Search

Your search keyword '"Fairley, S"' showing total 139 results
Start Over Author "Fairley, S"
139 results on '"Fairley, S"'

1. Protocol Variation in Functional Coronary Angiography Among Patients With Suspected Angina With Non-Obstructive Coronary Arteries: A Nationwide Snapshot of Current Practice Within Australia and New Zealand

Author

Watts, M., Somaratne, J., Farouque, O., Asrress, K., Ko, B., Sheikh, A.R., Ooi, E.L., Scott, P.J., Puri, A., Lambert, B., Yong, A., Ihdayhid, A.R., Singh, K., Ford, T., Turner, S., Al-Omary, M., Lo, S., Arstall, M., Ng, M.K., Khor, L., Van Gaal, W., Elder, A., Layland, J., Beltrame, J.F., Zeitz, C.J., Worthley, M., Lau, J.K., Wing-Lun, E., Adams, H.S.L., Spiro, J., Rajwani, A., rieger, D., Sidharta, S., Montarello, N., Pasupathy, S., Wong, D., Chan, W., Fairley, S., Shetty, P., Spiro, Jon, Ford, Thomas J., Yong, Andy, Zeitz, Chris, and Beltrame, John F.

Published
2024
Full Text
View/download PDF

8. Predictors of Major Adverse Cardiovascular Events: First Report From the Australian-New Zealand Spontaneous Coronary Artery Dissection (ANZ-SCAD) Registry

Author

Dang, Q., Psaltis, P., Burgess, S., Chandrasekhar, J., Mukherjee, S., Kritharides, L., Jepson, N., Fairley, S., Ihdayhid, A., Layland, J., Szirt, R., El-Jack, S., Puri, A., Davis, E., Shiekh, I., Arnold, R., Watts, M., Marathe, J., Bhagwandeen, R., Wing-Lun, E., Bhindi, R., Ford, T., Lo, S., Marschner, S., and Zaman, S.

Published
2024
Full Text
View/download PDF

10. GA4GH: International policies and standards for data sharing across genomic research and healthcare

Author

Rehm, HL, Page, AJH, Smith, L, Adams, JB, Alterovitz, G, Babb, LJ, Barkley, MP, Baudis, M, Beauvais, MJS, Beck, T, Beckmann, JS, Beltran, S, Bernick, D, Bernier, A, Bonfield, JK, Boughtwood, TF, Bourque, G, Bowers, SR, Brookes, AJ, Brudno, M, Brush, MH, Bujold, D, Burdett, T, Buske, OJ, Cabili, MN, Cameron, DL, Carroll, RJ, Casas-Silva, E, Chakravarty, D, Chaudhari, BP, Chen, SH, Cherry, JM, Chung, J, Cline, M, Clissold, HL, Cook-Deegan, RM, Courtot, M, Cunningham, F, Cupak, M, Davies, RM, Denisko, D, Doerr, MJ, Dolman, LI, Dove, ES, Dursi, LJ, Dyke, SOM, Eddy, JA, Eilbeck, K, Ellrott, KP, Fairley, S, Fakhro, KA, Firth, HV, Fitzsimons, MS, Fiume, M, Flicek, P, Fore, IM, Freeberg, MA, Freimuth, RR, Fromont, LA, Fuerth, J, Gaff, CL, Gan, W, Ghanaim, EM, Glazer, D, Green, RC, Griffith, M, Griffith, OL, Grossman, RL, Groza, T, Auvil, JMG, Guigo, R, Gupta, D, Haendel, MA, Hamosh, A, Hansen, DP, Hart, RK, Hartley, DM, Haussler, D, Hendricks-Sturrup, RM, Ho, CWL, Hobb, AE, Hoffman, MM, Hofmann, OM, Holub, P, Hsu, JS, Hubaux, J-P, Hunt, SE, Husami, A, Jacobsen, JO, Jamuar, SS, Janes, EL, Jeanson, F, Jene, A, Johns, AL, Joly, Y, Jones, SJM, Kanitz, A, Kato, K, Keane, TM, Kekesi-Lafrance, K, Kelleher, J, Kerry, G, Khor, S-S, Knoppers, BM, Konopko, MA, Kosaki, K, Kuba, M, Lawson, J, Leinonen, R, Li, S, Lin, MF, Linden, M, Liu, X, Liyanage, IU, Lopez, J, Lucassen, AM, Lukowski, M, Mann, AL, Marshall, J, Mattioni, M, Metke-Jimenez, A, Middleton, A, Milne, RJ, Molnar-Gabor, F, Mulder, N, Munoz-Torres, MC, Nag, R, Nakagawa, H, Nasir, J, Navarro, A, Nelson, TH, Niewielska, A, Nisselle, A, Niu, J, Nyronen, TH, O'Connor, BD, Oesterle, S, Ogishima, S, Wang, VO, Paglione, LAD, Palumbo, E, Parkinson, HE, Philippakis, AA, Pizarro, AD, Prlic, A, Rambla, J, Rendon, A, Rider, RA, Robinson, PN, Rodarmer, KW, Rodriguez, LL, Rubin, AF, Rueda, M, Rushton, GA, Ryan, RS, Saunders, GI, Schuilenburg, H, Schwede, T, Scollen, S, Senf, A, Sheffield, NC, Skantharajah, N, Smith, AV, Sofia, HJ, Spalding, D, Spurdle, AB, Stark, Z, Stein, LD, Suematsu, M, Tan, P, Tedds, JA, Thomson, AA, Thorogood, A, Tickle, TL, Tokunaga, K, Tomroos, J, Torrents, D, Upchurch, S, Valencia, A, Guimera, RV, Vamathevan, J, Varma, S, Vears, DF, Viner, C, Voisin, C, Wagner, AH, Wallace, SE, Walsh, BP, Williams, MS, Winkler, EC, Wold, BJ, Wood, GM, Woolley, JP, Yamasaki, C, Yates, AD, Yung, CK, Zass, LJ, Zaytseva, K, Zhang, J, Goodhand, P, North, K, Birney, E, Rehm, HL, Page, AJH, Smith, L, Adams, JB, Alterovitz, G, Babb, LJ, Barkley, MP, Baudis, M, Beauvais, MJS, Beck, T, Beckmann, JS, Beltran, S, Bernick, D, Bernier, A, Bonfield, JK, Boughtwood, TF, Bourque, G, Bowers, SR, Brookes, AJ, Brudno, M, Brush, MH, Bujold, D, Burdett, T, Buske, OJ, Cabili, MN, Cameron, DL, Carroll, RJ, Casas-Silva, E, Chakravarty, D, Chaudhari, BP, Chen, SH, Cherry, JM, Chung, J, Cline, M, Clissold, HL, Cook-Deegan, RM, Courtot, M, Cunningham, F, Cupak, M, Davies, RM, Denisko, D, Doerr, MJ, Dolman, LI, Dove, ES, Dursi, LJ, Dyke, SOM, Eddy, JA, Eilbeck, K, Ellrott, KP, Fairley, S, Fakhro, KA, Firth, HV, Fitzsimons, MS, Fiume, M, Flicek, P, Fore, IM, Freeberg, MA, Freimuth, RR, Fromont, LA, Fuerth, J, Gaff, CL, Gan, W, Ghanaim, EM, Glazer, D, Green, RC, Griffith, M, Griffith, OL, Grossman, RL, Groza, T, Auvil, JMG, Guigo, R, Gupta, D, Haendel, MA, Hamosh, A, Hansen, DP, Hart, RK, Hartley, DM, Haussler, D, Hendricks-Sturrup, RM, Ho, CWL, Hobb, AE, Hoffman, MM, Hofmann, OM, Holub, P, Hsu, JS, Hubaux, J-P, Hunt, SE, Husami, A, Jacobsen, JO, Jamuar, SS, Janes, EL, Jeanson, F, Jene, A, Johns, AL, Joly, Y, Jones, SJM, Kanitz, A, Kato, K, Keane, TM, Kekesi-Lafrance, K, Kelleher, J, Kerry, G, Khor, S-S, Knoppers, BM, Konopko, MA, Kosaki, K, Kuba, M, Lawson, J, Leinonen, R, Li, S, Lin, MF, Linden, M, Liu, X, Liyanage, IU, Lopez, J, Lucassen, AM, Lukowski, M, Mann, AL, Marshall, J, Mattioni, M, Metke-Jimenez, A, Middleton, A, Milne, RJ, Molnar-Gabor, F, Mulder, N, Munoz-Torres, MC, Nag, R, Nakagawa, H, Nasir, J, Navarro, A, Nelson, TH, Niewielska, A, Nisselle, A, Niu, J, Nyronen, TH, O'Connor, BD, Oesterle, S, Ogishima, S, Wang, VO, Paglione, LAD, Palumbo, E, Parkinson, HE, Philippakis, AA, Pizarro, AD, Prlic, A, Rambla, J, Rendon, A, Rider, RA, Robinson, PN, Rodarmer, KW, Rodriguez, LL, Rubin, AF, Rueda, M, Rushton, GA, Ryan, RS, Saunders, GI, Schuilenburg, H, Schwede, T, Scollen, S, Senf, A, Sheffield, NC, Skantharajah, N, Smith, AV, Sofia, HJ, Spalding, D, Spurdle, AB, Stark, Z, Stein, LD, Suematsu, M, Tan, P, Tedds, JA, Thomson, AA, Thorogood, A, Tickle, TL, Tokunaga, K, Tomroos, J, Torrents, D, Upchurch, S, Valencia, A, Guimera, RV, Vamathevan, J, Varma, S, Vears, DF, Viner, C, Voisin, C, Wagner, AH, Wallace, SE, Walsh, BP, Williams, MS, Winkler, EC, Wold, BJ, Wood, GM, Woolley, JP, Yamasaki, C, Yates, AD, Yung, CK, Zass, LJ, Zaytseva, K, Zhang, J, Goodhand, P, North, K, and Birney, E

Abstract

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.

Published
2021

11. How Do Music Activities Affect Health and Well-Being? A Scoping Review of Studies Examining Psychosocial Mechanisms

Author

Dingle, GA, Sharman, LS, Bauer, Z, Beckman, E, Broughton, M, Bunzli, E, Davidson, R, Draper, G, Fairley, S, Farrell, C, Flynn, LM, Gomersall, S, Hong, M, Larwood, J, Lee, C, Lee, J, Nitschinsk, L, Peluso, N, Reedman, SE, Vidas, D, Walter, ZC, Wright, ORL, Dingle, GA, Sharman, LS, Bauer, Z, Beckman, E, Broughton, M, Bunzli, E, Davidson, R, Draper, G, Fairley, S, Farrell, C, Flynn, LM, Gomersall, S, Hong, M, Larwood, J, Lee, C, Lee, J, Nitschinsk, L, Peluso, N, Reedman, SE, Vidas, D, Walter, ZC, and Wright, ORL

Abstract

Background: This scoping review analyzed research about how music activities may affect participants' health and well-being. Primary outcomes were measures of health (including symptoms and health behaviors) and well-being. Secondary measures included a range of psychosocial processes such as arousal, mood, social connection, physical activation or relaxation, cognitive functions, and identity. Diverse music activities were considered: receptive and intentional music listening; sharing music; instrument playing; group singing; lyrics and rapping; movement and dance; and songwriting, composition, and improvisation. Methods: Nine databases were searched with terms related to the eight music activities and the psychosocial variables of interest. Sixty-three papers met selection criteria, representing 6,975 participants of all ages, nationalities, and contexts. Results: Receptive and intentional music listening were found to reduce pain through changes in physiological arousal in some studies but not others. Shared music listening (e.g., concerts or radio programs) enhanced social connections and mood in older adults and in hospital patients. Music listening and carer singing decreased agitation and improved posture, movement, and well-being of people with dementia. Group singing supported cognitive health and well-being of older adults and those with mental health problems, lung disease, stroke, and dementia through its effects on cognitive functions, mood, and social connections. Playing a musical instrument was associated with improved cognitive health and well-being in school students, older adults, and people with mild brain injuries via effects on motor, cognitive and social processes. Dance and movement with music programs were associated with improved health and well-being in people with dementia, women with postnatal depression, and sedentary women with obesity through various cognitive, physical, and social processes. Rapping, songwriting, and composition help

Published
2021

15. Ensembl 2009

Author

Hubbard, T. J. P., Aken, B. L., Ayling, S., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Clarke, L., Coates, G., Fairley, S., Fitzgerald, S., Fernandez-Banet, J., Gordon, L., Graf, S., Haider, S., Hammond, M., Holland, R., Howe, K., Jenkinson, A., Johnson, N., Kahari, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Kulesha, E., Lawson, D., Longden, I., Megy, K., Meidl, P., Overduin, B., Parker, A., Pritchard, B., Rios, D., Schuster, M., Slater, G., Smedley, D., Spooner, W., Spudich, G., Trevanion, S., Vilella, A., Vogel, J., White, S., Wilder, S., Zadissa, A., Birney, E., Cunningham, F., Curwen, V., Durbin, R., Fernandez-Suarez, X. M., Herrero, J., Kasprzyk, A., Proctor, G., Smith, J., Searle, S., and Flicek, P.

Published
2009

16. The Effects of Common Structural Variants on {3D} Chromatin Structure

Author

Shanta, O., Noor, A., Sebat, J., Chaisson, M., Sanders, A., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E., Rodriguez, O., Guo, L., Collins, R., Fan, X., Wen, J., Handsaker, R., Fairley, S., Kronenberg, Z., Kong, X., Hormozdiari, F., Lee, D., Wenger, A., Hastie, A., Antaki, D., Anantharaman, T., Audano, P., Brand, H., Cantsilieris, S., Cao, H., Cerveira, E., Chen, C., Chen, X., Chin, C., Chong, Z., Chuang, N., Lambert, C., Church, D., Clarke, L., Farrell, A., Flores, J., Galeey, T., Gujral, M., Guryev, V., Heaton, W., Korlach, J., Kumar, S., Kwon, J., Lam, E., Lee, J., Lee, W., Lee, S., Li, S., Marks, P., Viaud-Martinez, K., Meiers, S., Munson, K., Navarro, F., Nelson, B., Nodzak, C., Kyriazopoulou-Panagiotopoulou, S., Pang, A., Rosanio, G., Ryan, M., Stuetz, A., Spierings, D., Ward, A., Welch, A., Xiao, M., Xu, W., Zhang, C., Zhu, Q., Zheng-Bradley, X., Lowy, E., Yakneen, S., McCarroll, S., Jun, G., Ding, L., Koh, C., Flicek, P., Chen, K., Gerstein, M., Kwok, P., Lansdorp, P., Marth, G., Shi, X., Bashir, A., Ye, K., Devine, S., Talkowski, M., Mills, R., Marschall, T., Korbel, J., Eichler, E., Lee, C., HGSVC, Intelligent Systems, Groningen Research Institute for Asthma and COPD (GRIAC), Stem Cell Aging Leukemia and Lymphoma (SALL), and Damage and Repair in Cancer Development and Cancer Treatment (DARE)

Subjects
Cancer Research, DOMAINS, lcsh:QH426-470, CFHR1, lcsh:Biotechnology, Population, Biology, Genome, Structural variation, Chromosome conformation capture, Deletion, 03 medical and health sciences, 0302 clinical medicine, Hi-C, lcsh:TP248.13-248.65, Cell Line, Tumor, Genetics, TAD fusion, Chromosomes, Human, Humans, 1000 Genomes Project, education, Gene, 030304 developmental biology, Sequence Deletion, 0303 health sciences, education.field_of_study, Sequence Inversion, Breakpoint, Inversion, TAD, Chromatin Assembly and Disassembly, Chromatin, GENOME, lcsh:Genetics, Enhancer Elements, Genetic, Genomic Structural Variation, Linear Models, 030217 neurology & neurosurgery, Biotechnology, Research Article
Abstract

Background Three-dimensional spatial organization of chromosomes is defined by highly self-interacting regions 0.1–1 Mb in size termed Topological Associating Domains (TADs). Genetic factors that explain dynamic variation in TAD structure are not understood. We hypothesize that common structural variation (SV) in the human population can disrupt regulatory sequences and thereby influence TAD formation. To determine the effects of SVs on 3D chromatin organization, we performed chromosome conformation capture sequencing (Hi-C) of lymphoblastoid cell lines from 19 subjects for which SVs had been previously characterized in the 1000 genomes project. We tested the effects of common deletion polymorphisms on TAD structure by linear regression analysis of nearby quantitative chromatin interactions (contacts) within 240 kb of the deletion, and we specifically tested the hypothesis that deletions at TAD boundaries (TBs) could result in large-scale alterations in chromatin conformation. Results Large (> 10 kb) deletions had significant effects on long-range chromatin interactions. Deletions were associated with increased contacts that span the deleted region and this effect was driven by large deletions that were not located within a TAD boundary (nonTB). Some deletions at TBs, including a 80 kb deletion of the genes CFHR1 and CFHR3, had detectable effects on chromatin contacts. However for TB deletions overall, we did not detect a pattern of effects that was consistent in magnitude or direction. Large inversions in the population had a distinguishable signature characterized by a rearrangement of contacts that span its breakpoints. Conclusions Our study demonstrates that common SVs in the population impact long-range chromatin structure, and deletions and inversions have distinct signatures. However, the effects that we observe are subtle and variable between loci. Genome-wide analysis of chromatin conformation in large cohorts will be needed to quantify the influence of common SVs on chromatin structure.

Published
2020

19. Alignment of 1000 Genomes Project reads to reference assembly GRCh38

Author

Zheng-Bradley, X., Streeter, I., Fairley, S., Richardson, D., Clarke, L., Flicek, P., 1000 Genomes Project , C., and Timmermann, B.

Subjects
0301 basic medicine, European Nucleotide Archive, Computer science, read mapping, Health Informatics, Computational biology, Data Note, Genome, 03 medical and health sciences, Contig Mapping, 0302 clinical medicine, Human Genome Project, Humans, 1000 Genomes Project, reference genome, Sequence (medicine), Information retrieval, Contig, Whole Genome Sequencing, alignment, Reference Standards, Short read, Computer Science Applications, 030104 developmental biology, 030220 oncology & carcinogenesis, sequence reads, GRCh38, Sequence Alignment, Project analysis, Algorithms, Reference genome
Abstract

The 1000 Genomes Project produced more than 100 trillion basepairs of short read sequence from more than 2600 samples in 26 populations over a period of five years. In its final phase, the project released over 85 million genotyped and phased variants on human reference genome assembly GRCh37. An updated reference assembly, GRCh38, was released in late 2013, but there was insufficient time for the final phase of the project analysis to change to the new assembly. Although it is possible to lift the coordinates of the 1000 Genomes Project variants to the new assembly, this is a potentially error-prone process as coordinate remapping is most appropriate only for non-repetitive regions of the genome and those that did not see significant change between the two assemblies. It will also miss variants in any region that was newly added to GRCh38. Thus, to produce the highest quality variants and genotypes on GRCh38, the best strategy is to realign the reads and recall the variants based on the new alignment. As the first step of variant calling for the 1000 Genomes Project data, we have finished remapping all of the 1000 Genomes sequence reads to GRCh38 with alternative scaffold–aware BWA-MEM. The resulting alignments are available as CRAM, a reference-based sequence compression format. The data have been released on our FTP site and are also available from European Nucleotide Archive to facilitate researchers discovering variants on the primary sequences and alternative contigs of GRCh38.

Published
2017

20. Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project

Author

Lowy-Gallego, E., Fairley, S., Zheng-Bradley, X., Ruffier, M., Clarke, L., Flicek, P., 1000 Genomes Project , C., and Timmermann, B.

Subjects
single nucleotide variation, 0303 health sciences, Computer science, variant calling, population genetics, Medicine (miscellaneous), Genomics, Computational biology, Articles, Data Note, General Biochemistry, Genetics and Molecular Biology, Set (abstract data type), Data set, variant discovery, 03 medical and health sciences, Resource (project management), 0302 clinical medicine, Benchmark (computing), 1000 Genomes Project, Indel, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

We present a set of biallelic SNVs and INDELs, from 2,548 samples spanning 26 populations from the 1000 Genomes Project, called de novo on GRCh38. We believe this will be a useful reference resource for those using GRCh38. It represents an improvement over the “lift-overs” of the 1000 Genomes Project data that have been available to date by encompassing all of the GRCh38 primary assembly autosomes and pseudo-autosomal regions, including novel, medically relevant loci. Here, we describe how the data set was created and benchmark our call set against that produced by the final phase of the 1000 Genomes Project on GRCh37 and the lift-over of that data to GRCh38.

Published
2019
Full Text
View/download PDF

21. Ensembl 2011

Author

Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gordon, L., Hendrix, M., Hourlier, T., Johnson, N., Kahari, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Kulesha, E., Larsson, P., Longden, I., McLaren, W., Overduin, B., Pritchard, B., Riat, H. S., Rios, D., Ritchie, G. R. S., Ruffier, M., Schuster, M., Sobral, D., Spudich, G., Tang, Y. A., Trevanion, S., Vandrovcova, J., Vilella, A. J., White, S., Wilder, S. P., Zadissa, A., Zamora, J., Aken, B. L., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernandez-Suarez, X. M., Herrero, J., Hubbard, T. J. P., Parker, A., Proctor, G., Vogel, J., and Searle, S. M. J.

Subjects
0303 health sciences, Genetic Variation, Molecular Sequence Annotation, Articles, Genomics, Regulatory Sequences, Nucleic Acid, Rats, Mice, 03 medical and health sciences, 0302 clinical medicine, Databases, Genetic, Genetics, Animals, Humans, Software, Zebrafish, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.

Published
2010
Full Text
View/download PDF

29. Ensembl 2012

Author

Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gil, L., Gordon, L., Hendrix, M., Hourlier, T., Johnson, N., Kahari, A. K., Keefe, D., Keenan, S., Kinsella, R., Komorowska, M., Koscielny, G., Kulesha, E., Larsson, P., Longden, I., McLaren, W., Muffato, M., Overduin, B., Pignatelli, M., Pritchard, B., Riat, H. S., Ritchie, G. R. S., Ruffier, M., Schuster, M., Sobral, D., Tang, Y. A., Taylor, K., Trevanion, S., Vandrovcova, J., White, S., Wilson, M., Wilder, S. P., Aken, B. L., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernandez-Suarez, X. M., Harrow, J., Herrero, J., Hubbard, T. J. P., Parker, A., Proctor, G., Spudich, G., Vogel, J., Yates, A., Zadissa, A., and Searle, S. M. J.

Subjects
0303 health sciences, Genetic Variation, Molecular Sequence Annotation, Genomics, Articles, Rats, 03 medical and health sciences, Mice, 0302 clinical medicine, Gene Expression Regulation, Databases, Genetic, Genetics, Animals, Humans, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human genome data as well as data for key model organisms such as mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) and Tasmanian devil (Sarcophilus harrisii) bringing the total number of supported species to 61 as of Ensembl release 64 (September 2011). Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project.

Published
2011

30. Ensembl 2009

Author

Hubbard, T J P, Aken, B L, Ayling, S, Ballester, Benoit, Beal, K, Bragin, E, Brent, S, Chen, Y, Clapham, P, Clarke, L, Coates, G, Fairley, S, Fitzgerald, S, Fernandez-Banet, J, Gordon, L, Graf, S, Haider, S, Hammond, M, Holland, R, Howe, K, Jenkinson, A, Johnson, N, Kahari, A, Keefe, D, Keenan, S, Kinsella, R, Kokocinski, F, Kulesha, E, Lawson, D, Longden, I, Megy, K, Meidl, P, Overduin, B, Parker, A, Pritchard, B, Rios, D, Schuster, M, Slater, G, Smedley, D, Spooner, W, Spudich, G, Trevanion, S, Vilella, A, Vogel, J, White, S, Wilder, S, Zadissa, A, Birney, E, Cunningham, F, Curwen, V, Durbin, R, Fernandez-Suarez, X M, Herrero, J, Kasprzyk, A, Proctor, G, Smith, J, Searle, S, Flicek, P, and Spinelli, Lionel

Subjects
[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

no abstract

Published
2009

31. The effect of English job titles in job advertisements on Dutch respondents

Author

Meurs, F. van, Korzilius, H.P.L.M., Planken, B.C., and Fairley, S

Subjects
Professional Communication, Organizational Cybernetics
Abstract

Contains fulltext : 44819.pdf (Publisher’s version ) (Closed access) This paper reports on a study that tested the effect on Dutch respondents of using English in job titles. One half of the respondents evaluated five English job titles, and the other half evaluated the equivalent Dutch job titles. The results of the experiment support claims about the effect of English in job titles in the Netherlands and other non-English-speaking countries which had not previously been tested experimentally. In those cases where there were statistically significant differences, English job titles were evaluated worse than their Dutch counterparts, while jobs with English titles were assessed more positively, were thought to have higher salaries, and were on the whole considered to be more international. Contrary to what is suggested in the literature, where there were significant differences, jobs with English titles were not considered more gender-neutral, but in fact were perceived to be more male-oriented than their Dutch equivalents. Although no statistically significant differences were found between the associations evoked by equivalent English and Dutch job titles, our findings support the hypothesis, formulated with respect to English in advertising in non-English-speaking countries, that English words do not just have referential meaning but also carry symbolic value. 17 p.

Published
2007

34. Analyses of pig genomes provide insight into porcine demography and evolution

Author

Groenen, M. A., Archibald, A. L., Uenishi, H., Tuggle, C. K., Takeuchi, Y., Rothschild, M. F., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H. J., Li, S., Larkin, D. M., Kim, H., Frantz, L. A., Caccamo, M., Ahn, H., Aken, B. L., Anselmo, A., Anthon, C., Auvil, L., Badaoui, B., Beattie, C. W., Bendixen, C., Berman, D., Blecha, F., Blomberg, Jonas, Bolund, L., Bosse, M., Botti, S., Bujie, Z., Byström, M., Capitanu, B., Carvalho-Silva, D., Chardon, P., Chen, C., Cheng, R., Choi, S. H., Chow, W., Clark, R. C., Clee, C., Crooijmans, R. P., Dawson, H. D., Dehais, P., De Sapio, F., Dibbits, B., Drou, N., Du, Z. Q., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G. J., Fowler, K. E., Fredholm, M., Fritz, E., Gilbert, J. G., Giuffra, E., Gorodkin, J., Griffin, D. K., Harrow, J. L., Hayward, Alexander, Howe, K., Hu, Z. L., Humphray, S. J., Hunt, T., Hornshoj, H., Jeon, J. T., Jern, Patric, Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Kim, J., Kim, J. H., Kim, K. W., Kim, T. H., Larson, G., Lee, K., Lee, K. T., Leggett, R., Lewin, H. A., Li, Y., Liu, W., Loveland, J. E., Lu, Y., Lunney, J. K., Ma, J., Madsen, O., Mann, K., Matthews, L., McLaren, S., Morozumi, T., Murtaugh, M. P., Narayan, J., Nguyen, D. T., Ni, P., Oh, S. J., Onteru, S., Panitz, F., Park, E. W., Park, H. S., Pascal, G., Paudel, Y., Perez-Enciso, M., Ramirez-Gonzalez, R., Reecy, J. M., Rodriguez-Zas, S., Rohrer, G. A., Rund, L., Sang, Y., Schachtschneider, K., Schraiber, J. G., Schwartz, J., Scobie, L., Scott, C., Searle, S., Servin, B., Southey, B. R., Sperber, Göran, Stadler, P., Sweedler, J. V., Tafer, H., Thomsen, B., Wali, R., Wang, J., White, S., Xu, X., Yerle, M., Zhang, G., Zhang, J., Zhao, S., Rogers, J., Churcher, C., Schook, L. B., Groenen, M. A., Archibald, A. L., Uenishi, H., Tuggle, C. K., Takeuchi, Y., Rothschild, M. F., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H. J., Li, S., Larkin, D. M., Kim, H., Frantz, L. A., Caccamo, M., Ahn, H., Aken, B. L., Anselmo, A., Anthon, C., Auvil, L., Badaoui, B., Beattie, C. W., Bendixen, C., Berman, D., Blecha, F., Blomberg, Jonas, Bolund, L., Bosse, M., Botti, S., Bujie, Z., Byström, M., Capitanu, B., Carvalho-Silva, D., Chardon, P., Chen, C., Cheng, R., Choi, S. H., Chow, W., Clark, R. C., Clee, C., Crooijmans, R. P., Dawson, H. D., Dehais, P., De Sapio, F., Dibbits, B., Drou, N., Du, Z. Q., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G. J., Fowler, K. E., Fredholm, M., Fritz, E., Gilbert, J. G., Giuffra, E., Gorodkin, J., Griffin, D. K., Harrow, J. L., Hayward, Alexander, Howe, K., Hu, Z. L., Humphray, S. J., Hunt, T., Hornshoj, H., Jeon, J. T., Jern, Patric, Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Kim, J., Kim, J. H., Kim, K. W., Kim, T. H., Larson, G., Lee, K., Lee, K. T., Leggett, R., Lewin, H. A., Li, Y., Liu, W., Loveland, J. E., Lu, Y., Lunney, J. K., Ma, J., Madsen, O., Mann, K., Matthews, L., McLaren, S., Morozumi, T., Murtaugh, M. P., Narayan, J., Nguyen, D. T., Ni, P., Oh, S. J., Onteru, S., Panitz, F., Park, E. W., Park, H. S., Pascal, G., Paudel, Y., Perez-Enciso, M., Ramirez-Gonzalez, R., Reecy, J. M., Rodriguez-Zas, S., Rohrer, G. A., Rund, L., Sang, Y., Schachtschneider, K., Schraiber, J. G., Schwartz, J., Scobie, L., Scott, C., Searle, S., Servin, B., Southey, B. R., Sperber, Göran, Stadler, P., Sweedler, J. V., Tafer, H., Thomsen, B., Wali, R., Wang, J., White, S., Xu, X., Yerle, M., Zhang, G., Zhang, J., Zhao, S., Rogers, J., Churcher, C., and Schook, L. B.

Abstract

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

Published
2012
Full Text
View/download PDF

35. Analyses of pig genomes provide insight into porcine demography and evolution

Author

Groenen, MAM, Archibald, AL, Uenishi, H, Tuggle, CK, Takeuchi, Y, Rothschild, MF, Rogel-Gaillard, C, Park, C, Milan, D, Megens, H-J, Li, S, Larkin, DM, Kim, H, Frantz, LAF, Caccamo, M, Ahn, H, Aken, BL, Anselmo, A, Anthon, C, Auvil, L, Badaoui, B, Beattie, CW, Bendixen, C, Berman, D, Blecha, F, Blomberg, J, Bolund, L, Bosse, M, Botti, S, Zhan, B, Bystrom, M, Capitanu, B, Carvalho-Silva, D, Chardon, P, Chen, C, Cheng, R, Choi, S-H, Chow, W, Clark, RC, Clee, C, Crooijmans, RPMA, Dawson, HD, Dehais, P, De Sapio, F, Dibbits, B, Drou, N, Du, Z-Q, Eversole, K, Fadista, J, Fairley, S, Faraut, T, Faulkner, GJ, Fowler, KE, Fredholm, M, Fritz, E, Gilbert, JGR, Giuffra, E, Gorodkin, J, Griffin, DK, Harrow, JL, Hayward, A, Howe, K, Hu, Z-L, Humphray, SJ, Hunt, T, Hornshoj, H, Jeon, J-T, Jern, P, Jones, M, Jurka, J, Kanamori, H, Kapetanovic, R, Kim, J, Kim, J-H, Kim, K-W, Kim, T-H, Larson, G, Lee, K, Lee, K-T, Leggett, R, Lewin, HA, Li, Y, Liu, W, Loveland, JE, Lu, Y, Lunney, JK, Ma, J, Madsen, O, Mann, K, Matthews, L, McLaren, S, Morozumi, T, Murtaugh, MP, Narayan, J, Dinh, TN, Ni, P, Oh, S-J, Onteru, S, Panitz, F, Park, E-W, Park, H-S, Pascal, G, Paudel, Y, Perez-Enciso, M, Ramirez-Gonzalez, R, Reecy, JM, Rodriguez-Zas, S, Rohrer, GA, Rund, L, Sang, Y, Schachtschneider, K, Schraiber, JG, Schwartz, J, Scobie, L, Scott, C, Searle, S, Servin, B, Southey, BR, Sperber, G, Stadler, P, Sweedler, JV, Tafer, H, Thomsen, B, Wali, R, Wang, J, White, S, Xu, X, Yerle, M, Zhang, G, Zhang, J, Zhao, S, Rogers, J, Churcher, C, Schook, LB, Groenen, MAM, Archibald, AL, Uenishi, H, Tuggle, CK, Takeuchi, Y, Rothschild, MF, Rogel-Gaillard, C, Park, C, Milan, D, Megens, H-J, Li, S, Larkin, DM, Kim, H, Frantz, LAF, Caccamo, M, Ahn, H, Aken, BL, Anselmo, A, Anthon, C, Auvil, L, Badaoui, B, Beattie, CW, Bendixen, C, Berman, D, Blecha, F, Blomberg, J, Bolund, L, Bosse, M, Botti, S, Zhan, B, Bystrom, M, Capitanu, B, Carvalho-Silva, D, Chardon, P, Chen, C, Cheng, R, Choi, S-H, Chow, W, Clark, RC, Clee, C, Crooijmans, RPMA, Dawson, HD, Dehais, P, De Sapio, F, Dibbits, B, Drou, N, Du, Z-Q, Eversole, K, Fadista, J, Fairley, S, Faraut, T, Faulkner, GJ, Fowler, KE, Fredholm, M, Fritz, E, Gilbert, JGR, Giuffra, E, Gorodkin, J, Griffin, DK, Harrow, JL, Hayward, A, Howe, K, Hu, Z-L, Humphray, SJ, Hunt, T, Hornshoj, H, Jeon, J-T, Jern, P, Jones, M, Jurka, J, Kanamori, H, Kapetanovic, R, Kim, J, Kim, J-H, Kim, K-W, Kim, T-H, Larson, G, Lee, K, Lee, K-T, Leggett, R, Lewin, HA, Li, Y, Liu, W, Loveland, JE, Lu, Y, Lunney, JK, Ma, J, Madsen, O, Mann, K, Matthews, L, McLaren, S, Morozumi, T, Murtaugh, MP, Narayan, J, Dinh, TN, Ni, P, Oh, S-J, Onteru, S, Panitz, F, Park, E-W, Park, H-S, Pascal, G, Paudel, Y, Perez-Enciso, M, Ramirez-Gonzalez, R, Reecy, JM, Rodriguez-Zas, S, Rohrer, GA, Rund, L, Sang, Y, Schachtschneider, K, Schraiber, JG, Schwartz, J, Scobie, L, Scott, C, Searle, S, Servin, B, Southey, BR, Sperber, G, Stadler, P, Sweedler, JV, Tafer, H, Thomsen, B, Wali, R, Wang, J, White, S, Xu, X, Yerle, M, Zhang, G, Zhang, J, Zhao, S, Rogers, J, Churcher, C, and Schook, LB

Abstract

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

Published
2012

36. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Author

Renfree, MB, Papenfuss, AT, Deakin, JE, Lindsay, J, Heider, T, Belov, K, Rens, W, Waters, PD, Pharo, EA, Shaw, G, Wong, ESW, Lefèvre, CM, Nicholas, KR, Kuroki, Y, Wakefield, MJ, Zenger, KR, Wang, C, Ferguson-Smith, M, Nicholas, FW, Hickford, D, Yu, H, Short, KR, Siddle, HV, Frankenberg, SR, Chew, KY, Menzies, BR, Stringer, JM, Suzuki, S, Hore, TA, Delbridge, ML, Mohammadi, A, Schneider, NY, Hu, Y, O'Hara, W, Al Nadaf, S, Wu, C, Feng, ZP, Cocks, BG, Wang, J, Flicek, P, Searle, SMJ, Fairley, S, Beal, K, Herrero, J, Carone, DM, Suzuki, Y, Sugano, S, Toyoda, A, Sakaki, Y, Kondo, S, Nishida, Y, Tatsumoto, S, Mandiou, I, Hsu, A, McColl, KA, Lansdell, B, Weinstock, G, Kuczek, E, McGrath, A, Wilson, P, Men, A, Hazar-Rethinam, M, Hall, A, Davis, J, Wood, D, Williams, S, Sundaravadanam, Y, Muzny, DM, Jhangiani, SN, Lewis, LR, Morgan, MB, Okwuonu, GO, Ruiz, SJ, Santibanez, J, Nazareth, L, Cree, A, Fowler, G, Kovar, CL, Dinh, HH, Joshi, V, Jing, C, Lara, F, Thornton, R, Chen, L, Deng, J, Liu, Y, Shen, JY, Song, XZ, Edson, J, Troon, C, Thomas, D, Stephens, A, Yapa, L, Levchenko, T, Gibbs, RA, Cooper, DW, Speed, TP, Fujiyama, A, M Graves, JA, O'Neill, RJ, Renfree, MB, Papenfuss, AT, Deakin, JE, Lindsay, J, Heider, T, Belov, K, Rens, W, Waters, PD, Pharo, EA, Shaw, G, Wong, ESW, Lefèvre, CM, Nicholas, KR, Kuroki, Y, Wakefield, MJ, Zenger, KR, Wang, C, Ferguson-Smith, M, Nicholas, FW, Hickford, D, Yu, H, Short, KR, Siddle, HV, Frankenberg, SR, Chew, KY, Menzies, BR, Stringer, JM, Suzuki, S, Hore, TA, Delbridge, ML, Mohammadi, A, Schneider, NY, Hu, Y, O'Hara, W, Al Nadaf, S, Wu, C, Feng, ZP, Cocks, BG, Wang, J, Flicek, P, Searle, SMJ, Fairley, S, Beal, K, Herrero, J, Carone, DM, Suzuki, Y, Sugano, S, Toyoda, A, Sakaki, Y, Kondo, S, Nishida, Y, Tatsumoto, S, Mandiou, I, Hsu, A, McColl, KA, Lansdell, B, Weinstock, G, Kuczek, E, McGrath, A, Wilson, P, Men, A, Hazar-Rethinam, M, Hall, A, Davis, J, Wood, D, Williams, S, Sundaravadanam, Y, Muzny, DM, Jhangiani, SN, Lewis, LR, Morgan, MB, Okwuonu, GO, Ruiz, SJ, Santibanez, J, Nazareth, L, Cree, A, Fowler, G, Kovar, CL, Dinh, HH, Joshi, V, Jing, C, Lara, F, Thornton, R, Chen, L, Deng, J, Liu, Y, Shen, JY, Song, XZ, Edson, J, Troon, C, Thomas, D, Stephens, A, Yapa, L, Levchenko, T, Gibbs, RA, Cooper, DW, Speed, TP, Fujiyama, A, M Graves, JA, and O'Neill, RJ

Abstract

Background: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development.Results: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements.Conclusions: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution. © 2011 Renfree et al.; licensee BioMed Central Ltd.

Published
2011

38. Transfer of fixation using affine structure: Extending the analysis to stereo

Author

Fairley, S, Reid, I, and Murray, D

Subjects
genetic structures, ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION
Abstract

This paper describes an algorithm for maintaining fixation upon a 3D body-centred point using 3D affine transfer, extending an earlier monocular method to stereo cameras. Transfer is based on corners detected in the image and matched over time and in stereo. The paper presents a method using all available matched data, providing immunity to noise and poor conditioning. The algorithm, implemented at video rates on a multi-processor machine, incorporates controlled degradation in the presence of insufficient data. Results are given from experiments using a four-axis active stereo camera platform, first which show the greater stability of the fixation point over the monocular method, both as it appears in the image and occurs in the scene; and, secondly, which show the recovery and evolution of 3D affine structure during fixation. It is shown that fixation and explicit structure recovery can occur separately, allowing the information required for gaze control to be computed in a fixed time.

Published
1998

40. Poster session IV * Friday 10 December 2010, 14:00-18:00

Author

Mora, B., primary, Base, E., additional, Schmid, W., additional, Andreas, M., additional, Weber, U., additional, Junreitmaier, M., additional, Foerster, F., additional, Hiesmayr, M., additional, Tschernich, H. D., additional, Guldbrand, D., additional, Goetzsche, O., additional, Eika, B., additional, Fumagalli, S., additional, Francini, S., additional, Gabbai, D., additional, Pedri, S., additional, Casalone Rinaldi, M., additional, Makhanian, Y., additional, Sollami, R., additional, Tarantini, F., additional, Marchionni, N., additional, Azcarate, P. M., additional, Castano, S., additional, Rodriguez-Manero, M., additional, Arraiza, M., additional, Levy, B., additional, Barba, J., additional, Rabago, G., additional, Bastarrika, G., additional, Rus, H., additional, Radoi, M., additional, Ciurea, C., additional, Boda, D., additional, Erdei, T., additional, Denes, M., additional, Mihalcz, A., additional, Kardos, A., additional, Foldesi, C. S., additional, Temesvari, A., additional, Lengyel, M., additional, Cameli, M., additional, Lisi, M., additional, Righini, F., additional, Ballo, P., additional, Henein, M., additional, Mondillo, S., additional, Nistri, S., additional, Galderisi, M., additional, Ballo, P. C., additional, Pagliani, L., additional, Olivotto, I., additional, Santoro, A., additional, Papesso, B., additional, Innelli, P., additional, Cecchi, F., additional, Hristova, K., additional, Katova, T. Z., additional, Kostova, V., additional, Simova, Y., additional, Nesheva, N., additional, Ivanovic, B., additional, Tadic, M. T., additional, Simic, D. S., additional, Rao, C. M., additional, Aguglia, D., additional, Casciola, G., additional, Imbesi, C., additional, Marvelli, A., additional, Sgro, M., additional, Benedetto, D., additional, Tripepi, G., additional, Zoccali, C., additional, Benedetto, F. A., additional, Mantziari, L., additional, Kamperidis, V., additional, Damvopoulou, E., additional, Ventoulis, I., additional, Giannakoulas, G., additional, Paraskevaidis, S., additional, Vassilikos, V., additional, Karvounis, H., additional, Styliadis, I. H., additional, Sonder, T. K., additional, Loegstrup, B. B., additional, Lambrechtsen, J., additional, Van Bortel, L. M., additional, Segers, P., additional, Egstrup, K., additional, Tho, A., additional, Moceri, P., additional, Bertora, D., additional, Gibelin, P., additional, Cho, E. J., additional, Choi, K. Y., additional, Kim, B. J., additional, Kim, D. B., additional, Jang, S. W., additional, Park, C. S., additional, Jung, H. O., additional, Jeon, H. K., additional, Youn, H. J., additional, Kim, J. H., additional, Donal, E., additional, Coquerel, N., additional, Bodi, S., additional, Thebault, C., additional, Kervio, G., additional, Carre, F., additional, Daly, M. J., additional, Fairley, S. L., additional, Doherty, R., additional, Ashfield, K., additional, Kirkpatrick, R., additional, Smith, B., additional, Buchanan, J., additional, Hill, L., additional, Dixon, L. J., additional, Rosca, M., additional, O' Connor, K., additional, Magne, J., additional, Romano, G., additional, Calin, A., additional, Popescu, B. A., additional, Beladan, C. C., additional, Pierard, L., additional, Ginghina, C., additional, Lancellotti, P., additional, Bochenek, T., additional, Wita, K., additional, Tabor, Z., additional, Grabka, M., additional, Elzbieciak, M., additional, Trusz-Gluza, M., additional, Moreau, O., additional, Leclercq, C., additional, Sahlen, A., additional, Shahgaldi, K., additional, Aminoff, A., additional, Aagaard, P., additional, Manouras, A., additional, Winter, R., additional, Ehrenborg, E., additional, Braunschweig, F., additional, Bedetti, G., additional, Gargani, L., additional, Pizzi, C., additional, Sicari, R., additional, Picano, E., additional, Zhang, J., additional, Zhang, H. B., additional, Duan, Y. Y., additional, Chen, L. L., additional, Li, J., additional, Liu, L. W., additional, Zhu, T., additional, Li, H. L., additional, Su, H. L., additional, Zhou, X. D., additional, Ruiz Ortiz, M., additional, Mesa Rubio, D., additional, Delgado Ortega, M., additional, Romo Penas, E., additional, Toledano Degado, F., additional, Leon Del Pino, C., additional, Lopez Aguilera, J., additional, Villanueva Fernandez, E., additional, Cejudo Diaz Del Campo, L., additional, Suarez De Lezo, J., additional, Abergel, E., additional, Simon, M., additional, Dehant, P., additional, Bogino, E., additional, Jimenez, M., additional, Verdier, J. C., additional, Chauvel, C., additional, Albertsen, A. E., additional, Nielsen, J. C., additional, Mortensen, P. T., additional, Egeblad, H., additional, Nasr, G. M., additional, Tawfik, S., additional, Omar, A., additional, Olofsson, M., additional, Boman, K., additional, Rezzoug, N., additional, Vaes, B., additional, Degryse, J., additional, Vanoverschelde, J.-L., additional, Pasquet, A. A., additional, Poggio, D., additional, Bonadies, M., additional, Pacher, V., additional, Mazzetti, S., additional, Grillo, M., additional, D'elia, E., additional, Khouri, T., additional, Specchia, G., additional, Mornos, C., additional, Rusinaru, D., additional, Cozma, D., additional, Ionac, A., additional, Petrescu, L., additional, Rotzak, R., additional, Rosenman, Y., additional, Patterson, R. D., additional, Ratnatheepan, S., additional, Bogle, R. G., additional, Goebel, B., additional, Gjesdal, O., additional, Kottke, D., additional, Otto, S., additional, Jung, C., additional, Edvardsen, T., additional, Figulla, H. R., additional, Poerner, T. C., additional, Otsuka, T., additional, Suzuki, M., additional, Yoshikawa, H., additional, Hashimoto, G., additional, Itou, N., additional, Ono, T., additional, Yamamoto, M., additional, Osaki, T., additional, Tsuchida, T., additional, Sugi, K., additional, Wolber, T., additional, Haegeli, L., additional, Huerlimann, D., additional, Brunckhorst, C., additional, Duru, F., additional, Wu, Z. M., additional, Shu, X. H., additional, Dong, L. L., additional, Fan, B., additional, Ge, J. B., additional, Greutmann, M., additional, Tobler, D., additional, Biaggi, P., additional, Mah, M., additional, Crean, A., additional, Oechslin, E. N., additional, Silversides, C. K., additional, Giusca, S., additional, Jurcut, R., additional, Ghiorghiu, I., additional, Coman, I. M., additional, Amzulescu, M., additional, Ionescu, R., additional, Delcroix, M., additional, Voigt, J. U., additional, Piatkowski, R., additional, Kochanowski, J., additional, Scislo, P., additional, Grabowski, M., additional, Marchel, M., additional, Roik, M., additional, Kosior, D., additional, Opolski, G., additional, Maceira Gonzalez, A. M., additional, Cosin-Sales, J., additional, Dalli, E., additional, Igual, B., additional, Monmeneu, J. V., additional, Lopez-Lereu, P., additional, Estornell, J., additional, Ruvira, J., additional, Sotillo, J., additional, Stevanovic, A., additional, Toncev, A., additional, Dimkovic, S., additional, Dekleva, M., additional, Paunovic, N., additional, Toncev, D., additional, Sekularac, N., additional, Yildirimturk, O., additional, Helvacioglu, F. F., additional, Tayyareci, Y., additional, Yurdakul, S., additional, Demiroglu, I. C. C., additional, Aytekin, S., additional, Pinedo Gago, M., additional, Amat Santos, I., additional, Revilla Orodea, A., additional, Lopez Diaz, J., additional, Arnold, R., additional, De La Fuente Galan, L., additional, Recio Platero, A., additional, Gomez Salvador, I., additional, Puerto Sanz, A., additional, San Roman Calvar, J. A., additional, Yotti, R., additional, Bermejo, J., additional, Mombiela, T., additional, Benito, Y., additional, Sanchez, P. L., additional, Solis, J., additional, Prieto, R., additional, Fernandez-Aviles, F., additional, Zilberszac, R., additional, Gabriel, H., additional, Graf, S., additional, Mundigler, G., additional, Maurer, G., additional, Rosenhek, R., additional, Zito, C., additional, Salvia, J., additional, Longordo, C., additional, Donato, D., additional, Alati, E., additional, Miceli, M., additional, Pardeo, A., additional, Arcidiaco, S., additional, Oreto, G., additional, Carerj, S., additional, Hadjimiltiades, S., additional, Sianos, G., additional, Anastasiadis, K., additional, Grosomanidis, V., additional, Efthimiadis, G., additional, Parcharidis, G., additional, Yousry, M., additional, Rickenlund, A., additional, Petrini, J., additional, Gustafsson, T., additional, Liska, J., additional, Hamsten, A., additional, Eriksson, P., additional, Franco-Cereceda, A., additional, Eriksson, M. J., additional, Caidahl, K., additional, Mizia-Stec, K., additional, Pysz, P., additional, Jasinski, M., additional, Drzewiecka-Gerber, A., additional, Krejca, M., additional, Bochenek, A., additional, Wos, S., additional, Gasior, Z., additional, Tendera, M., additional, Niki, K., additional, Sugawara, M., additional, Takamisawa, I., additional, Watanabe, H., additional, Sumiyoshi, T., additional, Hosoda, S., additional, Ida, T., additional, Takanashi, S., additional, Olsen, N. T., additional, Sogaard, P., additional, Jons, C., additional, Mogelvang, R., additional, Larsson, H. B. W., additional, Goetze, J. P., additional, Nielsen, O. W., additional, Fritz-Hansen, T., additional, Sayar, N., additional, Orhan, A. L., additional, Erer, H. B., additional, Eren, M., additional, Atmaca, H., additional, Yilmaz, H. Y., additional, Cakmak, N., additional, Altay, S., additional, Terzi, S., additional, Yesilcimen, K., additional, Garcia Orta, R., additional, Moreno, E., additional, Lopez, M., additional, Uribe, I., additional, Vidal, M., additional, Ruiz-Lopez, M. F., additional, Gonzalez-Molina, M., additional, Oyonarte, J. M., additional, Lopez, S., additional, Azpitarte, J., additional, Szymanski, C., additional, Levine, R. A., additional, Zheng, H., additional, Handschumacher, M. D., additional, Tawakol, A., additional, Hung, J., additional, Le Ven, F., additional, Etienne, Y., additional, Jobic, Y., additional, Frachon, I., additional, Castellant, P., additional, Fatemi, M., additional, Blanc, J. J., additional, Tribouilloy, C., additional, Grigioni, F., additional, Avierinos, J.-F., additional, Barbieri, A., additional, Buiciuc, O., additional, Enriquez-Sarano, M., additional, Said, K., additional, Farag, A. K., additional, El-Ramly, M., additional, Rizk, H., additional, Iorio, A., additional, Pinamonti, B., additional, Bobbo, M., additional, Merlo, M., additional, Massa, L., additional, Faganello, G., additional, Di Lenarda, A., additional, Sinagra, G., additional, Margato, R., additional, Ribeiro, H., additional, Ferreira, C., additional, Matias, A., additional, Fontes, P., additional, Moreira, J. I., additional, Milan, A., additional, Puglisi, E., additional, Magnino, C., additional, Fabbri, A., additional, Leone, D., additional, Vairo, A., additional, Crudo, V., additional, Iannaccone, A., additional, Milazzo, V., additional, Veglio, F., additional, Maroz-Vadalazhskaya, N., additional, Ostrovskiy, I., additional, Imbalzano, E., additional, Saitta, A., additional, Cusma-Piccione, M., additional, Di Bella, G., additional, Nava, R., additional, Ferro, M., additional, Falanga, G., additional, Frigy, A., additional, Buzogany, J., additional, Szabados, C. S., additional, Dan, L., additional, Carasca, E., additional, Ikonomidis, I., additional, Lekakis, J., additional, Tzortzis, S., additional, Kremastinos, D. T., additional, Papadopoulos, C., additional, Paraskevaidis, I., additional, Triantafyllidi, H., additional, Trivilou, P., additional, Venetsanou, K., additional, Anastasiou-Nana, M., additional, Wierzbowska-Drabik, K., additional, Kurpesa, M., additional, Trzos, E., additional, Rechcinski, T., additional, Mozdzan, M., additional, Kasprzak, J. D., additional, Kosmala, W., additional, Kotwica, T., additional, Przewlocka-Kosmala, M., additional, Mysiak, A., additional, Skultetyova, D., additional, Filipova, S., additional, Chnupa, P., additional, Pechlivanidis, G., additional, Dimitroula, H., additional, Tsai, W.-C., additional, Liu, Y.-W., additional, Lin, C.-C., additional, Huang, Y.-Y., additional, Tsai, L.-M., additional, Park, S. M., additional, Kim, Y. H., additional, Shin, S. M., additional, Shim, W. J., additional, Gonzalez Mansilla, A., additional, Torres Macho, J., additional, Sanchez Sanchez, V., additional, Diez, P., additional, Delgado, J., additional, Borruel, S., additional, Saenz De La Calzada, C., additional, Pyxaras, S., additional, Valentincic, M., additional, Barbati, G., additional, Lo Giudice, F., additional, Perkan, A., additional, Magnani, S., additional, Palecek, T., additional, Ambroz, D., additional, Jansa, P., additional, Lindner, J., additional, Vitovec, M., additional, Polacek, P., additional, Jiratova, K., additional, Linhart, A., additional, Baskurt, M., additional, Dogan, G. M., additional, Abaci, O., additional, Kaya, A., additional, Kucukoglu, S., additional, Duszanska, A., additional, Kukulski, T., additional, Skoczylas, I., additional, Majsnerowska, A., additional, Nowowiejska-Wiewiora, A., additional, Streb, W., additional, Szulik, M., additional, Polonski, L., additional, Kalarus, Z., additional, Yerly, P. O., additional, Prella, M., additional, Joly, A., additional, Nicod, L., additional, Aubert, J. D., additional, Aebischer, N., additional, Dores, H., additional, Leal, S., additional, Rosario, I., additional, Correia, M. J., additional, Monge, J., additional, Grilo, A. M., additional, Arroja, I., additional, Fonseca, C., additional, Aleixo, A., additional, Silva, A., additional, Perez-David, E., additional, Sanchez-Alegre, M., additional, Gomez Anta, I., additional, De La Torre, J., additional, Alarcon, J., additional, Garcia Robles, J. A., additional, Lafuente, J., additional, Garcia Alonso, C. J., additional, Vallejo Camazon, N., additional, Gonzalez Guardia, A., additional, Nunez, R., additional, Bosch Carabante, C., additional, Mateu, L., additional, Gual Capllonch, F., additional, Ferrer Sistach, E., additional, Lopez Ayerbe, J., additional, Bayes Genis, A., additional, Tomaszewski, A., additional, Kutarski, A., additional, Tomaszewski, M., additional, Bramos, D., additional, Kalantaridou, A., additional, Takos, D., additional, Skaltsiotis, E., additional, Trika, C., additional, Tsirikos, N., additional, Pamboukas, C., additional, Kottis, G., additional, Toumanidis, S., additional, Aggeli, C., additional, Felekos, I., additional, Roussakis, G., additional, Kazazaki, C., additional, Lampropoulos, K., additional, Lagoudakou, S., additional, Stergiou, C., additional, Pitsavos, C., additional, Stefanadis, C., additional, Kihara, C., additional, Murata, K., additional, Wada, Y., additional, Tanaka, T., additional, Uchida, K., additional, Okuda, S., additional, Susa, T., additional, Matsuzaki, M., additional, Abrahamsson, A., additional, Gudmundsson, P., additional, Brodin, L., additional, Knebel, F., additional, Schattke, S., additional, Sanad, W., additional, Schimke, I., additional, Schroeckh, S., additional, Brechtel, L., additional, Lock, J., additional, Makauskiene, R., additional, Baumann, G., additional, Borges, A. C., additional, Moelmen-Hansen, H. E., additional, Wisloff, U., additional, Aamot, I. L., additional, Stoylen, A., additional, Ingul, C. B., additional, Estensen, M.-E., additional, Beitnes, J. O., additional, Grindheim, G., additional, Henriksen, T., additional, Aaberge, L., additional, Smiseth, O. A., additional, Gullestad, L., additional, Aakhus, S., additional, Agoston, G., additional, Moggi Pignone, A., additional, Capati, E., additional, Badano, L., additional, Moreo, A., additional, Bombardieri, S., additional, Varga, A., additional, Carrideo, M., additional, Faricelli, S., additional, Corazzini, A., additional, Ippedico, R., additional, Ruggieri, B., additional, Di Blasio, A., additional, D'angelo, E., additional, Di Baldassarre, A., additional, Ripari, P., additional, Gallina, S., additional, Kentrschynskyj, A., additional, Hylander, B., additional, Jacobson, S., additional, Pagels, A., additional, Dumitrescu, S. I., additional, Tintoiu, I., additional, Greere, V., additional, Cristian, G., additional, Chiriac, L., additional, Pinte, F., additional, Droc, I., additional, Neagoe, G., additional, Stanciu, S., additional, Voicu, V. A., additional, Kuch-Wocial, A., additional, Pruszczyk, P., additional, Szmigielski, C. A., additional, Szulc, M., additional, Styczynski, G., additional, Sinski, M., additional, Kaczynska, A., additional, Ryabikov, A., additional, Malyutina, S., additional, Halcox, J., additional, Bobak, M., additional, Nikitin, Y. U., additional, Marmot, M., additional, Barbosa, D., additional, Kiss, G., additional, Orderud, F., additional, Amundsen, B., additional, Jasaityte, R., additional, Loeckx, D., additional, Claus, P., additional, Torp, H., additional, D'hooge, J., additional, Kuhl, J. T., additional, Lonborg, J., additional, Fuchs, A., additional, Andersen, M., additional, Vejlstrup, N., additional, Engstrom, T., additional, Moller, J. E., additional, Kofoed, K. F., additional, Smith, L. A., additional, Bhan, A., additional, Paul, M., additional, Monaghan, M. J., additional, Zaborska, B., additional, Stec, S., additional, Sikora-Frac, M., additional, Krynski, T., additional, Kulakowski, P., additional, Pushparajah, K., additional, Dashwood, D., additional, Barlow, A., additional, Nugent, K., additional, Miller, O., additional, Simpson, J., additional, Valeur, N., additional, Ersboll, M. K., additional, Kjaergaard, J., additional, Greibe, R., additional, Risum, N., additional, Hassager, C., additional, Kober, L., additional, Popovic, D., additional, Nedeljkovic, I., additional, Petrovic, M., additional, Vujisic-Tesic, B., additional, Arandjelovic, A., additional, Stojiljkovic, S., additional, Jakovljevic, B., additional, Damjanovic, S., additional, Ostojic, M., additional, Agrios, I. A., additional, Bramos, D. B., additional, Skaltsiotis, H. S., additional, Takos, D. T., additional, Kaladaridis, A., additional, Vasiladiotis, N. V., additional, Kottis, G. K., additional, Antoniou, A. A., additional, Pamboucas, C. P., additional, Toumanidis, S. T. T., additional, Locorotondo, G., additional, Porto, I., additional, Paraggio, L., additional, Fedele, E., additional, Barchetta, S., additional, De Caterina, A. R., additional, Rebuzzi, A. G., additional, Crea, F., additional, Galiuto, L., additional, Lipiec, P., additional, Szymczyk, E., additional, Michalski, B., additional, Wozniakowski, B., additional, Stefanczyk, L., additional, Rotkiewicz, A., additional, Shim, A., additional, Vainer, J., additional, Habets, J., additional, Lousberg, A., additional, Pont De, C., additional, Waltenberger, J., additional, Farouk, H., additional, Heshmat, H., additional, Adel, A., additional, El Chilali, K., additional, Baghdady, Y., additional, Sorour, K., additional, Gustafsson, U., additional, Larsson, M., additional, Bjallmark, A., additional, Lindqvist, P., additional, A'roch, R., additional, Haney, M., additional, Waldenstrom, A., additional, Mladenovic, Z., additional, Tavciovski, D., additional, Mijailovic, Z., additional, Djordjevic - Dikic, A., additional, Obradovic, S., additional, Matunovic, R., additional, Jovic, Z., additional, Djuric, P., additional, Aase, S., additional, Dalen, H., additional, Sarkola, T., additional, Redington, A. N., additional, Keeley, F., additional, Bradley, T., additional, Jaeggi, E., additional, and Sahlen, H., additional

Published
2010
Full Text
View/download PDF

42. Human enteric infection with canine hookworms.

Author

Croese, John, Loukas, Alex, Opdebeeck, Joan, Fairley, Stephen, Prociv, Paul, Croese, J, Loukas, A, Opdebeeck, J, Fairley, S, and Prociv, P

Subjects
INTESTINAL infections, ZOONOSES, HOOKWORM disease
Abstract

Objective: To describe a zoonotic ancylostomiasis (canine), acquired from domestic pets by patients living in developed, urban communities.Design: An 8-year, retrospective case study.Setting: A clinical gastroenterologic practice in Townsville and a university parasitology department in Brisbane, Australia.Patients: Nine patients, each with enteric hookworm infection diagnosed by finding a single organism in situ; five were treated by us, and the rest were referred to us for parasite identification.Measurements: Clinical and demographic data, complete blood examinations, total serum immunoglobulin E assay, and serologic testing with enzyme-linked immunosorbent assay and Western blot using excretory-secretory antigens of Ancylostoma caninum. Gut biopsy specimens were examined histologically, and hookworms were identified using morphologic criteria.Results: The infections in three of the patients were diagnosed during the initial 6 years and six in the last 2 years. All owned a dog and described activity potentially exposing them to infection with canine hookworm larvae. Three patients had a laparotomy for acute abdominal pain, and six had colonoscopies (five with pain and one without symptoms). Six of the nine had blood eosinophilia (mean, 0.97 x 10(9)/L), and five of eight had elevated immunoglobulin E levels (mean level, 756 micrograms/L); six of eight had eosinophilic inflammation of the gut. In six patients, the worm was identified as A. caninum, whereas in three, damage to the specimen did not allow specific identification; however, they were unlikely to be human parasite species. Although all parasites were in the adult stage, none were sexually mature. Positive serologic findings in seven of the eight patients tested confirmed presence of antibody to the parasite.Conclusions: Human enteric infections with A. caninum are being diagnosed more frequently in northeastern Australia. Although infection may be subclinical, the chief symptom is abdominal pain, sometimes sudden and severe. The pathologic finding is focal or diffuse eosinophilic inflammation caused by a type 1 hypersensitivity response to secreted antigens. Infection by sexually immature worms is scant and nonpatent, indicating poor adaptation to the human host. Serologic testing assists in identification of occult infection. Advanced hygiene and sanitation afford little protection because the parasite reservoir is a large and growing pool of infected domestic pets. [ABSTRACT FROM AUTHOR]

Published
1994
Full Text
View/download PDF

45. eSport: Construct specifications and implications for sport management

Author

Cunningham, G., Fairley, S., Ferkins, L., Lock, Daniel, Kerwin, S., Shaw, S., Wicker, P., Cunningham, G., Fairley, S., Ferkins, L., Lock, Daniel, Kerwin, S., Shaw, S., and Wicker, P.

Abstract

The purpose of this article is to add to the conceptual discussion on eSport, analyze the role of eSport within sport management, and suggest avenues for future eSport research. The authors suggest that debates surround the degree to which eSport represents formal sport, and disagreements likely stem from conceptualizations of sport and context. Irrespective of one’s notion of eSport as formal sport, the authors suggest the topic has a place in sport management scholarship and discourse. Such a position is consistent with the broad view of sport adopted by Sport Management Review, the perspective that eSport represents a form of sportification, and the association among eSport and various outcomes, including physical and psychological health, social well-being, sport consumption outcomes, and diversity and inclusion. Finally, the authors conclude that eSport scholarship can advance through the study of its governance, marketing, and management as well as by theorizing about eSport

47. ACUTE FULMINANT NECROTISING LYMPHOCYTIC MYOCARDITIS IN A PATIENT WITH MIXED CONNECTIVE TISSUE DISEASE: A RAPID CLINICAL RESPONSE TO IMMUNOSUPPRESSION.

Author

Fairley, S. L., Herron, B., Wilson, C. M., and Roberts, M. J. D.

Abstract

The article describes the case of a 53-year-old man presented with a history of chest pain and flu-like symptoms and mixed connective tissue disease (MCTD). Topics discussed include the clinical response to immunosuppression in patients with acute fulminant necrotising lymphocytic myocarditis with MCTD, the importance of myocarditis diagnosis in patients with acute heart failure, and the utilization of multiple endomyocardial biopsy samples to prevent sampling errors.

Published
2014

48. Professional reading.

Author

Fairley, S. and Williams, W.W.

Subjects
*VIDEO reviews, *UNIVERSITIES & colleges, *ACADEMIC libraries, *LIBRARIES, *PUBLIC libraries
Abstract

Reviews the videotapes "Discovering the College Library" and "Introduction to Research: Using Subject Indexes from Wilson," by H.W. Wilson.

Published
1991

49. Paired risk scores to predict ischaemic and bleeding risk twenty-eight days to one year after an acute coronary syndrome.

Author

Kerr AJ, Choi Y, Williams MJ, Stewart RA, White HD, Devlin G, Selak V, Lee MAW, El-Jack S, Adamson PD, Fairley S, Jackson RT, and Poppe K

Subjects
Humans, Platelet Aggregation Inhibitors adverse effects, Aftercare, Risk Assessment, Patient Discharge, Hemorrhage chemically induced, Hemorrhage epidemiology, Risk Factors, Ischemia drug therapy, Drug Therapy, Combination, Treatment Outcome, Acute Coronary Syndrome diagnosis, Acute Coronary Syndrome epidemiology, Acute Coronary Syndrome drug therapy, Stroke, Brain Ischemia diagnosis, Brain Ischemia epidemiology, Brain Ischemia etiology, Percutaneous Coronary Intervention
Abstract

Objective: The recommended duration of dual anti-platelet therapy (DAPT) following acute coronary syndrome (ACS) varies from 1 month to 1 year depending on the balance of risks of ischaemia and major bleeding. We designed paired ischaemic and major bleeding risk scores to inform this decision., Methods: New Zealand (NZ) patients with ACS investigated with coronary angiography are recorded in the All NZ ACS Quality Improvement registry and linked to national health datasets. Patients were aged 18-84 years (2012-2020), event free at 28 days postdischarge and without atrial fibrillation. Two 28-day to 1-year postdischarge multivariable risk prediction scores were developed: (1) cardiovascular mortality/rehospitalisation with myocardial infarction or ischaemic stroke (ischaemic score) and (2) bleeding mortality/rehospitalisation with bleeding (bleeding score)., Findings: In 27 755 patients, there were 1200 (4.3%) ischaemic and 548 (2.0%) major bleeding events. Both scores were well calibrated with moderate discrimination performance (Harrell's c-statistic 0.75 (95% CI, 0.74 to 0.77) and 0.69 (95% CI, 0.67 to 0 .71), respectively). Applying these scores to the 2020 European Society of Cardiology ACS antithrombotic treatment algorithm, the 31% of the cohort at elevated (>2%) bleeding and ischaemic risk would be considered for an abbreviated DAPT duration. For those at low bleeding risk, but elevated ischaemic risk (37% of the cohort), prolonged DAPT may be appropriate, and for those with low bleeding and ischaemic risk (29% of the cohort) short duration DAPT may be justified., Conclusion: We present a pair of ischaemic and bleeding risk scores specifically to assist clinicians and their patients in deciding on DAPT duration beyond the first month post-ACS., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Published
2023
Full Text
View/download PDF

50. A draft human pangenome reference.

Author

Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu TY, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Sirén J, Tomlinson C, Villani F, Vollger MR, Antonacci-Fulton LL, Baid G, Baker CA, Belyaeva A, Billis K, Carroll A, Chang PC, Cody S, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld AL, Formenti G, Frankish A, Gao Y, Garrison NA, Giron CG, Green RE, Haggerty L, Hoekzema K, Hourlier T, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson ND, Popejoy AB, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Smith MW, Sofia HJ, Abou Tayoun AN, Thibaud-Nissen F, Tricomi FF, Wagner J, Walenz B, Wood JMD, Zimin AV, Bourque G, Chaisson MJP, Flicek P, Phillippy AM, Zook JM, Eichler EE, Haussler D, Wang T, Jarvis ED, Miga KH, Garrison E, Marschall T, Hall IM, Li H, and Paten B

Subjects
Humans, Diploidy, Haplotypes genetics, Sequence Analysis, DNA, Reference Standards, Cohort Studies, Alleles, Genetic Variation, Genome, Human genetics, Genomics standards
Abstract

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals 1 . These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample., (© 2023. The Author(s).)

Published
2023
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results