Characteristics of severe acute respiratory infectionassociated hospitalization in Yemen, 2014/15

This study aims to describe etiological agents, demographic details of patients, seasonality and underlying conditions among patients hospitalized due to viral severe acute respiratory infection (SARI) in Yemen. We carried out a retrospective descriptive analysis of data from January 2014 to December 2015. Nasopharyngeal swabs were taken from each patient for laboratory testing. A total of 1346 diagnostic specimens were tested, of which 733 (54%) were positive for influenza viruses. Influenza A(H3) and A(H1N1) pdm09 predominated. Respiratory syncytial virus (RSV) was reported predominantly among children (41%). Males (61%) were more affected than females. The median age was 1 year (range 0.5-94.0). The median length of hospitalization was 6 days. Chronic cardiovascular disease was the most commonly reported underlying condition, but 67% had no documented underlying disease. Respiratory viruses, particularly RSV, adenovirus and influenza, were commonly associated with hospitalization for SARI.

The H1N1 influenza pandemic of 2009 in the Eastern Mediterranean Region: lessons learnt and future strategy

A novel strain of influenza A virus H1N1 surfaced in Mexico in April 2009 and quickly spread across the globe, turning an epidemic into a pandemic. Within two months, the World Health Organization (WHO) declared an international health emergency and raised the threat bar from level V to level VI, i.e. containment to mitigation. During this time, the WHO Regional Office for the Eastern Mediterranean worked closely with its Member States, other stakeholders and WHO headquarters to manage the situation. This report examines the steps taken as part of this response. Programme documents were reviewed and key personnel interviewed for this study. A hallmark of the response was the establishment of the Strategic Health Operations Centre to bring together experts from different technical backgrounds at regional level. Several lessons were learnt that can provide the basis for standard operating procedures, protocols and guidelines for emergency events in future.

Burden of acute respiratory disease of epidemic and pandemic potential in the WHO Eastern Mediterranean Region: A literature review

There are gaps in the knowledge about the burden of severe respiratory disease in the Eastern Mediterranean Region (EMR). This literature review was therefore conducted to describe the burden of epidemicand pandemic-prone acute respiratory infections (ARI) in the Region which may help in the development of evidence-based disease prevention and control policies. Relevant published and unpublished reports were identified from searches of various databases; 83 documents fulfilled the search criteria. The infections identified included: ARI, avian influenza A(H5N1), influenza A(H1N1)pdm09 and Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Pneumonia and ARIs were leading causes of disease and death in the Region. Influenza A(H1N1) was an important cause of morbidity during the 2009 pandemic. This review provides a descriptive summary of the burden of acute respiratory diseases in the Region, but there still remains a lack of necessary data.

Middle East respiratory syndrome coronavirus: current knowledge and future considerations

A literature review of publically available information was undertaken to summarize current understanding and gaps in knowledge about Middle East respiratory syndrome coronavirus (MERS-CoV), including its origin, transmission, effective control measures and management. Major databases were searched and relevant published papers and reports during 2012-2015 were reviewed. Of the 2520 publications initially retrieved, 164 were deemed relevant. The collected results suggest that much remains to be discovered about MERS-CoV. Improved surveillance, epidemiological research and development of new therapies and vaccines are important, and the momentum of recent gains in terms of better understanding of disease patterns should be maintained to enable the global community to answer the remaining questions about this disease.

Contribution of laboratories in the WHO Eastern Mediterranean Region to the selection of candidate seasonal influenza vaccine, 2010-2015

The World Health Organization (WHO) formulates recommendations for viruses to be included in vaccines for the influenza seasons in the northern and southern hemispheres on the basis of analyses by its collaborating centres (CCs). This report describes the contribution of influenza laboratories and national influenza centres in countries in the WHO Region for the Eastern Mediterranean to the selection process of seasonal and pre-pandemic influenza virus subtypes. Data submitted by 22 countries to FluNet and FluID between September 2010 and June 2015 were analysed. National Influenza Centres (NICs) in 12 countries (55%) reported data, 5 (23%) to both FluNet and FluID and 7 (32%) only to FluNet. The WHO CC in London characterized 78% of the samples, and the CC in Atlanta, characterized 21%. The contribution of influenza laboratories and NICs from this Region to global influenza surveillance is appreciable. However, enhancing the contribution through initiatives such as the Pandemic Influenza Preparedness Framework is still needed.

Adult native knee extensor mechanism ruptures

Extensor mechanism rupture is a serious event requiring prompt diagnosis and treatment. Patella fractures are reportedly six times more frequent than soft tissue injuries such as quadriceps or patella tendon ruptures. Classically quadriceps and patella tendon ruptures are seen more in males, with those over 40 predominantly suffering from quadriceps tendon ruptures, often associated with an underlying condition, whereas patella tendon ruptures are mostly associated with sport injuries and are commonly seen in the under 40s. Almost all types of extensor mechanism ruptures benefit from early management which typically involves surgery. Diagnosis can be deemed easy to make by demonstrating inability to actively extend the knee, this however can be easily overlooked and missed in a busy emergency department leading to a late diagnosis and necessitating more complex surgery. Earlier surgical intervention and rehabilitation tend to produce improved outcomes.

A Flexible, Micro-Lens-Coupled LED Stimulator for Optical Neuromodulation

Optogenetics is a fast growing neuromodulation method, which can remotely manipulate the specific activities of genetically-targeted neural cells and associated biological behaviors with millisecond temporal precision through light illumination. Application of optogenetics in neuroscience studies has created an increased need for the development of light sources and the instruments for light delivery. This paper presents a micro-lens-coupled LED neural stimulator which includes a backside reflector and a frontside microlens for light collection and collimation. The device structure has been optimized using optical simulation and the optimized device is able to increase the volume of excitable tissues by 70.4%. Device prototypes have been fabricated and integrated based on an optimization of the device structure. The measurement results show that the light power increases by 99% at an effective penetration depth of 5 000 [Formula: see text] by the fabricated device under various voltages of 2.4-3.2 V.

Can 'Hot Spotting' Prove to be a Useful Tool to Identify Disproportionate ED Use in the Rural General Hospital Setting?

'Hot spotting' allows the identification of areas with disproportionate use of Emergency Department (ED) services. To date, 'hot spotting' has focused on large urban centres. The aim of this study was to determine if there are geographic hotspots for ED use in the rural general hospital. ED attendances were logged between 1st July 2013 and 30th June 2014. Frequent users and super users were isolated. Addresses were cross referenced against national census data to determine number of users per 500 population in geographically distinct regions. The number of frequent users ranged from 1.00/500 population to 4.88/500 population. Four out of nineteen areas had > or equals; 4 frequent users per 500 population. There was no correlation between number of users and distance from MGH (p=0.44). 77% of frequent users presented with mixed aetiologies. Nineteen percent of frequent attenders presented via GP referral only, 13% attended via self-referral only and 88% attended via GP and self-referral routes.

Presence of microbial and chemical source tracking markers in roof-harvested rainwater and catchment systems for the detection of fecal contamination

Microbial source tracking (MST) and chemical source tracking (CST) markers were utilized to identify fecal contamination in harvested rainwater and gutter debris samples. Throughout the sampling period, Bacteroides HF183 was detected in 57.5 % of the tank water samples and 95 % of the gutter debris samples, while adenovirus was detected in 42.5 and 52.5 % of the tank water and gutter debris samples, respectively. Human adenovirus was then detected at levels ranging from below the detection limit to 316 and 1253 genome copies/μL in the tank water and debris samples, respectively. Results for the CST markers showed that salicylic acid (average 4.62 μg/L) was the most prevalent marker (100 %) in the gutter debris samples, caffeine (average 18.0 μg/L) was the most prevalent in the tank water samples (100 %) and acetaminophen was detected sporadically throughout the study period. Bacteroides HF183 and salicylic acid (95 %) and Bacteroides HF183 and caffeine (80 %) yielded high concurrence frequencies in the gutter debris samples. In addition, the highest concurrence frequency in the tank water samples was observed for Bacteroides HF183 and caffeine (60 %). The current study thus indicates that Bacteroides HF183, salicylic acid and caffeine may potentially be applied as source tracking markers in rainwater catchment systems in order to supplement fecal indicator analyses.

The S-Quattro in the Management of Acute Intraarticular Phalangeal Fractures of the Hand

Intraarticular phalangeal fractures of the hand are difficult and challenging to manage. Dynamic external fixation devices offer the advantages of allowing distraction of the impacted fracture and early joint mobilization. We present our study of 100 patients with a variety of fractures who were treated with the S-Quattro technique over a 6-year period, with an average follow-up of 10.5 months. The mean active range of motion regained was 92° for proximal interphalangeal joints (81 fractures), 82° for distal interphalangeal joints (10 fractures), 91° for metacarpophalangeal joints (6 fractures) and 80° for interphalangeal joints of the thumb (3 fractures). Only nine patients complained of mild or moderate pain. Postoperative radiographic appearances were satisfactory in all but five out of the 100 patients. This device is a simple and effective technique for the management of these difficult fractures. It offers advantages in terms of versatility, ease of application, good tolerance by patients, few complications and good outcome.

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3^rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar

EMA-qPCR to monitor the efficiency of a closed-coupled solar pasteurization system in reducing Legionella contamination of roof-harvested rainwater

Solar pasteurization is effective in reducing the level of indicator organisms in stored rainwater to within drinking water standards. However, Legionella spp. were detected at temperatures exceeding the recommended pasteurization temperatures using polymerase chain reaction assays. The aim of the current study was thus to apply EMA quantitative polymerase chain reaction (EMA-qPCR) to determine whether the Legionella spp. detected were intact cells and therefore possibly viable at pasteurization temperatures >70°C. The BacTiter-Glo™ Microbial Cell Viability Assay was also used to detect the presence of ATP in the tested samples, as ATP indicates the presence of metabolically active cells. Chemical analysis also indicated that all anions and cations were within the respective drinking water guidelines, with the exception of iron (mean: 186.76 μg/L) and aluminium (mean: 188.13 μg/L), which were detected in the pasteurized tank water samples at levels exceeding recommended guidelines. The BacTiter-Glo™ Microbial Cell Viability Assay indicated the presence of viable cells for all pasteurized temperatures tested, with the percentage of ATP (in the form of relative light units) decreasing with increasing temperature [70-79°C (96.7%); 80- 89°C (99.2%); 90-95°C (99.7%)]. EMA-qPCR then indicated that while solar pasteurization significantly reduced (p<0.05) the genomic copy numbers of intact Legionella cells in the pasteurized tank water (~99%), no significant difference (p>0.05) in the mean copy numbers was detected with an increase in the pasteurization temperature, with 6 × 10(3) genomic copies/mL DNA sample obtained at 95°C. As intact Legionella cells were detected in the pasteurized tank water samples, quantitative microbial risk assessment studies need to be conducted to determine the potential health risk associated with using the water for domestic purposes.

Isolation, antibiogram and pathogenicity of Salmonella spp. recovered from slaughtered food animals in Nagpur region of Central India

Aim:

To determine the prevalence, antibiogram and pathogenicity of Salmonella spp. in the common food animals slaughtered for consumption purpose at government approved slaughter houses located in and around Nagpur region during a period of 2010-2012.

Materials and Methods:

A total of 400 samples comprising 50 each of blood and meat from each slaughtered male cattle, buffaloes, pigs and goats were collected. Isolation was done by pre-enrichment in buffered peptone water and enrichment in Rappaport-Vassiliadis broth with subsequent selective plating onto xylose lysine deoxycholate agar. Presumptive Salmonella colonies were biochemically confirmed and analyzed for pathogenicity by hemolysin production and Congo red dye binding assay (CRDA). An antibiotic sensitivity test was performed to assess the antibiotic resistance pattern of the isolates.

Results:

A total of 10 isolates of Salmonella spp. from meat (3 from cattle, 1 from buffaloes and 6 from pigs) with an overall prevalence of 5% among food animals was recorded. No isolation was reported from any blood samples. Pathogenicity assays revealed 100% and 80% positivity for CRDA and hemolytic activity, respectively. Antimicrobial sensitivity test showed multi-drug resistance. The overall resistance of 50% was noted for trimethoprim followed by ampicillin (20%). A maximum sensitivity (80%) was reported to gentamycin followed by 40% each to ampicillin and trimethoprim, 30% to amikacin and 10% to kanamycin.

Conclusion:

The presence of multidrug resistant and potentially pathogenic Salmonella spp. in slaughtered food animals in Nagpur region can be a matter of concern for public health.

Utilisation of Clinical Networks to Facilitate Elective Surgical Workload; A Preliminary Analysis

Clinical networks have potential to increase elective surgical workload for benign conditions in non-cancer centres. The aims of this study were to determine outcomes for elective laparoscopic cholecystectomy in our unit and to evaluate early experience in managing benign surgical workload referred from the tertiary centre within our clinical network. An analysis of cholecystectomies performed at Mayo General Hospital was conducted (2003-2013). A review of elective procedures more recently referred from Galway University Hospital (GUH) waiting lists was also conducted. 1937 consecutive cholecystectomies were performed with an overall laparoscopic conversion rate of 1.7% (33/1875). The total major complication rate was 0.93% (18/1937). 151 selected procedures originating from GUH have been performed since December 2013 without adverse events. Laparoscopic cholecystectomy can be performed in significant volume in the general hospital environment. This and other appropriate benign surgical procedures may be performed outside of tertiary units according to network agreements.

Sedation for gastroscopy: Is it an adequately understood and informed choice?

INTRODUCTION

Sedation uptake rates for oesophagogastroduodenoscopy (OGD) vary greatly. Issues concerning adequate information and consent have been raised. Additionally, patient comprehension of sedation options is inconsistent.

METHODS

A closed ended questionnaire was created and delivered to assess patient understanding regarding sedation prior to OGD. The questionnaire was based on British Society of Gastroenterology guidelines.

RESULTS

One hundred and eleven patients were recruited. 90 % of the sedated and 73 % of the unsedated patients were satisfied with their respective decisions (OR 0.283, *p = 0.01). 65 % were unaware of basic differences between conscious sedation and general anesthesia, and 37 % were unaware that driving is permitted after having throat spray alone. The most informed of the age groups had the lowest uptake of sedation and the least informed had the highest uptake.

CONCLUSION

The decision to undergo gastroscopy with or without sedation is not a sufficiently informed one. This study highlights the need for the widespread dissemination of good quality information to inform patients better regarding sedation prior to OGD.

Low surrogate light chain in pro-B cells from old mice suppresses apoptosis and alters the idiotypes and proportions of phosphorylcholine reactive B cells (LYM6P.718)

The generation of new B cells is substantially decreased in old mice (&gt;2 years). Early B cell precursors (pro-B cells) are reduced in old mice and exhibit a reduction in the surrogate light chain (SLC) protein λ5. We hypothesize that this alters the expression and function of the pre-B cell receptor and influences the “read-out” of antibody specificities in the B cell repertoire. In old mice, the remaining pro-B cells, low in SLC, are resistant to apoptotic stimuli (TNFα), in contrast to young adult pro-B cells. Apoptotic sensitivity reflects levels of the SLC, since young pro-B cells partially or completely deficient in λ5 are also resistant to apoptosis. Age-associated B cells (ABC) represent a B cell subset which expands in old mice; ABC are pro-inflammatory and secrete TNFα. Adoptive transfer of ABC into young RAG-2 KO recipients results in partial loss of pro-B cells and, in particular, loss of pro-B cells with higher levels of SLC λ5. Anti-phosphorylcholine (PC) reactive B cells, especially those of the T15 idiotype, are important in defense against pneumococci. In old age, the proportion of PC reactive B cells, particularly with less protective T15 negative idiotypes, increases. Low SLC promotes both increased PC reactivity and T15 negative idiotypes. These studies suggest that ABC promote an “SLClow” B cell pathway that alters antibody specificities in old age.

Bisphosphonates and their influence on fracture healing: a systematic review

Bisphosphonates are commonly used in osteoporosis, but concerns have been raised about possible negative effects on fracture healing. We systematically reviewed the literature and found that bisphosphonates significantly prolong union times of distal radius fractures but not femoral fractures. The timing of bisphosphonate introduction does not affect fracture union time.

INTRODUCTION

Bisphosphonates are the most commonly prescribed drugs in patients suffering from and at higher risk of developing osteoporosis. However, concerns have been raised as to whether these drugs have a negative effect on fracture healing. The aim of this systematic review is to explore further these concerns.

METHODS

A literature review was performed in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. All relevant articles found via MEDLINE, Cochrane, CINAHL, EMBASE and Google Scholar were screened. Studies with information on bisphosphonates' effect on fracture healing in humans were included and systematically reviewed.

RESULTS

Patients with distal radius fractures on bisphosphonates had a significantly longer union time compared with controls, but not patients with femoral fractures. No correlation between timing of bisphosphonate introduction and union time for fractures was found. Although one study reported a higher humeral non-union associated with bisphosphonate introduction following the fracture, there was no evidence that bisphosphonate introduction, timing or dose resulted in a significant delay in union following other fractures.

CONCLUSIONS

This systematic review has shown that bisphosphonates significantly prolong union times of distal radius fractures. Some clinical findings are in contrast with preclinical studies highlighting the need to develop better animal models to study osteoporosis, treatment and fracture healing. There is also a need for more well-constructed studies looking at the clinical effect of bisphosphonate on fracture healing in a large number of patients. These robust studies need to look at union time and non-union rates as a function of duration and dose of different bisphosphonates in different upper and lower limb fractures.

Benign subcutaneous emphysema: A case report with bite

INTRODUCTION

Subcutaneous emphysema is the presence of air/gas within the subcutaneous tissue plane. Though there are numerous causative factors, benign subcutaneous emphysema is rare.

CASE REPORT

We report a very rare case of benign subcutaneous emphysema following an insect bite on the forearm of a 48-year old man. The puncture area was erythematous and the emphysema extended to the whole arm, axilla and superior mediastinum. Despite, conservative management, the patient had residual discomfort and erythema around the puncture site. Surgical debridement resulted in resolution of symptoms.

DISCUSSION

Subcutaneous emphysema affecting an isolated limb is extremely rare. It is vital to differentiate it from life-threatening soft-tissue infections secondary to a gas-forming organism. Immunodeficiency states are key factors in the development and the outcomes of patients with subcutaneous emphysema. Medical management successfully resolves symptoms in the majority of cases. However, surgical debridement of the puncture site and surrounding fibrotic tissue has been advocated for those with persistent symptoms.

CONCLUSION

This case highlights a rare cause of benign subcutaneous emphysema, highlighting key issues surrounding its management for a successful outcome.

Management of paediatric acute appendicitis in the general hospital setting: a national survey of preferred surgical technique

BACKGROUND

The advent of laparoscopic surgery has facilitated the management of acute appendicitis in the adult population. In the paediatric population (<12 years), management varies according to institution and/or consultant expertise. The aim of this study was to analyse consultant preference for laparoscopic versus open appendicectomy in the management of acute appendicitis in children under 12 years presenting to general hospitals.

METHODS

A 15-point questionnaire was distributed to 81 consultant surgeons identified from the specialist register of the Irish Medical Council and practicing as general surgeons outside of specialist paediatric centres.

RESULTS

A response rate of 83 % (67/81) was obtained. Of the 67 surgeons surveyed, 11 (16 %) had formal paediatric training. Sixty percent (40/67) of surgeons expressed a preference for the open technique. The median frequency of on-call rota was >1 in 5 (32/67) and only 3 % (2/67) claimed that the on-call commitment influenced decision-making regarding surgical approach. The average minimum age (9.3 years, range 1-14) and average minimum weight (25 kg, range 12-70) at which the operating surgeon would perform a laparoscopic appendicectomy were also recorded. Thirty percent (20/67) of consultant general surgeons had immediate access to specialist paediatric laparoscopic equipment.

DISCUSSION

This study has shown wide variability amongst consultant general surgeons when considering open versus laparoscopic appendicectomy in children under 12 years. Restricted access to specialist paediatric laparoscopic equipment, combined with declining exposure to paediatric surgical training, may continue to limit the numbers of paediatric laparoscopic appendicectomies performed in the general setting.

Follow-up arrangements for breast cancer patients; is it appropriate to transfer surveillance to general practitioners?

The aim of this study was to examine the evidence for hospital follow up of breast cancer survivors and to identify patient preferences for hospital or community follow-up. We surveyed General Practitioner attitudes towards community follow-up and quantified the incidence of new or recurrent cancers within a patient cohort to identify their primary symptoms and thus cancer detection in the community. A 22 item questionnaire was distributed to 101 breast cancer survivors from a cohort of 921 treated patients. A 9 item questionnaire was distributed to 81 General Practitioners. Patients are reassured by hospital outpatient appointments, n=63 (74%) but have high levels of confidence in General Practitioner follow-up, n=57 (67%). General Practitioners are equally divided regarding their support for the transfer of follow-up (51%, 49%). Ten of the 14 new cancer episodes were associated with obvious clinical signs (p < 0.05). The proposed transfer of follow-up for patients to general practice by the national cancer control programme is appropriate.