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1. Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach

Author

Magalhães, Tiago R, Palmer, Jessica, Tomancak, Pavel, and Pollard, Katherine S

Subjects
Biomedical and Clinical Sciences, Neurosciences, Genetics, Human Genome, Biotechnology, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Neurological, Animals, Animals, Genetically Modified, Axons, Body Patterning, Cell Cycle Proteins, Cluster Analysis, Drosophila, Drosophila Proteins, Gene Expression Profiling, Gene Expression Regulation, Developmental, Oligonucleotide Array Sequence Analysis, Time Factors, Biochemistry and Cell Biology, Cognitive Sciences, Neurology & Neurosurgery, Biological psychology
Abstract

BackgroundDuring the development of the Drosophila central nervous system the process of midline crossing is orchestrated by a number of guidance receptors and ligands. Many key axon guidance molecules have been identified in both invertebrates and vertebrates, but the transcriptional regulation of growth cone guidance remains largely unknown. It is established that translational regulation plays a role in midline crossing, and there are indications that transcriptional regulation is also involved. To investigate this issue, we conducted a genome-wide study of transcription in Drosophila embryos using wild type and a number of well-characterized Drosophila guidance mutants and transgenics. We also analyzed a previously published microarray time course of Drosophila embryonic development with an axon guidance focus.ResultsUsing hopach, a novel clustering method which is well suited to microarray data analysis, we identified groups of genes with similar expression patterns across guidance mutants and transgenics. We then systematically characterized the resulting clusters with respect to their relevance to axon guidance using two complementary controlled vocabularies: the Gene Ontology (GO) and anatomical annotations of the Atlas of Pattern of Gene Expression (APoGE) in situ hybridization database. The analysis indicates that regulation of gene expression does play a role in the process of axon guidance in Drosophila. We also find a strong link between axon guidance and hemocyte migration, a result that agrees with mounting evidence that axon guidance molecules are co-opted in vertebrate vascularization. Cell cyclin activity in the context of axon guidance is also suggested from our array data. RNA and protein expression patterns of cell cyclins in axon guidance mutants and transgenics support this possible link.ConclusionThis study provides important insights into the regulation of axon guidance in vivo.

Published
2007

2. Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

Author

Afshinnekoo, Ebrahim, Meydan, Cem, Chowdhury, Shanin, Jaroudi, Dyala, Boyer, Collin, Bernstein, Nick, Maritz, Julia M., Reeves, Darryl, Gandara, Jorge, Chhangawala, Sagar, Ahsanuddin, Sofia, Simmons, Amber, Nessel, Timothy, Sundaresh, Bharathi, Pereira, Elizabeth, Jorgensen, Ellen, Kolokotronis, Sergios-Orestis, Kirchberger, Nell, Garcia, Isaac, Gandara, David, Dhanraj, Sean, Nawrin, Tanzina, Saletore, Yogesh, Alexander, Noah, Vijay, Priyanka, Hénaff, Elizabeth M., Zumbo, Paul, Walsh, Michael, O’Mullan, Gregory D., Tighe, Scott, Dudley, Joel T., Dunaif, Anya, Ennis, Sean, O’Halloran, Eoghan, Magalhaes, Tiago R., Boone, Braden, Jones, Angela L., Muth, Theodore R., Paolantonio, Katie Schneider, Alter, Elizabeth, Schadt, Eric E., Garbarino, Jeanne, Prill, Robert J., Carlton, Jane M., Levy, Shawn, and Mason, Christopher E.

Published
2015
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3. Convergence of Genes and Cellular Pathways Dysregulated in Autism Spectrum Disorders

Author

Pinto, Dalila, Delaby, Elsa, Merico, Daniele, Barbosa, Mafalda, Merikangas, Alison, Klei, Lambertus, Thiruvahindrapuram, Bhooma, Xu, Xiao, Ziman, Robert, Wang, Zhuozhi, Vorstman, Jacob A.S., Thompson, Ann, Regan, Regina, Pilorge, Marion, Pellecchia, Giovanna, Pagnamenta, Alistair T., Oliveira, Bárbara, Marshall, Christian R., Magalhaes, Tiago R., Lowe, Jennifer K., Howe, Jennifer L., Griswold, Anthony J., Gilbert, John, Duketis, Eftichia, Dombroski, Beth A., De Jonge, Maretha V., Cuccaro, Michael, Crawford, Emily L., Correia, Catarina T., Conroy, Judith, Conceição, Inês C., Chiocchetti, Andreas G., Casey, Jillian P., Cai, Guiqing, Cabrol, Christelle, Bolshakova, Nadia, Bacchelli, Elena, Anney, Richard, Gallinger, Steven, Cotterchio, Michelle, Casey, Graham, Zwaigenbaum, Lonnie, Wittemeyer, Kerstin, Wing, Kirsty, Wallace, Simon, van Engeland, Herman, Tryfon, Ana, Thomson, Susanne, Soorya, Latha, Rogé, Bernadette, Roberts, Wendy, Poustka, Fritz, Mouga, Susana, Minshew, Nancy, McInnes, L. Alison, McGrew, Susan G., Lord, Catherine, Leboyer, Marion, Le Couteur, Ann S., Kolevzon, Alexander, Jiménez González, Patricia, Jacob, Suma, Holt, Richard, Guter, Stephen, Green, Jonathan, Green, Andrew, Gillberg, Christopher, Fernandez, Bridget A., Duque, Frederico, Delorme, Richard, Dawson, Geraldine, Chaste, Pauline, Café, Cátia, Brennan, Sean, Bourgeron, Thomas, Bolton, Patrick F., Bölte, Sven, Bernier, Raphael, Baird, Gillian, Bailey, Anthony J., Anagnostou, Evdokia, Almeida, Joana, Wijsman, Ellen M., Vieland, Veronica J., Vicente, Astrid M., Schellenberg, Gerard D., Pericak-Vance, Margaret, Paterson, Andrew D., Parr, Jeremy R., Oliveira, Guiomar, Nurnberger, John I., Monaco, Anthony P., Maestrini, Elena, Klauck, Sabine M., Hakonarson, Hakon, Haines, Jonathan L., Geschwind, Daniel H., Freitag, Christine M., Folstein, Susan E., Ennis, Sean, Coon, Hilary, Battaglia, Agatino, Szatmari, Peter, Sutcliffe, James S., Hallmayer, Joachim, Gill, Michael, Cook, Edwin H., Buxbaum, Joseph D., Devlin, Bernie, Gallagher, Louise, Betancur, Catalina, and Scherer, Stephen W.

Published
2014
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6. Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach

Author

Tomancak Pavel, Palmer Jessica, Magalhães Tiago R, and Pollard Katherine S

Subjects
Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571, Neurophysiology and neuropsychology, QP351-495
Abstract

Abstract Background During the development of the Drosophila central nervous system the process of midline crossing is orchestrated by a number of guidance receptors and ligands. Many key axon guidance molecules have been identified in both invertebrates and vertebrates, but the transcriptional regulation of growth cone guidance remains largely unknown. It is established that translational regulation plays a role in midline crossing, and there are indications that transcriptional regulation is also involved. To investigate this issue, we conducted a genome-wide study of transcription in Drosophila embryos using wild type and a number of well-characterized Drosophila guidance mutants and transgenics. We also analyzed a previously published microarray time course of Drosophila embryonic development with an axon guidance focus. Results Using hopach, a novel clustering method which is well suited to microarray data analysis, we identified groups of genes with similar expression patterns across guidance mutants and transgenics. We then systematically characterized the resulting clusters with respect to their relevance to axon guidance using two complementary controlled vocabularies: the Gene Ontology (GO) and anatomical annotations of the Atlas of Pattern of Gene Expression (APoGE) in situ hybridization database. The analysis indicates that regulation of gene expression does play a role in the process of axon guidance in Drosophila. We also find a strong link between axon guidance and hemocyte migration, a result that agrees with mounting evidence that axon guidance molecules are co-opted in vertebrate vascularization. Cell cyclin activity in the context of axon guidance is also suggested from our array data. RNA and protein expression patterns of cell cyclins in axon guidance mutants and transgenics support this possible link. Conclusion This study provides important insights into the regulation of axon guidance in vivo.

Published
2007
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7. Personalized Cardio-Metabolic Responses to an Anti-Inflammatory Nutrition Intervention in Obese Adolescents: A Randomized Controlled Crossover Trial

Author

McMorrow, Aoibheann M., primary, Connaughton, Ruth M., additional, Magalhães, Tiago R., additional, McGillicuddy, Fiona C., additional, Hughes, Maria F., additional, Cheishvili, David, additional, Morine, Melissa J., additional, Ennis, Sean, additional, Healy, Marie-Louise, additional, Roche, Edna F., additional, Tremblay, Richard E., additional, Szyf, Moshe, additional, Lithander, Fiona E., additional, and Roche, Helen M., additional

Published
2018
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9. Investigation of 15q11-q13, 16p11.2 and 22q13 CNVs in Autism Spectrum Disorder Brazilian Individuals with and without Epilepsy

Author

Moreira, Danielle P., primary, Griesi-Oliveira, Karina, additional, Bossolani-Martins, Ana L., additional, Lourenço, Naila C. V., additional, Takahashi, Vanessa N. O., additional, da Rocha, Kátia M., additional, Moreira, Eloisa S., additional, Vadasz, Estevão, additional, Meira, Joanna Goes Castro, additional, Bertola, Debora, additional, Halloran, Eoghan O’, additional, Magalhães, Tiago R., additional, Fett-Conte, Agnes C., additional, and Passos-Bueno, Maria Rita, additional

Published
2014
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10. 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., Jonge, Maretha de, 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., Magalhães, 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, Engeland, Herman van, Vincent, John B., Volkmar, Fred, Vorstman, JAS, Wallace, Simon, Wing, Kirsty, Wittemeyer, Kerstin, Wood, Shawn, Zurawiecki, Danielle, Zwaigenbaum, Lonnie, Bailey, Anthony J., Battaglia, Agatino, 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, John I., Oliveira, Guiomar, Parr, Jeremy R., Pericak-Vance, Margaret Ann, Piven, Joseph, Schellenberg, Gerard D., Scherer, Stephen W., Vicente, Astrid M., Wassink, Thomas H., Wijsman, Ellen M., Betancur, Catalina, Buxbaum, Joseph D., Cook, Edwin H., Gallagher, Louise, Gill, Michael, Hallmayer, Joachim, Paterson, Andrew D., Sutcliffe, James S., Szatmari, Peter, Vieland, Veronica J., Hakonarson, Hakon, Devlin, Bernie, 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., Jonge, Maretha de, 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., Magalhães, 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, Engeland, Herman van, Vincent, John B., Volkmar, Fred, Vorstman, JAS, Wallace, Simon, Wing, Kirsty, Wittemeyer, Kerstin, Wood, Shawn, Zurawiecki, Danielle, Zwaigenbaum, Lonnie, Bailey, Anthony J., Battaglia, Agatino, 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, John I., Oliveira, Guiomar, Parr, Jeremy R., Pericak-Vance, Margaret Ann, Piven, Joseph, Schellenberg, Gerard D., Scherer, Stephen W., Vicente, Astrid M., Wassink, Thomas H., Wijsman, Ellen M., Betancur, Catalina, Buxbaum, Joseph D., Cook, Edwin H., Gallagher, Louise, Gill, Michael, Hallmayer, Joachim, Paterson, Andrew D., Sutcliffe, James S., Szatmari, Peter, Vieland, Veronica J., Hakonarson, Hakon, and Devlin, Bernie

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

11. A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder

Author

Casey, Jillian P., Magalhães, Tiago R., Conroy, Judith M., Regan, Regina, Shah, Naisha, Anney, Richard, Shields, Denis C., Abrahams, Brett S., Almeida, Joana, Bacchelli, Elena, Bailey, Anthony J., Baird, Gillian, Battaglia, Agatino, Berney, Tom, Bolshakova, Nadia, Bolton, Patrick F., Bourgeron, Thomas, Brennan, Sean, Cali, Phil, Correia, Catarina, Corsello, Christina, Coutanche, Marc, Dawson, Geraldine, Jonge, Maretha de, Delorme, Richard, Duketis, Eftichia, Duque, Frederico, Estes, Annette, Farrar, Penny, Fernandez, Bridget A., Folstein, Susan E., Foley, Suzanne, Fombonne, Eric, Freitag, Christine M., Gilbert, John, Gillberg, Christopher, Glessner, Joseph T., Green, Jonathan, Guter, Stephen J., Hakonarson, Hakon, Holt, Richard, Hughes, Gillian, Hus, Vanessa, Igliozzi, Roberta, Kim, Cecilia, Klauck, Sabine M., Kolevzon, Alexander, Lamb, Janine A., Leboyer, Marion, Le Couteur, Ann, Leventhal, Bennett L., Lord, Catherine, Lund, Sabata C., Maestrini, Elena, Mantoulan, Carine, Marshall, Christian R., McConachie, Helen, McDougle, Christopher J., McGrath, Jane, McMahon, William M., Merikangas, Alison, Miller, Judith, Minopoli, Fiorella, Mirza, Ghazala K., Munson, Jeff, Nelson, Stanley F., Nygren, Gudrun, Oliveira, Guiomar, Pagnamenta, Alistair T., Papanikolaou, Katerina, Parr, Jeremy R., Parrini, Barbara, Pickles, Andrew, Pinto, Dalila, Piven, Joseph, Posey, David J., Poustka, Annemarie, Poustka, Fritz, Ragoussis, Jiannis, Roge, Bernadette, Rutter, Michael L., Sequeira, Ana F., Soorya, Latha, Sousa, Inês, Sykes, Nuala, Stoppioni, Vera, Tancredi, Raffaella, Tauber, Maïté, Thompson, Ann P., Thomson, Susanne, Tsiantis, John, Engeland, Herman van, Vincent, John B., Volkmar, Fred, Vorstman, Jacob A. S., Wallace, Simon, Wang, Kai, Wassink, Thomas H., White, Kathy, Wing, Kirsty, Wittemeyer, Kerstin, Yaspan, Brian L., Zwaigenbaum, Lonnie, Betancur, Catalina, Buxbaum, Joseph D., Cantor, Rita M., Cook, Edwin H., Coon, Hilary, Cuccaro, Michael L., Geschwind, Daniel H., Haines, Jonathan L., Hallmayer, Joachim, Monaco, Anthony P., Nurnberger, John I., Pericak-Vance, Margaret Ann, Schellenberg, Gerard D., Scherer, Stephen W., Sutcliffe, James S., Szatmari, Peter, Vieland, Veronica J., Wijsman, Ellen M., Green, Andrew, Gill, Michael, Gallagher, Louise, Vicente, Astrid M., Ennis, Sean, Casey, Jillian P., Magalhães, Tiago R., Conroy, Judith M., Regan, Regina, Shah, Naisha, Anney, Richard, Shields, Denis C., Abrahams, Brett S., Almeida, Joana, Bacchelli, Elena, Bailey, Anthony J., Baird, Gillian, Battaglia, Agatino, Berney, Tom, Bolshakova, Nadia, Bolton, Patrick F., Bourgeron, Thomas, Brennan, Sean, Cali, Phil, Correia, Catarina, Corsello, Christina, Coutanche, Marc, Dawson, Geraldine, Jonge, Maretha de, Delorme, Richard, Duketis, Eftichia, Duque, Frederico, Estes, Annette, Farrar, Penny, Fernandez, Bridget A., Folstein, Susan E., Foley, Suzanne, Fombonne, Eric, Freitag, Christine M., Gilbert, John, Gillberg, Christopher, Glessner, Joseph T., Green, Jonathan, Guter, Stephen J., Hakonarson, Hakon, Holt, Richard, Hughes, Gillian, Hus, Vanessa, Igliozzi, Roberta, Kim, Cecilia, Klauck, Sabine M., Kolevzon, Alexander, Lamb, Janine A., Leboyer, Marion, Le Couteur, Ann, Leventhal, Bennett L., Lord, Catherine, Lund, Sabata C., Maestrini, Elena, Mantoulan, Carine, Marshall, Christian R., McConachie, Helen, McDougle, Christopher J., McGrath, Jane, McMahon, William M., Merikangas, Alison, Miller, Judith, Minopoli, Fiorella, Mirza, Ghazala K., Munson, Jeff, Nelson, Stanley F., Nygren, Gudrun, Oliveira, Guiomar, Pagnamenta, Alistair T., Papanikolaou, Katerina, Parr, Jeremy R., Parrini, Barbara, Pickles, Andrew, Pinto, Dalila, Piven, Joseph, Posey, David J., Poustka, Annemarie, Poustka, Fritz, Ragoussis, Jiannis, Roge, Bernadette, Rutter, Michael L., Sequeira, Ana F., Soorya, Latha, Sousa, Inês, Sykes, Nuala, Stoppioni, Vera, Tancredi, Raffaella, Tauber, Maïté, Thompson, Ann P., Thomson, Susanne, Tsiantis, John, Engeland, Herman van, Vincent, John B., Volkmar, Fred, Vorstman, Jacob A. S., Wallace, Simon, Wang, Kai, Wassink, Thomas H., White, Kathy, Wing, Kirsty, Wittemeyer, Kerstin, Yaspan, Brian L., Zwaigenbaum, Lonnie, Betancur, Catalina, Buxbaum, Joseph D., Cantor, Rita M., Cook, Edwin H., Coon, Hilary, Cuccaro, Michael L., Geschwind, Daniel H., Haines, Jonathan L., Hallmayer, Joachim, Monaco, Anthony P., Nurnberger, John I., Pericak-Vance, Margaret Ann, Schellenberg, Gerard D., Scherer, Stephen W., Sutcliffe, James S., Szatmari, Peter, Vieland, Veronica J., Wijsman, Ellen M., Green, Andrew, Gill, Michael, Gallagher, Louise, Vicente, Astrid M., and Ennis, Sean

Abstract

Autism spectrum disorder (ASD) is a highly heritable disorder of complex and heterogeneous aetiology. It is primarily characterized by altered cognitive ability including impaired language and communication skills and fundamental deficits in social reciprocity. Despite some notable successes in neuropsychiatric genetics, overall, the high heritability of ASD (~90%) remains poorly explained by common genetic risk variants. However, recent studies suggest that rare genomic variation, in particular copy number variation, may account for a significant proportion of the genetic basis of ASD. We present a large scale analysis to identify candidate genes which may contain low-frequency recessive variation contributing to ASD while taking into account the potential contribution of population differences to the genetic heterogeneity of ASD. Our strategy, homozygous haplotype (HH) mapping, aims to detect homozygous segments of identical haplotype structure that are shared at a higher frequency amongst ASD patients compared to parental controls. The analysis was performed on 1,402 Autism Genome Project trios genotyped for 1 million single nucleotide polymorphisms (SNPs). We identified 25 known and 1,218 novel ASD candidate genes in the discovery analysis including CADM2, ABHD14A, CHRFAM7A, GRIK2, GRM3, EPHA3, FGF10, KCND2, PDZK1, IMMP2L and FOXP2. Furthermore, 10 of the previously reported ASD genes and 300 of the novel candidates identified in the discovery analysis were replicated in an independent sample of 1,182 trios. Our results demonstrate that regions of HH are significantly enriched for previously reported ASD candidate genes and the observed association is independent of gene size (odds ratio 2.10). Our findings highlight the applicability of HH mapping in complex disorders such as ASD and offer an alternative approach to the analysis of genome-wide association data.

Published
2011

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

Author

Anney, Richard, Klei, Lambertus, Pinto, Dalila, Regan, Regina, Conroy, Judith, Magalhães, 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, Jonge, Maretha de, 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, Poustka, Fritz, Prasad, Aparna, Ragoussis, Jiannis, Renshaw, Katy, Rickaby, Jessica, Roberts, Wendy, Roeder, Kathryn, Roge, Bernadette, Rutter, Michael L., Bierut, Laura Jean, Rice, John P., Salt, Jeff, Sansom, Katherine, Sato, Daisuke, Segurado, Ricardo, Senman, Lili, Shah, Naisha, Sheffield, Val C., Soorya, Latha, Sousa, Inês, Stoppioni, Vera, Strawbridge, Christina, Tancredi, Raffaella, Tansey, Katherine, Thiruvahindrapduram, Bhooma, Thompson, Ann P., Thomson, Susanne, Tryfon, Ana, Tsiantis, John, Engeland, Herman van, Vincent, John B., Volkmar, Fred, Wallace, Simon, Wang, Kai, Wang, Zhouzhi, Wassink, Thomas H., Wing, Kirsty, Wittemeyer, Kerstin, Wood, Shawn, Yaspan, Brian L., Zurawiecki, Danielle, Zwaigenbaum, Lonnie, Betancur, Catalina, Buxbaum, Joseph D., Cantor, Rita M., Cook, Edwin H., Coon, Hilary, Cuccaro, Michael L., Gallagher, Louise, Geschwind, Daniel H., Gill, Michael, Haines, Jonathan L., Miller, Judith, Monaco, Anthony P., Nurnberger, John I., Paterson, Andrew D., Pericak-Vance, Margaret Ann, Schellenberg, Gerard D., Scherer, Stephen W., Sutcliffe, James S., Szatmari, Peter, Vicente, Astrid M., Vieland, Veronica J., Wijsman, Ellen M., Devlin, Bernie, Ennis, Sean, Hallmayer, Joachim, Anney, Richard, Klei, Lambertus, Pinto, Dalila, Regan, Regina, Conroy, Judith, Magalhães, 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, Jonge, Maretha de, 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, Poustka, Fritz, Prasad, Aparna, Ragoussis, Jiannis, Renshaw, Katy, Rickaby, Jessica, Roberts, Wendy, Roeder, Kathryn, Roge, Bernadette, Rutter, Michael L., Bierut, Laura Jean, Rice, John P., Salt, Jeff, Sansom, Katherine, Sato, Daisuke, Segurado, Ricardo, Senman, Lili, Shah, Naisha, Sheffield, Val C., Soorya, Latha, Sousa, Inês, Stoppioni, Vera, Strawbridge, Christina, Tancredi, Raffaella, Tansey, Katherine, Thiruvahindrapduram, Bhooma, Thompson, Ann P., Thomson, Susanne, Tryfon, Ana, Tsiantis, John, Engeland, Herman van, Vincent, John B., Volkmar, Fred, Wallace, Simon, Wang, Kai, Wang, Zhouzhi, Wassink, Thomas H., Wing, Kirsty, Wittemeyer, Kerstin, Wood, Shawn, Yaspan, Brian L., Zurawiecki, Danielle, Zwaigenbaum, Lonnie, Betancur, Catalina, Buxbaum, Joseph D., Cantor, Rita M., Cook, Edwin H., Coon, Hilary, Cuccaro, Michael L., Gallagher, Louise, Geschwind, Daniel H., Gill, Michael, Haines, Jonathan L., Miller, Judith, Monaco, Anthony P., Nurnberger, John I., Paterson, Andrew D., Pericak-Vance, Margaret Ann, Schellenberg, Gerard D., Scherer, Stephen W., Sutcliffe, James S., Szatmari, Peter, Vicente, Astrid M., Vieland, Veronica J., Wijsman, Ellen M., Devlin, Bernie, Ennis, Sean, and Hallmayer, Joachim

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

15. Modern Methods for Delineating Metagenomic Complexity

Author

Afshinnekoo, Ebrahim, Meydan, Cem, Chowdhury, Shanin, Jaroudi, Dyala, Boyer, Collin, Bernstein, Nick, Maritz, Julia M., Reeves, Darryl, Gandara, Jorge, Chhangawala, Sagar, Ahsanuddin, Sofia, Simmons, Amber, Nessel, Timothy, Sundaresh, Bharathi, Pereira, Elizabeth, Jorgensen, Ellen, Kolokotronis, Sergios-Orestis, Kirchberger, Nell, Garcia, Isaac, Gandara, David, Dhanraj, Sean, Nawrin, Tanzina, Saletore, Yogesh, Alexander, Noah, Vijay, Priyanka, Hénaff, Elizabeth M., Zumbo, Paul, Walsh, Michael, O’Mullan, Gregory D., Tighe, Scott, Dudley, Joel T., Dunaif, Anya, Ennis, Sean, O’Halloran, Eoghan, Magalhaes, Tiago R., Boone, Braden, Jones, Angela L., Muth, Theodore R., Paolantonio, Katie Schneider, Alter, Elizabeth, Schadt, Eric E., Garbarino, Jeanne, Prill, Robert J., Carlton, Jane M., Levy, Shawn, and Mason, Christopher E.

Published
2015
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16. Ancestry of the Timorese: age-related macular degeneration associated genotype and allele sharing among human populations from throughout the world

Author

Morrison, Margaux A., Magalhaes, Tiago R., Ramke, Jacqueline, Smith, Silvia E., Ennis, Sean, Simpson, Claire L., Portas, Laura, Murgia, Federico, Ahn, Jeeyun, Dardenne, Caitlin, Mayne, Katie, Robinson, Rosann, Morgan, Denise J., Brian, Garry, Lee, Lucy, Woo, Se J., Zacharaki, Fani, Tsironi, Evangelia E., Miller, Joan W., Kim, Ivana K., Park, Kyu H., Bailey-Wilson, Joan E., Farrer, Lindsay A., Stambolian, Dwight, and DeAngelis, Margaret M.

Subjects
population genetics, ancestry, age-related macular degeneration, complex disease, and epidemiology
Abstract

We observed that the third leading cause of blindness in the world, age-related macular degeneration (AMD), occurs at a very low documented frequency in a population-based cohort from Timor-Leste. Thus, we determined a complete catalog of the ancestry of the Timorese by analysis of whole exome chip data and haplogroup analysis of SNP genotypes determined by sequencing the Hypervariable I and II regions of the mitochondrial genome and 17 genotyped YSTR markers obtained from 535 individuals. We genotyped 20 previously reported AMD-associated SNPs in the Timorese to examine their allele frequencies compared to and between previously documented AMD cohorts of varying ethnicities. For those without AMD (average age > 55 years), genotype and allele frequencies were similar for most SNPs with a few exceptions. The major risk allele of HTRA1 rs11200638 (10q26) was at a significantly higher frequency in the Timorese, as well as 3 of the 5 protective CFH (1q32) SNPs (rs800292, rs2284664, and rs12066959). Additionally, the most commonly associated AMD-risk SNP, CFH rs1061170 (Y402H), was also seen at a much lower frequency in the Korean and Timorese populations than in the assessed Caucasian populations (C ~7 vs. ~40%, respectively). The difference in allele frequencies between the Timorese population and the other genotyped populations, along with the haplogroup analysis, also highlight the genetic diversity of the Timorese. Specifically, the most common ancestry groupings were Oceanic (Melanesian and Papuan) and Eastern Asian (specifically Han Chinese). The low prevalence of AMD in the Timorese population (2 of 535 randomly selected participants) may be due to the enrichment of protective alleles in this population at the 1q32 locus.

Published
2015
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