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2. Genomic architecture of autism from comprehensive whole-genome sequence annotation.

Author

Trost, Brett, Thiruvahindrapuram, Bhooma, Chan, Ada, Engchuan, Worrawat, Higginbotham, Edward, Howe, Jennifer, Loureiro, Livia, Reuter, Miriam, Roshandel, Delnaz, Whitney, Joe, Zarrei, Mehdi, Bookman, Matthew, Somerville, Cherith, Shaath, Rulan, Abdi, Mona, Aliyev, Elbay, Patel, Rohan, Nalpathamkalam, Thomas, Pellecchia, Giovanna, Hamdan, Omar, Kaur, Gaganjot, Wang, Zhuozhi, MacDonald, Jeffrey, Wei, John, Sung, Wilson, Lamoureux, Sylvia, Hoang, Ny, Selvanayagam, Thanuja, Deflaux, Nicole, Geng, Melissa, Ghaffari, Siavash, Bates, John, Young, Edwin, Ding, Qiliang, Shum, Carole, DAbate, Lia, Bradley, Clarrisa, Rutherford, Annabel, Aguda, Vernie, Apresto, Beverly, Chen, Nan, Desai, Sachin, Du, Xiaoyan, Fong, Matthew, Pullenayegum, Sanjeev, Samler, Kozue, Wang, Ting, Ho, Karen, Paton, Tara, Pereira, Sergio, Herbrick, Jo-Anne, Wintle, Richard, Fuerth, Jonathan, Noppornpitak, Juti, Ward, Heather, Magee, Patrick, Al Baz, Ayman, Kajendirarajah, Usanthan, Kapadia, Sharvari, Vlasblom, Jim, Valluri, Monica, Green, Joseph, Seifer, Vicki, Quirbach, Morgan, Rennie, Olivia, Kelley, Elizabeth, Masjedi, Nina, Lord, Catherine, Szego, Michael, Zawati, Man, Lang, Michael, Strug, Lisa, Marshall, Christian, Costain, Gregory, Calli, Kristina, Iaboni, Alana, Yusuf, Afiqah, Ambrozewicz, Patricia, Gallagher, Louise, Amaral, David, Brian, Jessica, Elsabbagh, Mayada, Georgiades, Stelios, Messinger, Daniel, Ozonoff, Sally, Sebat, Jonathan, Sjaarda, Calvin, Smith, Isabel, Szatmari, Peter, Zwaigenbaum, Lonnie, Kushki, Azadeh, Frazier, Thomas, Vorstman, Jacob, Fakhro, Khalid, Fernandez, Bridget, Lewis, M, Weksberg, Rosanna, Fiume, Marc, Yuen, Ryan, and Anagnostou, Evdokia

Subjects
autism spectrum disorder, copy-number variation, neurodevelopmental disorders, phenotype measures, polygenic risk scores, rare variants, structural variation, whole-genome sequencing, Humans, Autism Spectrum Disorder, Autistic Disorder, Genetic Predisposition to Disease, DNA Copy Number Variations, Genomics
Abstract

Fully understanding autism spectrum disorder (ASD) genetics requires whole-genome sequencing (WGS). We present the latest release of the Autism Speaks MSSNG resource, which includes WGS data from 5,100 individuals with ASD and 6,212 non-ASD parents and siblings (total n = 11,312). Examining a wide variety of genetic variants in MSSNG and the Simons Simplex Collection (SSC; n = 9,205), we identified ASD-associated rare variants in 718/5,100 individuals with ASD from MSSNG (14.1%) and 350/2,419 from SSC (14.5%). Considering genomic architecture, 52% were nuclear sequence-level variants, 46% were nuclear structural variants (including copy-number variants, inversions, large insertions, uniparental isodisomies, and tandem repeat expansions), and 2% were mitochondrial variants. Our study provides a guidebook for exploring genotype-phenotype correlations in families who carry ASD-associated rare variants and serves as an entry point to the expanded studies required to dissect the etiology in the ∼85% of the ASD population that remain idiopathic.

Published
2022

4. KIF1A novel frameshift variant p.(Ser887Profs*64) exhibits clinical heterogeneity in a Pakistani family with hereditary sensory and autonomic neuropathy type IIC.

Author

Ghafoor, Saima, Rafiq, Muhammad Arshad, Abbas Shah, Syed Tahir, Ansar, Muhammad, Paton, Tara, Ajmal, Muhammad, Agha, Zehra, Qamar, Raheel, and Azam, Maleeha

Subjects
SINGLE nucleotide polymorphisms, FRAMESHIFT mutation, NEUROPATHY, GENETIC disorders, PERIPHERAL nervous system
Abstract

Background: Hereditary sensory and autonomic neuropathies (HSANs) are rare heterogeneous group of neurological disorders caused by peripheral nerve deterioration. The HSANs sub-clinical classes have clinical and genetic overlap which often lead to misdiagnosis. In the present study a Pakistani family with five affected members suffering from severe neuropathy were genetically analyzed to identify the disease causative element in the family. Methods: Genome wide high-density single nucleotide polymorphism (SNP) microarray analysis was carried out followed by whole exome sequencing of the affected proband and another affected sibling. Shared homozygous regions in all severely affected members were identified through homozygosity mapping approach. Results: The largest homozygous region of 14.1 Mb shared by the five severely affected members of the family was identified on chromosome 2. Subsequent exome sequencing identified a novel single nucleotide deletion c.2658del; p.(Ser887Profs*64) in KIF1A. Segregation analysis revealed that this mutation was homozygous in all five affected individuals of the family with severe clinical manifestation, while members of the family that were heterozygous carriers shared abnormal skin features (scaly skin) only with the homozygous affected members. Conclusions: A novel frameshift mutation p.(Ser887Profs*64) in KIF1A is the potential cause of severe HSANIIC in a Pakistani family along with incomplete penetrance in mutation carriers. We demonstrate that using a combination of different techniques not only strengthens the gene finding approach but also helps in proper sub-clinical characterization along with identification of mutated alleles exhibiting incomplete penetrance leading to intrafamilial clinical variability in HSAN group of inherited diseases. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Individual common variants exert weak effects on the risk for autism spectrum disorders

Author

Anney, Richard, Klei, Lambertus, Pinto, Dalila, Almeida, Joana, Bacchelli, Elena, Baird, Gillian, Bolshakova, Nadia, Bölte, Sven, Bolton, Patrick F, Bourgeron, Thomas, Brennan, Sean, Brian, Jessica, Casey, Jillian, Conroy, Judith, Correia, Catarina, Corsello, Christina, Crawford, Emily L, de Jonge, Maretha, Delorme, Richard, Duketis, Eftichia, Duque, Frederico, Estes, Annette, Farrar, Penny, Fernandez, Bridget A, Folstein, Susan E, Fombonne, Eric, Gilbert, John, Gillberg, Christopher, Glessner, Joseph T, Green, Andrew, Green, Jonathan, Guter, Stephen J, Heron, Elizabeth A, Holt, Richard, Howe, Jennifer L, Hughes, Gillian, Hus, Vanessa, Igliozzi, Roberta, Jacob, Suma, Kenny, Graham P, Kim, Cecilia, Kolevzon, Alexander, Kustanovich, Vlad, Lajonchere, Clara M, Lamb, Janine A, Law-Smith, Miriam, Leboyer, Marion, Le Couteur, Ann, Leventhal, Bennett L, Liu, Xiao-Qing, Lombard, Frances, Lord, Catherine, Lotspeich, Linda, Lund, Sabata C, Magalhaes, Tiago R, Mantoulan, Carine, McDougle, Christopher J, Melhem, Nadine M, Merikangas, Alison, Minshew, Nancy J, Mirza, Ghazala K, Munson, Jeff, Noakes, Carolyn, Nygren, Gudrun, Papanikolaou, Katerina, Pagnamenta, Alistair T, Parrini, Barbara, Paton, Tara, Pickles, Andrew, Posey, David J, Poustka, Fritz, Ragoussis, Jiannis, Regan, Regina, Roberts, Wendy, Roeder, Kathryn, Roge, Bernadette, Rutter, Michael L, Schlitt, Sabine, Shah, Naisha, Sheffield, Val C, Soorya, Latha, Sousa, Inês, Stoppioni, Vera, Sykes, Nuala, Tancredi, Raffaella, Thompson, Ann P, Thomson, Susanne, Tryfon, Ana, Tsiantis, John, Van Engeland, Herman, Vincent, John B, Volkmar, Fred, Vorstman, JAS, Wallace, Simon, Wing, Kirsty, Wittemeyer, Kerstin, Wood, Shawn, Zurawiecki, Danielle, Zwaigenbaum, Lonnie, and Bailey, Anthony J

Subjects
Behavioral and Social Science, Clinical Research, Human Genome, Mental Health, Genetics, Brain Disorders, Pediatric, Intellectual and Developmental Disabilities (IDD), Autism, Prevention, Aetiology, 2.1 Biological and endogenous factors, Alleles, Child, Child Development Disorders, Pervasive, Female, Gene Frequency, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Language Development, Male, Membrane Proteins, Nerve Tissue Proteins, Polymorphism, Single Nucleotide, Risk Factors, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASDs), the contribution of common variation to the risk of developing ASD is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating the association of individual single nucleotide polymorphisms (SNPs), we also sought evidence that common variants, en masse, might affect the risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest P-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. In contrast, allele scores derived from the transmission of common alleles to Stage 1 cases significantly predict case status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele score results, it is reasonable to conclude that common variants affect the risk for ASD but their individual effects are modest.

Published
2012

6. A genome-wide scan for common alleles affecting risk for autism

Author

Anney, Richard, Klei, Lambertus, Pinto, Dalila, Regan, Regina, Conroy, Judith, Magalhaes, Tiago R, Correia, Catarina, Abrahams, Brett S, Sykes, Nuala, Pagnamenta, Alistair T, Almeida, Joana, Bacchelli, Elena, Bailey, Anthony J, Baird, Gillian, Battaglia, Agatino, Berney, Tom, Bolshakova, Nadia, Bölte, Sven, Bolton, Patrick F, Bourgeron, Thomas, Brennan, Sean, Brian, Jessica, Carson, Andrew R, Casallo, Guillermo, Casey, Jillian, Chu, Su H, Cochrane, Lynne, Corsello, Christina, Crawford, Emily L, Crossett, Andrew, Dawson, Geraldine, de Jonge, Maretha, Delorme, Richard, Drmic, Irene, Duketis, Eftichia, Duque, Frederico, Estes, Annette, Farrar, Penny, Fernandez, Bridget A, Folstein, Susan E, Fombonne, Eric, Freitag, Christine M, Gilbert, John, Gillberg, Christopher, Glessner, Joseph T, Goldberg, Jeremy, Green, Jonathan, Guter, Stephen J, Hakonarson, Hakon, Heron, Elizabeth A, Hill, Matthew, Holt, Richard, Howe, Jennifer L, Hughes, Gillian, Hus, Vanessa, Igliozzi, Roberta, Kim, Cecilia, Klauck, Sabine M, Kolevzon, Alexander, Korvatska, Olena, Kustanovich, Vlad, Lajonchere, Clara M, Lamb, Janine A, Laskawiec, Magdalena, Leboyer, Marion, Le Couteur, Ann, Leventhal, Bennett L, Lionel, Anath C, Liu, Xiao-Qing, Lord, Catherine, Lotspeich, Linda, Lund, Sabata C, Maestrini, Elena, Mahoney, William, Mantoulan, Carine, Marshall, Christian R, McConachie, Helen, McDougle, Christopher J, McGrath, Jane, McMahon, William M, Melhem, Nadine M, Merikangas, Alison, Migita, Ohsuke, Minshew, Nancy J, Mirza, Ghazala K, Munson, Jeff, Nelson, Stanley F, Noakes, Carolyn, Noor, Abdul, Nygren, Gudrun, Oliveira, Guiomar, Papanikolaou, Katerina, Parr, Jeremy R, Parrini, Barbara, Paton, Tara, Pickles, Andrew, Piven, Joseph, Posey, David J, Poustka, Annemarie, and Poustka, Fritz

Subjects
Clinical Research, Human Genome, Mental Health, Genetics, Brain Disorders, Pediatric, Biotechnology, Intellectual and Developmental Disabilities (IDD), Autism, Prevention, Aetiology, 2.1 Biological and endogenous factors, Alleles, Autistic Disorder, DNA Copy Number Variations, Databases, Genetic, Genetic Predisposition to Disease, Genetic Variation, Genome, Human, Genome-Wide Association Study, Genotype, Humans, Polymorphism, Single Nucleotide, Risk Factors, White People, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.

Published
2010

8. A large data resource of genomic copy number variation across neurodevelopmental disorders

Author

Zarrei, Mehdi, Burton, Christie L., Engchuan, Worrawat, Young, Edwin J., Higginbotham, Edward J., MacDonald, Jeffrey R., Trost, Brett, Chan, Ada J. S., Walker, Susan, Lamoureux, Sylvia, Heung, Tracy, Mojarad, Bahareh A., Kellam, Barbara, Paton, Tara, Faheem, Muhammad, Miron, Karin, Lu, Chao, Wang, Ting, Samler, Kozue, Wang, Xiaolin, Costain, Gregory, Hoang, Ny, Pellecchia, Giovanna, Wei, John, Patel, Rohan V., Thiruvahindrapuram, Bhooma, Roifman, Maian, Merico, Daniele, Goodale, Tara, Drmic, Irene, Speevak, Marsha, Howe, Jennifer L., Yuen, Ryan K. C., Buchanan, Janet A., Vorstman, Jacob A. S., Marshall, Christian R., Wintle, Richard F., Rosenberg, David R., Hanna, Gregory L., Woodbury-Smith, Marc, Cytrynbaum, Cheryl, Zwaigenbaum, Lonnie, Elsabbagh, Mayada, Flanagan, Janine, Fernandez, Bridget A., Carter, Melissa T., Szatmari, Peter, Roberts, Wendy, Lerch, Jason, Liu, Xudong, Nicolson, Rob, Georgiades, Stelios, Weksberg, Rosanna, Arnold, Paul D., Bassett, Anne S., Crosbie, Jennifer, Schachar, Russell, Stavropoulos, Dimitri J., Anagnostou, Evdokia, and Scherer, Stephen W.

Published
2019
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9. Structural neuroimaging correlates of social deficits are similar in autism spectrum disorder and attention-deficit/hyperactivity disorder: analysis from the POND Network

Author

Baribeau, Danielle A., Dupuis, Annie, Paton, Tara A., Hammill, Christopher, Scherer, Stephen W., Schachar, Russell J., Arnold, Paul D., Szatmari, Peter, Nicolson, Rob, Georgiades, Stelios, Crosbie, Jennifer, Brian, Jessica, Iaboni, Alana, Kushki, Azadeh, Lerch, Jason P., and Anagnostou, Evdokia

Published
2019
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11. The Personal Genome Project Canada: findings from whole genome sequences of the inaugural 56 participants

Author

Reuter, Miriam S., Walker, Susan, Thiruvahindrapuram, Bhooma, Whitney, Joe, Cohn, Iris, Sondheimer, Neal, Yuen, Ryan K.C., Trost, Brett, Paton, Tara A., Pereira, Sergio L., Herbrick, Jo-Anne, Wintle, Richard F., Merico, Daniele, Howe, Jennifer, MacDonald, Jeffrey R., Lu, Chao, Nalpathamkalam, Thomas, Sung, Wilson W.L., Wang, Zhuozhi, Patel, Rohan V., Pellecchia, Giovanna, Wei, John, Strug, Lisa J., Bell, Sherilyn, Kellam, Barbara, Mahtani, Melanie M., Bassett, Anne S., Bombard, Yvonne, Weksberg, Rosanna, Shuman, Cheryl, Cohn, Ronald D., Stavropoulos, Dimitri J., Bowdin, Sarah, Hildebrandt, Matthew R., Wei, Wei, Romm, Asli, Pasceri, Peter, Ellis, James, Ray, Peter, Meyn, M. Stephen, Monfared, Nasim, Hosseini, S. Mohsen, Joseph-George, Ann M., Keeley, Fred W., Cook, Ryan A., Fiume, Marc, Lee, Hin C., Marshall, Christian R., Davies, Jill, Hazell, Allison, Buchanan, Janet A., Szego, Michael J., and Scherer, Stephen W.

Subjects
Health policy -- Analysis, DNA sequencing -- Analysis, Pharmacogenomics -- Analysis, Health
Abstract

BACKGROUND: The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers. METHODS: Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant. RESULTS: Whole genome sequencing of the first 56 participants identified 207662 805 sequence variants and 27494 copy number variations. We analyzed a prioritized disease-associated data set (n = 1606 variants) according to standardized guidelines, and interpreted 19 variants in 14 participants (25%) as having obvious health implications. Six of these variants (e.g., in BRCA1 or mosaic loss of an X chromosome) were pathogenic or likely pathogenic. Seven were risk factors for cancer, cardiovascular or neurobehavioural conditions. Four other variants--associated with cancer, cardiac or neurodegenerative phenotypes--remained of uncertain significance because of discrepancies among databases. We also identified a large structural chromosome aberration and a likely pathogenic mitochondrial variant. There were 172 recessive disease alleles (e.g., 5 individuals carried mutations for cystic fibrosis). Pharmacogenomics analyses revealed another 3.9 potentially relevant genotypes per individual. INTERPRETATION: Our analyses identified a spectrum of genetic variants with potential health impact in 25% of participants. When also considering recessive alleles and variants with potential pharmacologic relevance, all 56 participants had medically relevant findings. Although access is mostly limited to research, whole genome sequencing can provide specific and novel information with the potential of major impact for health care., Rapid technological advances are enabling a view of human genetic variation in ever-increasing detail and at plummeting costs. (1) Until recently, analysis has been targeted largely to defined genes, but [...]

Published
2018
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12. Deep intronic variant in MVK as a cause for mevalonic aciduria initially presenting as non‐syndromic retinitis pigmentosa

Author

Dvaladze, Anna, primary, Tavares, Erika, additional, Di Scipio, Matteo, additional, Nimmo, Graeme, additional, Grudzinska‐Pechhacker, Monika K., additional, Paton, Tara, additional, Tumber, Anupreet, additional, Li, Shuning, additional, Eileen, Christabel, additional, Ertl‐Wagner, Birgit, additional, Mamak, Eva, additional, Hoffmann, Georg, additional, Marshall, Christian R., additional, Haas, Dorothea, additional, Mayatepek, Ertan, additional, Schulze, Andreas, additional, Heon, Elise, additional, and Vincent, Ajoy, additional

Published
2022
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14. Genomic architecture of Autism Spectrum Disorder from comprehensive whole-genome sequence annotation

Author

Trost, Brett, primary, Thiruvahindrapuram, Bhooma, additional, Chan, Ada J.S., additional, Engchuan, Worrawat, additional, Higginbotham, Edward J., additional, Howe, Jennifer L., additional, Loureiro, Livia O., additional, Reuter, Miriam S., additional, Roshandel, Delnaz, additional, Whitney, Joe, additional, Zarrei, Mehdi, additional, Bookman, Matthew, additional, Somerville, Cherith, additional, Shaath, Rulan, additional, Abdi, Mona, additional, Aliyev, Elbay, additional, Patel, Rohan V., additional, Nalpathamkalam, Thomas, additional, Pellecchia, Giovanna, additional, Hamdan, Omar, additional, Kaur, Gaganjot, additional, Wang, Zhuozhi, additional, MacDonald, Jeffrey R., additional, Wei, John, additional, Sung, Wilson W.L., additional, Lamoureux, Sylvia, additional, Hoang, Ny, additional, Selvanayagam, Thanuja, additional, Deflaux, Nicole, additional, Geng, Melissa, additional, Ghaffari, Siavash, additional, Bates, John, additional, Young, Edwin J., additional, Ding, Qiliang, additional, Shum, Carole, additional, D’abate, Lia, additional, Bradley, Clarissa A., additional, Rutherford, Annabel, additional, Aguda, Vernie, additional, Apresto, Beverly, additional, Chen, Nan, additional, Desai, Sachin, additional, Du, Xiaoyan, additional, Fong, Matthew L.Y., additional, Pullenayegum, Sanjeev, additional, Samler, Kozue, additional, Wang, Ting, additional, Ho, Karen, additional, Paton, Tara, additional, Pereira, Sergio L., additional, Herbrick, Jo-Anne, additional, Wintle, Richard F., additional, Fuerth, Jonathan, additional, Noppornpitak, Juti, additional, Ward, Heather, additional, Magee, Patrick, additional, Baz, Ayman Al, additional, Kajendirarajah, Usanthan, additional, Kapadia, Sharvari, additional, Vlasblom, Jim, additional, Valluri, Monica, additional, Green, Joseph, additional, Seifer, Vicki, additional, Quirbach, Morgan, additional, Rennie, Olivia, additional, Kelley, Elizabeth, additional, Masjedi, Nina, additional, Lord, Catherine, additional, Szego, Michael J., additional, Zawati, Ma’n H., additional, Lang, Michael, additional, Strug, Lisa J., additional, Marshall, Christian R., additional, Costain, Gregory, additional, Calli, Kristina, additional, Iaboni, Alana, additional, Yusuf, Afiqah, additional, Ambrozewicz, Patricia, additional, Gallagher, Louise, additional, Amaral, David G., additional, Brian, Jessica, additional, Elsabbagh, Mayada, additional, Georgiades, Stelios, additional, Messinger, Daniel S., additional, Ozonoff, Sally, additional, Sebat, Jonathan, additional, Sjaarda, Calvin, additional, Smith, Isabel M., additional, Szatmari, Peter, additional, Zwaigenbaum, Lonnie, additional, Kushki, Azadeh, additional, Frazier, Thomas W., additional, Vorstman, Jacob A.S., additional, Fakhro, Khalid A., additional, Fernandez, Bridget A., additional, Lewis, M.E. Suzanne, additional, Weksberg, Rosanna, additional, Fiume, Marc, additional, Yuen, Ryan K.C., additional, Anagnostou, Evdokia, additional, Sondheimer, Neal, additional, Glazer, David, additional, Hartley, Dean M., additional, and Scherer, Stephen W., additional

Published
2022
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18. PMPCA mutations cause abnormal mitochondrial protein processing in patients with non-progressive cerebellar ataxia

Author

Jobling, Rebekah K., Assoum, Mirna, Gakh, Oleksandr, Blaser, Susan, Raiman, Julian A., Mignot, Cyril, Roze, Emmanuel, Dürr, Alexandra, Brice, Alexis, Lévy, Nicolas, Prasad, Chitra, Paton, Tara, Paterson, Andrew D., Roslin, Nicole M., Marshall, Christian R., Desvignes, Jean-Pierre, Roëckel-Trevisiol, Nathalie, Scherer, Stephen W., Rouleau, Guy A., Mégarbané, André, Isaya, Grazia, Delague, Valérie, and Yoon, Grace

Published
2015
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20. Assessment of the Implementation of Pharmacogenomic Testing in a Pediatric Tertiary Care Setting

Author

Cohn, Iris, primary, Manshaei, Roozbeh, additional, Liston, Eriskay, additional, Okello, John B. A., additional, Khan, Reem, additional, Curtis, Meredith R., additional, Krupski, Abby J., additional, Jobling, Rebekah K., additional, Kalbfleisch, Kelsey, additional, Paton, Tara A., additional, Reuter, Miriam S., additional, Hayeems, Robin Z., additional, Verstegen, Ruud H. J., additional, Goldman, Aaron, additional, Kim, Raymond H., additional, and Ito, Shinya, additional

Published
2021
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22. DYNC2H1 hypomorphic or retina-predominant variants cause nonsyndromic retinal degeneration

Author

Vig, Anjali, primary, Poulter, James A., additional, Ottaviani, Daniele, additional, Tavares, Erika, additional, Toropova, Katerina, additional, Tracewska, Anna Maria, additional, Mollica, Antonio, additional, Kang, Jasmine, additional, Kehelwathugoda, Oshini, additional, Paton, Tara, additional, Maynes, Jason T., additional, Wheway, Gabrielle, additional, Arno, Gavin, additional, Ambrose, J.C., additional, Arumugam, P., additional, Baple, E.L., additional, Bleda, M., additional, Boardman-Pretty, F., additional, Boissiere, J.M., additional, Boustred, C.R., additional, Brittain, H., additional, Caulfield, M.J., additional, Chan, G.C., additional, Craig, C.E.H., additional, Daugherty, L.C., additional, de Burca, A., additional, Devereau, A., additional, Elgar, G., additional, Foulger, R.E., additional, Fowler, T., additional, Furió-Tarí, P., additional, Hackett, J.M., additional, Halai, D., additional, Hamblin, A., additional, Henderson, S., additional, Holman, J.E., additional, Hubbard, T.J.P., additional, Ibáñez, K., additional, Jackson, R., additional, Jones, L.J., additional, Kasperaviciute, D., additional, Kayikci, M., additional, Lahnstein, L., additional, Lawson, K., additional, Leigh, S.E.A., additional, Leong, I.U.S., additional, Lopez, F.J., additional, Maleady-Crowe, F., additional, Mason, J., additional, McDonagh, E.M., additional, Moutsianas, L., additional, Mueller, M., additional, Murugaesu, N., additional, Need, A.C., additional, Odhams, C.A., additional, Patch, C., additional, Perez-Gil, D., additional, Polychronopoulos, D., additional, Pullinger, J., additional, Rahim, T., additional, Rendon, A., additional, Riesgo-Ferreiro, P., additional, Rogers, T., additional, Ryten, M., additional, Savage, K., additional, Sawant, K., additional, Scott, R.H., additional, Siddiq, A., additional, Sieghart, A., additional, Smedley, D., additional, Smith, K.R., additional, Sosinsky, A., additional, Spooner, W., additional, Stevens, H.E., additional, Stuckey, A., additional, Sultana, R., additional, Thomas, E.R.A., additional, Thompson, S.R., additional, Tregidgo, C., additional, Tucci, A., additional, Walsh, E., additional, Watters, S.A., additional, Welland, M.J., additional, Williams, E., additional, Witkowska, K., additional, Wood, S.M., additional, Zarowiecki, M., additional, Khan, Kamron N., additional, McKibbin, Martin, additional, Toomes, Carmel, additional, Ali, Manir, additional, Di Scipio, Matteo, additional, Li, Shuning, additional, Ellingford, Jamie, additional, Black, Graeme, additional, Webster, Andrew, additional, Rydzanicz, Małgorzata, additional, Stawiński, Piotr, additional, Płoski, Rafał, additional, Vincent, Ajoy, additional, Cheetham, Michael E., additional, Inglehearn, Chris F., additional, Roberts, Anthony, additional, and Heon, Elise, additional

Published
2020
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24. BCORInternal Tandem Duplication Associated Uterine Sarcoma: Expanding the Clinicopathologic Spectrum

Author

Thiryayi, Sakinah A., Ettler, Helen, Goebel, Emily A., Prefontaine, Michel, Paton, Tara A., Wong, Andrew, Yee, Denise, Agro, Evangeline, Mayers, Justin, Lerner-Ellis, Jordan, and Turashvili, Gulisa

Abstract

The diagnosis of high-grade endometrial stromal sarcoma has become more refined following molecular characterization of these tumors. Recently BCORinternal tandem duplications (ITD) have been identified in a small number of high-grade endometrial stromal sarcoma. Here we present an additional case of this rare entity in a young woman in her late teens. She presented with menorrhagia and underwent resection of 2 uterine lesions. The tumor was a spindle cell neoplasm composed of long fascicles with low to moderate cellularity, mild to moderate cytologic atypia, and up to 2 mitotic figures per 10 high power fields. Necrosis was not identified. Immunohistochemical stains showed the tumor to be positive for cyclin D1 in >50% of tumor cells, focally positive for CD10, and negative for SMA, desmin, h-caldesmon, and ALK1. BCORITD was confirmed by polymerase chain reaction with subsequent Sanger sequencing. Clues to the diagnosis of BCOR ITD uterine sarcoma include young patient age, uniform nuclear features, and diffuse positivity for cyclin D1. These features should prompt further molecular interrogation for definitive diagnosis, which is important for prognostication.

Published
2022
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26. Functional impact of global rare copy number variation in autism spectrum disorders

Author

Pinto, Dalila, Pagnamenta, Alistair T., Klei, Lambertus, Anney, Richard, Merico, Daniele, Regan, Regina, Conroy, Judith, Magalhaes, Tiago R., Correia, Catarina, Abrahams, Brett S., Almeida, Joana, Bacchelli, Elena, Bader, Gary D., Bailey, Anthony J., Baird, Gillian, Battaglia, Agatino, Berney, Tom, Bolshakova, Nadia, Bölte, Sven, Bolton, Patrick F., Bourgeron, Thomas, Brennan, Sean, Brian, Jessica, Bryson, Susan E., Carson, Andrew R., Casallo, Guillermo, Casey, Jillian, Chung, Brian H.Y., Cochrane, Lynne, Corsello, Christina, Crawford, Emily L., Crossett, Andrew, Cytrynbaum, Cheryl, Dawson, Geraldine, de Jonge, Maretha, Delorme, Richard, Drmic, Irene, Duketis, Eftichia, Duque, Frederico, Estes, Annette, Farrar, Penny, Fernandez, Bridget A., Folstein, Susan E., Fombonne, Eric, Freitag, Christine M., Gilbert, John, Gillberg, Christopher, Glessner, Joseph T., Goldberg, Jeremy, Green, Andrew, Green, Jonathan, Guter, Stephen J., Hakonarson, Hakon, Heron, Elizabeth A., Hill, Matthew, Holt, Richard, Howe, Jennifer L., Hughes, Gillian, Hus, Vanessa, Igliozzi, Roberta, Kim, Cecilia, Klauck, Sabine M., Kolevzon, Alexander, Korvatska, Olena, Kustanovich, Vlad, Lajonchere, Clara M., Lamb, Janine A., Laskawiec, Magdalena, Leboyer, Marion, Le Couteur, Ann, Leventhal, Bennett L., Lionel, Anath C., Liu, Xiao-Qing, Lord, Catherine, Lotspeich, Linda, Lund, Sabata C., Maestrini, Elena, Mahoney, William, Mantoulan, Carine, Marshall, Christian R., McConachie, Helen, McDougle, Christopher J., McGrath, Jane, McMahon, William M., Merikangas, Alison, Migita, Ohsuke, Minshew, Nancy J., Mirza, Ghazala K., Munson, Jeff, Nelson, Stanley F., Noakes, Carolyn, Noor, Abdul, Nygren, Gudrun, Oliveira, Guiomar, Papanikolaou, Katerina, Parr, Jeremy R., Parrini, Barbara, Paton, Tara, Pickles, Andrew, Pilorge, Marion, Piven, Joseph, Ponting, Chris P., Posey, David J., Poustka, Annemarie, Poustka, Fritz, Prasad, Aparna, Ragoussis, Jiannis, Renshaw, Katy, Rickaby, Jessica, Roberts, Wendy, Roeder, Kathryn, Roge, Bernadette, Rutter, Michael L., Bierut, Laura J., Rice, John P., Salt, Jeff, Sansom, Katherine, Sato, Daisuke, Segurado, Ricardo, Sequeira, Ana F., Senman, Lili, Shah, Naisha, Sheffield, Val C., Soorya, Latha, Sousa, Inês, Stein, Olaf, Sykes, Nuala, Stoppioni, Vera, Strawbridge, Christina, Tancredi, Raffaella, Tansey, Katherine, Thiruvahindrapduram, Bhooma, Thompson, Ann P., Thomson, Susanne, Tryfon, Ana, Tsiantis, John, Van Engeland, Herman, Vincent, John B., Volkmar, Fred, Wallace, Simon, Wang, Kai, Wang, Zhouzhi, Wassink, Thomas H., Webber, Caleb, Weksberg, Rosanna, Wing, Kirsty, Wittemeyer, Kerstin, Wood, Shawn, Wu, Jing, Yaspan, Brian L., Zurawiecki, Danielle, Zwaigenbaum, Lonnie, Buxbaum, Joseph D., Cantor, Rita M., Cook, Edwin H., Coon, Hilary, Cuccaro, Michael L., Devlin, Bernie, Ennis, Sean, Gallagher, Louise, Geschwind, Daniel H., Gill, Michael, Haines, Jonathan L., Hallmayer, Joachim, Miller, Judith, Monaco, Anthony P., Nurnberger, John I., Jr, Paterson, Andrew D., Pericak-Vance, Margaret A., Schellenberg, Gerard D., Szatmari, Peter, Vicente, Astrid M., Vieland, Veronica J., Wijsman, Ellen M., Scherer, Stephen W., Sutcliffe, James S., and Betancur, Catalina

Published
2010
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28. Transporters in Drug Development: 2018 ITC Recommendations for Transporters of Emerging Clinical Importance

Author

Zamek-Gliszczynski, Maciej J., Taub, Mitchell E., Chothe, Paresh P., Chu, Xiaoyan, Giacomini, Kathleen M., Kim, Richard B., Ray, Adrian S., Stocker, Sophie L., Bingham, Jashvant D., Wang, Zhuozhi, Pellecchia, Giovanna, Buchanan, Janet A., Walker, Susan, Marshall, Christian R., Uddin, Mohammed, Zarrei, Mehdi, Deneault, Eric, D'Abate, Lia, Chan, Ada J.S., Koyanagi, Stephanie, Paton, Tara, Pereira, Sergio L., Hoang, Ny, Engchuan, Worrawat, Higginbotham, Edward J., and Ho, Karen

Subjects
0301 basic medicine, Organ function, Pharmacology, 030226 pharmacology & pharmacy, Models, Biological, Risk Assessment, Prospective evaluation, Article, 03 medical and health sciences, 0302 clinical medicine, Vitamin deficiency, Drug Development, Membrane Transport Modulators, medicine, Animals, Humans, Pharmacology (medical), Drug Interactions, Pharmacokinetics, Organic cation transport proteins, biology, business.industry, Membrane Transport Proteins, Transporter, medicine.disease, Organic anion-transporting polypeptide, 030104 developmental biology, Drug development, Pharmaceutical Preparations, biology.protein, business
Abstract

This white paper provides updated International Transporter Consortium (ITC) recommendations on transporters that are important in drug development following the 3rd ITC workshop. New additions include prospective evaluation of organic cation transporter 1 (OCT1) and retrospective evaluation of organic anion transporting polypeptide (OATP)2B1 because of their important roles in drug absorption, disposition, and effects. For the first time, the ITC underscores the importance of transporters involved in drug-induced vitamin deficiency (THTR2) and those involved in the disposition of biomarkers of organ function (OAT2 and bile acid transporters).

Published
2018

31. Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder

Author

Yuen, Ryan K C, Merico, Daniele, Bookman, Matt, Howe, Jennifer L., Thiruvahindrapuram, Bhooma, Patel, Rohan V., Whitney, Joe, Deflaux, Nicole, Bingham, Jonathan, Wang, Zhuozhi, Pellecchia, Giovanna, Buchanan, Janet A., Walker, Susan, Marshall, Christian R., Uddin, Mohammed, Zarrei, Mehdi, Deneault, Eric, D'Abate, Lia, Chan, Ada J S, Koyanagi, Stephanie, Paton, Tara, Pereira, Sergio L., Hoang, Ny, Engchuan, Worrawat, Higginbotham, Edward J., Ho, Karen, Lamoureux, Sylvia, Li, Weili, MacDonald, Jeffrey R., Nalpathamkalam, Thomas, Sung, Wilson W L, Tsoi, Fiona J., Wei, John, Xu, Lizhen, Tasse, Anne Marie, Kirby, Emily, Van Etten, William, Twigger, Simon, Roberts, Wendy, Drmic, Irene, Jilderda, Sanne, Modi, Bonnie Mackinnon, Kellam, Barbara, Szego, Michael, Cytrynbaum, Cheryl, Weksberg, Rosanna, Zwaigenbaum, Lonnie, Woodbury-Smith, Marc, Brian, Jessica, Senman, Lili, Iaboni, Alana, Doyle-Thomas, Krissy, Thompson, Ann, Chrysler, Christina, Leef, Jonathan, Savion-Lemieux, Tal, Smith, Isabel M., Liu, Xudong, Nicolson, Rob, Seifer, Vicki, Fedele, Angie, Cook, Edwin H., Dager, Stephen, Estes, Annette, Gallagher, Louise, Malow, Beth A., Parr, Jeremy R., Spence, Sarah J., Vorstman, Jacob, Frey, Brendan J., Robinson, James T., Strug, Lisa J., Fernandez, Bridget A., Elsabbagh, Mayada, Carter, Melissa T., Hallmayer, Joachim, Knoppers, Bartha M., Anagnostou, Evdokia, Szatmari, Peter, Ring, Robert H., Glazer, David, Pletcher, Mathew T., and Scherer, Stephen W.

Subjects
Neuroscience(all), Next-generation sequencing, Journal Article, Autism spectrum disorders
Abstract

We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 × 10-4). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD.

Published
2017

32. Oxytocin Receptor Polymorphisms are Differentially Associated with Social Abilities across Neurodevelopmental Disorders

Author

Baribeau, Danielle A., primary, Dupuis, Annie, additional, Paton, Tara A., additional, Scherer, Stephen W., additional, Schachar, Russell J., additional, Arnold, Paul D., additional, Szatmari, Peter, additional, Nicolson, Rob, additional, Georgiades, Stelios, additional, Crosbie, Jennifer, additional, Brian, Jessica, additional, Iaboni, Alana, additional, Lerch, Jason, additional, and Anagnostou, Evdokia, additional

Published
2017
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34. Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder

Author

C Yuen, Ryan K, primary, Merico, Daniele, additional, Bookman, Matt, additional, L Howe, Jennifer, additional, Thiruvahindrapuram, Bhooma, additional, Patel, Rohan V, additional, Whitney, Joe, additional, Deflaux, Nicole, additional, Bingham, Jonathan, additional, Wang, Zhuozhi, additional, Pellecchia, Giovanna, additional, Buchanan, Janet A, additional, Walker, Susan, additional, Marshall, Christian R, additional, Uddin, Mohammed, additional, Zarrei, Mehdi, additional, Deneault, Eric, additional, D'Abate, Lia, additional, Chan, Ada J S, additional, Koyanagi, Stephanie, additional, Paton, Tara, additional, Pereira, Sergio L, additional, Hoang, Ny, additional, Engchuan, Worrawat, additional, Higginbotham, Edward J, additional, Ho, Karen, additional, Lamoureux, Sylvia, additional, Li, Weili, additional, MacDonald, Jeffrey R, additional, Nalpathamkalam, Thomas, additional, Sung, Wilson W L, additional, Tsoi, Fiona J, additional, Wei, John, additional, Xu, Lizhen, additional, Tasse, Anne-Marie, additional, Kirby, Emily, additional, Van Etten, William, additional, Twigger, Simon, additional, Roberts, Wendy, additional, Drmic, Irene, additional, Jilderda, Sanne, additional, Modi, Bonnie MacKinnon, additional, Kellam, Barbara, additional, Szego, Michael, additional, Cytrynbaum, Cheryl, additional, Weksberg, Rosanna, additional, Zwaigenbaum, Lonnie, additional, Woodbury-Smith, Marc, additional, Brian, Jessica, additional, Senman, Lili, additional, Iaboni, Alana, additional, Doyle-Thomas, Krissy, additional, Thompson, Ann, additional, Chrysler, Christina, additional, Leef, Jonathan, additional, Savion-Lemieux, Tal, additional, Smith, Isabel M, additional, Liu, Xudong, additional, Nicolson, Rob, additional, Seifer, Vicki, additional, Fedele, Angie, additional, Cook, Edwin H, additional, Dager, Stephen, additional, Estes, Annette, additional, Gallagher, Louise, additional, Malow, Beth A, additional, Parr, Jeremy R, additional, Spence, Sarah J, additional, Vorstman, Jacob, additional, Frey, Brendan J, additional, Robinson, James T, additional, Strug, Lisa J, additional, Fernandez, Bridget A, additional, Elsabbagh, Mayada, additional, Carter, Melissa T, additional, Hallmayer, Joachim, additional, Knoppers, Bartha M, additional, Anagnostou, Evdokia, additional, Szatmari, Peter, additional, Ring, Robert H, additional, Glazer, David, additional, Pletcher, Mathew T, additional, and Scherer, Stephen W, additional

Published
2017
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35. De NovoGenome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis)

Author

Lok, Si, primary, Paton, Tara A, additional, Wang, Zhuozhi, additional, Kaur, Gaganjot, additional, Walker, Susan, additional, Yuen, Ryan K C, additional, Sung, Wilson W L, additional, Whitney, Joseph, additional, Buchanan, Janet A, additional, Trost, Brett, additional, Singh, Naina, additional, Apresto, Beverly, additional, Chen, Nan, additional, Coole, Matthew, additional, Dawson, Travis J, additional, Ho, Karen, additional, Hu, Zhizhou, additional, Pullenayegum, Sanjeev, additional, Samler, Kozue, additional, Shipstone, Arun, additional, Tsoi, Fiona, additional, Wang, Ting, additional, Pereira, Sergio L, additional, Rostami, Pirooz, additional, Ryan, Carol Ann, additional, Tong, Amy Hin Yan, additional, Ng, Karen, additional, Sundaravadanam, Yogi, additional, Simpson, Jared T, additional, Lim, Burton K, additional, Engstrom, Mark D, additional, Dutton, Christopher J, additional, Kerr, Kevin C R, additional, Franke, Maria, additional, Rapley, William, additional, Wintle, Richard F, additional, and Scherer, Stephen W, additional

Published
2017
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37. Transcriptome-wide characterization of the endogenous miR-34A-p53 tumor suppressor network

Author

Samuel, Nardin, primary, Wilson, Gavin, additional, Said, Badr Id, additional, Pan, Anna, additional, Deblois, Genevieve, additional, Fischer, Nicholas W., additional, Alexandrova, Roumiana, additional, Casallo, Guillermo, additional, Paton, Tara, additional, Lupien, Mathieu, additional, Gariepy, Jean, additional, Merico, Daniele, additional, Hudson, Thomas J., additional, and Malkin, David, additional

Published
2016
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38. The genetic diversity of Epstein-Barr virus in the setting of transplantation relative to non-transplant settings: A feasibility study

Author

Allen, Upton D., primary, Hu, Pingzhao, additional, Pereira, Sergio L., additional, Robinson, Joan L., additional, Paton, Tara A., additional, Beyene, Joseph, additional, Khodai-Booran, Nasser, additional, Dipchand, Anne, additional, Hébert, Diane, additional, Ng, Vicky, additional, Nalpathamkalam, Thomas, additional, and Read, Stanley, additional

Published
2015
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39. Individual common variants exert weak effects on the risk for autism spectrum disorderspi

Author

Anney, Richard Klei, Lambertus Pinto, Dalila Almeida, Joana and Bacchelli, Elena Baird, Gillian Bolshakova, Nadia and Boelte, Sven Bolton, Patrick F. Bourgeron, Thomas Brennan, Sean Brian, Jessica Casey, Jillian Conroy, Judith and Correia, Catarina Corsello, Christina Crawford, Emily L. de Jonge, Maretha Delorme, Richard Duketis, Eftichia Duque, Frederico Estes, Annette Farrar, Penny Fernandez, Bridget A. and Folstein, Susan E. Fombonne, Eric Gilbert, John and Gillberg, Christopher Glessner, Joseph T. Green, Andrew and Green, Jonathan Guter, Stephen J. Heron, Elizabeth A. Holt, Richard Howe, Jennifer L. Hughes, Gillian Hus, Vanessa and Igliozzi, Roberta Jacob, Suma Kenny, Graham P. Kim, Cecilia and Kolevzon, Alexander Kustanovich, Vlad Lajonchere, Clara M. and Lamb, Janine A. Law-Smith, Miriam Leboyer, Marion Le Couteur, Ann Leventhal, Bennett L. Liu, Xiao-Qing Lombard, Frances Lord, Catherine Lotspeich, Linda Lund, Sabata C. and Magalhaes, Tiago R. Mantoulan, Carine McDougle, Christopher J. and Melhem, Nadine M. Merikangas, Alison Minshew, Nancy J. and Mirza, Ghazala K. Munson, Jeff Noakes, Carolyn Nygren, Gudrun Papanikolaou, Katerina Pagnamenta, Alistair T. and Parrini, Barbara Paton, Tara Pickles, Andrew Posey, David J. and Poustka, Fritz Ragoussis, Jiannis Regan, Regina Roberts, Wendy Roeder, Kathryn Roge, Bernadette Rutter, Michael L. and Schlitt, Sabine Shah, Naisha Sheffield, Val C. Soorya, Latha Sousa, Ines Stoppioni, Vera Sykes, Nuala Tancredi, Raffaella Thompson, Ann P. Thomson, Susanne Tryfon, Ana and Tsiantis, John Van Engeland, Herman Vincent, John B. and Volkmar, Fred Vorstman, J. A. S. Wallace, Simon Wing, Kirsty and Wittemeyer, Kerstin Wood, Shawn Zurawiecki, Danielle and Zwaigenbaum, Lonnie Bailey, Anthony J. Battaglia, Agatino and Cantor, Rita M. Coon, Hilary Cuccaro, Michael L. Dawson, Geraldine Ennis, Sean Freitag, Christine M. Geschwind, Daniel H. Haines, Jonathan L. Klauck, Sabine M. McMahon, William M. Maestrini, Elena Miller, Judith Monaco, Anthony P. Nelson, Stanley F. Nurnberger, Jr., John I. Oliveira, Guiomar Parr, Jeremy R. Pericak-Vance, Margaret A. Piven, Joseph Schellenberg, Gerard D. Scherer, StephenW. Vicente, Astrid M. Wassink, Thomas H. Wijsman, Ellen M. Betancur, Catalina Buxbaum, Joseph D. Cook, Edwin H. Gallagher, Louise and Gill, Michael Hallmayer, Joachim Paterson, Andrew D. and Sutcliffe, James S. Szatmari, Peter Vieland, Veronica J. and Hakonarson, Hakon Devlin, Bernie

Subjects
mental disorders
Abstract

While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASDs), the contribution of common variation to the risk of developing ASD is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating the association of individual single nucleotide polymorphisms (SNPs), we also sought evidence that common variants, en masse, might affect the risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest P-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. In contrast, allele scores derived from the transmission of common alleles to Stage 1 cases significantly predict case status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm 1). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele score results, it is reasonable to conclude that common variants affect the risk for ASD but their individual effects are modest.

Published
2012

42. PMPCAmutations cause abnormal mitochondrial protein processing in patients with non-progressive cerebellar ataxia

Author

Jobling, Rebekah K., primary, Assoum, Mirna, additional, Gakh, Oleksandr, additional, Blaser, Susan, additional, Raiman, Julian A., additional, Mignot, Cyril, additional, Roze, Emmanuel, additional, Dürr, Alexandra, additional, Brice, Alexis, additional, Lévy, Nicolas, additional, Prasad, Chitra, additional, Paton, Tara, additional, Paterson, Andrew D., additional, Roslin, Nicole M., additional, Marshall, Christian R., additional, Desvignes, Jean-Pierre, additional, Roëckel-Trevisiol, Nathalie, additional, Scherer, Stephen W., additional, Rouleau, Guy A., additional, Mégarbané, André, additional, Isaya, Grazia, additional, Delague, Valérie, additional, and Yoon, Grace, additional

Published
2015
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43. Whole-exome analysis of foetal autopsy tissue reveals a frameshift mutation in OBSL1, consistent with a diagnosis of 3-M Syndrome

Author

Marshall, Christian R, primary, Farrell, Sandra A, additional, Cushing, Donna, additional, Paton, Tara, additional, Stockley, Tracy L, additional, Stavropoulos, Dimitri J, additional, Ray, Peter N, additional, Szego, Michael, additional, Lau, Lynette, additional, Pereira, Sergio L, additional, Cohn, Ronald D, additional, Wintle, Richard F, additional, Abuzenadah, Adel M, additional, Abu-Elmagd, Muhammad, additional, and Scherer, Stephen W, additional

Published
2015
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45. De Novo Genome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis).

Author

Si Lok, Paton, Tara A., Zhuozhi Wang, Kaur, Gaganjot, Walker, Susan, Yuen, Ryan K. C., Sung, Wilson W. L., Whitney, Joseph, Buchanan, Janet A., Trost, Brett, Singh, Naina, Apresto, Beverly, Nan Chen, Coole, Matthew, Dawson, Travis J., Ho, Karen, Zhizhou Hu, Pullenayegum, Sanjeev, Samler, Kozue, and Shipstone, Arun

Subjects
*AMERICAN beaver, *LEUCOCYTES, *GENOMES
Abstract

The Canadian beaver (Castor canadensis) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (<30 x) long reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by short reads (80 x) and checked for accuracy by congruency against an independent short read assembly. We scaffolded the assembly using the exon-gene models derived from 9805 full-length open reading frames (FL-ORFs) constructed from the beaver leukocyte and muscle transcriptomes. The final assembly comprised 22,515 contigs with an N50 of 278,680 bp and an N50-scaffold of 317,558 bp. Maximum contig and scaffold lengths were 3.3 and 4.2 Mb, respectively, with a combined scaffold length representing 92% of the estimated genome size. The completeness and accuracy of the scaffold assembly was demonstrated by the precise exon placement for 91.1% of the 9805 assembled FL-ORFs and 83.1% of the BUSCO (Benchmarking Universal Single-Copy Orthologs) gene set used to assess the quality of genome assemblies. Well-represented were genes involved in dentition and enamel deposition, defining characteristics of rodents with which the beaver is well-endowed. The study provides insights for genome assembly and an important genomics resource for Castoridae and rodent evolutionary biology. [ABSTRACT FROM AUTHOR]

Published
2017
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48. Lethal Disorder of Mitochondrial Fission Caused by Mutations in DNM1L

Author

Boycott, Kym M., Friedman, Jan, Michaud, Jacques, Bernier, Francois, Brudno, Michael, Fernandez, Bridget, Knoppers, Bartha, Samuels, Mark, Yoon, Grace, Malam, Zeenat, Paton, Tara, Marshall, Christian R., Hyatt, Ella, Ivakine, Zhenya, Scherer, Stephen W., Lee, Kyong-Soon, Hawkins, Cynthia, and Cohn, Ronald D.

Published
2016
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