Impacts of signal processing factors on perceptual restoration in cochlear-implant users

Cochlear-implant (CI) users have previously demonstrated perceptual restoration, or successful repair of noise-interrupted speech, using the interrupted sentences paradigm [Bhargava, Gaudrain, and Başkent (2014). "Top-down restoration of speech in cochlear-implant users," Hear. Res. 309, 113-123]. The perceptual restoration effect was defined experimentally as higher speech understanding scores with noise-burst interrupted sentences compared to silent-gap interrupted sentences. For the perceptual restoration illusion to occur, it is often necessary for the masking or interrupting noise bursts to have a higher intensity than the adjacent speech signal to be perceived as a plausible masker. Thus, signal processing factors like noise reduction algorithms and automatic gain control could have a negative impact on speech repair in this population. Surprisingly, evidence that participants with cochlear implants experienced the perceptual restoration illusion was not observed across the two planned experiments. A separate experiment, which aimed to provide a close replication of previous work on perceptual restoration in CI users, also found no consistent evidence of perceptual restoration, contrasting the original study's previously reported findings. Typical speech repair of interrupted sentences was not observed in the present work's sample of CI users, and signal-processing factors did not appear to affect speech repair.

Access to semantic cues does not lead to perceptual restoration of interrupted speech in cochlear-implant users

Cochlear-implant (CI) users experience less success in understanding speech in noisy, real-world listening environments than normal-hearing (NH) listeners. Perceptual restoration is one method NH listeners use to repair noise-interrupted speech. Whereas previous work has reported that CI users can use perceptual restoration in certain cases, they failed to do so under listening conditions in which NH listeners can successfully restore. Providing increased opportunities to use top-down linguistic knowledge is one possible method to increase perceptual restoration use in CI users. This work tested perceptual restoration abilities in 18 CI users and varied whether a semantic cue (presented visually) was available prior to the target sentence (presented auditorily). Results showed that whereas access to a semantic cue generally improved performance with interrupted speech, CI users failed to perceptually restore speech regardless of the semantic cue availability. The lack of restoration in this population directly contradicts previous work in this field and raises questions of whether restoration is possible in CI users. One reason for speech-in-noise understanding difficulty in CI users could be that they are unable to use tools like restoration to process noise-interrupted speech effectively.

SAT0433 TRIAL SIMULATION TO INFORM ENROLLMENT CRITERIA AND OUTCOME MEASURES FOR PRAGMATIC TRIALS IN PsA

Background:

Randomized controlled trials (RCTs) in psoriatic arthritis (PsA) have traditionally enrolled a homogenous subgroup of patients with more polyarticular disease, and the outcome measure used in PsA RCTs (ACR20) may not be ideal to measure differences between two active therapies nor capture change in patients with lower joint counts.

Objectives:

We conducted a simulation study to determine how changing the inclusion criteria and the primary outcome measure would impact the outcome of a future RCT.

Methods:

We used the Tight Control of PsA (TICOPA)1trial to inform simulation of two hypothetical head-to head trials comparing MTX to TNFi with 100 patients per arm. Within TICOPA, we identified MTX and TNFi new users; the visit at drug initiation became the hypothetical trial baseline visit, and the follow up visit was 12 weeks later. These data informed prediction models to simulate enrolled patients. We utilized propensity score-adjusted outcome models to account for potential confounding by indication. Trial 1, modeled after the SEAM-PsA trial,2used typical enrollment criteria (≥3 tender joint count (TJC) and ≥3 swollen joint count (SJC))2; Trial 2 required ≥1 TJC/SJC.1For each trial, five binary outcomes were simulated: ACR20, Disease Activity in PsA (DAPSA), clinical DAPSA (cDAPSA), Routine Assessment of Patient Index Data (RAPID3), and PsA Disease Activity Score (PASDAS), where low disease activity was the cutoff for continuous measures. Each hypothetical trial was simulated 1000 times, and the distribution of estimated effects was summarized using standard summary statistics and graphs.

Results:

Among 188 patients in TICOPA, 179 patients initiated MTX, and 43 patients initiated TNFi within the first 36 weeks. Among these, 107 MTX initiators and 15 TNFi initiators had ≥3 TJC and ≥3 SJC at drug initiation. Baseline characteristics of those in the “severe” (≥3 TJC and ≥3 SJC) and not severe (not meeting ≥3 TJC and ≥3 SJC) are shown in Table 1. Among “severe” patients, the mean probability of achieving ACR20 across simulations was approximately 0.27 in both arms and the observed relative risk (RR) TNFi vs MTX severe cohort across simulations was 1.0, IQR 0.84-1.17 (the RR in the SEAM trial at 24 wks was 1.20, 95%CI:1.05-1.35). In the “full cohort”, the median RR was 1.0, IQR 0.81-1.04. Trials using PASDAS, cDAPSA, and RAPID3 were more likely to differentiate between TNFi and MTX in the severe cohort (figure) but in the full cohort the results favored MTX.

Table 1.

Observed characteristics at drug initiation

Severe (n=148)Not Severe (n=75)MTX (n=127)TNFi (n=21)SMDMTX (n=52)TNFi (n=23)SMDTICOPA Arm (no. (%))Standard Care57 (45%)4 (19%)0.5828 (54%)3 (13%)0.96Intensive Management70 (55%)17 (81%)24 (46%)20 (87%)Female (no. (%))65 (51%)11 (52%)0.0222 (42%)12 (52%)0.20TJC (mean (SD))17.8 (15.3)19.1 (17.3)0.083.5 (4.6)16.4 (19.1)0.93SJC (mean (SD))9.2 (7.4)10.2 (12.1)0.102.4 (3.4)2.2 (2.4)0.05

Severe = ≥3 tender and ≥3 swollen joints

Not-severe = <3 tender or <3 swollen joints

*Pseudo-baseline characteristics were at the time of drug initiation. In cases where the patient started a TNFi between visits, these were the values at the previous visit.

Abbreviations: SMD = standardized mean difference, TJC=tender joint count, SJC=swollen joint count

Conclusion:

Including patients with lower joint counts in an RCT reduced the ability to detect change with therapy. Additionally, among the outcome measures used to detect a difference between two active therapies, PASDAS, cDAPSA, and RAPID3 outperformed ACR20.

References:

[1]Coates et al. Lancet 2015; 2. Mease et al. Arthritis Rheumatol 2019

Figure 1.

Risk Ratios (TNFi vs MTX) by Outcome Across 1000 Simulations

Figure 2.

Risk Differences (TNFi – MTX) by Outcome Across 1000 Simulations

Disclosure of Interests:

Alexis Ogdie Grant/research support from: Pfizer, Novartis, Consultant of: Abbvie, Amgen, BMS, Celgene, Corrona, Janssen, Lilly, Pfizer, Novartis, Sarah Weinstein: None declared, Laura C Coates: None declared, Philip Helliwell: None declared, Alisa Stephens-Shields: None declared

Common Skiing and Snowboarding Injuries

Participation in skiing, and especially snowboarding, continues to rise. As participation and level of competition in these winter sports increases, the number of injuries increases as well. Upper-extremity injuries are more common in snowboarding, whereas lower-extremity injuries are more common in skiing. Head injuries, particularly concussions, are common in both sports. Special consideration in these sports should be given to environmental conditions, such as high altitude and ultraviolet radiation. The purpose of this review is to discuss the most common musculoskeletal injuries seen in skiing and snowboarding, as well as considerations for initial assessment of these injuries and triage to the appropriate level of care. It is important for sports medicine physicians covering these sports to understand initial assessment and treatment of these injuries. Due to the potential for severe injuries in these sports, it is important to be able to quickly recognize an injury that needs to be assessed and treated urgently or emergently. With the increased participation and number of injuries in these sports, it also is important to consider prevention strategies that may minimize risk of injury.

Special symposium issue: slipped capital femoral epiphysis (SCFE)

Up-date on the pathogenesis, epidemiology, pathology, histopathology, clinical findings, diagnosis & classification, imaging modalities and all treatment options in slipped capital femoral epiphysis. This symposium issue of JCO is based on lectures presented at the Pre-Course at the 35th Annual Congress of the European Paediatric Orthopaedic Society (EPOS) in 2016.

Extensibility Characteristics of the Human Cheek: A Pilot Study

Force displacement curves of the cheek in an edentulous area in the maxillary bicuspid-molar region on ten adults evidenced three segments: a power function, a plateau, and an exponential function. The plateau suggested an area in which the cheek could be displaced with no increase in force. The resting force was 1.54 g to 4.61 g. The cheek can be modeled by a fluid-filled double elastic membrane system.

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

Incidental biliary adenofibroma with dysplastic features

We present a case of an incidentally detected cystic liver mass on CT scan, with histology showing biliary epithelium embedded in fibrous stroma and dysplastic features, consistent with an adenofibroma. This is only the third case described in the literature with malignant histology and the first case with angiographic imaging and subsequent management with preoperative embolization prior to surgical resection. We discuss the differential of the imaging findings and the features of this rare entity. Because of the risk of malignant transformation, consideration of this tumour is important to ensure early detection and ultimately resection for improved survival.

Abstract P4-01-08: Effect of bilateral salpingo-oophrectomy on breast MRI fibroglandular volume and background parenchymal enhancement for BRCA 1/2 mutation carriers

PURPOSE: Bilateral salpingo-oophrectomy (BSO) reduces breast cancer risk in women with BRCA1/2 mutations by approximately 50%. Annual screening for these high-risk women includes breast MRI and mammography. It is unknown whether BSO affects fibroglandular volume (FG) and background enhancement (BG) on breast MRI in this population. The purpose of this study is to assess the difference in FG and BG in BRCA1/2 mutation carriers before and after BSO on breast MRI.

METHOD AND MATERIALS: We compared FG and BG on contrast-enhanced breast MRI before and after BSO. Two readers blinded to both clinical and imaging history scored FG according to the BI-RADS criteria from 1–4: fatty, scattered, heterogeneously dense, or extremely dense. BG was graded based on the MRI BI-RADS scale from 1–4: minimal, mild, moderate, and marked. Average BIRADS scores of each reader were used to calculate mean FG and BG (±SD) before and after BSO, and compared using a paired t-test for significance.

RESULTS: We examined 60 women with BRCA1/2 mutations who underwent breast MRI before and after BSO from 2001–2011 at our institution. Five patients were excluded from the final analysis as they underwent mastectomy or bilateral radiation therapy before post-BSO MRI. Mean time to post-BSO MRI was 8.3 months ± 7 months. Mean pre- and post-operative FG were 2.64±0.78 and 2.58±0.75, respectively (p = 0.622). Mean pre- and post-operative BG were 2.46±0.93 and 1.87±0.81, respectively (p = 0.0001). Breast cancer was detected in 8 women at a median time of 3.4 years following BSO. In these 8 women, mean pre- and post-operative FG were 3.10±0.57 and 2.55±0.69, respectively. Mean pre- and post-operative BG were 3.20±0.67 and 2.35±0.71, respectively.

CONCLUSION: In this population of 55 BRCA1/2 mutation carriers who underwent breast MRI before and after BSO, there was a significant reduction in BG following BSO. There was no difference in FG on MRI following BSO. For the 8 patients in this cohort who were diagnosed with breast cancer after BSO, there was a trend toward higher FG and BG both before and after BSO, in comparison to the patients who were not diagnosed with breast cancer, suggesting that rates of higher FG and BG may be associated with increased risk for developing breast cancer.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-01-08.

Ex vivo cryoablation of Wolff-Parkinson-white in a donor heart prior to pediatric heart transplantation

This report describes the use of a donor heart with ventricular pre-excitation for pediatric orthotopic heart transplantation and the successful surgical cryoablation of the donor heart prior to transplantation. The issues related to the preoperative evaluation and surgical management of the donor heart with Wolff-Parkinson White syndrome are discussed.

Ocular and orbital manifestations of the inherited bone marrow failure syndromes: Fanconi anemia and dyskeratosis congenita

PURPOSE

The inherited bone marrow failure syndromes (IBMFS) are a heterogeneous group of genetic disorders that share the inability of the bone marrow to produce an adequate number of blood cells. The 4 most frequent syndromes are Fanconi anemia (FA), dyskeratosis congenita (DC), Diamond-Blackfan anemia (DBA), and Shwachman-Diamond syndrome (SDS). All 4 syndromes have been associated with various physical abnormalities. As part of a genotype/phenotype/cancer susceptibility study, we determined the prevalence of ophthalmic manifestations in these 4 syndromes.

DESIGN

Cross-sectional study of a patient cohort.

PARTICIPANTS

Seventy-five patients with an IBMFS and 121 of their first-degree relatives were seen in the National Eye Institute, National Institutes of Health, from 2001 to 2007. The patient group included 22 with FA, 28 with DC, 19 with DBA, and 6 with SDS.

METHODS

Every participant underwent a complete ophthalmic evaluation and digital facial photography with an adhesive paper ruler on the patient's forehead for an internal measure of scale. Interpupillary distance (IPD), inner canthal distance (ICD), outer canthal distance (OCD), palpebral fissure length (PFL), and corneal diameter (CD) were measured. Thirteen of the 22 patients with FA underwent axial length (AL) measurements by A-scan ultrasonography.

MAIN OUTCOME MEASURES

Type and prevalence of ophthalmic manifestations.

RESULTS

Ninety-five percent of patients with FA had at least 1 abnormal parameter, and 25% of patients had at least 4 abnormal parameters. Eighty-two percent of patients had small palpebral fissures, 69% of patients had simple microphthalmia, 64% of patients had small OCD, 55% of patients had microcornea, 28% of patients had ptosis, and 6% of patients had epicanthal folds. In patients with DC, abnormalities of the lacrimal drainage system (29%) were the most prevalent findings, followed by retinal abnormalities (pigmentary changes, retinal neovascularization, retinal detachment, exudative retinopathy) in 21%, cicatricial entropion with trichiasis and blepharitis in 7% each, and sparse eyelashes and congenital cataract in 3.5% each. No significant ophthalmic abnormalities were seen in patients with DBA or SDS.

CONCLUSIONS

Syndrome-specific ocular findings are associated with FA and DC and may antedate diagnosis of the specific syndrome. Early recognition of these abnormalities is important for optimal management.

HER-2/neu over-expressing DCIS phenotypes and the transition from in situ to invasive breast cancer: implications for breast cancer prevention

Abstract #1161

Background: Prognostically significant invasive breast cancer subtypes, distinguishable through immunohistochemistry for ER, PR and HER-2/neu expression, have recently been identified. The implication of similar phenotypic patterns in ductal carcinoma in situ (DCIS) lesions remains uncertain. The objective of this study was to determine whether DCIS phenotypes are associated with different rates of progression to invasive cancer.&#x2028; Methods: Immunohistochemical staining for ER, PR and HER-2/neu was performed on biopsy and resection specimens from consecutive patients evaluated with DCIS between March 2003 and May 2008. DCIS lesions were characterized as luminal A (ER+ or PR+, HER-2/neu-), luminal B (ER+ or PR+, HER-2/neu+), HER-2/neu positive (ER- and PR-, HER-2/neu+) or basal-like (ER-, PR- and HER-2/neu-). All patients underwent breast MRI and those patients with evidence of invasive disease greater than 1cm in largest dimension were excluded from the analysis. Rates of invasive disease associated with DCIS lesions with different phenotypes were compared using a chi square test. Multivariate logistic regression was used to evaluate the relationship between phenotype and invasion adjusting for patient age, lesion size, nuclear grade, and the presence of comedo necrosis.&#x2028; Results: One hundred and seven patients were included in the analysis. Luminal A was the most common phenotype and accounted for 59% of lesions (63/107). Associated invasive disease was identified in 6 patients with such lesions (10%). The HER-2/neu positive phenotype accounted for 21% of lesions (23/107). Invasive disease was identified in 8 patients with such lesions (35%). Seventeen patients had luminal B DCIS (16%) and 8 of these patients had associated invasive disease (47%). Basal-like lesions were uncommon; only four patients with such lesions were identified. The rates of invasion differed significantly between groups (overall rxc chi square p=0.002). By univariate analysis, the rates of invasion associated with luminal B and HER-2/neu positive phenotypes were significantly higher than the rate of invasion associated with the luminal A phenotype (p&lt;0.001 and p=0.005, respectively). Luminal B DCIS was significantly associated with invasive disease after multivariate adjustment (OR=11.1 p &lt;0.001).&#x2028; Discussion: Invasive foci are more commonly associated with HER-2/neu over-expressing DCIS phenotypes. Moreover, co-expression of HER-2/neu and ER in DCIS lesions is an independent predictor for the presence of associated invasive disease. Novel therapies targeting HER-2/neu in addition to anti-estrogen therapies may, therefore, play a role in breast cancer prevention.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 1161.

Limitations to plasticity of language network reorganization in localization related epilepsy

Neural networks for processing language often are reorganized in patients with epilepsy. However, the extent and location of within and between hemisphere re-organization are not established. We studied 45 patients, all with a left hemisphere seizure focus (mean age 22.8, seizure onset 13.3), and 19 normal controls (mean age 24.8) with an fMRI word definition language paradigm to assess the location of language processing regions. Individual patient SPM maps were compared to the normal group in a voxel-wise comparison; a voxel was considered to be significant if its z-value exceeded mid R:2mid R:. Subsequently, we used principal component analysis with hierarchical clustering of variance patterns from individual difference maps to identify four patient sub-groups. One did not differ from normal controls; one had increased left temporal activation on the margin of regions activated in controls; two others had recruitment in right inferior frontal gyrus, middle frontal gyrus and temporal cortex. Right hemisphere activation in these two groups occurred in homologues of left hemisphere regions that sustained task activation. Our study used novel data driven methods to find evidence for constraints on inter-hemispheric reorganization of language in recruitment of right homologues, and, in a subpopulation of patients, evidence for intra-hemispheric reorganization of language limited to the margins of typical left temporal regional activation. These methods may be applied to investigate both normal and pathological variance in other developmental disorders and cognitive domains.

Prognosis of children with partial epilepsy: MRI and serial 18FDG-PET

OBJECTIVE

To study the evolution of cerebral glucose metabolism after partial seizure onset in children, and its relation to clinical variables.

METHODS

Thirty-eight children had 3.4 +/-.8 (18)FDG-PET scans over 3.0 +/- 1.3 years starting within a year after their third unprovoked partial seizure. (18)FDG-PET was analyzed with a region of interest template to measure normalized metabolism in 12 paired anatomic areas. Scans with absolute asymmetry index, |AI|, greater than 0.13 in at least one cortical region other than the cerebellum were considered abnormal. Standard clinical T1- and T2-weighted MRI (1.5 T) scans were obtained.

RESULTS

Patients with initial normal PET (n = 28) were significantly more likely to remain in good seizure control than those with abnormal initial PET. Patients with initially normal PET scans that became abnormal had longer epilepsy duration before the first PET scan, but not greater seizure frequency, than those with PET always normal. There was no evidence for progression of hypometabolism. Patients with shorter time since last seizure and higher seizure frequency were more likely to have abnormal PET scans. Six of the seven patients whose PET scans were always abnormal had poor seizure control. Febrile seizure history did not affect PET findings. MRI was strongly predictive of initial PET results (chi(2) = 13.1; p < 0.02) but did not predict fluctuation hypometabolism. A model combining MRI and initial PET was strongly predictive of clinical course.

CONCLUSIONS

Initial imaging studies can help predict clinical course for children who have had at least three partial seizures. Serial FDG-PET is affected by seizure frequency and time since last seizure.

Hemorrhagic corpus luteum is associated with ovarian edema

BACKGROUND

Most cases of ovarian edema are thought to result from intermittent ovarian/adnexal torsion. This study describes how, in some cases, this etiology was ruled out even though the edema was unexplained.

STUDY OBJECTIVE

To evaluate the association between ovarian edema and hemorrhagic corpus luteum.

SETTING

Department of gynecology in an urban medical center.

PARTICIPANTS

Five patients admitted to the department of gynecology with a sonographic diagnosis of ovarian edema of unexplained etiology.

RESULTS

Laparoscopy performed on three of five patients in whom a diagnosis of unexplained ovarian edema revealed hemorrhagic corpus luteum and ovarian edema. The remaining two patients displayed typical sonographic imaging of hemorrhagic corpus luteum and ovarian edema and they were managed expectantly. The affected ovaries were between 4.8 and 10 times larger than the unaffected ovaries. During follow-up, the affected ovaries returned to their normal size and appearance.

CONCLUSIONS

Hemorrhagic corpus luteum can cause ovarian edema without interrupting the blood flow supply. The outcome of expectant management without any surgical intervention is the gradual disappearance of the ovarian edema in these patients and the return of ovaries to a normal sonographic appearance.

Adverse effects to quality of life arising from treatment can recover with intermittent androgen suppression in men with prostate cancer

Health-related quality of life (HQOL) research is a means of broadening the assessment of treatment effects. This longitudinal study investigated the dynamic change to quality of life (QOL) and testosterone dependant physiology in men commencing an intermittent maximal androgen blockade program (IMAB). Two hundred and fifty men were accrued to the multi-centre study of IMAB (Flutamide 250 mg TDS, Leuprolide 22.5 mg depot) ceasing treatment after 9 months if PSA <4 ng/ml, and restarting when PSA >20 ng/ml. QOL was assessed every 3 months for 30 months using the EORTC QLQ-C30 and EORTC QLQ-PR25 module. Data completion for the whole study was 90%. At baseline, our cohort was less symptomatic and had better function than the EORTC reference cohort, which may be related to a shift in clinical practice with time. Testosterone suppression (AS) lead to a significant reduction in global HQOL and deterioration in most function and symptom scales. During the off period, there was a trend of progressive improvement in HQOL that paralleled testosterone recovery but was slower than the rate of deterioration during the treatment phase. Maximum recovery of HQOL occurred most frequently by months 9-12. Testosterone recovery was slower and less complete in older men, and lead to concomitant poorer HOQL recovery. Whilst the magnitude of mean change to scale scores was small, there was a consistent and simultaneous deterioration during maximal androgen blockade (MAB) and improvement during androgen recovery. Older men are more likely to show an impaired testosterone recovery, and this was paralleled by a slower HQOL recovery. Newer methods of analysis to describe results in a way that has meaning to the individual patient are warranted.

fMRI language task panel improves determination of language dominance

BACKGROUND

fMRI language tasks reliably identify language areas in presurgical epilepsy patients, but activation using single paradigms may disagree with the intracarotid amobarbital test (IAT).

OBJECTIVE

To determine whether a panel of fMRI tasks targeting different aspects of language processing increases accuracy in determining hemisphere language dominance.

METHODS

Twenty-six patients age 12 to 56 years, predominantly with temporal lobe epilepsy, were studied using whole-brain 1.5 T fMRI (echo planar imaging, blood oxygenation level-dependent) with three task categories using a block design: verbal fluency, reading comprehension, and auditory comprehension. fMRI t maps were visually rated at three thresholds. All patients had assessment of language lateralization by IAT.

RESULTS

fMRI showed left dominance in 21 patients, right dominance in 2, and bilateral activation in 2; raters disagreed over a left vs right bilateral rating in 1 patient. There was full agreement between IAT and fMRI in 21 of 25 patients (IAT failed in 1). In three instances of partial disparity with IAT, the fMRI panel showed consistent findings across raters. Agreement between raters was excellent (partial disagreement in only one patient); the panel of tasks was superior to any single task for interrater agreement (Cramer V 0.93 [range 0.91 to 1.0] vs 0.72 [range 0.60 to 0.86]).

CONCLUSIONS

A panel of fMRI language paradigms may be more accurate for evaluating partial epilepsy patients than a single task. A panel of tasks reduces the likelihood of nondiagnostic findings, improves interrater reliability, and helps confirm language laterality.

Language dominance in partial epilepsy patients identified with an fMRI reading task

BACKGROUND

fMRI language tasks readily identify frontal language areas; temporal activation has been less consistent. No studies have compared clinical visual judgment to quantitative region of interest (ROI) analysis.

OBJECTIVE

To identify temporal language areas in patients with partial epilepsy using a reading paradigm with clinical and ROI interpretation.

METHODS

Thirty patients with temporal lobe epilepsy, aged 8 to 56 years, had 1.5-T fMRI. Patients silently named an object described by a sentence compared to a visual control. Data were analyzed with ROI analysis from t-maps. Regional asymmetry indices (AI) were calculated ([L-R]/[L+R]) and language dominance defined as >0.20. t-Maps were visually rated by three readers at three t thresholds. Twenty-one patients had intracarotid amobarbital test (IAT).

RESULTS

The fMRI reading task provided evidence of language lateralization in 27 of 30 patients with ROI analysis. Twenty-five were left dominant, two right, one bilateral, and two were nondiagnostic; IAT and fMRI agreed in most patients, three had partial agreement, none overtly disagreed. Interrater agreement ranged between 0.77 to 0.82 (Cramer V; p < 0.0001); agreement between visual and ROI reading with IAT was 0.71 to 0.77 (Cramer V; p < 0.0001). Viewing data at lower thresholds added interpretation to 12 patients on visual analysis and 8 with ROI analysis.

CONCLUSIONS

An fMRI reading paradigm can identify language dominance in frontal and temporal areas. Clinical visual interpretation is comparable to quantitative ROI analysis.