activating mutations or gene amplification of EGFR and ERBB2 (HER2) are frequently found in non-small cell lung, breast, colorectal, glioblastoma and head and neck cancers. However, little is known regarding the prevalence or functionality of genomic alterations in the ERBB3 (HER3) isoform. Although ERBB3 has limited inherent kinase activity, ligand stimulation promotes its dimerization with active kinases like ERBB2 and EGFR that can phosphorylate ERBB3 which then promotes transformation. Thus genomic alterations in ERBB3 may be a key means of promoting oncogenic signaling despite the protein lacking robust enzymatic activity. We performed a meta-analysis of 40 cross-cancer next generation sequencing and copy number genomics data sets newly generated by our group (bladder) or found in recently published repositories (The Cancer Genome Atlas (TCGA), Broad, Genentech, Sanger, etc). Analogous to the singular 2013 publication on ERBB3 mutations to date, we found frequent mutations in ERBB3 in gastric tumors (∼11%). Preliminary analysis of our novel and expanding cohort of 109 high-grade bladder cancer tumors suggests that ERBB3 mutations are equally frequent in bladder cancer (∼10-12%). Collectively, EGFR, ERBB2 and ERBB3 alterations were found in 23-30% of all high-grade bladder cancers, typically in a mutually exclusive pattern suggesting that these may be driver events. ERBB3 mutations were distributed across all structural domains of the protein. We identified more than 15 novel ERBB3 mutations in our bladder cohort, including hotspot mutations in the extracellular domain (V104L/M, D297Y, others) that were recurrent across multiple cancers types. Stable retroviral overexpression of ERBB3 mutants into NIH-3T3 cells induced phosphorylation of ERBB3, activation of downstream signaling cascades and soft agar colony formation, all which were enhanced in the presence of neuregulin and inhibited by the dual EGFR/ERBB2 kinase inhibitor, neratinib, and a monoclonal antibody to ERBB3, AMG-888/U3-1287. These data highlight a large cohort of bladder cancer patients with novel, activating mutations in the tractable kinase ERBB3, that could potentially benefit from approved EGFR/ERBB2 targeted therapeutics in the clinic and novel ERBB3 therapeutics in early clinical trials.

Citation Format: Aphrothiti J. Hanrahan, John P. Sfakianos, Ricardo Ramirez, Phillip H. Kim, Gopa Iyer, Hikmat A. Al-Ahmadie, Sasinya N. Scott, Dean F. Bajorin, Bernard H. Bochner, Jonathan A. Coleman, Jonathan E. Rosenberg, Michael F. Berger, Sarat Chandarlapaty, David B. Solit. Frequency and function of ERBB3 mutations in bladder cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3419. doi:10.1158/1538-7445.AM2014-3419

Synthetic lethality in ATM-deficient RAD50-mutant tumors underlies outlier response to cancer therapy

Metastatic solid tumors are almost invariably fatal. Patients with disseminated small-cell cancers have a particularly unfavorable prognosis, with most succumbing to their disease within two years. Here, we report on the genetic and functional analysis of an outlier curative response of a patient with metastatic small-cell cancer to combined checkpoint kinase 1 (CHK1) inhibition and DNA-damaging chemotherapy. Whole-genome sequencing revealed a clonal hemizygous mutation in the Mre11 complex gene RAD50 that attenuated ATM signaling which in the context of CHK1 inhibition contributed, via synthetic lethality, to extreme sensitivity to irinotecan. As Mre11 mutations occur in a diversity of human tumors, the results suggest a tumor-specific combination therapy strategy in which checkpoint inhibition in combination with DNA-damaging chemotherapy is synthetically lethal in tumor cells but not normal cells with somatic mutations that impair Mre11 complex function.

SIGNIFICANCE

Strategies to effect deep and lasting responses to cancer therapy in patients with metastatic disease have remained difficult to attain, especially in early-phase clinical trials. Here, we present an in-depth genomic and functional genetic analysis identifying RAD50 hypomorphism as a contributing factor to a curative response to systemic combination therapy in a patient with recurrent, metastatic small-cell cancer.

Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions

Background

Colorectal cancer is the second leading cause of cancer death in the United States, with over 50,000 deaths estimated in 2014. Molecular profiling for somatic mutations that predict absence of response to anti-EGFR therapy has become standard practice in the treatment of metastatic colorectal cancer; however, the quantity and type of tissue available for testing is frequently limited. Further, the degree to which the primary tumor is a faithful representation of metastatic disease has been questioned. As next-generation sequencing technology becomes more widely available for clinical use and additional molecularly targeted agents are considered as treatment options in colorectal cancer, it is important to characterize the extent of tumor heterogeneity between primary and metastatic tumors.

Results

We performed deep coverage, targeted next-generation sequencing of 230 key cancer-associated genes for 69 matched primary and metastatic tumors and normal tissue. Mutation profiles were 100% concordant for KRAS, NRAS, and BRAF, and were highly concordant for recurrent alterations in colorectal cancer. Additionally, whole genome sequencing of four patient trios did not reveal any additional site-specific targetable alterations.

Conclusions

Colorectal cancer primary tumors and metastases exhibit high genomic concordance. As current clinical practices in colorectal cancer revolve around KRAS, NRAS, and BRAF mutation status, diagnostic sequencing of either primary or metastatic tissue as available is acceptable for most patients. Additionally, consistency between targeted sequencing and whole genome sequencing results suggests that targeted sequencing may be a suitable strategy for clinical diagnostic applications.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0454-7) contains supplementary material, which is available to authorized users.

Tumor genetic analyses of patients with metastatic renal cell carcinoma and extended benefit from mTOR inhibitor therapy

PURPOSE

Rapalogs are allosteric mTOR inhibitors and approved agents for advanced kidney cancer. Reports of clonal heterogeneity in this disease challenge the concept of targeted monotherapy, yet a small subset of patients derives extended benefit. Our aim was to analyze such outliers and explore the genomic background of extreme rapalog sensitivity in the context of intratumor heterogeneity.

EXPERIMENTAL DESIGN

We analyzed archived tumor tissue of 5 patients with renal cell carcinoma, who previously achieved durable disease control with rapalogs (median duration, 28 months). DNA was extracted from spatially separate areas of primary tumors and metastases. Custom target capture and ultradeep sequencing was used to identify alterations across 230 target genes. Whole-exome sequence analysis was added to investigate genes beyond this original target list.

RESULTS

Five long-term responders contributed 14 specimens to explore clonal heterogeneity. Genomic alterations with activating effect on mTOR signaling were detected in 11 of 14 specimens, offering plausible explanation for exceptional treatment response through alterations in two genes (TSC1 and MTOR). In two subjects, distinct yet functionally convergent alterations activated the mTOR pathway in spatially separate sites. In 1 patient, concurrent genomic events occurred in two separate pathway components across different tumor regions.

CONCLUSIONS

Analysis of outlier cases can facilitate identification of potential biomarkers for targeted agents, and we implicate two genes as candidates for further study in this class of drugs. The previously reported phenomenon of clonal convergence can occur within a targetable pathway which might have implications for biomarker development beyond this disease and this class of agents.

Branched evolution and intratumor heterogeneity of urothelial carcinoma of the bladder

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Background: Genomic characterization of urothelial carcinoma of the bladder (UCB) has begun to reveal significant intertumor heterogeneity when comparing samples from different subjects. As in other malignancies, intratumor heterogeneity, which may allow for tumor evolution and adaption, poses a significant challenge to personalized-medicine strategies. Methods: To examine UCB tumor evolution and heterogeneity, we performed next-generation targeted sequencing on multiple temporally and spatially separated bladder tumors obtained at time of transurethral resection (TUR) and radical cystectomy (RC). Specimens were analyzed using a next-generation, targeted sequencing assay designed to identify point mutations, indels, and copy number alterations in 300 cancer-associated genes. Results: Phylogenetic reconstruction revealed evidence of branched evolutionary growth. Evaluation of multiple tumors from individual subjects identified both shared and unique potential driver mutations. Evidence of convergent phenotypic evolution was detected through analysis of multiple distinct tumors from several subjects. For example, three separate tumors in one subject shared a common PIK3CA mutation (E453K) and had unique second mutations in PIK3CA (E542V, E545K, and E545Q, respectively). In another subject, distinct inactivating mutations of EP300 were identified in two temporally separated tumor samples. Macrodissection of single tumors into non-invasive and invasive components revealed significant intratumor heterogeneity; one case illustrates how analysis of a muscle-invasive TUR specimen could result in undersampling and thereby miss the tumor clone that persisted at time of RC. Conclusions: We demonstrate branched evolution of UCB through genomic analyses of multiple temporally and spatially distinct bladder tumors from individual subjects. Macrodissection of individual tumor samples identified significant intratumor heterogeneity. These concepts may present major challenges to personalized-medicine approaches that rely on sampling of a single tumor at a specific timepoint in the evolution of a patient’s UCB.

Targeted sequencing of upper tract urothelial carcinoma

309

Background: Regardless of the anatomic location (renal pelvis or ureter (upper tract), bladder or urethra) urothelial carcinoma is considered a single entity. Outcomes differ depending on site of initial diagnosis. Moreover, little is known about the comparative biology across primary sites. To define the genomic profile of urothelial carcinoma arising from the upper tract, we used a next generation sequencing technology to analyze 26 sporadic high-grade urothelial tumors of the renal pelvis. Methods: Frozen tumor samples and matched germline blood or normal kidney DNA from 26 nephroureterectomy specimens were obtained under an IRB-approved protocol. DNA was analyzed using a next generation, targeted sequencing assay. We compared these tumors to a set of 108 bladder tumors. Fisher’s exact test analyzed associations with pathological stage and Cox regression with log-rank p-values examined associations with bladder recurrence and disease-free survival. Fisher’s exact test was used to compare mutation frequencies between upper tract and bladder tumors. P-values were adjusted for multiple comparisons using the Benjamini-Hochberg method. Results: Surgical pathology was Ta, T1, T2 and T3 in 7 (26.9%), 5 (19.2%), 4 (15.4%) and 10 (38.5%) patients, respectively. High-grade disease was found in 24 (92.3%) patients with 6 (27.3%) patients having node positive disease. The most frequently altered genes included FGFR3 (42.3%), KDM6A (38.5%), MLL2 (26.9%), TSC1 (26.9%), CREBBP (23.1%), CDKN2A (19.2%) and HRAS (19.2%). No significant differences in tumor and patient characteristics were found between the bladder and upper tract cohorts. A significant difference in the frequency of alterations between the upper tract and bladder cohorts was found in HRAS (19.2% vs 2.8%, p=0.032), TP53 (7.7% vs 57.4%, p<0.001) and TSC1(26.9% vs 5.6%, p=0.024). Conclusions: We identified unique patterns of genomic alterations within upper tract urothelial carcinoma compared to bladder cancers. Upper tract tumors are characterized by a higher frequency of activating FGFR3 and HRAS mutations, TSC1 nonsense mutations, and a lower frequency of TP53 alterations. These findings may have future implications on the utility of targeted therapies in this disease subtype.

Using exon-capture, deep sequencing of high-grade bladder urothelial carcinoma to identify recurrent genetic alterations and potential therapeutic targets

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Background: Urothelial carcinoma (UC) is highly lethal malignancy with limited therapeutic options in the advanced setting. Using a targeted, deep sequencing approach, we analyzed high grade bladder tumors to determine the prevalence of known cancer genes and to identify potential targets for therapy. Methods: High-grade bladder UC frozen tumor and matched germline blood was obtained from 109 patients (pts) undergoing transurethral resection or cystectomy. Tumor and normal DNA were analyzed using IMPACT (Integrated Molecular Profiling of Actionable Cancer Targets), a next generation, exon-capture targeted deep sequencing assay designed to identify point mutations, indels, and copy number alterations in the coding regions of 300 cancer-associated genes. Results: Median age was 68 and 82 pts (75%) were male. Mean target coverage for all sequenced exons was 579X. The most commonly mutated gene was TP53 (63 pts, 58%). Alterations in genes regulating cell cycle were also prevalent, including mutations in Rb (25 pts, 23%), and copy number gains of CCND1 (19 pts, 17%) and CCNE1 (8 patients, 7%). Mutations in several chromatin remodeling genes were also highly prevalent, including KDM6A (46 pts, 42%), MLL2 (34 pts, 31%), and ARID1A (31 pts, 28%). Alterations within recognized cancer-related signaling pathways were common. PI3K pathway alterations were prevalent, with PIK3CA mutations found in 25 pts (23%), 23 of which were recurrent missense mutations. Six pts (6%) had mutations in PTEN. Mutations in TSC1 were also found in six pts (6%). Alterations in select MAPK pathway genes were common, including FGFR3 (21 pts, 19%) and ERBB2(15 pts, 14%). Conclusions: High-grade bladder UC is a genetically heterogenous disease. However, over half of the tumors analyzed in this study harbor alterations in genes that have been targeted for therapeutic benefit in other cancers. Results from our targeted exon-sequencing analysis therefore provide a compelling case for clinical trials using novel agents in UC. Moreover, this deep sequencing assay may be used clinically to prospectively identify pts for trials enriched for patients with specific alterations.

Detecting somatic genetic alterations in tumor specimens by exon capture and massively parallel sequencing

Efforts to detect and investigate key oncogenic mutations have proven valuable to facilitate the appropriate treatment for cancer patients. The establishment of high-throughput, massively parallel "next-generation" sequencing has aided the discovery of many such mutations. To enhance the clinical and translational utility of this technology, platforms must be high-throughput, cost-effective, and compatible with formalin-fixed paraffin embedded (FFPE) tissue samples that may yield small amounts of degraded or damaged DNA. Here, we describe the preparation of barcoded and multiplexed DNA libraries followed by hybridization-based capture of targeted exons for the detection of cancer-associated mutations in fresh frozen and FFPE tumors by massively parallel sequencing. This method enables the identification of sequence mutations, copy number alterations, and select structural rearrangements involving all targeted genes. Targeted exon sequencing offers the benefits of high throughput, low cost, and deep sequence coverage, thus conferring high sensitivity for detecting low frequency mutations.

Effective monotherapy despite intratumor heterogeneity: Clonal convergence within the PI3K pathway and sensitivity to mTOR inhibitors in patients with advanced renal cell carcinoma (RCC)

4573

Background: Rapalogs, inhibitors of mTOR, are approved for treatment of advanced RCC. Recent reports of clonal heterogeneity challenge the concept of targeted monotherapy and the development of genomic biomarkers. Still, a subset of patients (pts) derives extended benefit from single agent rapalogs. This study analyzed such outliers so as to explore the genomic background of rapalog sensitivity in the setting of clonal heterogeneity. Methods: Cases were chosen based on time to treatment failure > 20 mos and tissue availability. DNA was extracted from spatially separate areas in primary tumors, metastases and the germline. Custom target capture and ultra-deep sequencing identified small indels, single base pair substitutions and copy number changes across all exons of 230 target genes. Results: 4 pts contributed 13 specimens (11 primary tumor samples, 2 metastases); mean exon coverage was 443X. Genomic alterations with activating effect on PI3K pathway signaling were seen in 11 of 13 specimens (Table). Clonal heterogeneity was present in all pts. For 2 pts, different mechanisms activated the pathway in separate sites, in 1 pt through separate genes. Conclusions: Pathway-activating genomic events across all sites explain rapalog benefit in 3 of 4 pts. Different disease sites in the same pt can harbor separate mechanisms activating the targeted pathway. This suggests that clonal convergence within the PI3K pathway can create an oncogenomic landscape sensitive to rapalogs despite branching clonal evolution. It supports the notion of sampling >1 disease site during future biomarker development. [Table: see text]

Phase II trial of MEK inhibitor selumetinib (AZD6244, ARRY-142886) in patients with BRAFV600E/K-mutated melanoma

PURPOSE

Test the hypothesis that in BRAF-mutated melanomas, clinical responses to selumetinib, a MEK inhibitor, will be restricted to tumors in which the PI3K/AKT pathway is not activated.

EXPERIMENTAL DESIGN

We conducted a phase II trial in patients with melanoma whose tumors harbored a BRAF mutation. Patients were stratified by phosphorylated-AKT (pAKT) expression (high vs. low) and treated with selumetinib 75 mg per os twice daily. Pretreatment tumors were also analyzed for genetic changes in 230 genes of interest using an exon-capture approach.

RESULTS

The high pAKT cohort was closed after no responses were seen in the first 10 patients. The incidence of low pAKT melanoma tumors was low (∼25% of melanomas tested) and this cohort was eventually closed because of poor accrual. However, among the five patients with melanoma accrued in the low pAKT cohort, there was one partial response (PR). Two other patients had near PRs before undergoing surgical resection of residual disease (one patient) or discontinuation of treatment due to toxicity (one patient). Among the two nonresponding, low pAKT patients with melanoma, co-mutations in MAP2K1, NF1, and/or EGFR were detected.

CONCLUSIONS

Tumor regression was seen in three of five patients with BRAF-mutated, low pAKT melanomas; no responses were seen in the high pAKT cohort. These results provide rationale for co-targeting MEK and PI3K/AKT in patients with BRAF mutant melanoma whose tumors express high pAKT. However, the complexity of genetic changes in melanoma indicates that additional genetic information will be needed for optimal selection of patients likely to respond to MEK inhibitors.

Abstract 392: Delineating genomic heterogeneity in paired primary and metastatic colorectal cancer by massively parallel sequencing

Colorectal cancer (CRC) is the third most common cause of cancer and cancer death for men and women in the United States. While the genetic steps necessary for carcinogenesis are well-defined, the subsequent genetic alterations driving tumor evolution to metastasis are not well characterized. We have performed deep sequencing of 230 key cancer-associated genes in 60 patient-matched primary tumor, metastatic tumor, and normal samples from CRC patients. Genes were selected on the basis of recurrent and/or “actionable” mutations reported in human tumors. Our custom captured-based sequencing assay, termed IMPACT (Integrated Mutation Profiling of Actionable Cancer Targets), provided a median sequence coverage of 644-fold, allowing for the identification of low frequency genetic events involving target genes. Somatic mutations, insertions/deletions (indels), and copy number alterations were identified and compared in both primary and metastatic samples. The most frequently mutated genes have all been previously implicated in CRC: APC, TP53, KRAS, PIK3CA, and SMAD4. Most genetic events were identical between primary and metastatic tumors; however, we identified particular alterations specific to the metastatic samples. The majority of these alterations were members of two important proliferative pathways, further lending credence that they might play an important role in metastatic progression. For patients with metastasis-specific mutations, we have sampled multiple microdissected regions from primary tumors to quantify the extent of intratumor heterogeneity and ascertain whether these differences are caused by sampling biases. The identification of these genetic variations between primary and metastatic tumors could have significant impact on biomarker analysis as well as treatment decisions for CRC patients.

Citation Format: Angela Rose Brannon, Efsevia Vakiani, Sasinya N. Scott, Brooke Sylvester, Krishan Kania, Agnes Viale, Nancy Kemeny, Martin Weiser, David B. Solit, Michael F. Berger. Delineating genomic heterogeneity in paired primary and metastatic colorectal cancer by massively parallel sequencing. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 392. doi:10.1158/1538-7445.AM2013-392

Abstract 2284: Phase II trial of MEK inhibitor selumetinib (AZD6244) in patients with BRAFV600E/K- or NRAS-mutated melanoma

Our pre-clinical in vitro data suggested that all BRAF-mutated cell lines, and some NRAS-mutated melanoma are sensitive to MEK inhibition. BRAFwt/NRASwt were uniformly resistant. Among the sensitive cell lines, those with enhanced activation of the PI3K/AKT pathway did not undergo apoptosis. This is consistent with a recent phase II trial with Selumetinib, an allosteric MEK inhibitor, which showed a 6% response rate in unselected melanoma patients. Retrospectively, 5 of 6 of the responders were found to harbor BRAFV600E mutations. We hypothesized that treatment of BRAF-mutated or NRAS-mutated melanomas with Selumetinib will induce clinical responses only in the subset of tumors in which the PI3K/AKT pathway is not activated. In this phase II trial, melanoma patients with either BRAF or NRAS mutation were stratified based on phospho-AKT (pAKT) expression (high vs. low), as measured by immunohistochemistry staining of pre-treatment tumor specimens. Patients were treated with Selumetinib 75 mg p.o. daily in 28-day cycles. We found that the incidence of high pAKT melanoma tumors was about 4 times higher than low pAKT tumors. None of the 10 patients in the high pAKT cohort responded, although 4 patients showed stable disease for ≥4 months. This cohort was closed to further accrual. In contrast, in the low pAKT group, 1 patient had a true partial response (PR) and 2 others had near PRs. One of these patients had to discontinue treatment due to toxicity; the other had his remaining tumor resected. This cohort was closed due to slow patient accrual. We used an exon capture, next-generation sequencing assay to define the mutational status of 230 cancer associated genes in pre-treatment tumors, derived from patients belonging to both cohorts. The assay detects point mutations, small indels and copy number alterations. Among the two low pAKT patients who were resistant to MEK inhibition, one had a mutation in MAP2K1 that encodes for a K57N mutation in helix A of MEK1. We speculate that this is an activating mutation, since a missense mutation in the amino acid just proximal (Q56P) was previously shown to be highly activating. The other non-responding patient in the low pAKT cohort had an activating mutation in EGFR. Both of these could drive increased activation of the MAPK pathway, thus explaining the resistance to the drug. We conclude that future trials with MEK inhibitors in melanoma should exclude patients with high pAKT tumors. The occurrence of complex genetic changes in melanoma requires studies to better stratify the patients according the prediction of response to MEK inhibitors.

Citation Format: Federica Catalanotti, David B. Solit, Melissa P. Pulitzer, Michael F. Berger, Sasinya N. Scott, Tunc Iyriboz, Mario E. Lacouture, Katherine S. Panageas, Jedd D. Wolchok, Richard D. Carvajal, Gary K. Schwartz, Neal Rosen, Paul B. Chapman. Phase II trial of MEK inhibitor selumetinib (AZD6244) in patients with BRAFV600E/K- or NRAS-mutated melanoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2284. doi:10.1158/1538-7445.AM2013-2284

Abstract 3515: Pathway convergent evolution underscores treatment response to MTOR inhibitors in kidney cancers

Despite the established role of MTOR inhibitors (rapalogs) in treating advanced kidney cancer, therapeutic benefit varies and predictive biomarkers are lacking. Intratumor branching heterogeneity, a recently discovered hallmark of this disease, has raised concerns about the feasibility of developing genomic biomarkers for targeted agents in kidney cancer. We undertook an outlier approach to interrogate the genetic determinants underlying long-term therapeutic response (&gt;20 months) to rapalogs in 6 patients. An integrated ultra-deep targeted-exome (∼500x) and standard whole-exome (∼100x) sequencing was performed. Additionally, to address intratumor and intertumor heterogeneity, spatially separated tumor specimens from the same individuals were analyzed whenever possible. Multiregional sequencing unveiled surprising MTOR pathway convergent evolution, manifested by MTOR pathway activation by means of distinct genomic events in spatially separate sites of disease within the same individual. Amongst the core components of the MTORC1 pathway, complete functional loss of TSC1 and TSC2, and a hyperactive MTOR mutant were discovered in 4 of 6 long-term responders. Mutations in MTOR Clustered at FAT and kinase domains confer hyperactivity and yet remain sensitive to rapamycin. Here, we affirm intratumor heterogeneity, identify genomic determinants of drug response, and discover pathway convergent evolution in the majority of long-term responders. We propose a “river” model in which intratumor and intertumor clonal heterogeneity in cancer patients evolves like a branching river that converges at critical nodes. These convergent points provide unique opportunities for the treatment of genetically diverged yet functionally converged cancers in any given patient.

Citation Format: Martin H. Voss, A Ari Hakimi, Can G. Pham, A Rose Brannon, Ying-Bei Chen, Luis F. Cunha, Oguz Akin, Han Liu, Shugaku Takeda, Sasinya N. Scott, Nicholas D. Socci, Agnes Viale, Nikolaus Schultz, Chris Sander, Victor E. Reuter, Paul Russo, Emily H. Cheng, Robert J. Motzer, Michael F. Berger, James J. Hsieh. Pathway convergent evolution underscores treatment response to MTOR inhibitors in kidney cancers. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3515. doi:10.1158/1538-7445.AM2013-3515

Genome sequencing identifies a basis for everolimus sensitivity

Cancer drugs often induce dramatic responses in a small minority of patients. We used whole-genome sequencing to investigate the genetic basis of a durable remission of metastatic bladder cancer in a patient treated with everolimus, a drug that inhibits the mTOR (mammalian target of rapamycin) signaling pathway. Among the somatic mutations was a loss-of-function mutation in TSC1 (tuberous sclerosis complex 1), a regulator of mTOR pathway activation. Targeted sequencing revealed TSC1 mutations in about 8% of 109 additional bladder cancers examined, and TSC1 mutation correlated with everolimus sensitivity. These results demonstrate the feasibility of using whole-genome sequencing in the clinical setting to identify previously occult biomarkers of drug sensitivity that can aid in the identification of patients most likely to respond to targeted anticancer drugs.

Genetic determinants of long-term response to rapalog therapy in advanced renal cell carcinoma (RCC)

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Background: Temsirolimus (T) and everolimus (E) are rapalog inhibitors of the mammalian target of rapamycin (mTOR) with efficacy in advanced RCC [NEJM;356(22):227-81; Lancet;372(9637):449-56]. With reported median progression-free survival (PFS) of 5.5 and 4.9 months (mo), respectively, benefit is typically modest, yet a subset of patients (pts) achieves long-term disease control evident by extended PFS. The oncogenomic background for this is unclear. Methods: We analyzed frozen specimens of tumor and adjacent normal kidney from pts with advanced RCC and documented long-term response to T or E, defined as PFS of ≥ 20mo. Samples from pts with PFS ≤ 2mo served as comparators. Specimens were subjected to whole exome sequencing; a targeted next-generation sequencing platform was used for deep sequencing and investigation of copy number variations (CNV) in 230 genes of interest. Results: In 5 pts with long-term response to T [n=3] or E [n=2], histologic subtypes were clear cell [n=3] and unclassified [n=2] RCC. Median number of prior treatments was 2 (1-3). Two pts remain on therapy, 3 have stopped drug for disease progression; treatment duration was 20, 25+, 27, 28, and 28+ mo. Three control pts progressed after 1, 2, and 2 mo on therapy. Mean target coverage was 86x for whole exome and 443x for targeted sequencing. Three of 5 long-term responders harbored acquired somatic mutations and/or CNV in genes encoding for members of the Phosphoinositide 3-Kinase (PI3K) / mTOR pathway. Effects on amino acid sequence and gene function suggest a hyperactive pathway in all 3. For the other 2 long-term responders genomic changes with possible indirect link to the pathway, but no apparent determinants of treatment response were seen. In 3 control patients with rapid disease progression no genomic alterations suggesting hyperactivation of the pathway were seen. Conclusions: In this retrospective discovery set of RCC pts with unusually long response to rapalog therapy, next generation sequencing using pre-treatment tissue specimens revealed plausible oncogenomic determinants of treatment benefit in 3 of 5 cases. These findings provide basis for further biomarker development and studies in a larger sample set are ongoing.

Influence of biological, behavioural, health service and social risk factors on the trend towards more frequent

OBJECTIVES

To analyse the trend in rising acute hospital admission rates in the Renfrew Paisley MIDSPAN cohort and assess the influence of baseline risk factor data, morbidity patterns, deprivation category and characteristics of GP practice on the increase.

DESIGN

Cohort analysis which, using a linked data set covering a 23 year follow-up period, combined original 'risk'-related data with subsequent routine hospital admissions data. A multiple logistic regression model predicted changes in hospital admissions patterns.

SETTING

Renfrew and Paisley, two post-industrial towns in Scotland.

SUBJECTS

Eight thousand three hundred and fifty four women and 7,052 men, aged 45-64 in the early 1970s.

MAIN OUTCOME MEASURES

The contribution that each of the factors investigated made to the likelihood of admission over time.

RESULTS

While risk status in middle life, diagnosis reached after admission, deprivation category and characteristics of GP practice influence the absolute chance of being admitted to hospital, changes in these factors do not explain much, if any, of the quite marked increase in admission rates observed during the last 10 year of the follow-up period.

CONCLUSIONS

Whatever the reasons for the trend of rising admission, the most likely explanation appears to be a combination of social and health service related factors. For the Paisley-Renfrew cohort, factors like smoking status, FEV1, deprivation category and GP practice remain important predictors of admission throughout the time period but changes in these factors explain little of the rising trend in admissions.

The link between major risk factors and important categories of admission in an ageing cohort

BACKGROUND

Record linkage of routine hospital data to population-based research findings presents an opportunity to explore the relationships between classical risk factors and hospital activity.

METHODS

The objectives of this study were to examine, in Paisley and Renfrew, the effect of risk factor variables on the likelihood of experiencing an acute hospital admission with six major medical conditions. The subjects were 8,349 women and 7,057 men, aged 45-64 in the early to mid-1970s. The main outcome measures were acute hospital admission with principal diagnosis of: any malignant neoplasm; malignant neoplasm of trachea, bronchus and lung; ischaemic heart disease; respiratory disease; cerebrovascular disease; or diabetes mellitus.

RESULTS

Smokers were almost eight times more likely to be admitted with lung cancer and, to a lesser extent, were more likely to be admitted for the other conditions investigated with the exception of diabetes mellitus. Forced expiratory volume was also an independent risk factor for admission with lung cancer and strokes. Higher levels of cholesterol were associated with increased risk of admission with ischaemic heart disease but less with cancer (including lung cancer). With the exception of admissions for cerebrovascular disease, deprivation category was found to have no independent effect on the likelihood of experiencing any of the morbidity outcomes examined.

CONCLUSIONS

These data confirm that associations first established between risk factors and mortality outcomes (e.g. smoking and lung cancer) are also found between risk factors and hospital admissions for the same causes. This in itself is unremarkable, but the results are of interest for three reasons. First, they illustrate the potential of record linkage to map the effects of risk factors. Second, they demonstrate the size of the effect risk factors have on the risk of admission. Third, they provide a surprising finding that deprivation category does not act as an independent risk factor for the majority of the categories of admission investigated.

Hospital use by an ageing cohort: an investigation into the association between biological, behavioural and social risk markers and subsequent hospital utilization

BACKGROUND

The aims of the study were to describe the pattern of hospital utilization (acute and mental health sectors) of the Paisley-Renfrew MIDSPAN cohort and assess the influence of biological, behavioural and social 'risk factors' (established at the time of screening) on subsequent hospital admissions.

METHOD

A cohort analysis was carried out in Paisley and Renfrew, two post-industrial towns in West Central Scotland. This used a linked data set covering a 23 year follow-up period to combine original 'risk'-related data with subsequent routine hospital admissions data. The subjects were 8349 women and 7057 men, aged 45-64 in the early to mid-1970s, and representing approximately 80 per cent of the eligible population. The main outcome measures were patterns of hospital utilization (acute and mental health sectors), 'any acute hospital admission', 'a serious acute hospital admission' and 'death' (relative risks of each outcome were calculated for all risk factors).

RESULTS

The following patterns of hospital utilization were found. Only 5 per cent experienced a mental health admission but mean stay was long (265 bed days per cohort member admitted). In contrast, 79 per cent experienced at least one acute hospital stay. The age-specific proportions of cohort members requiring admission increased over time but the growth in acute episodes was even higher (suggesting increasing rates of multiple admission). For non-survivors, 42 per cent of all acute episodes (55 per cent of bed days) took place during the 12 months before death. Analysis of risk factors (using Cox's proportional hazards model) of 'any admission' and 'a serious admission' showed forced expiratory volume (FEV1), age, sex, smoking status, blood pressure, blood sugar, body mass index, cholesterol and deprivation category to be important predictors.

CONCLUSIONS

Despite the desirability of alternative settings of care for the chronically ill and dying, a high proportion of hospital bed days were required near the time of death. The absolute size of the demand for hospital services within the cohort was strikingly large and increasing over time. Strategies to address the tide of rising admissions will have to confront the increasing proportion of individuals requiring admission as well as the growth in multiple admissions. Those who were at higher risk of admission were the older members of the cohort (especially men), those with low FEV1, smokers, those who were underweight or obese, the small number with abnormal levels of blood sugar, those with high blood pressure and those who lived in the most deprived areas. Thus, programmes which affect these determinants of ill health may be useful in reducing age-specific admission rates.

Eligibility criteria for NHS long stay care: the relationship between clinical need, dependency, and staff perception

A study was undertaken by a Scottish Health Authority to determine future provision of NHS long stay in-patient beds for young physically disabled people (aged < 65), and eligibility criteria for admission to such care. As part of the development of care in the community, only patients requiring specialist medical and nursing care should continue to be placed in NHS care. Resources freed from the resulting closure of NHS beds will be transferred to Social Services to develop alternative packages of care in the community, based on need rather than precedent. Achieving the balance, in terms of the correct level of continuance of NHS long stay care and redeployment of resources, requires careful planning. This study, involving all young physically disabled patients in NHS care in Argyll and Clyde Health Board, combined the assessment of dependency using validated scales (CAPE, FIM, and ERSS), with staff perception of dependency and with clinical criteria developed for a series of balance of care studies in this authority. These clinical criteria indicate the need for specialist medical and nursing care. By examining the relationship between dependency and staff perception, it has been possible to plan long stay provision on a population basis. The criteria for admission have been adopted for local clinical use and form the basis for appeals procedures for patients deemed appropriate for discharge.