Shared-decision-making and communication in paediatric palliative care within Uganda

The first palliative care services were started in Uganda 30 years ago with services continuing to develop since then. The Ministry of Health and the Palliative Care Association of Uganda have played key roles in the development of paediatric palliative care in the country. There are a range of paediatric palliative care service providers in Uganda, and these have developed alongside educational programmes and research in PPC. Care is provided across the Uganda health system and across the age range from neonates through to adolescents and young adults. Whilst recognising the importance of shared decision-making there is little literature with regards to this in the Ugandan context. However, a variety of factors have been shown to influence decision-making, along with the challenges and recommendations for the future. Uganda has made significant strides in the provision of paediatric palliative care although there is still a way to go before all children with palliative care needs, and their families, can access palliative care.

Physiological and Pathological Factors Affecting Drug Delivery to the Brain by Nanoparticles

The prevalence of neurological/neurodegenerative diseases, such as Alzheimer's disease is known to be increasing due to an aging population and is anticipated to further grow in the decades ahead. The treatment of brain diseases is challenging partly due to the inaccessibility of therapeutic agents to the brain. An increasingly important observation is that the physiology of the brain alters during many brain diseases, and aging adds even more to the complexity of the disease. There is a notion that the permeability of the blood-brain barrier (BBB) increases with aging or disease, however, the body has a defense mechanism that still retains the separation of the brain from harmful chemicals in the blood. This makes drug delivery to the diseased brain, even more challenging and complex task. Here, the physiological changes to the diseased brain and aged brain are covered in the context of drug delivery to the brain using nanoparticles. Also, recent and novel approaches are discussed for the delivery of therapeutic agents to the diseased brain using nanoparticle based or magnetic resonance imaging guided systems. Furthermore, the complement activation, toxicity, and immunogenicity of brain targeting nanoparticles as well as novel in vitro BBB models are discussed.

Experimental Models of SARS-CoV-2 Infection: Possible Platforms to Study COVID-19 Pathogenesis and Potential Treatments

In December 2019, a novel coronavirus crossed species barriers to infect humans and was effectively transmitted from person to person, leading including vaccines and antiviral drugs that could prevent or limit the burden or transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global health priority. It is thus of utmost importance to assess possible therapeutic strategies against SARS-CoV-2 using experimental models that recapitulate aspects of the human disease. Here, we review available models currently being developed and used to study SARS-CoV-2 infection and highlight their application to screen potential therapeutic approaches, including repurposed antiviral drugs and vaccines. Each identified model provides a valuable insight into SARS-CoV-2 cellular tropism, replication kinetics, and cell damage that could ultimately enhance understanding of SARS-CoV-2 pathogenesis and protective immunity. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Inclusion of a Matrix Metalloproteinase-9 Responsive Sequence in Self-assembled Peptide-based Brain-Targeting Nanoparticles Improves the Efficiency of Nanoparticles Crossing the Blood-Brain Barrier at Elevated MMP-9 Levels

This study investigated whether the inclusion of a matrix metalloproteinase-9 (MMP-9) responsive sequence in self-assembled peptide-based brain-targeting nanoparticles (NPs) would enhance the blood-brain barrier (BBB) penetration when MMP-9 levels are elevated both in the brain and blood circulation. Brain-targeting peptides were conjugated at the N-terminus to MMP-9-responsive peptides, and these were conjugated at the N-terminus to lipid moiety (cholesteryl chloroformate or palmitic acid). Two constructs did not have MMP-9-responsive peptides. NPs were characterised for size, charge, critical micelle concentration, toxicity, blood compatibility, neural cell uptake, release profiles, and in vitro BBB permeability simulating normal or elevated MMP-9 levels. The inclusion of MMP-9-sensitive sequences did not improve the release of a model drug in the presence of active MMP-9 from NPs compared to distilled water. ¹⁹F NMR studies suggested the burial of MMP-9-sensitive sequences inside the NPs making them inaccessible to MMP-9. Only cholesterol-GGGCKAPETALC (responsive to MMP-9) NPs showed <5% haemolysis, <1 pg/mL release of IL-1β at 500 μg/mL from THP1 cells, with 70.75 ± 5.78% of NPs crossing the BBB at 24 h in presence of active MMP-9. In conclusion, brain-targeting NPs showed higher transport across the BBB model when MMP-9 levels were elevated and the brain-targeting ligand was responsive to MMP-9.

DNA Methylation Clusters and Their Relation to Cytogenetic Features in Pediatric AML

Acute Myeloid Leukemia (AML) is characterized by recurrent genetic and cytogenetic lesions that are utilized for risk stratification and for making treatment decisions. In recent years, methylation dysregulation has been extensively studied and associated with risk groups and prognosis in adult AML, however, such studies in pediatric AML are limited. Moreover, the mutations in epigenetic genes such as DNMT3A, IDH1 or IDH2 are almost absent or rare in pediatric patients as compared to their abundance in adult AML. In the current study, we evaluated methylation patterns that occur with or independent of the well-defined cytogenetic features in pediatric AML patients enrolled on multi-site AML02 clinical trial (NCT00136084). Our results demonstrate that unlike adult AML, cytosine DNA methylation does not result in significant unique clusters in pediatric AML, however, DNA methylation signatures correlated significantly with the most common and recurrent cytogenetic features. Paired evaluation of DNA methylation and expression identified genes and pathways of biological relevance that hold promise for novel therapeutic strategies. Our results further demonstrate that epigenetic signatures occur complimentary to the well-established chromosomal/mutational landscape, implying that dysregulation of oncogenes or tumor suppressors might be leveraging both genetic and epigenetic mechanisms to impact biological pathways critical for leukemogenesis.

Development of Brain Targeting Peptide Based MMP-9 Inhibiting Nanoparticles for the Treatment of Brain Diseases with Elevated MMP-9 Activity

Latent and active levels of cerebral matrix metalloproteinase 9 (MMP-9) are elevated in neurological diseases and brain injuries, contributing to neurological damage and poor clinical outcomes. This study aimed developing peptide-based nanoparticles with ability to cross the blood-brain-barrier (BBB) and inhibit MMP-9. Three amphiphilic peptides were synthesised containing brain-targeting ligands (HAIYPRH or CKAPETALC) conjugated with MMP-9 inhibiting peptide (CTTHWGFTLC) linked by glycine (spacer) at the N-terminus, and the peptide sequences were conjugated at the N- terminus to cholesterol. ¹⁹F NMR assay was developed to measure MMP-9 inhibition. Cell toxicity was evaluated by the LDH assay, and dialysis studies were conducted with/without fetal bovine serum. An in vitro model was employed to evaluate the ability of nanoparticles crossing the BBB. The amphiphilic peptide (Cholesterol-GGGCTTHWGFTLCHAIYPRH) formed nanoparticles (average size of 202.8 nm) with ability to cross the BBB model. MMP-9 inhibiting nanoparticles were non-toxic to cells, and reduced MMP-9 activity from kobs of 4.5 × 10^-6s^-1 to complete inhibition. Dialysis studies showed that nanoparticles did not disassemble by extreme dilution (40 folds), but gradually hydrolysed by serum enzymes. In conclusion, the MMP-9 inhibiting nanoparticles reduced the activity of MMP-9, with acceptable serum stability, minimal cell toxicity and ability to cross the in vitro BBB model.

Abstract 2872: Acquisition of drug resistance mutations during chemotherapy treatment in pediatric acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) is a leading cause of cancer-associated death in children. To study the mechanisms of drug resistance in ALL, we performed whole-genome sequencing of diagnosis-relapse-germline trios from 103 Chinese patients and ultra-deep sequencing of 208 serial bone marrow samples from 17 of them. Relapse-specific somatic alterations were enriched in 12 genes (NR3C1, NR3C2, TP53, NT5C2, FPGS, CREBBP, MSH2, MSH6, PMS2, WHSC1, PRPS1, and PRPS2), which were predominantly involved in response to thiopurines, glucocorticoids, methotrexate, and other drugs. Four lines of evidence indicate that these resistance mutations frequently developed during treatment, rather than pre-existing at diagnosis. First, two novel, relapse-specific mutational signatures (novel signatures 1 and 2), most likely caused by chemotherapeutic regimens, were detected in 15% and 14% of relapsed cases, respectively. Drug resistance mutations frequently appeared at novel signature-associated trinucleotide contexts, indicating that chemotherapy may directly cause drug resistance mutations in ALL. The signatures were validated in NCI TARGET relapsed ALL samples, 2% and 23% of which harbored novel signatures 1 and 2, respectively. The varying signature prevalence between cohorts may reflect treatment differences. The novel signatures were not detected in &gt;2,000 adult cancers from the PCAWG study. Novel signature 1 induced C&gt;G transversions, particularly at GCC and TCT trinucleotides, and showed transcription-strand bias indicating guanine adducts. Novel signature 2 favored C&gt;T and C&gt;G mutations at CCG, and correlated with relapse-specific dinucleotide variants and structural variants, indicating an agent causing multiple mutation types. The drugs inducing these novel signatures are being explored in vitro. Second, mathematical modeling using growth curves of drug-resistant ALL indicated that drug resistance mutations occur, in some cases, long after diagnosis, during active treatment. Third, some patients acquired multiple drug resistance mutations sequentially through successive relapses, a finding inconsistent with their pre-existence at diagnosis. Indeed, 20% of relapses had multiple drug resistance mutations targeting different drug classes. Fourth, most relapsed ALLs derived from a subclone detected at diagnosis, which then evolved additional mutations, including drug resistance mutations, not detectable at diagnosis using 2000X targeted sequencing. Drug resistance mutations were often subclonal at relapse, suggesting later appearance. Together these data indicate that fully drug-resistant clones may not necessarily pre-exist at diagnosis in ALL, but may be acquired later during treatment. Thus, early intensive or targeted treatment strategies in slow responders may forestall the subsequent development of drug resistance mutations.

Citation Format: Benshang Li, Samuel W. Brady, Xiaotu Ma, Shuhong Shen, Yingchi Zhang, Yongjin Li, Yu Liu, Ningling Wang, Diane Flasch, Matthew Myers, Heather Mulder, Lixia Ding, Yanling Lu, Liqing Tian, Kohei Hagiwara, Ke Xu, Edgar Sioson, Tianyi Wang, Liu Yang, Jie Zhao, Hui Zhang, Ying Shao, Hongye Sun, Lele Sun, Jiaoyang Cai, Ting-Nien Lin, Lijuan Du, Fan Yang, Michael Rusch, Michael Edmonson, John Easton, Xiaofan Zhu, Jingliao Zhang, Cheng Cheng, Benjamin Raphael, Jingyan Tang, James Downing, Bin-Bing Zhou, Ching-Hon Pui, Jun Yang, Jinghui Zhang. Acquisition of drug resistance mutations during chemotherapy treatment in pediatric acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2872.

Real-time sharing of comprehensive clinical genomics sequencing data in St. Jude Cloud

10019

Background: As tumor and germline genomic data from pediatric cancer patients is scarce in existing genomic databases, there is an urgent need for more comprehensive datasets. Such data will allow us to fully assess the actionable pediatric cancer genome, facilitate biomarker discovery, and identify new clinical associations. Methods: We sequenced 1002 tumor/normal pairs as part of a real-time clinical genomics service including whole genome, exome and transcriptome for 775 and exome/transcriptome for 227 samples. Tumor types were representative of the common and rare diseases treated at our institution (37% hematological, 31% brain and 32% solid tumors). A multidisciplinary team assessed every case, and after clinical reporting was complete, genomics data and basic clinical information (primary diagnosis, age, sex, ethnicity, primary/relapse/metastasis status), was made securely available online through St. Jude Cloud (www.stjude.cloud). Results: Based on analysis of 253 initial cases from the Genomes for Kids study, our multi-platform sequencing approach uncovered diagnostic, prognostic and/or therapeutically relevant findings in 78% of patients. We estimate 11-16% of clinically-relevant gene mutations could be missed by less comprehensive sequencing approaches. One quarter of patients had a potentially druggable mutation. This surprisingly high proportion was driven, in part, by BRAF fused low-grade gliomas and diverse JAK/STAT pathway alterations in B-Cell acute lymphoblastic leukemias. Whole genome/transcriptome sequencing allowed us to detect rare and novel gene fusions in 8% of cases and facilitated discovery of a new recurrent fusion gene in pediatric melanoma. All data is available online for others to mine and it is likely that additional clinically-relevant mutations can be uncovered. Conclusions: These data demonstrate the value of incorporating comprehensive sequencing into clinical diagnostics and patient care. We endeavor to make this large and richly annotated dataset available to others in real time rather than holding it back for months or years until publication. We anticipate adding approximately 500 additional cases per year at regular intervals, and as the resource grows, expect users to identify new targetable alterations that may be incorporated into patient care.

Polygenic risk of subsequent thyroid cancer after childhood cancer: A report from St. Jude lifetime cohort (SJLIFE) and Childhood Cancer Survivor Study (CCSS)

10060

Background: Subsequent thyroid cancer (STC) is among the most common malignancies in childhood cancer survivors, especially those with thyroid exposure to radiotherapy (RT). Identification of genetic risk factors may inform screening practices. Methods: Twelve SNPs were previously identified as thyroid cancer risk loci in the general population of European ancestry. A polygenic risk score (PRS) was calculated as a sum of risk alleles carried by a survivor, weighted by the natural logarithm of the published per-allele odds ratios (range: 1.2-1.8). With piecewise exponential models, associations of STC rates with PRS were assessed, both overall and stratified by neck RT exposure. Models were adjusted for sex, age at primary diagnosis, attained age, neck RT dose, epipodophyllotoxin therapy, and eigenvectors within survivors of European ancestry from SJLIFE with whole-genome sequencing data and CCSS with SNP data imputed to Haplotype Reference Consortium. Results: Among 2,324 SJLIFE survivors, 61 (43 with, 18 without neck RT) developed STC. The rate of STC was increased by 5.3-fold (95% confidence interval (CI), 2.2-12.6) and 3.1-fold (CI, 1.3-7.7) for survivors in the third and second PRS tertiles, respectively, compared to those in the first tertile, with corresponding cumulative incidence at age of 40 years of 5.3% (CI, 3.3-7.3%), 2.5% (CI, 1.1-3.9%), and 1.0% (CI, 0.005-2.0%), respectively. Stratified by neck RT, the corresponding rate increases were 7.6 (CI, 2.3-25.3) and 3.8 (CI, 1.1-13.4), respectively, among survivors exposed to neck RT; however, no association was observed among survivors without neck RT (only 18 STC cases). Replication was performed among 4,302 CCSS survivors, 100 (61 with, 39 without neck RT) developed STC. The rates of STC were increased by 2.3-fold (CI, 1.4-3.9) and 1.7-fold (CI, 1.0-2.9) for survivors in the third and the second PRS tertiles, compared to those in the first tertile. The similar significant associations were observed in survivors with and without neck RT ( Ptrend = 0.04 and 0.02, respectively). Conclusions: High PRS conferring STC risk can inform screening practices and help personalize and improve survivorship care.

Assessment of Palliative Care Needs in Hospital Settings in Rwanda

Background: Rwanda is among the first African countries with a palliative care (PC) policy and implementation plan. A partnership with the Ministry of Health (MoH) through the Rwanda Biomedical Centre (RBC) and the University of Edinburgh has supported an integrated approach including expanding the evidence base. Aim: To assessing the need for (PC) to inform policy, service delivery and training. Methods: A point prevalence PC needs assessment was conducted in nine public hospitals (referral, provincial and district). A records census identified those with life-limiting illness (LLI) who were then invited to participate by interview. The assessment tool included the APCA African POS, POS S, WHO performance status and demographic information. Results: 608 case notes were reviewed, 152 eligible and 124 completed assessment. 25% of all patients admitted had LLI, of which 99.2% had evidence of unmet need determined by at least one score on the APCA POS ≥ 3. Diagnoses 29% cancer, 29% cardiovascular disease, 16.9% end-stage organ failure and 13.7% HIV. Symptoms with greatest impact; nausea and vomiting (34.7%) and pain (32.3%). 63.7% with WHO performance status 4 or 5. 8.1% seen by existing PC services. Conclusion: Although the MoH and RBC are making bold steps toward developing PC in Rwanda, there remains a significant amount of unmet PC needs. Meeting this need requires recognition of the scope of PC needs beyond cancer, feedback to the hospitals and health care workers, thinking strategically how to further strengthen the health system and further capacity building and training.

Home-Based Care Practitioners: A Strategy for Continuum of Care for Very Ill Patient

Background: Rwanda Ministry of Health in collaboration with partners has initiated an innovative initiative named Home Based Care Practitioners (HBCPs) to respond to the burden of long-term hospitalization for end of life patients. Aim: The program aims at providing home-based care to accompany patients and their families in their home, reduce unnecessary pain and suffering for those with chronic or terminal conditions, provide counseling to the patients and their families, early diagnosis of NCDs and improve awareness on prevention of NCDs risk factors and effectively refer them to either health facilities or community-based resources that can be of further help. Methods: The HBCPs is implemented into phases; phase one has started with a pilot of 200 HBCPs in 100 cells surrounding nine provincial and referral hospitals of Rwanda; 2 practitioners for both gender in each cell, with a criteria of completion at least secondary school. They have undergone a training of 120 credits (900 hours), equivalent of four months for theory and two months of practice. After training they have been deployed into the community with a supervision of health centers in collaboration with hospitals and Rwanda Biomedical Center. Results: During the implementation period of 6 months, 1663 NCDs patients have been transferred from health facility (OPD) to HBCPs for routine follow-up, 482 palliative care patients have been reported on end of life care by HBCPs, there is a remarkable linkage between facilities and community care ensured by supervisory relationship between health services providers and home based care practitioners, long-term admission has reduced the cost for the family and the facility due to the discharge of care from hospital to home. Conclusion: In a limited setting of social and economic cost of providing frivolous care in an expensive hospital for chronic or terminal conditions that would be better managed through treatment or palliative care at home (or less acute setting) home based care effort can better meet the needs of Rwandans at the community level and has started to show the efficiency in providing quality care to people in need of palliative care.

The Wave2 scaffold Hem-1 is required for transition of fetal liver hematopoiesis to bone marrow

The transition of hematopoiesis from the fetal liver (FL) to the bone marrow (BM) is incompletely characterized. We demonstrate that the Wiskott–Aldrich syndrome verprolin-homologous protein (WAVE) complex 2 is required for this transition, as complex degradation via deletion of its scaffold Hem-1 causes the premature exhaustion of neonatal BM hematopoietic stem cells (HSCs). This exhaustion of BM HSC is due to the failure of BM engraftment of Hem-1^−/− FL HSCs, causing early death. The Hem-1^−/− FL HSC engraftment defect is not due to the lack of the canonical function of the WAVE2 complex, the regulation of actin polymerization, because FL HSCs from Hem-1^−/− mice exhibit no defects in chemotaxis, BM homing, or adhesion. Rather, the failure of Hem-1^−/− FL HSC engraftment in the marrow is due to the loss of c-Abl survival signaling from degradation of the WAVE2 complex. However, c-Abl activity is dispensable for the engraftment of adult BM HSCs into the BM. These findings reveal a novel function of the WAVE2 complex and define a mechanism for FL HSC fitness in the embryonic BM niche.

Hematopoietic stem cells (HSCs) migrate from the fetal liver to the bone marrow (BM) during embryogenesis. Here the authors show that the WAVE2 complex scaffold Hem1 is required for engraftment of HSCs in BM, not through its canonical role regulating actin polymerization, but through c-Abl survival signaling.

Communication with young people in paediatric and adult endocrine consultations: an intervention development and feasibility study

BACKGROUND

Communication is complex in endocrine care, particularly during transition from paediatric to adult services. The aims of this study were to examine the feasibility of interventions to support young people to interact with clinicians.

METHODS

Development and evaluation of a complex intervention in 2 phases: Pre-intervention observational study; Intervention feasibility study. Purposive sample of recordings of 62 consultations with 58 young people aged 11-25 years with long-term endocrine conditions in two paediatric and two adult endocrine clinics. Proportion of time talked during consultations, number and direction of questions asked; Paediatric Consultation Assessment Tool (PCAT); OPTION shared decision making tool; Medical Information Satisfaction Scale (MISS- 21). Young people were invited to use one or more of: a prompt sheet to help them influence consultation agendas and raise questions; a summary sheet to record key information; and the www.explain.me.uk website.

RESULTS

Nearly two thirds of young people (63%) chose to use at least one communication intervention. Higher ratings for two PCAT items (95% CI 0.0 to 1.1 and 0.1 to 1.7) suggest interventions can support consultation skills. A higher proportion of accompanying persons (83%) than young people (64%) directed questions to clinicians. The proportion of young people asking questions was higher (84%) in the intervention phase than in the observation phase (71%).

CONCLUSIONS

Interventions were acceptable and feasible. The Intervention phase was associated with YP asking more questions, which implies that the availability of interventions could promote interactivity.

Population-based cohort study of variation in the use of emergency cholecystectomy for benign gallbladder diseases

Background

The aims of this prospective population-based cohort study were to identify the patient and hospital characteristics associated with emergency cholecystectomy, and the influences of these in determining variations between hospitals.

Methods

Data were collected for consecutive patients undergoing cholecystectomy in acute UK and Irish hospitals between 1 March and 1 May 2014. Potential explanatory variables influencing the performance of emergency cholecystectomy were analysed by means of multilevel, multivariable logistic regression modelling using a two-level hierarchical structure with patients (level 1) nested within hospitals (level 2).

Results

Data were collected on 4744 cholecystectomies from 165 hospitals. Increasing age, lower ASA fitness grade, biliary colic, the need for further imaging (magnetic retrograde cholangiopancreatography), endoscopic interventions (endoscopic retrograde cholangiopancreatography) and admission to a non-biliary centre significantly reduced the likelihood of an emergency cholecystectomy being performed. The multilevel model was used to calculate the probability of receiving an emergency cholecystectomy for a woman aged 40 years or over with an ASA grade of I or II and a BMI of at least 25·0 kg/m2, who presented with acute cholecystitis with an ultrasound scan showing a thick-walled gallbladder and a normal common bile duct. The mean predicted probability of receiving an emergency cholecystectomy was 0·52 (95 per cent c.i. 0·45 to 0·57). The predicted probabilities ranged from 0·02 to 0·95 across the 165 hospitals, demonstrating significant variation between hospitals.

Conclusion

Patients with similar characteristics presenting to different hospitals with acute gallbladder pathology do not receive comparable care.

CC-PROMISE effectively integrates two forms of molecular data with multiple biologically related endpoints

BACKGROUND

As new technologies allow investigators to collect multiple forms of molecular data (genomic, epigenomic, transcriptomic, etc) and multiple endpoints on a clinical trial cohort, it will become necessary to effectively integrate all these data in a way that reliably identifies biologically important genes.

METHODS

We introduce CC-PROMISE as an integrated data analysis method that combines components of canonical correlation (CC) and projection onto the most interesting evidence (PROMISE). For each gene, CC-PROMISE first uses CC to compute scores that represent the association of two forms of molecular data with each other. Next, these scores are substituted into PROMISE to evaluate the statistical evidence that the molecular data show a biologically meaningful relationship with the endpoints.

RESULTS

CC-PROMISE shows outstanding performance in simulation studies and an example application involving pediatric leukemia. In simulation studies, CC-PROMISE controls the type I error (misleading significance) rate very near the nominal level across 100 distinct null settings in which no molecular-endpoint association exists. Also, CC-PROMISE has better statistical power than three other methods that control type I error in 396 of 400 (99 %) alternative settings for which a molecular-endpoint association is present; the power advantage of CC-PROMISE exceeds 30 % in 127 of the 400 (32 %) alternative settings. These advantages of CC-PROMISE are also observed in an example application.

CONCLUSION

CC-PROMISE very effectively identifies genes for which some form of molecular data shows a biologically meaningful association with multiple related endpoints.

AVAILABILITY

The R package CCPROMISE is currently available from www.stjuderesearch.org/site/depts/biostats/software .

Children's palliative care now! Highlights from the second ICPCN conference on children's palliative care, 18-21 May 2016, Buenos Aires, Argentina

The International Children's Palliative Care Network held its second international conference on children's palliative care in Buenos Aires, Argentina, from the 18th-21st May 2016. The theme of the conference was 'Children's Palliative Care…. Now!' emphasising the need for palliative care for children now, as the future will be too late for many of them. Six pre-conference workshops were held, addressing issues connected to pain assessment and management, adolescent palliative care, ethics and decision-making, developing programmes, the basics of children's palliative care, and hidden aspects of children's palliative care. The conference brought together 410 participants from 40 countries. Plenary, concurrent, and poster presentations covered issues around the status of children's palliative care, genetics, perinatal and neonatal palliative care, the impact of children's palliative care and the experiences of parents and volunteers, palliative care as a human right, education in children's palliative care, managing complex pain in children, spiritual care and when to initiate palliative care. The 'Big Debate' explored issues around decision-making and end of life care in children, and gave participants the opportunity to explore a sensitive and thought provoking topic. At the end of the conference, delegates were urged to sign the Commitment of Buenos Aires which called for governments to implement the WHA resolution and ensure access to palliative care for neonates, children and their families, and also commits us as palliative care providers to share all that we can and collaborate with each other to achieve the global vision of palliative care for all children who need it. The conference highlighted the ongoing issues in children's palliative care and participants were continually challenged to ensure that children can access palliative care NOW.

Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016

I1 Proceedings of the Fifteenth Annual UT- KBRIN Bioinformatics Summit 2016

Eric C. Rouchka, Julia H. Chariker, Benjamin J. Harrison, Juw Won Park

P1 CC-PROMISE: Projection onto the Most Interesting Statistical Evidence (PROMISE) with Canonical Correlation to integrate gene expression and methylation data with multiple pharmacologic and clinical endpoints

Xueyuan Cao, Stanley Pounds, Susana Raimondi, James Downing, Raul Ribeiro, Jeffery Rubnitz, Jatinder Lamba

P2 Integration of microRNA-mRNA interaction networks with gene expression data to increase experimental power

Bernie J Daigle, Jr.

P3 Designing and writing software for in silico subtractive hybridization of large eukaryotic genomes

Deborah Burgess, Stephanie Gehrlich, John C Carmen

P4 Tracking the molecular evolution of Pax gene

Nicholas Johnson; Chandrakanth Emani

P5 Identifying genetic differences in thermally dimorphic and state specific fungi using in silico genomic comparison

Stephanie Gehrlich, Deborah Burgess, John C Carmen

P6 Identification of conserved genomic regions and variation therein amongst Cetartiodactyla species using next generation sequencing

Kalpani De Silva, Michael P Heaton, Theodore S Kalbfleisch

P7 Mining physiological data to identify patients with similar medical events and phenotypes

Teeradache Viangteeravat, Rahul Mudunuri, Oluwaseun Ajayi, Fatih Şen, Eunice Y Huang

P8 Smart brief for home health monitoring

Mohammad Mohebbi, Luaire Florian, Douglas J Jackson, John F Naber

P9 Side-effect term matching for computational adverse drug reaction predictions

AKM Sabbir, Sally R Ellingson

P10 Enrichment vs robustness: A comparison of transcriptomic data clustering metrics

Yuping Lu, Charles A Phillips, Michael A Langston

P11 Deep neural networks for transcriptome-based cancer classification

Rahul K Sevakula, Raghuveer Thirukovalluru, Nishchal K. Verma, Yan Cui

P12 Motif discovery using K-means clustering

Mohammed Sayed, Juw Won Park

P13 Large scale discovery of active enhancers from nascent RNA sequencing

Jing Wang, Qi Liu, Yu Shyr

P14 Computationally characterizing genomic pipelines and benchmarking results using GATK best practices on the high performance computing cluster at the University of Kentucky

Xiaofei Zhang, Sally R Ellingson

P15 Development of approaches enabling the identification of abnormal gene expression from RNA-Seq in personalized oncology

Naresh Prodduturi, Gavin R Oliver, Diane Grill, Jie Na, Jeanette Eckel-Passow, Eric W Klee

P16 Processing RNA-Seq data of plants infected with coffee ringspot virus

Michael M Goodin, Mark Farman, Harrison Inocencio, Chanyong Jang, Jerzy W Jaromczyk, Neil Moore, Kelly Sovacool

P17 Comparative transcriptomics of three Acinetobacter baumanii clinical isolates with different antibiotic resistance patterns

Leon Dent, Mike Izban, Sammed Mandape, Shruti Sakhare, Siddharth Pratap, Dana Marshall

P18 Metagenomic assessment of possible microbial contamination in the equine reference genome assembly

M Scotty DePriest, James N MacLeod, Theodore S Kalbfleisch

P19 Molecular evolution of cancer driver genes

Chandrakanth Emani, Hanady Adam, Ethan Blandford, Joel Campbell, Joshua Castlen, Brittany Dixon, Ginger Gilbert, Aaron Hall, Philip Kreisle, Jessica Lasher, Bethany Oakes, Allison Speer, Maximilian Valentine

P20 Biorepository Laboratory Information Management System

Naga Satya V Rao Nagisetty, Rony Jose, Teeradache Viangteeravat, Robert Rooney, David Hains

Multi-aperture foveated imaging

Foveated imaging, such as that evolved by biological systems to provide high angular resolution with a reduced space-bandwidth product, also offers advantages for man-made task-specific imaging. Foveated imaging systems using exclusively optical distortion are complex, bulky, and high cost, however. We demonstrate foveated imaging using a planar array of identical cameras combined with a prism array and superresolution reconstruction of a mosaicked image with a foveal variation in angular resolution of 5.9:1 and a quadrupling of the field of view. The combination of low-cost, mass-produced cameras and optics with computational image recovery offers enhanced capability of achieving large foveal ratios from compact, low-cost imaging systems.

The personal value of being part of a Tropical Health Education Trust (THET) links programme to develop a palliative care degree programme in Sub Saharan Africa: a descriptive study of the views of volunteer UK health care professionals

BACKGROUND

There is a global need to expand palliative care services to reach the increasing number requiring end of life care. In developing countries where the incidences of cancer are rising there is an urgent need to develop the palliative care workforce. This paper reports on a UK Department for international development (DFID) initiative funded through the Tropical Health Education Trust (THET) where palliative care staff, both clinical and academic, volunteered to help to develop, support and deliver a degree in palliative care in sub-Saharan Africa. The objective of the study was to explore the personal impact on the health care professionals of being part of this initiative.

METHODS

An evaluation approach using a confidential electronic survey containing quantitative and qualitative questions was distributed to all 17 volunteers on the programme, three months after completion of the first cohort. Data were analysed using descriptive statistics and content thematic analysis. Ethical review deemed the study to be service evaluation.

RESULTS

82 % (14) responded and several themes emerged from the data including the positive impact on teaching and educational skills; clinical practice and finally personal development. Using a score of 1-10 (1-no impact, 10 maximum impact) 'Lifestyle choices - life work balance' (rating 7.83) had the most impact.

CONCLUSIONS

This approach to supporting the development of palliative care in Sub-Saharan Africa through skill sharing in supporting the delivery of a degree programme in palliative care was successful in terms of delivery of the degree programme, material development and mentorship of local staff. Additionally, this study shows it provided a range of positive impacts on the volunteer health care professionals from the UK. Professional impacts including increased management skills, and being better prepared to undertake a senior role. However it is the personal impact including lifestyle choices which the volunteers reported as the highest impact. Interestingly, several of the faculty have joined other volunteer programmes to continue to support the international development of palliative care.

Effects of dietary electrolyte balance and addition of electrolyte-betaine supplements in feed or water on performance, acid-base balance and water retention in heat-stressed broilers

The effects of dietary electrolyte balance (DEB) and electrolyte-betaine (El-Be) supplements on heat-stressed broiler performance, acid-base balance and water retention were evaluated during the period 31-40 d of age in a 2 × 3 factorial arrangement of treatments. A total of 240 broilers were assigned to 6 treatment groups each with 8 replicates of 5 birds per cage and were exposed to cyclic high temperature (32 - 24 ± 1°C). Birds were provided with diets having DEB of either 180 or 220 mEq/kg. El-Be supplements were either added to the diet, water or not added to either of them to complete the array of 6 treatment groups. An additional 80 birds were kept at thermoneutral temperature (20 ± 1°C) and were provided with tap water and diets with DEB of either 180 or 220 mEq/kg to serve as negative controls. Exposure to high temperature depressed growth performance, increased rectal temperature and decreased potassium (K(+)) retention. In high-temperature room, birds fed on diets with DEB of 220 mEq/kg tended to increase BW from 35-40 d of age. However, at thermoneutral temperature, broilers fed on diets with DEB of 220 mEq/kg increased K(+) retention. Adding El-Be supplements in feed or water improved feed conversion ratio (FCR), enhanced water consumption and increased K(+) and sodium (Na(+)) retention. Interactions between DEB and El-Be supplements tended to affect body weight gain and FCR during the periods 35-40 and 31-40 d of age, respectively. It is suggested that when using a diet with DEB of 180 mEq/kg, adding the El-Be supplements in drinking water was more beneficial than in feed. Adding the supplements in feed or water was equally useful when using DEB of 220 mEq/kg.

The current situation in education and training of health-care professionals across Africa to optimise the delivery of palliative care for cancer patients

The need for palliative care education remains vital to contribute to the quality of life of patients, both adults and children, with cancer in Africa. The number of patients with cancer continues to rise, and with them the burden of palliative care needs. Palliative care has been present in Africa for nearly four decades, and a number of services are developing in response to the HIV/AIDS epidemic. However, the needs of cancer patients remain a challenge. Education and training initiatives have developed throughout this time, using a combination of educational methods, including, more recently, e-learning initiatives. The role of international and national organisations in supporting education has been pivotal in developing models of education and training that are robust, sustainable, and affordable. Developing a material for education and professional development needs to continue in close collaboration with that already in production in order to optimise available resources. Seeking ways to evaluate programmes in terms of their impact on patient care remains an important part of programme delivery. This article reviews the current situation.

Abstract 3083: The genetic landscape of Ph-like acute lymphoblastic leukemia

BCR-ABL1-like, or “Ph-like” B-progenitor acute lymphoblastic leukemia (B-ALL) constitutes up to 15% of childhood and 30% of adult ALL, and is characterized by a gene expression profile similar to BCR-ABL1 ALL, alteration of IKZF1, and poor outcome. A pilot next-generation sequencing study identified kinase activating alterations in 15 Ph-like ALL cases. The goals of this study were to define the genomic landscape of Ph-like ALL in children and young adults, and to examine the utility of tyrosine kinase inhibitors (TKIs) in patients harboring genetic alterations activating kinase signaling.

We studied 1665 B-ALL cases, including 309 childhood standard risk (10.8% Ph-like), 826 childhood high risk (14% Ph-like), 370 adolescent (16-21 years, 21% Ph-like) and 160 young adult (21-39 years; 26% Ph-like) cases. Approximately 50% of Ph-like cases harbored a CRLF2 rearrangement (IGH-CRLF2 or P2RY8-CRLF2). Next-generation sequencing was performed for 160 non-CRLF2 expressing Ph-like cases, including mRNA-seq (141 cases), whole genome sequencing (30 cases) and/or exome sequencing (12 cases). Fusion transcripts were identified using CICERO, a novel mRNA-seq assembly-based structural variation detection method.

Over 100 chimeric in-frame fusions were identified, including 29 involving 12 tyrosine kinase or cytokine receptor genes, 15 of which were recurrent: JAK2 (10 partners), ABL1 (6), ABL2 (3), PDGFRB (3), CSF1R, TYK2, NTRK3, PTK2B, IL2RB (1 partner each), and rearrangements of EPOR into the IGH and IGK loci. Together, these rearrangements were present in ∼30% of Ph-like ALL cases. Additional sequence and structural alterations activating kinase signaling were identified in ∼10% of cases (e.g IL7R, FLT3, SH2B3).

Despite the diversity of kinase alterations, the majority are predicted to respond to a limited number of TKIs, but many are novel or have not been tested in suitable preclinical models of ALL. We show that expression of RCSD1-ABL1, RANBP2-ABL1, ZMIZ1-ABL1, RCSD1-ABL2, SSBP2-CFS1R and PAX5-JAK2 in Ba/F3 and primary mouse pre-B cultures induces cytokine-independent proliferation and constitutive activation of JAK/STAT signaling. Furthermore, the ABL1, ABL2 and CSF1R fusions were sensitive to dasatinib (IC50 range 1-2nM), whilst PAX5-JAK2 only responded to the JAK2 inhibitor, ruxolitinib. Notably, we show efficacy of dasatinib (20mg/kg/day p.o) in a xenograft model of ETV6-ABL1, with reduction of circulating human CD45+ cells (17.4 vs 88.2%; p&lt;0.0001) and spleen weight (117 vs 321mg; p&lt;0.0001) in dasatinib treated mice (n=5) compared to vehicle treated mice (n=5).

These data define the genomic landscape of Ph-like ALL and show that the majority of cases harbor genetic alterations that activate a limited number of kinase signaling pathways. These results provide the basis for prospective precision medicine clinical trials that identify and direct patients with Ph-like ALL to logical TKI therapy.

Citation Format: Kathryn G. Roberts, Yongjin Li, Debbie Payne-Turner, Jinghui Zhang, Richard C. Harvey, Yung-Li Yang, Guangchun Song, Jing Ma, Shann-Ching Chen, Jinjun Cheng, Natalia Santiago-Morales, Ilaria Iacobucci, Meenakshi Devidas, I-Ming Chen, Shalini Reshmi, Michael Rusch, Pankaj Gupta, Naomi J. Winick, William L. Carroll, Nyla A. Heerema, Andrew J. Carroll, Elizabeth A. Raetz, Guido Marcucci, Clara D. Bloomfield, Wendy Stock, Steven M. Kornblau, Elisabeth Paietta, Ching-Hon Pui, Sima Jeha, James Downing, Daniela S. Gerhard, Julie M. Gastier-Foster, Mignon L. Loh, Cheryl Willman, Stephen P. Hunger, Charles G. Mullighan. The genetic landscape of Ph-like acute lymphoblastic leukemia. [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 3083. doi:10.1158/1538-7445.AM2014-3083

Genomic landscape of Ewing sarcoma defines an aggressive subtype with co-association of STAG2 and TP53 mutations

Ewing sarcoma is a primary bone tumor initiated by EWSR1-ETS gene fusions. To identify secondary genetic lesions that contribute to tumor progression, we performed whole-genome sequencing of 112 Ewing sarcoma samples and matched germline DNA. Overall, Ewing sarcoma tumors had relatively few single-nucleotide variants, indels, structural variants, and copy-number alterations. Apart from whole chromosome arm copy-number changes, the most common somatic mutations were detected in STAG2 (17%), CDKN2A (12%), TP53 (7%), EZH2, BCOR, and ZMYM3 (2.7% each). Strikingly, STAG2 mutations and CDKN2A deletions were mutually exclusive, as confirmed in Ewing sarcoma cell lines. In an expanded cohort of 299 patients with clinical data, we discovered that STAG2 and TP53 mutations are often concurrent and are associated with poor outcome. Finally, we detected subclonal STAG2 mutations in diagnostic tumors and expansion of STAG2-immunonegative cells in relapsed tumors as compared with matched diagnostic samples.

SIGNIFICANCE

Whole-genome sequencing reveals that the somatic mutation rate in Ewing sarcoma is low. Tumors that harbor STAG2 and TP53 mutations have a particularly dismal prognosis with current treatments and require alternative therapies. Novel drugs that target epigenetic regulators may constitute viable therapeutic strategies in a subset of patients with mutations in chromatin modifiers.

RRM1 and RRM2 pharmacogenetics: association with phenotypes in HapMap cell lines and acute myeloid leukemia patients

BACKGROUND

Ribonucleotide reductase catalyzes an essential step in the cellular production of deoxyribonucleotide triphosphates and has been associated with clinical outcome in cancer patients receiving nucleoside analog-based chemotherapy.

MATERIALS & METHODS

In the current study, we sequenced the genes RRM1 and RRM2 in genomic DNA from HapMap cell lines with European (Utah residents with northern and western European ancestry [CEU]; n = 90) or African (Yoruba people in Ibadan, Nigeria [YRI]; n = 90) ancestry.

RESULTS

We identified 44 genetic variants including eight coding SNPs in RRM1 and 15 SNPs including one coding SNP in RRM2. RRM1 and RRM2 mRNA expression levels were significantly correlated with each other in both CEU and YRI lymphoblast cell lines, and in leukemic blasts from acute myeloid leukemia (AML) patients (AML97, n = 89; AML02, n = 187). Additionally, RRM1 expression was higher among patient features indicative of a high relapse hazard. We evaluated SNPs within the RRM1 and RRM2 genes in the HapMap lymphoblast cell lines from CEU and YRI panels for association with expression and cytarabine chemosensitivity. SNPs of potential significance were further evaluated in AML patients. RRM1 SNPs rs1042919 (which occurs in linkage disequilbrium with multiple other SNPs) and promoter SNP rs1561876 were associated with intracellular 1-β-D-arabinofuranosyl-CTP levels, response after remission induction therapy, risk of relapse and overall survival in AML patients receiving cytarabine and cladribine.

CONCLUSION

These results suggest that SNPs within ribonucleotide reductase might be helpful predictive markers of response to nucleoside analogs and should be further validated in larger cohorts.

Super-resolution imaging using a camera array

The angular resolution of many commercial imaging systems is limited, not by diffraction or optical aberrations, but by pixilation effects. Multiaperture imaging has previously demonstrated the potential for super-resolution (SR) imaging using a lenslet array and single detector array. We describe the practical demonstration of SR imaging using an array of 25 independent commercial-off-the-shelf cameras. This technique demonstrates the potential for increasing the angular resolution toward the diffraction limit, but without the limit on angular resolution imposed by the use of a single detector array.

Transforming children's palliative care-from ideas to action: highlights from the first ICPCN conference on children's palliative care

The International Children’s Palliative Care Network (ICPCN) held its first international conference on children’s palliative care, in conjunction with Tata Memorial Centre, in Mumbai, India, from 10–12 February 2014. The theme of the conference, Transforming children’s palliative care—from ideas to action, reflected the vision of the ICPCN to live in a world where every child who needs it, can access palliative care, regardless of where they live. Key to this is action, to develop service provision and advocate for children’s palliative care. Three pre-conference workshops were held on 9 February, aimed at doctors, nurses, social workers, and volunteers, and focused around the principles of children’s palliative care, and in particular pain and symptom management. The conference brought together 235 participants representing 38 countries. Key themes identified throughout the conference included: the need for advocacy and leadership; for education and research, with great strides having been taken in the development of an evidence base for children’s palliative care, along with the provision of education; the importance of communication and attention to spirituality in children, and issues around clinical care, in particular for neonates. Delegates were continually challenged to transform children’s palliative care in their parts of the world and the conference culminated in the signing of the ICPCN Mumbai Declaration. The Declaration calls upon governments around the world to improve access to quality children’s palliative care services and made a call on the Belgian government not to pass a bill allowing children to be euthanised in that country. The conference highlighted many of the ongoing developments in children’s palliative care around the world, and as she closed the conference, Joan Marston (ICPCN CEO) challenged participants to take positive action and be the champions that the children need, thus transforming children’s palliative care.

LIM domain only-2 (LMO2) induces T-cell leukemia by two distinct pathways

The LMO2 oncogene is deregulated in the majority of human T-cell leukemia cases and in most gene therapy-induced T-cell leukemias. We made transgenic mice with enforced expression of Lmo2 in T-cells by the CD2 promoter/enhancer. These transgenic mice developed highly penetrant T-ALL by two distinct patterns of gene expression: one in which there was concordant activation of Lyl1, Hhex, and Mycn or alternatively, with Notch1 target gene activation. Most strikingly, this gene expression clustering was conserved in human Early T-cell Precursor ALL (ETP-ALL), where LMO2, HHEX, LYL1, and MYCN were most highly expressed. We discovered that HHEX is a direct transcriptional target of LMO2 consistent with its concordant gene expression. Furthermore, conditional inactivation of Hhex in CD2-Lmo2 transgenic mice markedly attenuated T-ALL development, demonstrating that Hhex is a crucial mediator of Lmo2's oncogenic function. The CD2-Lmo2 transgenic mice offer mechanistic insight into concordant oncogene expression and provide a model for the highly treatment-resistant ETP-ALL subtype.

The net effect: spanning diseases, crossing borders-highlights from the fourth triennial APCA conference and annual HPCA conference for palliative care

The African Palliative Care Association (APCA) jointly hosted its triennial palliative care conference for Africa with the Hospice and Palliative Care Association of South Africa (HPCA) on 17-20 September 2013 in Johannesburg, South Africa. At the heart of the conference stood a common commitment to see patient care improved across the continent. The theme for the conference, 'The Net Effect: Spanning Diseases, Crossing Borders', reflected this joint vision and the drive to remember the 'net effect' of our work in palliative care-that is, the ultimate impact of the care that we provide for our patients and their families across the disease and age spectrum and across the borders of African countries. The conference, held in Johannesburg, brought together 471 delegates from 34 countries. The key themes and messages from the conference are encapsulated in ten 'C's of commitment to political will and support at the highest levels of governance; engaging national, regional, and international bodies; collaboration; diversity; palliative care for children; planning for human resources and capacity building; palliative care integration at all levels; developing an evidence base for palliative care in Africa; using new technologies; and improved quality of care. Participants found the conference to be a forum that challenged their understanding of the topics presented, as well as enlightening in terms of applying best practice in their own context. Delegates found a renewed commitment and passion for palliative care and related health interventions for children and adults with life-limiting and life-threatening illnesses within the region. This conference highlighted many of the developments in palliative care in the region and served as a unique opportunity to bring people together and serve as a lynchpin for palliative care provision and development in Africa. The delegates were united in the fact that together we can 'span diseases,' 'cross borders,' and realise the 'African Dream' for palliative care.

Dominant role of oncogene dosage and absence of tumor suppressor activity in Nras-driven hematopoietic transformation

Biochemical properties of Ras oncoproteins and their transforming ability strongly support a dominant mechanism of action in tumorigenesis. However, genetic studies unexpectedly suggested that wild-type (WT) Ras exerts tumor suppressor activity. Expressing oncogenic Nras(G12D) in the hematopoietic compartment of mice induces an aggressive myeloproliferative neoplasm that is exacerbated in homozygous mutant animals. Here, we show that increased Nras(G12D) gene dosage, but not inactivation of WT Nras, underlies the aggressive in vivo behavior of Nras(G12D/G12D) hematopoietic cells. Modulating Nras(G12D) dosage had discrete effects on myeloid progenitor growth, signal transduction, and sensitivity to MAP-ERK kinase (MEK) inhibition. Furthermore, enforced WT N-Ras expression neither suppressed the growth of Nras-mutant cells nor inhibited myeloid transformation by exogenous Nras(G12D). Importantly, NRAS expression increased in human cancer cell lines with NRAS mutations. These data have therapeutic implications and support reconsidering the proposed tumor suppressor activity of WT Ras in other cancers.

SIGNIFICANCE

Understanding the mechanisms of Ras -induced transformation and adaptive cellular responses is fundamental. The observation that oncogenic Nras lacks tumor suppressor activity, whereas increased dosage strongly modulates cell growth and alters sensitivity to MEK inhibition, suggests new therapeutic opportunities in cancer.

Preferences for place of death if faced with advanced cancer: a population survey in England, Flanders, Germany, Italy, the Netherlands, Portugal and Spain

BACKGROUND

Cancer end-of-life care (EoLC) policies assume people want to die at home. We aimed to examine variations in preferences for place of death cross-nationally.

METHODS

A telephone survey of a random sample of individuals aged ≥16 in England, Flanders, Germany, Italy, the Netherlands, Portugal and Spain. We determined where people would prefer to die if they had a serious illness such as advanced cancer, facilitating circumstances, personal values and experiences of illness, death and dying.

RESULTS

Of 9344 participants, between 51% (95% CI: 48% to 54%) in Portugal and 84% (95% CI: 82% to 86%) in the Netherlands would prefer to die at home. Cross-national analysis found there to be an influence of circumstances and values but not of experiences of illness, death and dying. Four factors were associated with a preference for home death in more than one country: younger age up to 70+ (Germany, the Netherlands, Portugal, Spain), increased importance of dying in the preferred place (England, Germany, Portugal, Spain), prioritizing keeping a positive attitude (Germany, Spain) and wanting to involve family in decisions if incapable (Flanders, Portugal).

CONCLUSIONS

At least two-thirds of people prefer a home death in all but one country studied. The strong association with personal values suggests keeping home care at the heart of cancer EoLC.

Children's palliative care: a global concern

Children's palliative care (CPC) is a specialty in itself, albeit closely related to adult palliative care (World Health Organization (WHO), 2002). However, although there are many children who require palliative care, in much of the world CPC has a poor profile and is inaccessible to those who need it (Downing et al, 2010; Knapp et al, 2011). The provision of high-quality palliative care for children is a global concern, with 27% of the world population being under the age of 15, rising to as many as 49% in countries such as Uganda (WHO, 2010). It has been estimated that as many as 7 million of these children around the world will need palliative care each year (Rushton et al, 2002), although the true figure is likely to be higher. The public health approach to palliative care is key to the development of CPC services, as is the development of models that integrate services into existing health structures.

Education in children's palliative care across Europe and internationally

Ongoing education and training is essential in health care, particularly in palliative care, which is still expanding both in terms of its global reach and its scope. Children's palliative care (CPC) is a specialty in its own right, but one that is still relatively new, and so appropriate and ongoing education and training of CPC staff is especially important. However, such education and training is not always accessible to those who need it, and only recently have significant attempts been made to quantify the extent and nature of these deficiencies. This paper discusses CPC education and training from a European and global perspective, highlighting some of the principles and challenges. It also looks at the recent efforts of the European Association for Palliative Care and the International Children's Palliative Care Network to attain a clearer picture of the state of global CPC education, presenting some initial findings from their research and discussing preliminary recommendations and future directions.

Multichanneled finite-conjugate imaging

Multichanneled imaging systems rely on nonredundant images recorded by an array of low-resolution imagers to enable construction of a high-resolution image. We show how the varying degree of redundancy associated with imaging throughout the imaged volume effects image quality. Using ray-traced image simulations and a metric used as a proxy for human perception, we show that robust recovery of high-resolution images can be obtained by avoiding excessive redundancy and that this is a felicitous consequence of typical manufacturing tolerances.

Use of whole genome sequencing to identify novel mutations in distinct subgroups of medulloblastoma

9518

Background: Medulloblastoma is a malignant childhood brain tumor comprising four discrete subgroups (SHH-subgroup, WNT-subgroup, subgroup-3 and subgroup-4). The genetic alterations that drive these subgroups and that might serve as treatment targets are largely unknown. Methods: We sequenced entire genomes of 37 tumors and matched normal blood. 136 somatically mutated genes identified in this discovery cohort were sequenced in an additional 56 medulloblastomas. All tumors were classified into the 4 subgroups by expression profiling and immunohistochemistry. All mutations were validated by custom capture, 454, or Sanger sequencing. Results: Recurrent mutations were detected in 49 genes: 41 are not yet implicated in medulloblastoma. Several target distinct components of the epigenetic machinery in different disease subgroups, e.g., regulators of H3K27 and H3K4 trimethylation in subgroup-3 and 4 (e.g., KDM6A and ZMYM3), and CTNNB1-associated chromatin remodellers in WNT-subgroup tumors (e.g., SMARCA4 and CREBBP). Modelling of mutations in mouse lower rhombic lip progenitors that generate WNT-subgroup tumours, identified genes that maintain this cell lineage (DDX3X) as well as mutated genes that initiate (CDH1) or cooperate (PIK3CA) in tumourigenesis. Conclusions: We have identified several new recurrent somatic mutations that are enriched in specific subgroups of medulloblastoma. Alterations affecting subgroup-3 and 4 tumors appear to disrupt chromatin marking, most notably H3K27me3, potentially preserving a stem cell-like state in tumor cells. Mutations in WNT subgroup tumors affect binding partners of CTNNB1 that regulate WNT-response gene transcription. These data provide important new insights into the pathogenesis of medulloblastoma subgroups and highlight targets for therapeutic development.

Abstract 2487: CONSERTING: an accurate method for detecting focal and gross somatic copy number alterations in cancer genome by next generation sequencing

The Identification of somatically acquired DNA copy number alterations (CNA) is extremely important for finding causal genes in cancer. Although next-generation sequencing (NGS) can assay a genome at base-pair resolution, accurate identification of CNA from NGS data has been hindered by sequencing artifacts, coverage bias and paralogous genomic duplication. As a result, existing algorithms tend to generate many CNA segments that are not corroborated by an alternative assay such as SNP array, suggesting high false discovery rate. To improve CNA analysis for NGS data, we developed Copy Number Segmentation by Regression Tree in Next Generation Sequencing (CONSERTING), a novel copy number detection method that integrates read depth analysis with structural variation (SV) detection and adjustment for sequencing artifacts. Analysis of simulated data shown that CONSERTING outperforms existing methods by achieving high sensitivity of focal copy number detection (CONSERTING: 0.80, CNV-Seq: 0.26, SegSeq: 0.19, FREEC: 0.02) at a low false discovery rate (CONSERTING: 0.09, CNV-Seq: 0.19, SegSeq: 0.46, FREEC: 0.07). When applied to matching tumor/normal samples of hematopoietic malignancies and solid tumors, CONSERTING showed a high concordance with SNP array, with a mean of 18 uncorroborated CNA segments compared with 104 by CNVSeq, 182 by SegSeq and 63 by FREEC. In addition, CONSERTING is able to discover bona fide focal CNAs in genes of biological importance that were not detectable by SNP array, such as a 36 kb homozygous deletion in SH2B3 and a 20 kb deletion in CDK6. Finally, CONSERTING is able to find CNAs and SVs present in tumor subclone that are missed by SNP array or SV analysis of NGS data. The novel CNAs and SVs reported here were experimentally validated, demonstrating that the high sensitivity and accuracy of CONSERTING enable discovery of key genetic lesions in cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2487. doi:1538-7445.AM2012-2487

Abstract 4869: Whole genome sequence analysis of MLL rearranged infant acute lymphoblastic leukemias reveals remarkably few somatic mutations: A Report From the St Jude Children's Research Hospital - Washington University Pediatric Cancer Genome Project

Infant acute lymphoblastic leukemia (ALL) is characterized by MLL rearrangements (MLLr) and poor prognosis. To determine the complement of somatic mutations in this high risk leukemia, we performed whole genome sequencing (WGS) on 22 infants with MLL rearranged ALL. An analysis of the structure of the MLLr revealed that over half had complex rearrangements involving either three or more chromosomes, carried cryptic rearrangements, or contained at the breakpoints deletions, amplifications, insertions, or inversion of sequences. In three cases, genetic rearrangements were predicted to generate in addition to the MLL-partner gene fusion, novel in-frame fusions including KRAS-MLL; RAD51B-MLL / AFF1-RAD51B, AFF1-RAD51B-MLL; MLLT10-ATP5L-YPEL4 / ATP5L-YPEL4. An analysis of the number of non-silent mutations revealed infant ALL to have the lowest frequency of somatic mutations of any cancer sequenced to date. After removal of SVs and CNAs associated with the MLLr, a mean of only 3.5 SVs and 2.2 SNVs affecting the coding region of annotated genes or regulatory RNAs were detected per case. Despite the paucity of mutations several pathways were recurrently targeted including PI3K/RAS pathway in 45% (KRAS (n=4), NRAS (n=2), and non-recurrent mutations in NF1, PTPN11, PIK3R1, and ARHGAP32 (p200Rho/GAP)), B cell differentiation in 23% as a result of mono-allelic deletion or gains of PAX5, 14% with deletions of the CDKN2A/B, and 2 cases with focal deletions of the non-coding RNA genes DLEU1/2. WGS of two infant ALL relapse samples and comparison with their matched diagnostic samples revealed a marked increase in the number of mutations at relapse. Moreover, an analysis of the allelic ratios of mutated genes revealed clonal heterogeneity at diagnosis with relapse appearing to arise from a minor diagnostic clone. Because of the exceedingly low number of mutations detected in infant ALL, we used exome sequencing to determine the frequency of non-silent SNVs in 20 MLLr leukemias (9 ALLs, 10 AMLs and 1 AUL) in older children (7-19 yrs). This analysis revealed that non-infant pediatric MLL leukemias harbor a significantly higher number of non-silent somatic SNVs than infant ALL (mean 7.4/case in older patients vs 2.2/case in infants, p&lt;0.001). Although the higher frequency of mutations may be a reflection of age, the low number of cooperating mutations in infants raises the possibility that the target cell of transformation differs between infants and older children, with the cells present during early development requiring fewer cooperating mutations to induce leukemia. In summary our data demonstrated an exceedingly small number of mutations in infant leukemia. The number of detected somatic mutations may represent the lower limit required to transform a normal human cell into cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4869. doi:1538-7445.AM2012-4869

Abstract 1353: Inactivation of ribosomal protein L22 promotes transformation by induction of Lin28B

The molecular basis by which mutations in some ribosomal proteins (RP) predispose to development of hematologic malignancies remains unclear. We show here that germline inactivation of the ribosomal protein L22 (Rpl22), which selectively blocks T cell development, also predisposes T lineage progenitors to transformation. Indeed, RPL22 was found to be inactivated in ∼9% of human T-acute lymphoblastic leukemias (T-ALL). Moreover, mono-allelic loss of Rpl22 accelerates development of thymic lymphoma in a mouse model of T cell malignancy and in acute transformation assays in vitro. Furthermore, we show that Rpl22 inactivation enhances transformation potential through induction of Lin28B. These findings represent the first mechanistic insight into how an RP mutation promotes transformation.Our finding that Rpl22 inactivation promotes transformation by inducing expression of Lin28B provides insight into the mechanistic basis by which mutations in Rpl22, and perhaps other RP genes, increase cancer risk. In addition, because we have determined that Lin28B induction is dependent upon NF-kB activity, our findings may provide new opportunities for therapeutic intervention both in aggressive forms of T-ALL, where we have found Rpl22 to be inactivated, and perhaps in other diseases caused by mutations in RP genes.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1353. doi:1538-7445.AM2012-1353

Abstract 4873: Comprehensive analysis of 160 whole-genome sequences reveals striking telomere alteration patterns in 9 pediatric cancers

Although telomere shortening has long been recognized as a feature of cancer genomes, a comprehensive characterization of telomere alteration in pediatric cancer has not yet been performed. As part of the St. Jude Children's Research Hospital-Washington University Pediatric Cancer Genome Project (PCGP), we are performing whole genome sequence analysis on 600 pediatric cancers and matched germ line samples. This database will allow us to carry out a systematic investigation of telomere alteration across a broad range of pediatric cancers. To characterize the relative level of telomere length within a tumor, we have developed an approach that utilizes the WGS data and identifies all sequencing reads containing the telomeric repeat (TTAGGG)4. This read count is then normalized for genome-wide coverage and compared to the result from the matched germline sample to define the relative level of telomere amplification or loss in the tumor. To date we have analyzed 160 tumor/normal pairs collected from 9 distinct pediatric cancers types (Early T Progenitor Acute Lymphoblastic Leukemia (ALL), Infant ALL, Hypo-diploid ALL, Medulloblastoma, Retinoblastoma, Neuroblastoma, Osteosarcoma, Rhabdomyosarcoma, and Adrenocortical Carcinoma). Our analysis revealed normal telomere length or minimal loss in Early T Progenitor Acute Lymphoblastic Leukemia (ALL), Hypo-Diploid ALL, Infant-ALL, Medulloblastoma, Retinoblastoma, and Rhabdomyosarcoma. By contrast a subset of three distinct tumor types (Neurobalstoma, Oteosarcoma, and Adrenocortical Carcinoma) were characterized by marked increases in the number of telomere reads in the tumor consistent with telomere lengthening. These latter findings were validated in neuroblastoma by quantitative polymerase chain reaction (13/14) and fluorescence in situ hybridization (7/7). The presence of long telomeres was statistically associated with an increase in the number of somatic structural variations in tumor, with this association most evident in osteosarcoma. These data suggest that some pediatric cancers are associated with marked abnormalities in telomere maintenance leading to expansion in the telomere repeats. Defining the specific mutational processes that are responsible for these telomere defects and expanding the dataset to all 600 cancers in the project should help to define the mechanisms through which these alterations contribute to the transformed phenotypes.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4873. doi:1538-7445.AM2012-4873