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10. Pathway Analysis Integrating Genome-Wide and Functional Data Identifies PLCG2 as a Candidate Gene for Age-Related Macular Degeneration

Author

Waksmunski, Andrea R., Grunin, Michelle, Kinzy, Tyler G., Igo, Robert P., Jr., Haines, Jonathan L., Bailey, Jessica N. Cooke, Fritsche, Lars G., Igl, Wilmar, Grassmann, Felix, Sengupta, Sebanti, Bragg-Gresham, Jennifer L., Burdon, Kathryn P., Hebbring, Scott J., Wen, Cindy, Gorski, Mathias, Kim, Ivana K., Cho, David, Zack, Donald, Souied, Eric, Scholl, Hendrik P. N., Bala, Elisa, Lee, Kristine E., Hunter, David J., Sardell, Rebecca J., Mitchell, Paul, Merriam, Joanna E., Cipriani, Valentina, Hoffman, Joshua D., Schick, Tina, Lechanteur, Yara T. E., Guymer, Robyn H., Johnson, Matthew P., Jiang, Yingda, Stanton, Chloe M., Buitendijk, Gabrielle H. S., Zhan, Xiaowei, Kwong, Alan M., Boleda, Alexis, Brooks, Matthew, Gieser, Linn, Ratnapriya, Rinki, Branham, Kari E., Foerster, Johanna R., Heckenlively, John R., Othman, Mohammad, I, Vote, Brendan J., Liang, Helena Hai, Souzeau, Emmanuelle, McAllister, Ian L., Isaacs, Timothy, Hall, Janette, Lake, Stewart, Mackey, David A., Constable, Ian J., Craig, Jamie E., Kitchner, Terrie E., Yang, Zhenglin, Su, Zhiguang, Luo, Hongrong, Chen, Daniel, Ouyang, Hong, Flagg, Ken, Lin, Danni, Mao, Guanping, Ferreyra, Henry, Stark, Klaus, von Strachwitz, Claudia N., Wolf, Armin, Brandl, Caroline, Rudolph, Guenther, Olden, Matthias, Morrison, Margaux A., Morgan, Denise J., Schu, Matthew, Ahn, Jeeyun, Silvestri, Giuliana, Tsironi, Evangelia E., Park, Kyu Hyung, Farrer, Lindsay A., Orlin, Anton, Brucker, Alexander, Li, Mingyao, Curcio, Christine A., Mohand-Said, Saddek, Sahel, Jose-Alain, Audo, Isabelle, Benchaboune, Mustapha, Cree, Angela J., Rennie, Christina A., Goverdhan, Srinivas, V, Hagbi-Levi, Shira, Campochiaro, Peter, Katsanis, Nicholas, Holz, Frank G., Blond, Frederic, Blanche, Helene, Deleuze, Jean-Francois, Truitt, Barbara, Peachey, Neal S., Meuer, Stacy M., Myers, Chelsea E., Moore, Emily L., Klein, Ronald, Hauser, Michael A., Postel, Eric A., Courtenay, Monique D., Schwartz, Stephen G., Kovach, Jaclyn L., Scott, William K., Liew, Gerald, Tan, Ava G., Gopinath, Bamini, Merriam, John C., Smith, R. Theodore, Khan, Jane C., Shahid, Humma, Moore, Anthony T., McGrath, J. Allie, Laux, Renee, Brantley, Milam A., Jr., Agarwal, Anita, Ersoy, Lebriz, Caramoy, Albert, Langmann, Thomas, Saksens, Nicole T. M., de Jong, Eiko K., Hoyng, Carel B., Cain, Melinda S., Richardson, Andrea J., Martin, Tammy M., Blangero, John, Weeks, Daniel E., Dhillon, Bal, van Duijn, Cornelia M., Doheny, Kimberly F., Romm, Jane, Klaver, Caroline C. W., Hayward, Caroline, Gorin, Michael B., Klein, Michael L., Baird, Paul N., den Hollander, Anneke, I, Fauser, Sascha, Yates, John R. W., Allikmets, Rando, Wang, Jie Jin, Schaumberg, Debra A., Klein, Barbara E. K., Hagstrom, Stephanie A., Chowers, Itay, Lotery, Andrew J., Leveillard, Thierry, Zhang, Kang, Brilliant, Murray H., Hewitt, Alex W., Swaroop, Anand, Chew, Emily Y., Pericak-Vance, Margaret A., DeAngelis, Margaret, Stambolian, Dwight, Iyengar, Sudha K., Weber, Bernhard H. F., Abecasis, Goncalo R., Heid, Iris M., Waksmunski, Andrea R., Grunin, Michelle, Kinzy, Tyler G., Igo, Robert P., Jr., Haines, Jonathan L., Bailey, Jessica N. Cooke, Fritsche, Lars G., Igl, Wilmar, Grassmann, Felix, Sengupta, Sebanti, Bragg-Gresham, Jennifer L., Burdon, Kathryn P., Hebbring, Scott J., Wen, Cindy, Gorski, Mathias, Kim, Ivana K., Cho, David, Zack, Donald, Souied, Eric, Scholl, Hendrik P. N., Bala, Elisa, Lee, Kristine E., Hunter, David J., Sardell, Rebecca J., Mitchell, Paul, Merriam, Joanna E., Cipriani, Valentina, Hoffman, Joshua D., Schick, Tina, Lechanteur, Yara T. E., Guymer, Robyn H., Johnson, Matthew P., Jiang, Yingda, Stanton, Chloe M., Buitendijk, Gabrielle H. S., Zhan, Xiaowei, Kwong, Alan M., Boleda, Alexis, Brooks, Matthew, Gieser, Linn, Ratnapriya, Rinki, Branham, Kari E., Foerster, Johanna R., Heckenlively, John R., Othman, Mohammad, I, Vote, Brendan J., Liang, Helena Hai, Souzeau, Emmanuelle, McAllister, Ian L., Isaacs, Timothy, Hall, Janette, Lake, Stewart, Mackey, David A., Constable, Ian J., Craig, Jamie E., Kitchner, Terrie E., Yang, Zhenglin, Su, Zhiguang, Luo, Hongrong, Chen, Daniel, Ouyang, Hong, Flagg, Ken, Lin, Danni, Mao, Guanping, Ferreyra, Henry, Stark, Klaus, von Strachwitz, Claudia N., Wolf, Armin, Brandl, Caroline, Rudolph, Guenther, Olden, Matthias, Morrison, Margaux A., Morgan, Denise J., Schu, Matthew, Ahn, Jeeyun, Silvestri, Giuliana, Tsironi, Evangelia E., Park, Kyu Hyung, Farrer, Lindsay A., Orlin, Anton, Brucker, Alexander, Li, Mingyao, Curcio, Christine A., Mohand-Said, Saddek, Sahel, Jose-Alain, Audo, Isabelle, Benchaboune, Mustapha, Cree, Angela J., Rennie, Christina A., Goverdhan, Srinivas, V, Hagbi-Levi, Shira, Campochiaro, Peter, Katsanis, Nicholas, Holz, Frank G., Blond, Frederic, Blanche, Helene, Deleuze, Jean-Francois, Truitt, Barbara, Peachey, Neal S., Meuer, Stacy M., Myers, Chelsea E., Moore, Emily L., Klein, Ronald, Hauser, Michael A., Postel, Eric A., Courtenay, Monique D., Schwartz, Stephen G., Kovach, Jaclyn L., Scott, William K., Liew, Gerald, Tan, Ava G., Gopinath, Bamini, Merriam, John C., Smith, R. Theodore, Khan, Jane C., Shahid, Humma, Moore, Anthony T., McGrath, J. Allie, Laux, Renee, Brantley, Milam A., Jr., Agarwal, Anita, Ersoy, Lebriz, Caramoy, Albert, Langmann, Thomas, Saksens, Nicole T. M., de Jong, Eiko K., Hoyng, Carel B., Cain, Melinda S., Richardson, Andrea J., Martin, Tammy M., Blangero, John, Weeks, Daniel E., Dhillon, Bal, van Duijn, Cornelia M., Doheny, Kimberly F., Romm, Jane, Klaver, Caroline C. W., Hayward, Caroline, Gorin, Michael B., Klein, Michael L., Baird, Paul N., den Hollander, Anneke, I, Fauser, Sascha, Yates, John R. W., Allikmets, Rando, Wang, Jie Jin, Schaumberg, Debra A., Klein, Barbara E. K., Hagstrom, Stephanie A., Chowers, Itay, Lotery, Andrew J., Leveillard, Thierry, Zhang, Kang, Brilliant, Murray H., Hewitt, Alex W., Swaroop, Anand, Chew, Emily Y., Pericak-Vance, Margaret A., DeAngelis, Margaret, Stambolian, Dwight, Iyengar, Sudha K., Weber, Bernhard H. F., Abecasis, Goncalo R., and Heid, Iris M.

Abstract

PURPOSE. Age-related macular degeneration (AMD) is the worldwide leading cause of blindness among the elderly. Although genome-wide association studies (GWAS) have identified AMD risk variants, their roles in disease etiology are not well-characterized, and they only explain a portion of AMD heritability. METHODS. We performed pathway analyses using summary statistics from the International AMD Genomics Consortium's 2016 GWAS and multiple pathway databases to identify biological pathways wherein genetic association signals for AMD may be aggregating. We determined which genes contributed most to significant pathway signals across the databases. We characterized these genes by constructing protein-protein interaction networks and performing motif analysis. RESULTS. We determined that eight genes (C2, C3, LIPC, MICA, NOTCH4, PLCG2, PPARA, and RAD51B) drive'' the statistical signals observed across pathways curated in the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and Gene Ontology (GO) databases. We further refined our definition of statistical driver gene to identify PLCG2 as a candidate gene for AMD due to its significant gene-level signals (P < 0.0001) across KEGG, Reactome, GO, and NetPath pathways. CONCLUSIONS. We performed pathway analyses on the largest available collection of advanced AMD cases and controls in the world. Eight genes strongly contributed to significant pathways from the three larger databases, and one gene (PLCG2) was central to significant pathways from all four databases. This is, to our knowledge, the first study to identify PLCG2 as a candidate gene for AMD based solely on genetic burden. Our findings reinforce the utility of integrating in silico genetic and biological pathway data to investigate the genetic architecture of AMD.

Published
2019

21. Identification of the Tuberous Sclerosis Gene TSC1 on Chromosome 9q34

Author

van Slegtenhorst, Marjon, de Hoogt, Ronald, Hermans, Caroline, Nellist, Mark, Janssen, Bart, Verhoef, Senno, Lindhout, Dick, van den Ouweland, Ans, Halley, Dicky, Young, Janet, Burley, Mariwyn, Jeremiah, Steve, Woodward, Karen, Nahmias, Joseph, Fox, Margaret, Ekong, Rosemary, Osborne, John, Wolfe, Jonathan, Povey, Sue, Snell, Russell G., Cheadle, Jeremy P., Jones, Alistair C., Tachataki, Maria, Ravine, David, Sampson, Julian R., Reeve, Mary Pat, Richardson, Paul, Wilmer, Friederike, Munro, Cheryl, Hawkins, Trevor L., Sepp, Tiina, Ali, Johari B. M., Ward, Susannah, Green, Andrew J., Yates, John R. W., Kwiatkowska, Jolanta, Henske, Elizabeth P., Short, M. Priscilla, Haines, Jonathan H., Jozwiak, Sergiusz, and Kwiatkowski, David J.

Published
1997

25. Long-term cognitive outcomes in tuberous sclerosis complex.

Author

Tye, Charlotte, Mcewen, Fiona S, Liang, Holan, Underwood, Lisa, Woodhouse, Emma, Barker, Edward D, Sheerin, Fintan, Yates, John R W, Bolton, Patrick F, Higgins, N, Attard, V, Clarke, A, Elmslie, FV, Saggar, AK, Baines, D, Kerr, BA, Brayne, C, Carcani‐Rathwell, I, Connolly, C, and Clifford, M

Subjects
TUBEROUS sclerosis, INTELLECTUAL disabilities, SEIZURES (Medicine), INTELLECTUAL development, EPILEPSY, DISEASE risk factors, COGNITION, NEUROPSYCHOLOGICAL tests, RESEARCH funding, LONGITUDINAL method, DISEASE complications
Abstract

Aim: To investigate the interdependence between risk factors associated with long-term intellectual development in individuals with tuberous sclerosis complex (TSC).Method: The Tuberous Sclerosis 2000 Study is a prospective longitudinal study of individuals with TSC. In phase 1 of the study, baseline measures of intellectual ability, epilepsy, cortical tuber load, and mutation were obtained for 125 children (63 females, 62 males; median age=39mo). In phase 2, at an average of 8 years later, intellectual abilities were estimated for 88 participants with TSC and 35 unaffected siblings. Structural equation modelling was used to determine the risk pathways from genetic mutation through to IQ at phase 2.Results: Intellectual disability was present in 57% of individuals with TSC. Individuals without intellectual disability had significantly lower mean IQ compared to unaffected siblings, supporting specific genetic factors associated with intellectual impairment. Individuals with TSC who had a slower gain in IQ from infancy to middle childhood were younger at seizure onset and had increased infant seizure severity. Structural equation modelling indicated indirect pathways from genetic mutation, to tuber count, to seizure severity in infancy, through to IQ in middle childhood and adolescence.Interpretation: Early-onset and severe epilepsy in the first 2 years of life are associated with increased risk of long-term intellectual disability in individuals with TSC, emphasizing the importance of early and effective treatment or prevention of epilepsy.What This Paper Adds: Intellectual disability was present in 57% of individuals with tuberous sclerosis complex (TSC). Those with TSC without intellectual disability had significantly lower mean IQ compared to unaffected siblings. Earlier onset and greater severity of seizures in the first 2 years were observed in individuals with a slower gain in intellectual ability. Risk pathways through seizures in the first 2 years predict long-term cognitive outcomes in individuals with TSC. [ABSTRACT FROM AUTHOR]

Published
2020
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29. A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants

Author

Fritsche, Lars G., Igl, Wilmar, Bailey, Jessica N. Cooke, Grassmann, Felix, Sengupta, Sebanti, Bragg-Gresham, Jennifer L., Burdon, Kathryn P., Hebbring, Scott J., Wen, Cindy, Gorski, Mathias, Kim, Ivana K., Cho, David, Zack, Donald, Souied, Eric, Scholl, Hendrik P. N., Bala, Elisa, Lee, Kristine E., Hunter, David J., Sardell, Rebecca J., Mitchell, Paul, Merriam, Joanna E., Cipriani, Valentina, Hoffman, Joshua D., Schick, Tina, Lechanteur, Yara T. E., Guymer, Robyn H., Johnson, Matthew P., Jiang, Yingda, Stanton, Chloe M., Buitendijk, Gabrielle H. S., Zhan, Xiaowei, Kwong, Alan M., Boleda, Alexis, Brooks, Matthew, Gieser, Linn, Ratnapriya, Rinki, Branham, Kari E., Foerster, Johanna R., Heckenlively, John R., Othman, Mohammad I., Vote, Brendan J., Liang, Helena Hai, Souzeau, Emmanuelle, McAllister, Ian L., Isaacs, Timothy, Hall, Janette, Lake, Stewart, Mackey, David A., Constable, Ian J., Craig, Jamie E., Kitchner, Terrie E., Yang, Zhenglin, Su, Zhiguang, Luo, Hongrong, Chen, Daniel, Flagg, Ken, Lin, Danni, Mao, Guanping, Ferreyra, Henry, Starke, Klaus, von Strachwitz, Claudia N., Wolf, Armin, Brandl, Caroline, Rudolph, Guenther, Olden, Matthias, Morrison, Margaux A., Morgan, Denise J., Schu, Matthew, Ahn, Jeeyun, Silvestri, Giuliana, Tsironi, Evangelia E., Park, Kyu Hyung, Farrer, Lindsay A., Orlin, Anton, Brucker, Alexander, Li, Mingyao, Curcio, Christine A., Mohand-Said, Saddek, Sahel, Jose-Main, Audo, Isabelle, Benchaboune, Mustapha, Cree, Angela J., Rennie, Christina A., Goverdhan, Srinivas V., Grunin, Michelle, Hagbi-Levi, Shira, Campochiaro, Peter, Katsanis, Nicholas, Holz, Frank G., Blond, Frederic, Blanche, Helene, Deleuze, Jean-Francois, Igo, Robert P., Jr., Truitt, Barbara, Peachey, Neal S., Meuer, Stacy M., Myers, Chelsea E., Moore, Emily L., Klein, Ronald, Hauser, Michael A., Postel, Eric A., Courtenay, Monique D., Schwartz, Stephen G., Kovach, Jaclyn L., Scott, William K., Liew, Gerald, Tan, Ava G., Gopinath, Bamini, Merriam, John C., Smith, R. Theodore, Khan, Jane C., Shahid, Humma, Moore, Anthony T., McGrath, J. Allie, Laux, Renee, Brantley, Milam A., Jr., Agarwal, Anita, Ersoy, Lebriz, Caramoy, Albert, Langmann, Thomas, Saksens, Nicole T. M., de Jong, Eiko K., Hoyng, Carel B., Cain, Melinda S., Richardson, Andrea J., Martin, Tammy M., Blangero, John, Weeks, Daniel E., Dhillon, Bal, van Duijn, Cornelia M., Doheny, Kimberly F., Romm, Jane, Klaver, Caroline C. W., Hayward, Caroline, Gorin, Michael B., Klein, Michael L., Baird, Paul N., den Hollander, Anneke I., Fauser, Sascha, Yates, John R. W., Allikmets, Rando, Wang, Jie Jin, Schaumberg, Debra A., Klein, Barbara E. K., Hagstrom, Stephanie A., Chowers, Itay, Lotery, Andrew J., Leveillard, Thierry, Zhang, Kang, Brilliant, Murray H., Hewitt, Alex W., Swaroop, Anand, Chew, Emily Y., Pericak-Vance, Margaret A., DeAngelis, Margaret, Stambolian, Dwight, Haines, Jonathan L., Iyengar, Sudha K., Weber, Bernhard H. F., Abecasis, Goncalo R., Heid, Iris M., Fritsche, Lars G., Igl, Wilmar, Bailey, Jessica N. Cooke, Grassmann, Felix, Sengupta, Sebanti, Bragg-Gresham, Jennifer L., Burdon, Kathryn P., Hebbring, Scott J., Wen, Cindy, Gorski, Mathias, Kim, Ivana K., Cho, David, Zack, Donald, Souied, Eric, Scholl, Hendrik P. N., Bala, Elisa, Lee, Kristine E., Hunter, David J., Sardell, Rebecca J., Mitchell, Paul, Merriam, Joanna E., Cipriani, Valentina, Hoffman, Joshua D., Schick, Tina, Lechanteur, Yara T. E., Guymer, Robyn H., Johnson, Matthew P., Jiang, Yingda, Stanton, Chloe M., Buitendijk, Gabrielle H. S., Zhan, Xiaowei, Kwong, Alan M., Boleda, Alexis, Brooks, Matthew, Gieser, Linn, Ratnapriya, Rinki, Branham, Kari E., Foerster, Johanna R., Heckenlively, John R., Othman, Mohammad I., Vote, Brendan J., Liang, Helena Hai, Souzeau, Emmanuelle, McAllister, Ian L., Isaacs, Timothy, Hall, Janette, Lake, Stewart, Mackey, David A., Constable, Ian J., Craig, Jamie E., Kitchner, Terrie E., Yang, Zhenglin, Su, Zhiguang, Luo, Hongrong, Chen, Daniel, Flagg, Ken, Lin, Danni, Mao, Guanping, Ferreyra, Henry, Starke, Klaus, von Strachwitz, Claudia N., Wolf, Armin, Brandl, Caroline, Rudolph, Guenther, Olden, Matthias, Morrison, Margaux A., Morgan, Denise J., Schu, Matthew, Ahn, Jeeyun, Silvestri, Giuliana, Tsironi, Evangelia E., Park, Kyu Hyung, Farrer, Lindsay A., Orlin, Anton, Brucker, Alexander, Li, Mingyao, Curcio, Christine A., Mohand-Said, Saddek, Sahel, Jose-Main, Audo, Isabelle, Benchaboune, Mustapha, Cree, Angela J., Rennie, Christina A., Goverdhan, Srinivas V., Grunin, Michelle, Hagbi-Levi, Shira, Campochiaro, Peter, Katsanis, Nicholas, Holz, Frank G., Blond, Frederic, Blanche, Helene, Deleuze, Jean-Francois, Igo, Robert P., Jr., Truitt, Barbara, Peachey, Neal S., Meuer, Stacy M., Myers, Chelsea E., Moore, Emily L., Klein, Ronald, Hauser, Michael A., Postel, Eric A., Courtenay, Monique D., Schwartz, Stephen G., Kovach, Jaclyn L., Scott, William K., Liew, Gerald, Tan, Ava G., Gopinath, Bamini, Merriam, John C., Smith, R. Theodore, Khan, Jane C., Shahid, Humma, Moore, Anthony T., McGrath, J. Allie, Laux, Renee, Brantley, Milam A., Jr., Agarwal, Anita, Ersoy, Lebriz, Caramoy, Albert, Langmann, Thomas, Saksens, Nicole T. M., de Jong, Eiko K., Hoyng, Carel B., Cain, Melinda S., Richardson, Andrea J., Martin, Tammy M., Blangero, John, Weeks, Daniel E., Dhillon, Bal, van Duijn, Cornelia M., Doheny, Kimberly F., Romm, Jane, Klaver, Caroline C. W., Hayward, Caroline, Gorin, Michael B., Klein, Michael L., Baird, Paul N., den Hollander, Anneke I., Fauser, Sascha, Yates, John R. W., Allikmets, Rando, Wang, Jie Jin, Schaumberg, Debra A., Klein, Barbara E. K., Hagstrom, Stephanie A., Chowers, Itay, Lotery, Andrew J., Leveillard, Thierry, Zhang, Kang, Brilliant, Murray H., Hewitt, Alex W., Swaroop, Anand, Chew, Emily Y., Pericak-Vance, Margaret A., DeAngelis, Margaret, Stambolian, Dwight, Haines, Jonathan L., Iyengar, Sudha K., Weber, Bernhard H. F., Abecasis, Goncalo R., and Heid, Iris M.

Abstract

Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, with limited therapeutic options. Here we report on a study of >12 million variants, including 163,714 directly genotyped, mostly rare, protein-altering variants. Analyzing 16,144 patients and 17,832 controls, we identify 52 independently associated common and rare variants (P < 5 x 10(-8)) distributed across 34 loci. Although wet and dry AMD subtypes exhibit predominantly shared genetics, we identify the first genetic association signal specific to wet AMD, near MMP9 (difference P value = 4.1 x 10(-10)). Very rare coding variants (frequency <0.1 %) in CFH, CFI and TIMP3 suggest causal roles for these genes, as does a splice variant in SLC16A8. Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.

Published
2016

30. p63 Gene Mutations in EEC Syndrome, Limb-Mammary Syndrome, and Isolated Split Hand--Split Foot Malformation Suggest a Genotype-Phenotype Correlation

Author

van Bokhoven, Hans, Hamel, Ben C. J., Bamshad, Mike, Sangiorgi, Eugenio, Gurrieri, Fiorella, Duijf, Pascal H. G., Vanmolkot, Kate R. J., van Beusekom, Ellen, van Beersum, Sylvia E. C., Celli, Jacopo, Merkx, Gerard F. M., Tenconi, Romano, Fryns, Jean Pierre, Verloes, Alain, Newbury-Ecob, Ruth A., Raas-Rotschild, Annick, Majewski, Frank, Beemer, Frits A., Janecke, Andreas, Chitayat, David, Crisponi, Giangiorgio, Kayserili, Hulya, Yates, John R. W., Neri, Giovanni, and Brunner, Han G.

Subjects
Gene mutations -- Analysis, Orthopedics -- Research, Genetic disorders -- Analysis, Genetic epistasis -- Analysis, Biological sciences
Published
2001

33. A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants

Author

Fritsche, Lars G, primary, Igl, Wilmar, additional, Bailey, Jessica N Cooke, additional, Grassmann, Felix, additional, Sengupta, Sebanti, additional, Bragg-Gresham, Jennifer L, additional, Burdon, Kathryn P, additional, Hebbring, Scott J, additional, Wen, Cindy, additional, Gorski, Mathias, additional, Kim, Ivana K, additional, Cho, David, additional, Zack, Donald, additional, Souied, Eric, additional, Scholl, Hendrik P N, additional, Bala, Elisa, additional, Lee, Kristine E, additional, Hunter, David J, additional, Sardell, Rebecca J, additional, Mitchell, Paul, additional, Merriam, Joanna E, additional, Cipriani, Valentina, additional, Hoffman, Joshua D, additional, Schick, Tina, additional, Lechanteur, Yara T E, additional, Guymer, Robyn H, additional, Johnson, Matthew P, additional, Jiang, Yingda, additional, Stanton, Chloe M, additional, Buitendijk, Gabriëlle H S, additional, Zhan, Xiaowei, additional, Kwong, Alan M, additional, Boleda, Alexis, additional, Brooks, Matthew, additional, Gieser, Linn, additional, Ratnapriya, Rinki, additional, Branham, Kari E, additional, Foerster, Johanna R, additional, Heckenlively, John R, additional, Othman, Mohammad I, additional, Vote, Brendan J, additional, Liang, Helena Hai, additional, Souzeau, Emmanuelle, additional, McAllister, Ian L, additional, Isaacs, Timothy, additional, Hall, Janette, additional, Lake, Stewart, additional, Mackey, David A, additional, Constable, Ian J, additional, Craig, Jamie E, additional, Kitchner, Terrie E, additional, Yang, Zhenglin, additional, Su, Zhiguang, additional, Luo, Hongrong, additional, Chen, Daniel, additional, Ouyang, Hong, additional, Flagg, Ken, additional, Lin, Danni, additional, Mao, Guanping, additional, Ferreyra, Henry, additional, Stark, Klaus, additional, von Strachwitz, Claudia N, additional, Wolf, Armin, additional, Brandl, Caroline, additional, Rudolph, Guenther, additional, Olden, Matthias, additional, Morrison, Margaux A, additional, Morgan, Denise J, additional, Schu, Matthew, additional, Ahn, Jeeyun, additional, Silvestri, Giuliana, additional, Tsironi, Evangelia E, additional, Park, Kyu Hyung, additional, Farrer, Lindsay A, additional, Orlin, Anton, additional, Brucker, Alexander, additional, Li, Mingyao, additional, Curcio, Christine A, additional, Mohand-Saïd, Saddek, additional, Sahel, José-Alain, additional, Audo, Isabelle, additional, Benchaboune, Mustapha, additional, Cree, Angela J, additional, Rennie, Christina A, additional, Goverdhan, Srinivas V, additional, Grunin, Michelle, additional, Hagbi-Levi, Shira, additional, Campochiaro, Peter, additional, Katsanis, Nicholas, additional, Holz, Frank G, additional, Blond, Frédéric, additional, Blanché, Hélène, additional, Deleuze, Jean-François, additional, Igo, Robert P, additional, Truitt, Barbara, additional, Peachey, Neal S, additional, Meuer, Stacy M, additional, Myers, Chelsea E, additional, Moore, Emily L, additional, Klein, Ronald, additional, Hauser, Michael A, additional, Postel, Eric A, additional, Courtenay, Monique D, additional, Schwartz, Stephen G, additional, Kovach, Jaclyn L, additional, Scott, William K, additional, Liew, Gerald, additional, Tan, Ava G, additional, Gopinath, Bamini, additional, Merriam, John C, additional, Smith, R Theodore, additional, Khan, Jane C, additional, Shahid, Humma, additional, Moore, Anthony T, additional, McGrath, J Allie, additional, Laux, Reneé, additional, Brantley, Milam A, additional, Agarwal, Anita, additional, Ersoy, Lebriz, additional, Caramoy, Albert, additional, Langmann, Thomas, additional, Saksens, Nicole T M, additional, de Jong, Eiko K, additional, Hoyng, Carel B, additional, Cain, Melinda S, additional, Richardson, Andrea J, additional, Martin, Tammy M, additional, Blangero, John, additional, Weeks, Daniel E, additional, Dhillon, Bal, additional, van Duijn, Cornelia M, additional, Doheny, Kimberly F, additional, Romm, Jane, additional, Klaver, Caroline C W, additional, Hayward, Caroline, additional, Gorin, Michael B, additional, Klein, Michael L, additional, Baird, Paul N, additional, den Hollander, Anneke I, additional, Fauser, Sascha, additional, Yates, John R W, additional, Allikmets, Rando, additional, Wang, Jie Jin, additional, Schaumberg, Debra A, additional, Klein, Barbara E K, additional, Hagstrom, Stephanie A, additional, Chowers, Itay, additional, Lotery, Andrew J, additional, Léveillard, Thierry, additional, Zhang, Kang, additional, Brilliant, Murray H, additional, Hewitt, Alex W, additional, Swaroop, Anand, additional, Chew, Emily Y, additional, Pericak-Vance, Margaret A, additional, DeAngelis, Margaret, additional, Stambolian, Dwight, additional, Haines, Jonathan L, additional, Iyengar, Sudha K, additional, Weber, Bernhard H F, additional, Abecasis, Gonçalo R, additional, and Heid, Iris M, additional

Published
2015
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34. Complement Factor D in Age-Related Macular Degeneration

Author

Stanton, Chloe M., Yates, John R. W., den Hollander, Anneke I., Seddon, Johanna M., Swaroop, Anand, Stambolian, Dwight, Fauser, Sascha, Hoyng, Carel, Yu, Yi, Atsuhiro, Kanda, Branham, Kari, Othman, Mohammad, Chen, Wei, Kortvely, Elod, Chalmers, Kevin, Hayward, Caroline, Moore, Anthony T., Dhillon, Baljean, Ueffing, Marius, Wright, Alan F., Stanton, Chloe M., Yates, John R. W., den Hollander, Anneke I., Seddon, Johanna M., Swaroop, Anand, Stambolian, Dwight, Fauser, Sascha, Hoyng, Carel, Yu, Yi, Atsuhiro, Kanda, Branham, Kari, Othman, Mohammad, Chen, Wei, Kortvely, Elod, Chalmers, Kevin, Hayward, Caroline, Moore, Anthony T., Dhillon, Baljean, Ueffing, Marius, and Wright, Alan F.

Abstract

PURPOSE. To examine the role of complement factor D (CFD) in age-related macular degeneration (AMD) by analysis of genetic association, copy number variation, and plasma CFD concentrations. METHODS. Single nucleotide polymorphisms (SNPs) in the CFD gene were genotyped and the results analyzed by binary logistic regression. CFD gene copy number was analyzed by gene copy number assay. Plasma CFD was measured by an enzyme-linked immunosorbent assay. RESULTS. Genetic association was found between CFD gene SNP rs3826945 and AMD (odds ratio 1.44; P = 0.028) in a small discovery case-control series (462 cases and 325 controls) and replicated in a combined cohorts meta-analysis of 4765 cases and 2693 controls, with an odds ratio of 1.11 (P = 0.032), with the association almost confined to females. Copy number variation in the CFD gene was identified in 13 out of 640 samples examined but there was no difference in frequency between AMD cases (1.3%) and controls (2.7%). Plasma CFD concentration was measured in 751 AMD cases and 474 controls and found to be elevated in AMD cases (P = 0.00025). The odds ratio for those in the highest versus lowest quartile for plasma CFD was 1.81. The difference in plasma CFD was again almost confined to females. CONCLUSIONS. CFD regulates activation of the alternative complement pathway, which is implicated in AMD pathogenesis. The authors found evidence for genetic association between a CFD gene SNP and AMD and a significant increase in plasma CFD concentration in AMD cases compared with controls, consistent with a role for CFD in AMD pathogenesis. (Invest Ophthalmol Vis Sci. 2011;52:8828-8834) DOI:10.1167/iovs.11-7933

Published
2011

35. Identification of a rare coding variant in complement 3 associated with age-related macular degeneration

Author

Zhan, Xiaowei, primary, Larson, David E, additional, Wang, Chaolong, additional, Koboldt, Daniel C, additional, Sergeev, Yuri V, additional, Fulton, Robert S, additional, Fulton, Lucinda L, additional, Fronick, Catrina C, additional, Branham, Kari E, additional, Bragg-Gresham, Jennifer, additional, Jun, Goo, additional, Hu, Youna, additional, Kang, Hyun Min, additional, Liu, Dajiang, additional, Othman, Mohammad, additional, Brooks, Matthew, additional, Ratnapriya, Rinki, additional, Boleda, Alexis, additional, Grassmann, Felix, additional, von Strachwitz, Claudia, additional, Olson, Lana M, additional, Buitendijk, Gabriëlle H S, additional, Hofman, Albert, additional, van Duijn, Cornelia M, additional, Cipriani, Valentina, additional, Moore, Anthony T, additional, Shahid, Humma, additional, Jiang, Yingda, additional, Conley, Yvette P, additional, Morgan, Denise J, additional, Kim, Ivana K, additional, Johnson, Matthew P, additional, Cantsilieris, Stuart, additional, Richardson, Andrea J, additional, Guymer, Robyn H, additional, Luo, Hongrong, additional, Ouyang, Hong, additional, Licht, Christoph, additional, Pluthero, Fred G, additional, Zhang, Mindy M, additional, Zhang, Kang, additional, Baird, Paul N, additional, Blangero, John, additional, Klein, Michael L, additional, Farrer, Lindsay A, additional, DeAngelis, Margaret M, additional, Weeks, Daniel E, additional, Gorin, Michael B, additional, Yates, John R W, additional, Klaver, Caroline C W, additional, Pericak-Vance, Margaret A, additional, Haines, Jonathan L, additional, Weber, Bernhard H F, additional, Wilson, Richard K, additional, Heckenlively, John R, additional, Chew, Emily Y, additional, Stambolian, Dwight, additional, Mardis, Elaine R, additional, Swaroop, Anand, additional, and Abecasis, Goncalo R, additional

Published
2013
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36. Erratum: Corrigendum to: CASK mutations are frequent in males and cause X-linked nystagmus and variable XLMR phenotypes

Author

Hackett, Anna, primary, Tarpey, Patrick S, additional, Licata, Andrea, additional, Cox, James, additional, Whibley, Annabel, additional, Boyle, Jackie, additional, Rogers, Carolyn, additional, Grigg, John, additional, Partington, Michael, additional, Stevenson, Roger E, additional, Tolmie, John, additional, Yates, John R W, additional, Turner, Gillian, additional, Wilson, Meredith, additional, Futreal, Andrew P, additional, Corbett, Mark, additional, Shaw, Marie, additional, Gecz, Jozef, additional, Raymond, F Lucy, additional, Stratton, Michael R, additional, Schwartz, Charles E, additional, and Abidi, Fatima E, additional

Published
2010
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42. A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants

Author

Fritsche, Lars G, Igl, Wilmar, Bailey, Jessica N Cooke, Grassmann, Felix, Sengupta, Sebanti, Bragg-Gresham, Jennifer L, Burdon, Kathryn P, Hebbring, Scott J, Wen, Cindy, Gorski, Mathias, Kim, Ivana K, Cho, David, Zack, Donald, Souied, Eric, Scholl, Hendrik P N, Bala, Elisa, Lee, Kristine E, Hunter, David J, Sardell, Rebecca J, Mitchell, Paul, Merriam, Joanna E, Cipriani, Valentina, Hoffman, Joshua D, Schick, Tina, Lechanteur, Yara T E, Guymer, Robyn H, Johnson, Matthew P, Jiang, Yingda, Stanton, Chloe M, Buitendijk, Gabriëlle H S, Zhan, Xiaowei, Kwong, Alan M, Boleda, Alexis, Brooks, Matthew, Gieser, Linn, Ratnapriya, Rinki, Branham, Kari E, Foerster, Johanna R, Heckenlively, John R, Othman, Mohammad I, Vote, Brendan J, Liang, Helena Hai, Souzeau, Emmanuelle, McAllister, Ian L, Isaacs, Timothy, Hall, Janette, Lake, Stewart, Mackey, David A, Constable, Ian J, Craig, Jamie E, Kitchner, Terrie E, Yang, Zhenglin, Su, Zhiguang, Luo, Hongrong, Chen, Daniel, Ouyang, Hong, Flagg, Ken, Lin, Danni, Mao, Guanping, Ferreyra, Henry, Stark, Klaus, von Strachwitz, Claudia N, Wolf, Armin, Brandl, Caroline, Rudolph, Guenther, Olden, Matthias, Morrison, Margaux A, Morgan, Denise J, Schu, Matthew, Ahn, Jeeyun, Silvestri, Giuliana, Tsironi, Evangelia E, Park, Kyu Hyung, Farrer, Lindsay A, Orlin, Anton, Brucker, Alexander, Li, Mingyao, Curcio, Christine A, Mohand-Saïd, Saddek, Sahel, José-Alain, Audo, Isabelle, Benchaboune, Mustapha, Cree, Angela J, Rennie, Christina A, Goverdhan, Srinivas V, Grunin, Michelle, Hagbi-Levi, Shira, Campochiaro, Peter, Katsanis, Nicholas, Holz, Frank G, Blond, Frédéric, Blanché, Hélène, Deleuze, Jean-François, Igo, Robert P, Truitt, Barbara, Peachey, Neal S, Meuer, Stacy M, Myers, Chelsea E, Moore, Emily L, Klein, Ronald, Hauser, Michael A, Postel, Eric A, Courtenay, Monique D, Schwartz, Stephen G, Kovach, Jaclyn L, Scott, William K, Liew, Gerald, Tan, Ava G, Gopinath, Bamini, Merriam, John C, Smith, R Theodore, Khan, Jane C, Shahid, Humma, Moore, Anthony T, McGrath, J Allie, Laux, Reneé, Brantley, Milam A, Agarwal, Anita, Ersoy, Lebriz, Caramoy, Albert, Langmann, Thomas, Saksens, Nicole T M, de Jong, Eiko K, Hoyng, Carel B, Cain, Melinda S, Richardson, Andrea J, Martin, Tammy M, Blangero, John, Weeks, Daniel E, Dhillon, Bal, van Duijn, Cornelia M, Doheny, Kimberly F, Romm, Jane, Klaver, Caroline C W, Hayward, Caroline, Gorin, Michael B, Klein, Michael L, Baird, Paul N, den Hollander, Anneke I, Fauser, Sascha, Yates, John R W, Allikmets, Rando, Wang, Jie Jin, Schaumberg, Debra A, Klein, Barbara E K, Hagstrom, Stephanie A, Chowers, Itay, Lotery, Andrew J, Léveillard, Thierry, Zhang, Kang, Brilliant, Murray H, Hewitt, Alex W, Swaroop, Anand, Chew, Emily Y, Pericak-Vance, Margaret A, DeAngelis, Margaret, Stambolian, Dwight, Haines, Jonathan L, Iyengar, Sudha K, Weber, Bernhard H F, Abecasis, Gonçalo R, and Heid, Iris M

Abstract

Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, with limited therapeutic options. Here we report on a study of >12 million variants, including 163,714 directly genotyped, mostly rare, protein-altering variants. Analyzing 16,144 patients and 17,832 controls, we identify 52 independently associated common and rare variants (P < 5 × 10−8) distributed across 34 loci. Although wet and dry AMD subtypes exhibit predominantly shared genetics, we identify the first genetic association signal specific to wet AMD, near MMP9 (difference P value = 4.1 × 10−10). Very rare coding variants (frequency <0.1%) in CFH, CFI and TIMP3 suggest causal roles for these genes, as does a splice variant in SLC16A8. Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.

Published
2016
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43. Identification of the Tuberous Sclerosis Gene TSC1 on Chromosome 9q34

Author

Slegtenhorst, Marjon van, primary, Hoogt, Ronald de, additional, Hermans, Caroline, additional, Nellist, Mark, additional, Janssen, Bart, additional, Verhoef, Senno, additional, Lindhout, Dick, additional, Ouweland, Ans van den, additional, Halley, Dicky, additional, Young, Janet, additional, Burley, Mariwyn, additional, Jeremiah, Steve, additional, Woodward, Karen, additional, Nahmias, Joseph, additional, Fox, Margaret, additional, Ekong, Rosemary, additional, Osborne, John, additional, Wolfe, Jonathan, additional, Povey, Sue, additional, Snell, Russell G., additional, Cheadle, Jeremy P., additional, Jones, Alistair C., additional, Tachataki, Maria, additional, Ravine, David, additional, Sampson, Julian R., additional, Reeve, Mary Pat, additional, Richardson, Paul, additional, Wilmer, Friederike, additional, Munro, Cheryl, additional, Hawkins, Trevor L., additional, Sepp, Tiina, additional, Ali, Johari B. M., additional, Ward, Susannah, additional, Green, Andrew J., additional, Yates, John R. W., additional, Kwiatkowska, Jolanta, additional, Henske, Elizabeth P., additional, Short, M. Priscilla, additional, Haines, Jonathan H., additional, Jozwiak, Sergiusz, additional, and Kwiatkowski, David J., additional

Published
1997
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44. Nine novel L1 CAM mutations in families with X-linked hydrocephalus

Author

MacFarlane, John R., primary, Du, Jian-Sheng, additional, Pepys, Miriam E., additional, Ramsden, Simon, additional, Donnai, Dian, additional, Charlton, Ruth, additional, Garrett, Christine, additional, Tolmie, John, additional, Yates, John R. W., additional, Berry, Caroline, additional, Goudie, David, additional, Moncla, Anne, additional, Lunt, Peter, additional, Hodgson, Shirley, additional, Jouet, Monique, additional, and Kenwrick, Susan, additional

Published
1997
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47. The Tuberous Sclerosis 2000 Study: presentation, initial assessments and implications for diagnosis and management.

Author

Yates JR, Maclean C, Higgins JN, Humphrey A, le Maréchal K, Clifford M, Carcani-Rathwell I, Sampson JR, Bolton PF, Tuberous Sclerosis 2000 Study Group, Yates, John R W, Maclean, Cathy, Higgins, J Nicholas P, Humphrey, Ayla, le Maréchal, Kate, Clifford, Michelle, Carcani-Rathwell, Iris, Sampson, Julian R, and Bolton, Patrick F

Abstract

Aims: The Tuberous Sclerosis 2000 Study is the first comprehensive longitudinal study of tuberous sclerosis (TS) and aims to identify factors that determine prognosis. Mode of presentation and findings at initial assessments are reported here. Methods: Children aged 0-16 years newly diagnosed with TS in the UK were evaluated. Results: 125 children with TS were studied. 114 (91%) met clinical criteria for a definite diagnosis and the remaining 11 (9%) had pathogenic TSC1 or TSC2 mutations. In families with a definite clinical diagnosis, the detection rate for pathogenic mutations was 89%. 21 cases (17%) were identified prenatally, usually with abnormalities found at routine antenatal ultrasound examination. 30 cases (24%) presented before developing seizures and in 10 of these without a definite diagnosis at onset of seizures, genetic testing could have confirmed TS. 77 cases (62%) presented with seizures. Median age at recruitment assessment was 2.7 years (range: 4 weeks-18 years). Dermatological features of TS were present in 81%. The detection rate of TS abnormalities was 20/107 (19%) for renal ultrasound including three cases with polycystic kidney disease, 51/88 (58%) for echocardiography, 29/35 (83%) for cranial CT and 95/104 (91%) for cranial MRI. 91% of cases had epilepsy and 65% had intellectual disability (IQ<70). Conclusions: Genetic testing can be valuable in confirming the diagnosis. Increasing numbers of cases present prenatally or in early infancy, before onset of seizures, raising important questions about whether these children should have EEG monitoring and concerning the criteria for starting anticonvulsant therapy. [ABSTRACT FROM AUTHOR]

Published
2011
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48. CASK mutations are frequent in males and cause X-linked nystagmus and variable XLMR phenotypes.

Author

Hackett, Anna, Tarpey, Patrick S., Licata, Andrea, Cox, James, Whibley, Annabel, Boyle, Jackie, Rogers, Carolyn, Grigg, John, Partington, Michael, Stevenson, Roger E., Tolmie, John, Yates, John R. W., Turner, Gillian, Wilson, Meredith, Futreal, Andrew P., Corbett, Mark, Shaw, Marie, Gecz, Jozef, Raymond, F. Lucy, and Stratton, Michael R.

Subjects
GENETIC mutation, NYSTAGMUS, EYE movement disorders, PHENOTYPES, PATHOLOGICAL psychology
Abstract

Mutations of the calcium/calmodulin-dependent serine protein kinase (CASK) gene have recently been associated with X-linked mental retardation (XLMR) with microcephaly, optic atrophy and brainstem and cerebellar hypoplasia, as well as with an X-linked syndrome having some FG-like features. Our group has recently identified four male probands from 358 probable XLMR families with missense mutations (p.Y268H, p.P396S, p.D710G and p.W919R) in the CASK gene. Congenital nystagmus, a rare and striking feature, was present in two of these families. We screened a further 45 probands with either nystagmus or microcephaly and mental retardation (MR), and identified two further mutations, a missense mutation (p.Y728C) and a splice mutation (c.2521-2A>T) in two small families with nystagmus and MR. Detailed clinical examinations of all six families, including an ophthalmological review in four families, were undertaken to further characterise the phenotype. We report on the clinical features of 24 individuals, mostly male, from six families with CASK mutations. The phenotype was variable, ranging from non-syndromic mild MR to severe MR associated with microcephaly and dysmorphic facial features. Carrier females were variably affected. Congenital nystagmus was found in members of four of the families. Our findings reinforce the CASK gene as a relatively frequent cause of XLMR in females and males. We further define the phenotypic spectrum and demonstrate that affected males with missense mutations or in-frame deletions in CASK are frequently associated with congenital nystagmus and XLMR, a striking feature not previously reported. [ABSTRACT FROM AUTHOR]

Published
2010
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50. Nonsense-mediated RNA decay in the TSC1 gene suggests a useful tool pre- and post-positional cloning.

Author

Jeganathan, Dharini, Fox, Margaret F., Young, Janet M., Yates, John R. W., Osborne, John P., and Povey, Sue

Subjects
MESSENGER RNA, RNA, GENETIC mutation, CLONING, GENETIC engineering, ASEXUAL reproduction, GENETIC recombination, GENETICS
Abstract

Many mRNAs carrying mutations that are predicted to encode a truncated protein are subject to a mechanism known as nonsense-mediated mRNA decay (NMD), which results in reduced levels of mutant transcript. Tuberous sclerosis (TSC), an autosomal dominant neurocutaneous disorder with mutations in either of two genes, TSC1 or TSC2, requires comprehensive screening of both genes for molecular diagnosis. Virtually all TSC1 mutations are predicted to truncate the protein product. Coding and newly identified 3′ untranslated region polymorphisms in TSC1 were used to develop a transcript imbalance assay to investigate TSC1 transcript levels in patients. This approach allowed the correct identification of six out of seven TSC1 patients tested blind from a panel of TSC1 and TSC2 patients, with no false positives. The extent of NMD in TSC1 was found to correlate with each individual mutation regardless of intra-familial variation in clinical features and with no strong evidence for positional bias. NMD in TSC1 was more pronounced in cultured cells than in RNA prepared directly from peripheral lymphocytes (in which novel splicing of exon 5 was observed). The advent of a dense SNP map of transcribed regions of the genome may allow a similar transcript imbalance assay in the assessment of candidate genes for diseases whose causes are still unknown. [ABSTRACT FROM AUTHOR]

Published
2002
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