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4. A 600 kb deletion syndrome at 16p11.2 leads to energy imbalance and neuropsychiatric disorders.

Author

Beckmann, Noam, Hanson, Ellen, Maillard, Anne, Hippolyte, Loyse, Macé, Aurélien, Ferrari, Carina, Kutalik, Zoltán, Andrieux, Joris, Aylward, Elizabeth, Barker, Mandy, Bernier, Raphael, Bouquillon, Sonia, Conus, Philippe, Delobel, Bruno, Faucett, W, Goin-Kochel, Robin, Grant, Ellen, Harewood, Louise, Hunter, Jill, Lebon, Sébastien, Ledbetter, David, Martin, Christa, Männik, Katrin, Martinet, Danielle, Ramocki, Melissa, Spence, Sarah, Steinman, Kyle, Tjernagel, Jennifer, Spiro, John, Reymond, Alexandre, Beckmann, Jacques, Chung, Wendy, Jacquemont, Sébastien, Zufferey, Flore, Mukherjee, Pratik, and Sherr, Elliott

Subjects
Adolescent, Adult, Body Mass Index, Child, Child Development Disorders, Pervasive, Chromosome Deletion, Chromosomes, Human, Pair 16, Developmental Disabilities, Female, Gene Order, Heterozygote, Humans, Intelligence Tests, Male, Phenotype, Syndrome, Young Adult
Abstract

BACKGROUND: The recurrent ~600 kb 16p11.2 BP4-BP5 deletion is among the most frequent known genetic aetiologies of autism spectrum disorder (ASD) and related neurodevelopmental disorders. OBJECTIVE: To define the medical, neuropsychological, and behavioural phenotypes in carriers of this deletion. METHODS: We collected clinical data on 285 deletion carriers and performed detailed evaluations on 72 carriers and 68 intrafamilial non-carrier controls. RESULTS: When compared to intrafamilial controls, full scale intelligence quotient (FSIQ) is two standard deviations lower in carriers, and there is no difference between carriers referred for neurodevelopmental disorders and carriers identified through cascade family testing. Verbal IQ (mean 74) is lower than non-verbal IQ (mean 83) and a majority of carriers require speech therapy. Over 80% of individuals exhibit psychiatric disorders including ASD, which is present in 15% of the paediatric carriers. Increase in head circumference (HC) during infancy is similar to the HC and brain growth patterns observed in idiopathic ASD. Obesity, a major comorbidity present in 50% of the carriers by the age of 7 years, does not correlate with FSIQ or any behavioural trait. Seizures are present in 24% of carriers and occur independently of other symptoms. Malformations are infrequently found, confirming only a few of the previously reported associations. CONCLUSIONS: The 16p11.2 deletion impacts in a quantitative and independent manner FSIQ, behaviour and body mass index, possibly through direct influences on neural circuitry. Although non-specific, these features are clinically significant and reproducible. Lastly, this study demonstrates the necessity of studying large patient cohorts ascertained through multiple methods to characterise the clinical consequences of rare variants involved in common diseases.

Published
2012

5. Disease-associated balanced chromosomal rearrangements : molecular characterisation of two cases, with a review of the impact of published cases in human genetic research

Author

Harewood, Louise

Subjects
572.8
Abstract

Disease associated balanced chromosomal rearrangements (DBCRs) are large-scale alterations in normal genomic sequence, which occur without copy number change in a phenotypically abnormal individual. Complete ascertainment of published DBCRs was attempted via recursive searches of the literature. 775 cases were identified with 1672 breakpoints and 406 different phenotypes. Physical mapping of DBCR breakpoints has elucidated the genetic basis of Mendelian disorders in 29 cases and was the first indication of a subsequently verified disease locus in a further 30 cases. Two interesting DBCR cases, which had no cell-lines or fixed cell suspensions, were available for study: Case 1 had a t(2;12)(p25;q23.3) translocation associated with upper limb peromelia and lower limb phocomelia; Case 2 had a t(1;2)(q41;p25.3) associated with lethal bilateral renal adysplasia. In case 1, the 2p25 breakpoint was found to interrupt the ROCK2 gene, which, on the basis of the phenotype of null mice, was considered to be a poor candidate for the peromelia/phocomelia phenotype. The 12q23.3 breakpoint lay 0-25 kb from the 5’ end of the CMKLR1gene, which encodes a chemokine-like receptor, the sole ligand for which is encoded by the retinoic acid responsive gene, RARRES2. Site and stage-specific expression of both the receptor and the ligand in the developing limb bud suggested that CMKLR1 was a good candidate for a causative gene. A phenotypically similar case was screened for mutations in CMKLR1 and a candidate regulatory region, but none could be identified. A mouse model is being developed to further elucidate the developmental role of this gene. In case 2, the 2p25.3 breakpoint mapped to a gap in the genome sequence. No good candidate gene could be identified in the vicinity of this gap.

Published
2006

8. Karyosequencing: Integrating Genome-Wide and Targeted Sequencing for Comprehensive Diagnosis of Lymphoproliferative Disorders

Author

Stewart, James Peter, primary, Harewood, Louise, additional, Srivastava, Shambhavi, additional, Gazdova, Jana, additional, Maurya, Manisha, additional, Nakjang, Sirintra, additional, Hodges, Elizabeth, additional, Chiecchio, Laura, additional, Cross, Nicholas C.P., additional, Jenner, Matthew W, additional, Catherwood, Mark, additional, Ryan, Sarra, additional, Moorman, Anthony V., additional, Darzentas, Nikos, additional, and Gonzalez, David, additional

Published
2021
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9. The Potential of Digital Image Analysis to Determine Tumor Cell Content in Biobanked Formalin-Fixed, Paraffin-Embedded Tissue Samples

Author

Greene, Christine, primary, O'Doherty, Edwina, additional, Abdullahi Sidi, Fatima, additional, Bingham, Victoria, additional, Fisher, Natalie C., additional, Humphries, Matthew P., additional, Craig, Stephanie G., additional, Harewood, Louise, additional, McQuaid, Stephen, additional, Lewis, Claire, additional, and James, Jacqueline, additional

Published
2021
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12. Detection of Structural Variants in Circulating Cell-Free DNA from Sarcoma Patients Using Next Generation Sequencing

Author

Mc Connell, Lauren, primary, Gazdova, Jana, additional, Beck, Katja, additional, Srivastava, Shambhavi, additional, Harewood, Louise, additional, Stewart, JP, additional, Hübschmann, Daniel, additional, Stenzinger, Albrecht, additional, Glimm, Hanno, additional, Heilig, Christoph E., additional, Fröhling, Stefan, additional, and Gonzalez, David, additional

Published
2020
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14. A 600 kb deletion syndrome at 16p11.2 leads to energy imbalance and neuropsychiatric disorders

Author

Zufferey, Flore, Sherr, Elliott H, Beckmann, Noam D, Hanson, Ellen, Maillard, Anne M, Hippolyte, Loyse, Macé, Aurélien, Ferrari, Carina, Kutalik, Zoltán, Andrieux, Joris, Aylward, Elizabeth, Barker, Mandy, Bernier, Raphael, Bouquillon, Sonia, Conus, Philippe, Delobel, Bruno, Faucett, W Andrew, Goin-Kochel, Robin P, Grant, Ellen, Harewood, Louise, Hunter, Jill V, Lebon, Sébastien, Ledbetter, David H, Martin, Christa Lese, Männik, Katrin, Martinet, Danielle, Mukherjee, Pratik, Ramocki, Melissa B, Spence, Sarah J, Steinman, Kyle J, Tjernagel, Jennifer, Spiro, John E, Reymond, Alexandre, Beckmann, Jacques S, Chung, Wendy K, and Jacquemont, Sébastien

Published
2012
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15. Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus

Author

Jacquemont, Sébastien, Reymond, Alexandre, Zufferey, Flore, Harewood, Louise, Walters, Robin G., Kutalik, Zoltán, Martinet, Danielle, Shen, Yiping, Valsesia, Armand, Beckmann, Noam D., Thorleifsson, Gudmar, Belfiore, Marco, Bouquillon, Sonia, Campion, Dominique, de Leeuw, Nicole, de Vries, Bert B. A., Esko, Tõnu, Fernandez, Bridget A., Fernández-Aranda, Fernando, Fernández-Real, José Manuel, Gratacòs, Mònica, Guilmatre, Audrey, Hoyer, Juliane, Jarvelin, Marjo-Riitta, Kooy, Frank R., Kurg, Ants, Le Caignec, Cédric, Männik, Katrin, Platt, Orah S., Sanlaville, Damien, Van Haelst, Mieke M., Gomez, Sergi Villatoro, Walha, Faida, Wu, Bai-lin, Yu, Yongguo, Aboura, Azzedine, Addor, Marie-Claude, Alembik, Yves, Antonarakis, Stylianos E., Arveiler, Benoît, Barth, Magalie, Bednarek, Nathalie, Béna, Frédérique, Bergmann, Sven, Beri, Mylène, Bernardini, Laura, Blaumeiser, Bettina, Bonneau, Dominique, Bottani, Armand, Boute, Odile, Brunner, Han G., Cailley, Dorothée, Callier, Patrick, Chiesa, Jean, Chrast, Jacqueline, Coin, Lachlan, Coutton, Charles, Cuisset, Jean-Marie, Cuvellier, Jean-Christophe, David, Albert, de Freminville, Bénédicte, Delobel, Bruno, Delrue, Marie-Ange, Demeer, Bénédicte, Descamps, Dominique, Didelot, Gérard, Dieterich, Klaus, Disciglio, Vittoria, Doco-Fenzy, Martine, Drunat, Séverine, Duban-Bedu, Bénédicte, Dubourg, Christèle, Moustafa, Julia S. El-Sayed, Elliott, Paul, Faas, Brigitte H. W., Faivre, Laurence, Faudet, Anne, Fellmann, Florence, Ferrarini, Alessandra, Fisher, Richard, Flori, Elisabeth, Forer, Lukas, Gaillard, Dominique, Gerard, Marion, Gieger, Christian, Gimelli, Stefania, Gimelli, Giorgio, Grabe, Hans J., Guichet, Agnès, Guillin, Olivier, Hartikainen, Anna-Liisa, Heron, Délphine, Hippolyte, Loyse, Holder, Muriel, Homuth, Georg, Isidor, Bertrand, Jaillard, Sylvie, Jaros, Zdenek, Jiménez-Murcia, Susana, Helas, Géraldine Joly, Jonveaux, Philippe, Kaksonen, Satu, Keren, Boris, Kloss-Brandstätter, Anita, Knoers, Nine V. A. M., Koolen, David A., Kroisel, Peter M., Kronenberg, Florian, Labalme, Audrey, Landais, Emilie, Lapi, Elisabetta, Layet, Valérie, Legallic, Solenn, Leheup, Bruno, Leube, Barbara, Lewis, Suzanne, Lucas, Josette, MacDermot, Kay D., Magnusson, Pall, Marshall, Christian, Mathieu-Dramard, Michèle, McCarthy, Mark I., Meitinger, Thomas, Mencarelli, Maria Antonietta, Merla, Giuseppe, Moerman, Alexandre, Mooser, Vincent, Morice-Picard, Fanny, Mucciolo, Mafalda, Nauck, Matthias, Ndiaye, Ndeye Coumba, Nordgren, Ann, Pasquier, Laurent, Petit, Florence, Pfundt, Rolph, Plessis, Ghislaine, Rajcan-Separovic, Evica, Ramelli, Gian Paolo, Rauch, Anita, Ravazzolo, Roberto, Reis, Andre, Renieri, Alessandra, Richart, Cristobal, Ried, Janina S., Rieubland, Claudine, Roberts, Wendy, Roetzer, Katharina M., Rooryck, Caroline, Rossi, Massimiliano, Saemundsen, Evald, Satre, Véronique, Schurmann, Claudia, Sigurdsson, Engilbert, Stavropoulos, Dimitri J., Stefansson, Hreinn, Tengström, Carola, Thorsteinsdóttir, Unnur, Tinahones, Francisco J., Touraine, Renaud, Vallée, Louis, van Binsbergen, Ellen, Van der Aa, Nathalie, Vincent-Delorme, Catherine, Visvikis-Siest, Sophie, Vollenweider, Peter, Völzke, Henry, Vulto-van Silfhout, Anneke T., Waeber, Gérard, Wallgren-Pettersson, Carina, Witwicki, Robert M., Zwolinksi, Simon, Andrieux, Joris, Estivill, Xavier, Gusella, James F., Gustafsson, Omar, Metspalu, Andres, Scherer, Stephen W., Stefansson, Kari, Blakemore, Alexandra I. F., Beckmann, Jacques S., and Froguel, Philippe

Published
2011
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20. NF-κB-Dependent Lymphoid Enhancer Co-option Promotes Renal Carcinoma Metastasis

Author

Rodrigues, Paulo, Patel, Saroor A, Harewood, Louise, Olan, Ioana, Vojtasova, Erika, Syafruddin, Saiful E, Zaini, M Nazhif, Richardson, Emma K, Burge, Johanna, Warren, Anne Y, Stewart, Grant D, Saeb-Parsy, Kourosh, Samarajiwa, Shamith A, Vanharanta, Sakari, Olan, Ioana [0000-0003-0692-1831], Samarajiwa, Shamith A [0000-0003-1046-0601], and Apollo - University of Cambridge Repository

Subjects
Gene Expression Regulation, Neoplastic, Male, Mice, Enhancer Elements, Genetic, Lung Neoplasms, Mice, Inbred NOD, Cell Line, Tumor, Basic Helix-Loop-Helix Transcription Factors, NF-kappa B, Animals, Humans, Mice, SCID, Kidney Neoplasms
Abstract

Metastases, the spread of cancer cells to distant organs, cause the majority of cancer-related deaths. Few metastasis-specific driver mutations have been identified, suggesting aberrant gene regulation as a source of metastatic traits. However, how metastatic gene expression programs arise is poorly understood. Here, using human-derived metastasis models of renal cancer, we identify transcriptional enhancers that promote metastatic carcinoma progression. Specific enhancers and enhancer clusters are activated in metastatic cancer cell populations, and the associated gene expression patterns are predictive of poor patient outcome in clinical samples. We find that the renal cancer metastasis-associated enhancer complement consists of multiple coactivated tissue-specific enhancer modules. Specifically, we identify and functionally characterize a coregulatory enhancer cluster, activated by the renal cancer driver HIF2A and an NF-κB-driven lymphoid element, as a mediator of metastasis in vivo We conclude that oncogenic pathways can acquire metastatic phenotypes through cross-lineage co-option of physiologic epigenetic enhancer states.Significance: Renal cancer is associated with significant mortality due to metastasis. We show that in metastatic renal cancer, functionally important metastasis genes are activated via co-option of gene regulatory enhancer modules from distant developmental lineages, thus providing clues to the origins of metastatic cancer. Cancer Discov; 8(7); 850-65. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 781.

Published
2018

21. Genetic Analysis of 'PAX6-Negative' Individuals with Aniridia or Gillespie Syndrome

Author

Ansari, Morad, Rainger, Jacqueline, Hanson, Isabel M, Williamson, Kathleen A, Sharkey, Freddie, Harewood, Louise, Sandilands, Angela, Clayton-Smith, Jill, Dollfus, Helene, Bitoun, Pierre, Meire, Francoise, Fantes, Judy, Franco, Brunella, Lorenz, Birgit, Taylor, David S, Stewart, Fiona, Willoughby, Colin E, McEntagart, Meriel, Khaw, Peng Tee, Clericuzio, Carol, Van Maldergem, Lionel, Williams, Denise, Newbury-Ecob, Ruth, Traboulsi, Elias I, Silva, Eduardo D, Madlom, Mukhlis M, Goudie, David R, Fleck, Brian W, Wieczorek, Dagmar, Kohlhase, Juergen, McTrusty, Alice D, Gardiner, Carol, Yale, Christopher, Moore, Anthony T, Russell-Eggitt, Isabelle, Islam, Lily, Lees, Melissa, Beales, Philip L, Tuft, Stephen J, Solano, Juan B, Splitt, Miranda, Hertz, Jens Michael, Prescott, Trine E, Shears, Deborah J, Nischal, Ken K, Doco-Fenzy, Martine, Prieur, Fabienne, Temple, I Karen, Lachlan, Katherine L, Damante, Giuseppe, Morrison, Danny A, van Heyningen, Veronica, FitzPatrick, David R, Ansari, Morad, Rainger, Jacqueline, Hanson, Isabel M., Williamson, Kathleen A., Sharkey, Freddie, Harewood, Louise, Sandilands, Angela, Clayton Smith, Jill, Dollfus, Helene, Bitoun, Pierre, Meire, Francoise, Fantes, Judy, Franco, Brunella, Lorenz, Birgit, Taylor, David S., Stewart, Fiona, Willoughby, Colin E., Mcentagart, Meriel, Khaw, Peng Tee, Clericuzio, Carol, Van Maldergem, Lionel, Williams, Denise, Newbury Ecob, Ruth, Traboulsi, Elias I., Silva, Eduardo D., Madlom, Mukhlis M., Goudie, David R., Fleck, Brian W., Wieczorek, Dagmar, Kohlhase, Juergen, Mctrusty, Alice D., Gardiner, Carol, Yale, Christopher, Moore, Anthony T., Russell Eggitt, Isabelle, Islam, Lily, Lees, Melissa, Beales, Philip L., Tuft, Stephen J., Solano, Juan B., Splitt, Miranda, Hertz, Jens Michael, Prescott, Trine E., Shears, Deborah J., Nischal, Ken K., Doco Fenzy, Martine, Prieur, Fabienne, Temple, I. Karen, Lachlan, Katherine L., Damante, Giuseppe, Morrison, Danny A., Van Heyningen, Veronica, and Fitzpatrick, David R.

Subjects
Male, Genetics and Molecular Biology (all), Eye Diseases, PAX6 Transcription Factor, Mutagenesis and Gene Deletion Techniques, Gene Identification and Analysis, Iris, lcsh:Medicine, Artificial Gene Amplification and Extension, Polymerase Chain Reaction, Biochemistry, axenfeld-rieger syndrome gtpase-activating protein linear skin defects cerebellar-ataxia mental-retardation pax6 gene missense mutations impaired accommodation pitx2 mutations phenotype Science & Technology - Other Topics, Medicine and Health Sciences, Pair 11, lcsh:Science, Aniridia, Comparative Genomic Hybridization, Medicine (all), GTPase-Activating Proteins, Forkhead Transcription Factors, Genomics, Deletion Mutation, Female, Anatomy, Research Article, Human, congenital, hereditary, and neonatal diseases and abnormalities, Cerebellar Ataxia, Ocular Anatomy, Research and Analysis Methods, Human Genomics, Chromosomes, Histone Deacetylases, Ocular System, Intellectual Disability, Genetics, Humans, Genetic Testing, Molecular Biology Techniques, Molecular Biology, Mutation Detection, Homeodomain Proteins, Chromosomes, Human, X, Biochemistry, Genetics and Molecular Biology (all), Chromosomes, Human, Pair 11, lcsh:R, Biology and Life Sciences, Glaucoma, Mutation, Transcription Factors, Agricultural and Biological Sciences (all), eye diseases, Ophthalmology, Mutational Analysis, Genetic Loci, lcsh:Q, sense organs
Abstract

We report molecular genetic analysis of 42 affected individuals referred with a diagnosis of aniridia who previously screened as negative for intragenic PAX6 mutations. Of these 42, the diagnoses were 31 individuals with aniridia and 11 individuals referred with a diagnosis of Gillespie syndrome (iris hypoplasia, ataxia and mild to moderate developmental delay). Array-based comparative genomic hybridization identified six whole gene deletions: four encompassing PAX6 and two encompassing FOXC1. Six deletions with plausible cis-regulatory effects were identified: five that were 3′ (telomeric) to PAX6 and one within a gene desert 5′ (telomeric) to PITX2. Sequence analysis of the FOXC1 and PITX2 coding regions identified two plausibly pathogenic de novo FOXC1 missense mutations (p.Pro79Thr and p. Leu101Pro). No intragenic mutations were detected in PITX2. FISH mapping in an individual with Gillespie-like syndrome with an apparently balanced X;11 reciprocal translocation revealed disruption of a gene at each breakpoint: ARHGAP6 on the X chromosome and PHF21A on chromosome 11. In the other individuals with Gillespie syndrome no mutations were identified in either of these genes, or in HCCS which lies close to the Xp breakpoint. Disruption of PHF21A has previously been implicated in the causation of intellectual disability (but not aniridia). Plausibly causative mutations were identified in 15 out of 42 individuals (12/32 aniridia; 3/11 Gillespie syndrome). Fourteen of these mutations presented in the known aniridia genes; PAX6, FOXC1 and PITX2. The large number of individuals in the cohort with no mutation identified suggests greater locus heterogeneity may exist in both isolated and syndromic aniridia than was previously appreciated.

Published
2016

24. NF-κB–Dependent Lymphoid Enhancer Co-option Promotes Renal Carcinoma Metastasis

Author

Rodrigues, Paulo, primary, Patel, Saroor A., additional, Harewood, Louise, additional, Olan, Ioana, additional, Vojtasova, Erika, additional, Syafruddin, Saiful E., additional, Zaini, M. Nazhif, additional, Richardson, Emma K., additional, Burge, Johanna, additional, Warren, Anne Y., additional, Stewart, Grant D., additional, Saeb-Parsy, Kourosh, additional, Samarajiwa, Shamith A., additional, and Vanharanta, Sakari, additional

Published
2018
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27. A potential contributory role for ciliary dysfunction in the 16p11.2 600 kb BP4-BP5 pathology

Author

Migliavacca, Eugenia, Golzio, Christelle, Männik, Katrin, Blumenthal, Ian, Oh, Edwin C., Harewood, Louise, Kosmicki, Jack A., Loviglio, Maria Nicla, Giannuzzi, Giuliana, Hippolyte, Loyse, Maillard, Anne M., Alfaiz, Ali Abdullah, Witwicki, Robert, Didelot, Gérard, Van Der Werf, Ilse, Alfaiz, Ali A., Zazhytska, Marianna, Chrast, Jacqueline, Macé, Aurélien, Bergmann, Sven, Kutalik, Zoltan, Siffredi, Vanessa, Zufferey, Flore, Martinet, Danielle, Bena, Frédérique, Rauch, Anita, Bouquillon, Sonia, Delobel, Bruno, Boute, Odile, Duban-Bedu, Bénédicte, Le Caignec, Cédric, Isidor, Bertrand, Chiesa, Jean, Keren, Boris, Gilbert-Dussardier, Brigitte, Touraine, Renaud, Campion, Dominique, Thambo, Caroline Rooryck, Mathieu-Dramard, Michèle, Plessis, Ghislaine, Kooy, Frank, Peeters, Hilde, Ounap, Katrin, Vulto-Van Silfhout, Anneke T., De Vries, Bert B., Van Binsbergen, Ellen, Nordgren, Ann, Mucciolo, Mafalda, Renieri, Alessandra, Rajcan-Separovic, Evica, Philipps, John A., Ellis, Richard J., Van Haelst, Mieke M., Andrieux, Joris, Gusella, James F., Daly, Mark J., Beckmann, Jacques S., Jacquemont, Sébastien, Talkowski, Michael E., Katsanis, Nicholas, Reymond, Alexandre, Migliavacca, Eugenia, Golzio, Christelle, Männik, Katrin, Blumenthal, Ian, Oh, Edwin C., Harewood, Louise, Kosmicki, Jack A., Loviglio, Maria Nicla, Giannuzzi, Giuliana, Hippolyte, Loyse, Maillard, Anne M., Alfaiz, Ali Abdullah, Witwicki, Robert, Didelot, Gérard, Van Der Werf, Ilse, Alfaiz, Ali A., Zazhytska, Marianna, Chrast, Jacqueline, Macé, Aurélien, Bergmann, Sven, Kutalik, Zoltan, Siffredi, Vanessa, Zufferey, Flore, Martinet, Danielle, Bena, Frédérique, Rauch, Anita, Bouquillon, Sonia, Delobel, Bruno, Boute, Odile, Duban-Bedu, Bénédicte, Le Caignec, Cédric, Isidor, Bertrand, Chiesa, Jean, Keren, Boris, Gilbert-Dussardier, Brigitte, Touraine, Renaud, Campion, Dominique, Thambo, Caroline Rooryck, Mathieu-Dramard, Michèle, Plessis, Ghislaine, Kooy, Frank, Peeters, Hilde, Ounap, Katrin, Vulto-Van Silfhout, Anneke T., De Vries, Bert B., Van Binsbergen, Ellen, Nordgren, Ann, Mucciolo, Mafalda, Renieri, Alessandra, Rajcan-Separovic, Evica, Philipps, John A., Ellis, Richard J., Van Haelst, Mieke M., Andrieux, Joris, Gusella, James F., Daly, Mark J., Beckmann, Jacques S., Jacquemont, Sébastien, Talkowski, Michael E., Katsanis, Nicholas, and Reymond, Alexandre

Published
2015

28. A potential contributory role for ciliary dysfunction in the 16p11.2 600 kb BP4-BP5 pathology

Author

Genetica Klinische Genetica, Child Health, Genetica Sectie Genoomdiagnostiek, Migliavacca, Eugenia, Golzio, Christelle, Männik, Katrin, Blumenthal, Ian, Oh, Edwin C., Harewood, Louise, Kosmicki, Jack A., Loviglio, Maria Nicla, Giannuzzi, Giuliana, Hippolyte, Loyse, Maillard, Anne M., Alfaiz, Ali Abdullah, Witwicki, Robert, Didelot, Gérard, Van Der Werf, Ilse, Alfaiz, Ali A., Zazhytska, Marianna, Chrast, Jacqueline, Macé, Aurélien, Bergmann, Sven, Kutalik, Zoltan, Siffredi, Vanessa, Zufferey, Flore, Martinet, Danielle, Bena, Frédérique, Rauch, Anita, Bouquillon, Sonia, Delobel, Bruno, Boute, Odile, Duban-Bedu, Bénédicte, Le Caignec, Cédric, Isidor, Bertrand, Chiesa, Jean, Keren, Boris, Gilbert-Dussardier, Brigitte, Touraine, Renaud, Campion, Dominique, Thambo, Caroline Rooryck, Mathieu-Dramard, Michèle, Plessis, Ghislaine, Kooy, Frank, Peeters, Hilde, Ounap, Katrin, Vulto-Van Silfhout, Anneke T., De Vries, Bert B., Van Binsbergen, Ellen, Nordgren, Ann, Mucciolo, Mafalda, Renieri, Alessandra, Rajcan-Separovic, Evica, Philipps, John A., Ellis, Richard J., Van Haelst, Mieke M., Andrieux, Joris, Gusella, James F., Daly, Mark J., Beckmann, Jacques S., Jacquemont, Sébastien, Talkowski, Michael E., Katsanis, Nicholas, Reymond, Alexandre, Genetica Klinische Genetica, Child Health, Genetica Sectie Genoomdiagnostiek, Migliavacca, Eugenia, Golzio, Christelle, Männik, Katrin, Blumenthal, Ian, Oh, Edwin C., Harewood, Louise, Kosmicki, Jack A., Loviglio, Maria Nicla, Giannuzzi, Giuliana, Hippolyte, Loyse, Maillard, Anne M., Alfaiz, Ali Abdullah, Witwicki, Robert, Didelot, Gérard, Van Der Werf, Ilse, Alfaiz, Ali A., Zazhytska, Marianna, Chrast, Jacqueline, Macé, Aurélien, Bergmann, Sven, Kutalik, Zoltan, Siffredi, Vanessa, Zufferey, Flore, Martinet, Danielle, Bena, Frédérique, Rauch, Anita, Bouquillon, Sonia, Delobel, Bruno, Boute, Odile, Duban-Bedu, Bénédicte, Le Caignec, Cédric, Isidor, Bertrand, Chiesa, Jean, Keren, Boris, Gilbert-Dussardier, Brigitte, Touraine, Renaud, Campion, Dominique, Thambo, Caroline Rooryck, Mathieu-Dramard, Michèle, Plessis, Ghislaine, Kooy, Frank, Peeters, Hilde, Ounap, Katrin, Vulto-Van Silfhout, Anneke T., De Vries, Bert B., Van Binsbergen, Ellen, Nordgren, Ann, Mucciolo, Mafalda, Renieri, Alessandra, Rajcan-Separovic, Evica, Philipps, John A., Ellis, Richard J., Van Haelst, Mieke M., Andrieux, Joris, Gusella, James F., Daly, Mark J., Beckmann, Jacques S., Jacquemont, Sébastien, Talkowski, Michael E., Katsanis, Nicholas, and Reymond, Alexandre

Published
2015

29. A Potential Contributory Role for Ciliary Dysfunction in the 16p11.2 600 kb BP4-BP5 Pathology

Author

Migliavacca, Eugenia, primary, Golzio, Christelle, additional, Männik, Katrin, additional, Blumenthal, Ian, additional, Oh, Edwin C., additional, Harewood, Louise, additional, Kosmicki, Jack A., additional, Loviglio, Maria Nicla, additional, Giannuzzi, Giuliana, additional, Hippolyte, Loyse, additional, Maillard, Anne M., additional, Alfaiz, Ali Abdullah, additional, van Haelst, Mieke M., additional, Andrieux, Joris, additional, Gusella, James F., additional, Daly, Mark J., additional, Beckmann, Jacques S., additional, Jacquemont, Sébastien, additional, Talkowski, Michael E., additional, Katsanis, Nicholas, additional, Reymond, Alexandre, additional, Migliavacca, Eugenia, additional, Witwicki, Robert, additional, Didelot, Gérard, additional, van der Werf, Ilse, additional, Alfaiz, Ali A., additional, Zazhytska, Marianna, additional, Chrast, Jacqueline, additional, Macé, Aurélien, additional, Bergmann, Sven, additional, Kutalik, Zoltan, additional, Siffredi, Vanessa, additional, Zufferey, Flore, additional, Martinet, Danielle, additional, Bena, Frédérique, additional, Rauch, Anita, additional, Bouquillon, Sonia, additional, Delobel, Bruno, additional, Boute, Odile, additional, Duban-Bedu, Bénédicte, additional, Le Caignec, Cédric, additional, Isidor, Bertrand, additional, Chiesa, Jean, additional, Keren, Boris, additional, Gilbert-Dussardier, Brigitte, additional, Touraine, Renaud, additional, Campion, Dominique, additional, Thambo, Caroline Rooryck, additional, Mathieu-Dramard, Michèle, additional, Plessis, Ghislaine, additional, Kooy, Frank, additional, Peeters, Hilde, additional, Ounap, Katrin, additional, Vulto-van Silfhout, Anneke T., additional, de Vries, Bert B., additional, van Binsbergen, Ellen, additional, van Haelst, Mieke M., additional, Nordgren, Ann, additional, Mucciolo, Mafalda, additional, Renieri, Alessandra, additional, Rajcan-Separovic, Evica, additional, Philipps, John A., additional, Ellis, Richard J., additional, and Beckmann, Jacques S., additional

Published
2015
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37. Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours

Author

Steven W. Wingett, Matthew D. Eldridge, Kamal Kishore, Stefan Schoenfelder, Danita M. Pearson, V. Peter Collins, Louise Harewood, Peter Fraser, Harewood, Louise [0000-0002-6398-6714], Kishore, Kamal [0000-0002-4650-8745], Eldridge, Matthew [0000-0002-5799-8911], Schoenfelder, Stefan [0000-0002-3200-8133], Collins, Peter [0000-0002-0381-8516], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, DNA Copy Number Variations, lcsh:QH426-470, Population, Chromosome Breakpoints, Method, Chromosomal translocation, Chromosomal rearrangement, Biology, Translocation, Genetic, Chromosome conformation capture, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Hi-C, Neoplasms, Humans, Copy-number variation, education, lcsh:QH301-705.5, In Situ Hybridization, Fluorescence, Cancer, Chromosomal inversion, Gene Rearrangement, Chromosome Aberrations, Genetics, education.field_of_study, Genome, Chromosome rearrangement, Copy number variation, Human genetics, lcsh:Genetics, 030104 developmental biology, lcsh:Biology (General), Chromosome Inversion, Tumour, Glioblastoma, Anaplastic astrocytoma
Abstract

Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, is troublesome, which is particularly detrimental in oncology where rearrangements play diagnostic and prognostic roles. Here we describe the use of Hi-C as a tool for detection of both balanced and unbalanced chromosomal rearrangements in primary human tumour samples, with the potential to define chromosome breakpoints to bp resolution. In addition, we show copy number profiles can also be obtained from the same data, all at a significantly lower cost than standard sequencing approaches. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1253-8) contains supplementary material, which is available to authorized users.

Published
2017

38. Immunoglobulin/T Cell Receptor Capture Strategy for Comprehensive Immunogenetics.

Author

Stewart JP, Gazdova J, Srivastava S, Revolta J, Harewood L, Maurya M, Darzentas N, and Gonzalez D

Subjects
DNA Copy Number Variations, High-Throughput Nucleotide Sequencing methods, Humans, Immunoglobulins genetics, Immunogenetics, Receptors, Antigen, T-Cell genetics
Abstract

In the era of genomic medicine, targeted next generation sequencing strategies (NGS) are becoming increasingly adopted by clinical molecular diagnostic laboratories to identify genetic diagnostic and prognostic biomarkers in hemato-oncology. We describe the EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay, which is designed to simultaneously detect B and T cell clonal rearrangements, translocations, copy number alterations, and sequence variants. The accompanying validated bioinformatics pipeline enables production of an integrated report. The combination of the laboratory protocol and bioinformatics pipeline in the EuroClonality-NDC minimizes the potential for human error, reduces economic costs compared to current molecular testing strategies, and should improve diagnostic outcomes., (© 2022. The Author(s).)

Published
2022
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39. Structural variation and its effect on expression.

Author

Harewood L, Chaignat E, and Reymond A

Subjects
Chromosome Mapping, DNA Copy Number Variations, Gene Deletion, Gene Dosage, Gene Duplication, Gene Rearrangement, Humans, Phenotype, Quantitative Trait Loci, Regulatory Sequences, Nucleic Acid, Translocation, Genetic, Gene Expression, Genetic Variation, Genome, Human
Abstract

Structural variation, whether it is caused by copy number variants or present in a balanced form, such as reciprocal translocations and inversions, can have a profound and dramatic effect on the expression of genes mapping within and close to the rearrangement, as well as affecting others genome wide. These effects can be caused by altering the copy number of one or more genes or regulatory elements (dosage effect) or from physical disruption of links between regulatory elements and their associated gene or genes, resulting in perturbation of expression. Similarly, large-scale structural variants can result in genome-wide expression changes by altering the positions that chromosomes occupy within the nucleus, potentially disrupting not only local cis interactions, but also trans interactions that occur throughout the genome. Structural variation is, therefore, a significant factor in the study of gene expression and is discussed here in more detail.

Published
2012
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