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818 results on '"Hirst M"'

101. De novo transcriptome assembly with ABySS

Author

Birol, I., Jackman, S., Nielsen, C., Qian, J., Varhol, Richard, Stazyk, G., Morin, R., Zhao, Y., Hirst, M., Schein, J., Horsman, D., Connors, J., Gascoyne, R., Marra, M., Jones, S., Birol, I., Jackman, S., Nielsen, C., Qian, J., Varhol, Richard, Stazyk, G., Morin, R., Zhao, Y., Hirst, M., Schein, J., Horsman, D., Connors, J., Gascoyne, R., Marra, M., and Jones, S.

Abstract

Motivation: Whole transcriptome shotgun sequencing data from non-normalized samples offer unique opportunities to study the metabolic states of organisms. One can deduce gene expression levels using sequence coverage as a surrogate, identify coding changes or discover novel isoforms or transcripts. Especially for discovery of novel events, de novo assembly of transcriptomes is desirable. Results: Transcriptome from tumor tissue of a patient with follicular lymphoma was sequenced with 36 base pair (bp) single- and paired-end reads on the Illumina Genome Analyzer II platform. We assembled ~194 million reads using ABySS into 66 921 contigs 100 bp or longer, with a maximum contig length of 10 951 bp, representing over 30 million base pairs of unique transcriptome sequence, or roughly 1% of the genome. © The Author 2009. Published by Oxford University Press. All rights reserved.

Published
2009

102. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

Author

Shah, S., Morin, R., Khattra, J., Prentice, L., Pugh, T., Burleigh, A., Delaney, A., Gelmon, K., Guliany, R., Senz, J., Steidl, C., Holt, R., Jones, S., Sun, M., Leung, G., Moore, R., Severson, T., Taylor, G., Teschendorff, A., Tse, K., Turashvili, G., Varhol, Richard, Warren, R., Watson, P., Zhao, Y., Caldas, C., Huntsman, D., Hirst, M., Marra, M., Aparicio, S., Shah, S., Morin, R., Khattra, J., Prentice, L., Pugh, T., Burleigh, A., Delaney, A., Gelmon, K., Guliany, R., Senz, J., Steidl, C., Holt, R., Jones, S., Sun, M., Leung, G., Moore, R., Severson, T., Taylor, G., Teschendorff, A., Tse, K., Turashvili, G., Varhol, Richard, Warren, R., Watson, P., Zhao, Y., Caldas, C., Huntsman, D., Hirst, M., Marra, M., and Aparicio, S.

Abstract

Recent advances in next generation sequencing have made it possible to precisely characterize all somatic coding mutations that occur during the development and progression of individual cancers. Here we used these approaches to sequence the genomes (43-fold coverage) and transcriptomes of an oestrogen-receptor-a-positive metastatic lobular breast cancer at depth. We found 32 somatic non-synonymous coding mutations present in the metastasis, and measured the frequency of these somatic mutations in DNA from the primary tumour of the same patient, which arose 9 years earlier. Five of the 32 mutations (in ABCB11, HAUS3, SLC24A4, SNX4 and PALB2) were prevalent in the DNA of the primary tumour removed at diagnosis 9 years earlier, six (in KIF1C, USP28, MYH8, MORC1, KIAA1468 and RNASEH2A) were present at lower frequencies (1-13%), 19 were not detected in the primary tumour, and two were undetermined. The combined analysis of genome and transcriptome data revealed two new RNA-editing events that recode the amino acid sequence of SRP9 and COG3. Taken together, our data show that single nucleotide mutational heterogeneity can be a property of low or intermediate grade primary breast cancers and that significant evolution can occur with disease progression. © 2009 Macmillan Publishers Limited. All rights reserved.

Published
2009

103. Mutation of FOXL2 in granulosa-cell tumors of the ovary

Author

Shah, S., Köbel, M., Senz, J., Morin, R., Clarke, B., Wiegand, K., Leung, G., Zayed, A., Mehl, E., Kalloger, S., Sun, M., Giuliany, R., Yorida, E., Jones, S., Varhol, Richard, Swenerton, K., Miller, D., Clement, P., Crane, C., Madore, J., Provencher, D., Leung, P., DeFazio, A., Khattra, J., Turashvili, G., Zhao, Y., Zeng, T., Glover, J., Vanderhyden, B., Zhao, C., Parkinson, C., Jimenez-Linan, M., Bowtell, D., Mes-Masson, A., Brenton, J., Aparicio, S., Boyd, N., Hirst, M., Gilks, C., Marra, M., Huntsman, D., Shah, S., Köbel, M., Senz, J., Morin, R., Clarke, B., Wiegand, K., Leung, G., Zayed, A., Mehl, E., Kalloger, S., Sun, M., Giuliany, R., Yorida, E., Jones, S., Varhol, Richard, Swenerton, K., Miller, D., Clement, P., Crane, C., Madore, J., Provencher, D., Leung, P., DeFazio, A., Khattra, J., Turashvili, G., Zhao, Y., Zeng, T., Glover, J., Vanderhyden, B., Zhao, C., Parkinson, C., Jimenez-Linan, M., Bowtell, D., Mes-Masson, A., Brenton, J., Aparicio, S., Boyd, N., Hirst, M., Gilks, C., Marra, M., and Huntsman, D.

Abstract

BACKGROUND: Granulosa-cell tumors (GCTs) are the most common type of malignant ovarian sex cord-stromal tumor (SCST). The pathogenesis of these tumors is unknown. Moreover, their histopathological diagnosis can be challenging, and there is no curative treatment beyond surgery. METHODS: We analyzed four adult-type GCTs using whole-transcriptome paired-end RNA sequencing. We identified putative GCT-specific mutations that were present in at least three of these samples but were absent from the transcriptomes of 11 epithelial ovarian tumors, published human genomes, and databases of single-nucleotide polymorphisms. We confirmed these variants by direct sequencing of complementary DNA and genomic DNA. We then analyzed additional tumors and matched normal genomic DNA, using a combination of direct sequencing, analyses of restriction-fragment-length polymorphisms, and TaqMan assays. RESULTS: All four index GCTs had a missense point mutation, 402C?G (C134W), in FOXL2, a gene encoding a transcription factor known to be critical for granulosa-cell development. The FOXL2 mutation was present in 86 of 89 additional adult-type GCTs (97%), in 3 of 14 thecomas (21%), and in 1 of 10 juvenile-type GCTs (10%). The mutation was absent in 49 SCSTs of other types and in 329 unrelated ovarian or breast tumors. CONCLUSIONS: Whole-transcriptome sequencing of four GCTs identified a single, recurrent somatic mutation (402C?G) in FOXL2 that was present in almost all morphologically identified adult-type GCTs. Mutant FOXL2 is a potential driver in the pathogenesis of adult-type GCTs. Copyright © 2009 Massachusetts Medical Society. All rights reserved.

Published
2009

104. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

Author

Morin, R., Bainbridge, M., Fejes, A., Hirst, M., Krzywinski, M., Pugh, T., McDonald, H., Varhol, Richard, Jones, S., Marra, M., Morin, R., Bainbridge, M., Fejes, A., Hirst, M., Krzywinski, M., Pugh, T., McDonald, H., Varhol, Richard, Jones, S., and Marra, M.

Abstract

Sequence-based methods for transcriptome characterization have typically relied on generation of either serial analysis of gene expression tags or expressed sequence tags. Although such approaches have the potential to enumerate transcripts by counting sequence tags derived from them, they typically do not robustly survey the majority of transcripts along their entire length. Here we show that massively parallel sequencing of randomly primed cDNAs, using a next-generation sequencing-by-synthesis technology, offers the potential to generate relative measures of mRNA and individual exon abundance while simultaneously profiling the prevalence of both annotated and novel exons and exon-splicing events. This technique identifies known single nucleotide polymorphisms (SNPs) as well as novel single-base variants. Analysis of these variants, and previously unannotated splicing events in the HeLa S3 cell line, reveals an overrepresentation of gene categories including those previously implicated in cancer.

Published
2008

105. Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing

Author

Wederell, E., Bilenky, M., Cullum, R., Thiessen, N., Dagpinar, M., Delaney, A., Varhol, Richard, Zhao, Y., Zeng, T., Bernier, B., Ingham, M., Hirst, M., Robertson, G., Marra, M., Jones, S., Hoodless, P., Wederell, E., Bilenky, M., Cullum, R., Thiessen, N., Dagpinar, M., Delaney, A., Varhol, Richard, Zhao, Y., Zeng, T., Bernier, B., Ingham, M., Hirst, M., Robertson, G., Marra, M., Jones, S., and Hoodless, P.

Abstract

Foxa2 (HNF3ß) is a one of three, closely related transcription factors that are critical to the development and function of the mouse liver. We have used chromatin immunoprecipitation and massively parallel Illumina 1G sequencing (ChIP-Seq) to create a genome-wide profile of in vivo Foxa2-binding sites in the adult liver. More than 65% of the ~ 11.5 k genomic sites associated with Foxa2 binding, mapped to extended gene regions of annotated genes, while more than 30% of intragenic sites were located within first introns. 20.5% of all sites were further than 50 kb from any annotated gene, suggesting an association with novel gene regions. QPCR analysis demonstrated a strong positive correlation between peak height and fold enrichment for Foxa2-binding sites. We measured the relationship between Foxa2 and liver gene expression by overlapping Foxa2-binding sites with a SAGE transcriptome profile, and found that 43.5% of genes expressed in the liver were also associated with Foxa2 binding. We also identified potential Foxa2-interacting transcription factors whose motifs were enriched near Foxa2-binding sites. Our comprehensive results for in vivo Foxa2-binding sites in the mouse liver will contribute to resolving transcriptional regulatory networks that are important for adult liver function. © 2008 The Author(s).

Published
2008

107. OMICS AND PROGNSTIC MARKERS

Author

Adachi, K., primary, Sasaki, H., additional, Nagahisa, S., additional, Yoshida, K., additional, Hattori, N., additional, Nishiyama, Y., additional, Kawase, T., additional, Hasegawa, M., additional, Abe, M., additional, Hirose, Y., additional, Alentorn, A., additional, Marie, Y., additional, Poggioli, S., additional, Alshehhi, H., additional, Boisselier, B., additional, Carpentier, C., additional, Mokhtari, K., additional, Capelle, L., additional, Figarella-Branger, D., additional, Hoang-Xuan, K., additional, Sanson, M., additional, Delattre, J.-Y., additional, Idbaih, A., additional, Yust-Katz, S., additional, Anderson, M., additional, Olar, A., additional, Eterovic, A., additional, Ezzeddine, N., additional, Chen, K., additional, Zhao, H., additional, Fuller, G., additional, Aldape, K., additional, de Groot, J., additional, Andor, N., additional, Harness, J., additional, Lopez, S. G., additional, Fung, T. L., additional, Mewes, H. W., additional, Petritsch, C., additional, Arivazhagan, A., additional, Somasundaram, K., additional, Thennarasu, K., additional, Pandey, P., additional, Anandh, B., additional, Santosh, V., additional, Chandramouli, B., additional, Hegde, A., additional, Kondaiah, P., additional, Rao, M., additional, Bell, R., additional, Kang, R., additional, Hong, C., additional, Song, J., additional, Costello, J., additional, Nagarajan, R., additional, Zhang, B., additional, Diaz, A., additional, Wang, T., additional, Bie, L., additional, Li, Y., additional, Liu, H., additional, Luyo, W. F. C., additional, Carnero, M. H., additional, Iruegas, M. E. P., additional, Morell, A. R., additional, Figueiras, M. C., additional, Lopez, R. L., additional, Valverde, C. F., additional, Chan, A. K.-Y., additional, Pang, J. C.-S., additional, Chung, N. Y.-F., additional, Li, K. K.-W., additional, Poon, W. S., additional, Chan, D. T.-M., additional, Wang, Y., additional, Ng, H.-a. K., additional, Chaumeil, M., additional, Larson, P., additional, Yoshihara, H., additional, Vigneron, D., additional, Nelson, S., additional, Pieper, R., additional, Phillips, J., additional, Ronen, S., additional, Clark, V., additional, Omay, Z. E., additional, Serin, A., additional, Gunel, J., additional, Omay, B., additional, Grady, C., additional, Youngblood, M., additional, Bilguvar, K., additional, Baehring, J., additional, Piepmeier, J., additional, Gutin, P., additional, Vortmeyer, A., additional, Brennan, C., additional, Pamir, M. N., additional, Kilic, T., additional, Krischek, B., additional, Simon, M., additional, Yasuno, K., additional, Gunel, M., additional, Cohen, A. L., additional, Sato, M., additional, Aldape, K. D., additional, Mason, C., additional, Diefes, K., additional, Heathcock, L., additional, Abegglen, L., additional, Shrieve, D., additional, Couldwell, W., additional, Schiffman, J. D., additional, Colman, H., additional, D'Alessandris, Q. G., additional, Cenci, T., additional, Martini, M., additional, Ricci-Vitiani, L., additional, De Maria, R., additional, Larocca, L. M., additional, Pallini, R., additional, Theeler, B., additional, Lang, F., additional, Rao, G., additional, Gilbert, M., additional, Sulman, E., additional, Luthra, R., additional, Eterovic, K., additional, Routbort, M., additional, Verhaak, R., additional, Mills, G., additional, Mendelsohn, J., additional, Meric-Bernstam, F., additional, Yung, A., additional, MacArthur, K., additional, Hahn, S., additional, Kao, G., additional, Lustig, R., additional, Alonso-Basanta, M., additional, Chandrasekaran, S., additional, Wileyto, E. P., additional, Reyes, E., additional, Dorsey, J., additional, Fujii, K., additional, Kurozumi, K., additional, Ichikawa, T., additional, Onishi, M., additional, Ishida, J., additional, Shimazu, Y., additional, Kaur, B., additional, Chiocca, E. A., additional, Date, I., additional, Geisenberger, C., additional, Mock, A., additional, Warta, R., additional, Schwager, C., additional, Hartmann, C., additional, von Deimling, A., additional, Abdollahi, A., additional, Herold-Mende, C., additional, Gevaert, O., additional, Achrol, A., additional, Gholamin, S., additional, Mitra, S., additional, Westbroek, E., additional, Loya, J., additional, Mitchell, L., additional, Chang, S., additional, Steinberg, G., additional, Plevritis, S., additional, Cheshier, S., additional, Xu, J., additional, Napel, S., additional, Zaharchuk, G., additional, Harsh, G., additional, Gutman, D., additional, Holder, C., additional, Colen, R., additional, Dunn, W., additional, Jain, R., additional, Cooper, L., additional, Hwang, S., additional, Flanders, A., additional, Brat, D., additional, Hayes, J., additional, Droop, A., additional, Thygesen, H., additional, Boissinot, M., additional, Westhead, D., additional, Short, S., additional, Lawler, S., additional, Bady, P., additional, Kurscheid, S., additional, Delorenzi, M., additional, Hegi, M. E., additional, Crosby, C., additional, Faulkner, C., additional, Smye-Rumsby, T., additional, Kurian, K., additional, Williams, M., additional, Hopkins, K., additional, Palmer, A., additional, Williams, H., additional, Wragg, C., additional, Haynes, H. R., additional, Kurian, K. M., additional, White, P., additional, Oka, T., additional, Jalbert, L., additional, Elkhaled, A., additional, Jensen, R., additional, Salzman, K., additional, Schabel, M., additional, Gillespie, D., additional, Mumert, M., additional, Johnson, B., additional, Mazor, T., additional, Barnes, M., additional, Yamamoto, S., additional, Ueda, H., additional, Tatsuno, K., additional, Aihara, K., additional, Bollen, A., additional, Hirst, M., additional, Marra, M., additional, Mukasa, A., additional, Saito, N., additional, Aburatani, H., additional, Berger, M., additional, Taylor, B., additional, Popov, S., additional, Mackay, A., additional, Ingram, W., additional, Burford, A., additional, Jury, A., additional, Vinci, M., additional, Jones, C., additional, Jones, D. T. W., additional, Hovestadt, V., additional, Picelli, S., additional, Wang, W., additional, Northcott, P. A., additional, Kool, M., additional, Reifenberger, G., additional, Pietsch, T., additional, Sultan, M., additional, Lehrach, H., additional, Yaspo, M.-L., additional, Borkhardt, A., additional, Landgraf, P., additional, Eils, R., additional, Korshunov, A., additional, Zapatka, M., additional, Radlwimmer, B., additional, Pfister, S. M., additional, Lichter, P., additional, Joy, A., additional, Smirnov, I., additional, Reiser, M., additional, Shapiro, W., additional, Kim, S., additional, Feuerstein, B., additional, Jungk, C., additional, Friauf, S., additional, Unterberg, A., additional, Juratli, T. A., additional, McElroy, J., additional, Meng, W., additional, Huebner, A., additional, Geiger, K. D., additional, Krex, D., additional, Schackert, G., additional, Chakravarti, A., additional, Lautenschlaeger, T., additional, Kim, B. Y., additional, Jiang, W., additional, Beiko, J., additional, Prabhu, S., additional, DeMonte, F., additional, Sawaya, R., additional, Cahill, D., additional, McCutcheon, I., additional, Lau, C., additional, Wang, L., additional, Terashima, K., additional, Yamaguchi, S., additional, Burstein, M., additional, Sun, J., additional, Suzuki, T., additional, Nishikawa, R., additional, Nakamura, H., additional, Natsume, A., additional, Terasaka, S., additional, Ng, H.-K., additional, Muzny, D., additional, Gibbs, R., additional, Wheeler, D., additional, Zhang, X.-q., additional, Sun, S., additional, Lam, K.-f., additional, Kiang, K. M. Y., additional, Pu, J. K. S., additional, Ho, A. S. W., additional, Leung, G. K. K., additional, Loebel, F., additional, Curry, W. T., additional, Barker, F. G., additional, Lelic, N., additional, Chi, A. S., additional, Cahill, D. P., additional, Lu, D., additional, Yin, J., additional, Teo, C., additional, McDonald, K., additional, Madhankumar, A., additional, Weston, C., additional, Slagle-Webb, B., additional, Sheehan, J., additional, Patel, A., additional, Glantz, M., additional, Connor, J., additional, Maire, C., additional, Francis, J., additional, Zhang, C.-Z., additional, Jung, J., additional, Manzo, V., additional, Adalsteinsson, V., additional, Homer, H., additional, Blumenstiel, B., additional, Pedamallu, C. S., additional, Nickerson, E., additional, Ligon, A., additional, Love, C., additional, Meyerson, M., additional, Ligon, K., additional, Jalbert, L. E., additional, Nelson, S. J., additional, Bollen, A. W., additional, Smirnov, I. V., additional, Song, J. S., additional, Olshen, A. B., additional, Berger, M. S., additional, Chang, S. M., additional, Taylor, B. S., additional, Costello, J. F., additional, Mehta, S., additional, Armstrong, B., additional, Peng, S., additional, Bapat, A., additional, Berens, M., additional, Melendez, B., additional, Mollejo, M., additional, Mur, P., additional, Hernandez-Iglesias, T., additional, Fiano, C., additional, Ruiz, J., additional, Rey, J. A., additional, Stadler, V., additional, Schulte, A., additional, Lamszus, K., additional, Schichor, C., additional, Westphal, M., additional, Tonn, J.-C., additional, Morozova, O., additional, Katzman, S., additional, Grifford, M., additional, Salama, S., additional, Haussler, D., additional, Olshen, A., additional, Fouse, S., additional, Nakamizo, S., additional, Sasayama, T., additional, Tanaka, H., additional, Tanaka, K., additional, Mizukawa, K., additional, Yoshida, M., additional, Kohmura, E., additional, Northcott, P., additional, Jones, D., additional, Pfister, S., additional, Otani, R., additional, Takayanagi, S., additional, Saito, K., additional, Tanaka, S., additional, Shin, M., additional, Ozawa, T., additional, Riester, M., additional, Cheng, Y.-K., additional, Huse, J., additional, Helmy, K., additional, Charles, N., additional, Squatrito, M., additional, Michor, F., additional, Holland, E., additional, Perrech, M., additional, Dreher, L., additional, Rohn, G., additional, Goldbrunner, R., additional, Timmer, M., additional, Pollo, B., additional, Palumbo, V., additional, Calatozzolo, C., additional, Patane, M., additional, Nunziata, R., additional, Farinotti, M., additional, Silvani, A., additional, Lodrini, S., additional, Finocchiaro, G., additional, Lopez, E., additional, Rioscovian, A., additional, Ruiz, R., additional, Siordia, G., additional, de Leon, A. P., additional, Rostomily, C., additional, Rostomily, R., additional, Silbergeld, D., additional, Kolstoe, D., additional, Chamberlain, M., additional, Silber, J., additional, Roth, P., additional, Keller, A., additional, Hoheisel, J., additional, Codo, P., additional, Bauer, A., additional, Backes, C., additional, Leidinger, P., additional, Meese, E., additional, Thiel, E., additional, Korfel, A., additional, Weller, M., additional, Nagae, G., additional, Nagane, M., additional, Sanborn, J. Z., additional, Mikkelsen, T., additional, Jhanwar, S., additional, Chin, L., additional, Nishihara, M., additional, Schliesser, M., additional, Grimm, C., additional, Weiss, E., additional, Claus, R., additional, Weichenhan, D., additional, Weiler, M., additional, Hielscher, T., additional, Sahm, F., additional, Wiestler, B., additional, Klein, A.-C., additional, Blaes, J., additional, Plass, C., additional, Wick, W., additional, Stragliotto, G., additional, Rahbar, A., additional, Soderberg-Naucler, C., additional, Won, M., additional, Ezhilarasan, R., additional, Sun, P., additional, Blumenthal, D., additional, Vogelbaum, M., additional, Jenkins, R., additional, Jeraj, R., additional, Brown, P., additional, Jaeckle, K., additional, Schiff, D., additional, Dignam, J., additional, Atkins, J., additional, Brachman, D., additional, Werner-Wasik, M., additional, Mehta, M., additional, Shen, J., additional, Luan, J., additional, Yu, A., additional, Matsutani, M., additional, Liang, Y., additional, Man, T.-K., additional, Trister, A., additional, Tokita, M., additional, Mikheeva, S., additional, Mikheev, A., additional, Friend, S., additional, van den Bent, M., additional, Erdem, L., additional, Gorlia, T., additional, Taphoorn, M., additional, Kros, J., additional, Wesseling, P., additional, Dubbink, H., additional, Ibdaih, A., additional, French, P., additional, van Thuijl, H., additional, Heimans, J., additional, Ylstra, B., additional, Reijneveld, J., additional, Prabowo, A., additional, Scheinin, I., additional, van Essen, H., additional, Spliet, W., additional, Ferrier, C., additional, van Rijen, P., additional, Veersema, T., additional, Thom, M., additional, Meeteren, A. S.-v., additional, Aronica, E., additional, Kim, H., additional, Zheng, S., additional, Brat, D. J., additional, Virk, S., additional, Amini, S., additional, Sougnez, C., additional, Barnholtz-Sloan, J., additional, Verhaak, R. G. W., additional, Watts, C., additional, Sottoriva, A., additional, Spiteri, I., additional, Piccirillo, S., additional, Touloumis, A., additional, Collins, P., additional, Marioni, J., additional, Curtis, C., additional, Tavare, S., additional, Tews, B., additional, Yeung, T. P. C., additional, Al-Khazraji, B., additional, Morrison, L., additional, Hoffman, L., additional, Jackson, D., additional, Lee, T.-Y., additional, Yartsev, S., additional, Bauman, G., additional, Fu, J., additional, Vegesna, R., additional, Mao, Y., additional, Heathcock, L. E., additional, Torres-Garcia, W., additional, Wang, S., additional, McKenna, A., additional, Brennan, C. W., additional, Yung, W. K. A., additional, Weinstein, J. N., additional, Sulman, E. P., additional, and Koul, D., additional

Published
2013
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113. Evaluation of Disability Living Allowance and Attendance Allowance

Author

Sainsbury, R, Hirst, M, and Lawton, D

Abstract

Major changes were made to disability benefits in 1992. Disability Living Allowance (DLA) was introduced, making new lower rates of benefit available to people with less severe care and mobility needs. Attendance Allowance (AA) remained for people who became disabled in later life, but substantial changes were being made to the claim process. This report presents the findings of research carried out by the Social Policy Research Unit at York University to evaluate the changes. The research asks whether the new lower rates of DLA are extending help to less severely disabled people, and evaluates the quality of service provided to people who claim the benefits, ask for a review of the claim, or appeal against the decision.

Published
1995

114. Two new cases of FMR1 deletion associated with mental impairment

Author

Hirst, M, Grewal, P, Flannery, A, Slatter, R, Maher, E, Barton, D, Fryns, J P, and Davies, K

Subjects
Adult, Male, congenital, hereditary, and neonatal diseases and abnormalities, Base Sequence, Mosaicism, Molecular Sequence Data, RNA-Binding Proteins, Nerve Tissue Proteins, Minisatellite Repeats, Polymerase Chain Reaction, nervous system diseases, Pedigree, Fragile X Mental Retardation Protein, Fragile X Syndrome, Intellectual Disability, Humans, RNA, Messenger, Child, Promoter Regions, Genetic, Research Article, Sequence Deletion
Abstract

Screening of families clinically ascertained for the fragile X syndrome phenotype revealed two mentally impaired males who were cytogenetically negative for the fragile X chromosome. In both cases, screening for the FMR1 trinucleotide expansion mutation revealed a rearrangement within the FMR1 gene. In the first case, a 660-bp deletion is present in 40% of peripheral lymphocytes. PCR and sequence analysis revealed it to include the CpG island and the CGG trinucleotide repeat, thus removing the FMR1 promoter region and putative mRNA start site. In the second case, PCR analysis demonstrated that a deletion extended from a point proximal to FMR1 to 25 kb into the gene, removing all the region 5' to exon 11. The distal breakpoint was confirmed by Southern blot analysis and localized to a 600-bp region, and FMR1-mRNA analysis in a cell line established from this individual confirmed the lack of a transcript. These deletion patients provide further confirmatory evidence that loss of FMR1 gene expression is indeed responsible for mental retardation. Additionally, these cases highlight the need for the careful examination of the FMR1 gene, even in the absence of cytogenetic expression, particularly when several fragile X-like clinical features are present.

Published
1995

116. Triplet repeat expansion at the FRAXE locus and X-linked mild mental handicap

Author

Knight, S, Voelckel, M, Hirst, M, Flannery, A, Moncla, A, and Davies, K

Subjects
Male, Phenotype, Fragile X Syndrome, Restriction Mapping, Humans, Female, DNA, Down Syndrome, Dinucleoside Phosphates, Research Article, Pedigree, Repetitive Sequences, Nucleic Acid
Abstract

We have recently shown that the expression of the FRAXE fragile site in Xq28 is associated with the expansion of a GCC trinucleotide repeat. In the families studied, FRAXE expression is also associated with mild mental handicap. Here we present data on families that previously had been diagnosed as having the fragile X syndrome but that later were found to be negative for trinucleotide repeat expansion at the FRAXA locus. In these families we demonstrate the presence of a GCC trinucleotide repeat expansion at the FRAXE locus. Studies of the FRAXE locus of normal individuals show that they have 6-25 copies of the repeat, whereas affected individuals have > 200 copies. As in the fragile X syndrome, the amplified CpG residues are methylated in affected males.

Published
1994

126. Book review: Culture And Politics: Issues In Australian Journalism On Indonesia, 1975-1993

Author

Hirst, M. and Hirst, M.

Abstract

Kingsbury Damien (1997) Culture And Politics: Issues In Australian Journalism On Indonesia, 1975-93 Australia-Asia Papers No. 80. Centre for the Study of Australia Asia Relations.Griffith University, Brisbane, Qld. September. ISBN 0 86857 782 O Review Essay by Martin Hirst Culture and Politics is a timely reminder of the delicate nature of the Australian news media's relationship with the Indonesian regime and that so-called "cultural sensitivities' are really no more than political expediency (inter alia p.149). Indonesian journalists, as well as those visiting from Australia, are subject to harsh criticism when it suits the Jakarta government. Even worse, local journalists are banned, or have their publications closed down, if they transgress the tough written and unwritten rules of behaviour. As Kingsbury notes, for their sins (real and imagined) several Australian journalists have been expelled from Indonesia over the past 15 years. We're also reminded that in 1975 six Australian reporters were murdered by Indonesian soldiers when they tried to cover the invasion of East Timor.

Published
1998

127. Looking out from Terra Nullius: Journalism, modernity and the 'vacant lot'

Author

Hirst, M. and Hirst, M.

Abstract

Keith Windschuttle's recent defence of journalism education (1998a: 41)brought a storm of protest from cultural and media studies theorists (The Australian, 25 March 1998). It is with faint damnation that I find myself praising Windschuttle. While I acknowledge that some media theory is good for journalism students, I question the usefulness and validity of much that the postmodernists believe in. I criticise cultural studies as an attempt to colonise the "terra nullius" of journalism theory (Hartley 1996: 39) and would argue strongly that journalism education should be taken seriously in universities as a legitimate cross-disciplinary field of study (Guerke & Hirst 1996, Hirst 1998).

Published
1998

133. Book review: Racism, ethnicity and the media

Author

Hirst, M. and Hirst, M.

Abstract

Jakubowicz, Andrew; GoodallL, Heather; Martin, Jeannie; Mitchell, Tony; Randall, Lois; Seneviratne, Kalinga (1994)Racism, ethnicity and the media. Allen & Unwin: Sydney ISBN: 1-86373-364-7 Reviewed by Martin Hirst A central concern of this book is that the myths of Australian national identity, especially as generated and communicated by the mass media, do not accord with the multicultural diversity of Australian life. This dissonance has varied and related causes. Some of them, such as declining national economic fortunes are locally-generated, though with an international context. Other factors are external, but impinge explicitly on national life and consciousness in Australia.

Published
1996

150. 'REALITY WORLDS' COLLIDE: FILM AND VIDEOGAMES AS PEDAGOGICAL TOOLS FOR THE CLASSICS.

Author

Karam, B. and Kirby-Hirst, M.

Subjects
MOTION pictures & video games, TIE-ins (Marketing), MOTION pictures in education, CLASSICAL education, BLOCKBUSTERS (Motion pictures)
Abstract

Since the early eighties, the personal computer has come to form an integral part of most aspects of our existence. In Hollywood this is no different. Indeed, the influence of the computer is so powerful that it is rare for an action-adventure film to be able to call itself a 'blockbuster' unless it is released with some sort of videogame tie-in following closely in its wake, as the case of James Cameron's Avatar (2010) suggests. It is the relationship between film and videogame and their combined strengths as a teaching tool that are the concerns of this article. The analysis therefore centres on two examples of film and videogame tie-in: Clash of the Titans and Percy Jackson & the Olympians: The lightning thief, both 2010 releases. The investigation" targets this film / videogame complex through the use of a new concept, the 'reality world', to be defined in the course of the article that better allows an assessment of the relevance and utility of films and their videogame tie-ins as pedagogical tools for the teaching and study of the discipline of Classics. [ABSTRACT FROM AUTHOR]

Published
2011

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