Search

Your search keyword '"Brodeur, Wendy"' showing total 15 results
Start Over Author "Brodeur, Wendy"
15 results on '"Brodeur, Wendy"'

1. Neptune: an environment for the delivery of genomic medicine

Author

Eric, Venner, Yi, Victoria, Murdock, David, Kalla, Sara E., Wu, Tsung-Jung, Sabo, Aniko, Li, Shoudong, Meng, Qingchang, Tian, Xia, Murugan, Mullai, Cohen, Michelle, Kovar, Christie, Wei, Wei-Qi, Chung, Wendy K., Weng, Chunhua, Wiesner, Georgia L., Jarvik, Gail P., Muzny, Donna, Gibbs, Richard A., Abrams, Debra, Adunyah, Samuel E., Albertson-Junkans, Ladia, Almoguera, Berta, Ames, Darren C., Appelbaum, Paul, Aronson, Samuel, Aufox, Sharon, Babb, Lawrence J., Balasubramanian, Adithya, Bangash, Hana, Basford, Melissa, Bastarache, Lisa, Baxter, Samantha, Behr, Meckenzie, Benoit, Barbara, Bhoj, Elizabeth, Bielinski, Suzette J., Bland, Harris T., Blout, Carrie, Borthwick, Kenneth, Bottinger, Erwin P., Bowser, Mark, Brand, Harrison, Brilliant, Murray, Brodeur, Wendy, Caraballo, Pedro, Carrell, David, Carroll, Andrew, Castillo, Lisa, Castro, Victor, Chandanavelli, Gauthami, Chiang, Theodore, Chisholm, Rex L., Christensen, Kurt D., Chung, Wendy, Chute, Christopher G., City, Brittany, Cobb, Beth L., Connolly, John J., Crane, Paul, Crew, Katherine, Crosslin, David R., Dayal, Jyoti, De Andrade, Mariza, De la Cruz, Jessica, Denny, Josh C., Denson, Shawn, DeSmet, Tim, Dikilitas, Ozan, Dinsmore, Michael J., Dodge, Sheila, Dunlea, Phil, Edwards, Todd L., Eng, Christine M., Fasel, David, Fedotov, Alex, Feng, Qiping, Fleharty, Mark, Foster, Andrea, Freimuth, Robert, Friedrich, Christopher, Fullerton, Stephanie M., Funke, Birgit, Gabriel, Stacey, Gainer, Vivian, Gharavi, Ali, Glazer, Andrew M., Glessner, Joseph T., Goehringer, Jessica, Gordon, Adam S., Graham, Chet, Green, Robert C., Gundelach, Justin H., Hain, Heather S., Hakonarson, Hakon, Harden, Maegan V., Harley, John, Harr, Margaret, Hartzler, Andrea, Hayes, M. Geoffrey, Hebbring, Scott, Henrikson, Nora, Hershey, Andrew, Hoell, Christin, Holm, Ingrid, Howell, Kayla M., Hripcsak, George, Hu, Jianhong, Hynes, Elizabeth Duffy, Jayaseelan, Joy C., Jiang, Yunyun, Joo, Yoonjung Yoonie, Jose, Sheethal, Josyula, Navya Shilpa, Justice, Anne E., Kalra, Divya, Karlson, Elizabeth W., Keating, Brendan J., Kelly, Melissa A., Kenny, Eimear E., Key, Dustin, Kiryluk, Krzysztof, Kitchner, Terrie, Klanderman, Barbara, Klee, Eric, Kochan, David C., Korchina, Viktoriya, Kottyan, Leah, Kudalkar, Emily, Rahm, Alanna Kulchak, Kullo, Iftikhar J., Lammers, Philip, Larson, Eric B., Lebo, Matthew S., Leduc, Magalie, Lee, Ming Ta (Michael), Lennon, Niall J., Leppig, Kathleen A., Leslie, Nancy D., Li, Rongling, Liang, Wayne H., Lin, Chiao-Feng, Linder, Jodell E., Lindor, Noralane M., Lingren, Todd, Linneman, James G., Liu, Cong, Liu, Wen, Liu, Xiuping, Lynch, John, Lyon, Hayley, Macbeth, Alyssa, Mahadeshwar, Harshad, Mahanta, Lisa, Malin, Bradley, Manolio, Teri, Marasa, Maddalena, Marsolo, Keith, McGowan, Michelle L., McNally, Elizabeth, Meldrim, Jim, Mentch, Frank, Rasouly, Hila Milo, Mosley, Jonathan, Mukherjee, Shubhabrata, Mullen, Thomas E., Muniz, Jesse, Murdock, David R., Murphy, Shawn, Myers, Melanie F., Namjou, Bahram, Ni, Yizhao, Onofrio, Robert C., Obeng, Aniwaa Owusu, Person, Thomas N., Peterson, Josh F., Petukhova, Lynn, Pisieczko, Cassandra J., Pratap, Siddharth, Prows, Cynthia A., Puckelwartz, Megan J., Raj, Ritika, Ralston, James D., Ramaprasan, Arvind, Ramirez, Andrea, Rasmussen, Luke, Rasmussen-Torvik, Laura, Raychaudhuri, Soumya, Rehm, Heidi L., Ritchie, Marylyn D., Rives, Catherine, Riza, Beenish, Roden, Dan M., Rosenthal, Elisabeth A., Santani, Avni, Dan, Schaid, Scherer, Steven, Scott, Stuart, Scrol, Aaron, Sengupta, Soumitra, Shang, Ning, Sharma, Himanshu, Sharp, Richard R., Singh, Rajbir, Sleiman, Patrick M.A., Slowik, Kara, Smith, Joshua C., Smith, Maureen E., Smoot, Duane T., Smoller, Jordan W., Sohn, Sunghwan, Stanaway, Ian B., Starren, Justin, Stroud, Mary, Su, Jessica, Taylor, Casey Overby, Tolwinski, Kasia, Van Driest, Sara L., Vargas, Sean M., Varugheese, Matthew, Veenstra, David, Venner, Eric, Verbitsky, Miguel, Vicente, Gina, Wagner, Michael, Walker, Kimberly, Walunas, Theresa, Wang, Liwen, Wang, Qiaoyan, Weiss, Scott T., Wells, Quinn S., White, Peter S., Wiley, Ken L., Jr, Williams, Janet L., Williams, Marc S., Wilson, Michael W., Witkowski, Leora, Woods, Laura Allison, Woolf, Betty, Wynn, Julia, Yang, Yaping, Zhang, Ge, Zhang, Lan, and Zouk, Hana

Published
2021
Full Text
View/download PDF

2. Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network

Author

Zouk, Hana, Venner, Eric, Lennon, Niall J., Muzny, Donna M., Abrams, Debra, Adunyah, Samuel, Albertson-Junkans, Ladia, Ames, Darren C., Appelbaum, Paul, Aronson, Samuel, Aufox, Sharon, Babb, Lawrence J., Balasubramanian, Adithya, Bangash, Hana, Basford, Melissa, Bastarache, Lisa, Baxter, Samantha, Behr, Meckenzie, Benoit, Barbara, Bhoj, Elizabeth, Bielinski, Suzette J., Bland, Sarah T., Blout, Carrie, Borthwick, Kenneth, Bottinger, Erwin P., Bowser, Mark, Brand, Harrison, Brilliant, Murray, Brodeur, Wendy, Caraballo, Pedro, Carrell, David, Carroll, Andrew, Almoguera, Berta, Castillo, Lisa, Castro, Victor, Chandanavelli, Gauthami, Chiang, Theodore, Chisholm, Rex L., Christensen, Kurt D., Chung, Wendy, Chute, Christopher G., City, Brittany, Cobb, Beth L., Connolly, John J., Crane, Paul, Crew, Katherine, Crosslin, David, De Andrade, Mariza, De la Cruz, Jessica, Denson, Shawn, Denny, Josh, DeSmet, Tim, Dikilitas, Ozan, Friedrich, Christopher, Fullerton, Stephanie M., Funke, Birgit, Gabriel, Stacey, Gainer, Vivian, Gharavi, Ali, Glazer, Andrew M., Glessner, Joseph T., Goehringer, Jessica, Gordon, Adam S., Graham, Chet, Green, Robert C., Gundelach, Justin H., Dayal, Jyoti, Hain, Heather S., Hakonarson, Hakon, Harden, Maegan V., Harley, John, Harr, Margaret, Hartzler, Andrea, Hayes, M. Geoffrey, Hebbring, Scott, Henrikson, Nora, Hershey, Andrew, Hoell, Christin, Holm, Ingrid, Howell, Kayla M., Hripcsak, George, Hu, Jianhong, Jarvik, Gail P., Jayaseelan, Joy C., Jiang, Yunyun, Joo, Yoonjung Yoonie, Jose, Sheethal, Josyula, Navya Shilpa, Justice, Anne E., Kalla, Sara E., Kalra, Divya, Karlson, Elizabeth, Kelly, Melissa A., Keating, Brendan J., Kenny, Eimear E., Key, Dustin, Kiryluk, Krzysztof, Kitchner, Terrie, Klanderman, Barbara, Klee, Eric, Kochan, David C., Korchina, Viktoriya, Kottyan, Leah, Kovar, Christie, Kudalkar, Emily, Kullo, Iftikhar J., Lammers, Philip, Larson, Eric B., Lebo, Matthew S., Leduc, Magalie, Lee, Ming Ta (Michael), Leppig, Kathleen A., Leslie, Nancy D., Li, Rongling, Liang, Wayne H., Lin, Chiao-Feng, Linder, Jodell, Lindor, Noralane M., Lingren, Todd, Linneman, James G., Liu, Cong, Liu, Wen, Liu, Xiuping, Lynch, John, Lyon, Hayley, Macbeth, Alyssa, Mahadeshwar, Harshad, Mahanta, Lisa, Malin, Brad, Manolio, Teri, Marasa, Maddalena, Marsolo, Keith, Dinsmore, Michael J., Dodge, Sheila, Hynes, Elizabeth Duffy, Dunlea, Phil, Edwards, Todd L., Eng, Christine M., Fasel, David, Fedotov, Alex, Feng, Qiping, Fleharty, Mark, Foster, Andrea, Freimuth, Robert, McGowan, Michelle L., McNally, Elizabeth, Meldrim, Jim, Mentch, Frank, Mosley, Jonathan, Mukherjee, Shubhabrata, Mullen, Thomas E., Muniz, Jesse, Murdock, David R., Murphy, Shawn, Murugan, Mullai, Myers, Melanie F., Namjou, Bahram, Ni, Yizhao, Obeng, Aniwaa Owusu, Onofrio, Robert C., Taylor, Casey Overby, Person, Thomas N., Peterson, Josh F., Petukhova, Lynn, Pisieczko, Cassandra J., Pratap, Siddharth, Prows, Cynthia A., Puckelwartz, Megan J., Rahm, Alanna Kulchak, Raj, Ritika, Ralston, James D., Ramaprasan, Arvind, Ramirez, Andrea, Rasmussen, Luke, Rasmussen-Torvik, Laura, Rasouly, Hila Milo, Raychaudhuri, Soumya, Ritchie, Marylyn D., Rives, Catherine, Riza, Beenish, Roden, Dan, Rosenthal, Elisabeth A., Santani, Avni, Schaid, Dan, Scherer, Steven, Scott, Stuart, Scrol, Aaron, Sengupta, Soumitra, Shang, Ning, Sharma, Himanshu, Sharp, Richard R., Singh, Rajbir, Sleiman, Patrick M.A., Slowik, Kara, Smith, Joshua C., Smith, Maureen E., Smoller, Jordan W., Sohn, Sunghwan, Stanaway, Ian B., Starren, Justin, Stroud, Mary, Su, Jessica, Tolwinski, Kasia, Van Driest, Sara L., Vargas, Sean M., Varugheese, Matthew, Veenstra, David, Verbitsky, Miguel, Vicente, Gina, Wagner, Michael, Walker, Kimberly, Walunas, Theresa, Wang, Liwen, Wang, Qiaoyan, Wei, Wei-Qi, Weiss, Scott T., Wiesner, Georgia L., Wells, Quinn, Weng, Chunhua, White, Peter S., Wiley, Ken L., Jr., Williams, Janet L., Williams, Marc S., Wilson, Michael W., Witkowski, Leora, Woods, Laura Allison, Woolf, Betty, Wu, Tsung-Jung, Wynn, Julia, Yang, Yaping, Yi, Victoria, Zhang, Ge, Zhang, Lan, Rehm, Heidi L., and Gibbs, Richard A.

Published
2019
Full Text
View/download PDF

3. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

Author

De Jager, Philip L, Srivastava, Gyan, Lunnon, Katie, Burgess, Jeremy, Schalkwyk, Leonard C, Yu, Lei, Eaton, Matthew L, Keenan, Brendan T, Ernst, Jason, McCabe, Cristin, Tang, Anna, Raj, Towfique, Replogle, Joseph, Brodeur, Wendy, Gabriel, Stacey, Chai, High S, Younkin, Curtis, Younkin, Steven G, Zou, Fanggeng, Szyf, Moshe, Epstein, Charles B, Schneider, Julie A, Bernstein, Bradley E, Meissner, Alex, Ertekin-Taner, Nilufer, Chibnik, Lori B, Kellis, Manolis, Mill, Jonathan, and Bennett, David A

Subjects
Neurosciences, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Brain Disorders, Alzheimer's Disease, Human Genome, Genetics, Dementia, Neurodegenerative, Acquired Cognitive Impairment, Aging, 2.1 Biological and endogenous factors, Aetiology, Neurological, Adaptor Proteins, Signal Transducing, Aged, Aged, 80 and over, Alzheimer Disease, Amyloidosis, Ankyrins, Brain, Carrier Proteins, CpG Islands, DNA Methylation, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Intracellular Signaling Peptides and Proteins, Male, Middle Aged, Nuclear Proteins, Protein Interaction Maps, Tumor Suppressor Proteins, Psychology, Cognitive Sciences, Neurology & Neurosurgery
Abstract

We used a collection of 708 prospectively collected autopsied brains to assess the methylation state of the brain's DNA in relation to Alzheimer's disease (AD). We found that the level of methylation at 71 of the 415,848 interrogated CpGs was significantly associated with the burden of AD pathology, including CpGs in the ABCA7 and BIN1 regions, which harbor known AD susceptibility variants. We validated 11 of the differentially methylated regions in an independent set of 117 subjects. Furthermore, we functionally validated these CpG associations and identified the nearby genes whose RNA expression was altered in AD: ANK1, CDH23, DIP2A, RHBDF2, RPL13, SERPINF1 and SERPINF2. Our analyses suggest that these DNA methylation changes may have a role in the onset of AD given that we observed them in presymptomatic subjects and that six of the validated genes connect to a known AD susceptibility gene network.

Published
2014

4. Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico

Author

Williams, Amy L, Jacobs, Suzanne BR, Moreno-Macías, Hortensia, Huerta-Chagoya, Alicia, Churchhouse, Claire, Márquez-Luna, Carla, García-Ortíz, Humberto, José Gómez-Vázquez, María, Burtt, Noël P, Aguilar-Salinas, Carlos A, González-Villalpando, Clicerio, Florez, Jose C, Orozco, Lorena, Haiman, Christopher A, Tusié-Luna, Teresa, Altshuler, David, Ripke, Stephan, Manning, Alisa K, Neale, Benjamin, Reich, David, Stram, Daniel O, Fernández-López, Juan Carlos, Romero-Hidalgo, Sandra, Patterson, Nick, Aguilar-Delfín, Irma, Martínez-Hernández, Angélica, Centeno-Cruz, Federico, Mendoza-Caamal, Elvia, Revilla-Monsalve, Cristina, Islas-Andrade, Sergio, Córdova, Emilio, Rodríguez-Arellano, Eunice, Soberón, Xavier, González-Villalpando, María Elena, Henderson, Brian E, Monroe, Kristine, Wilkens, Lynne, Kolonel, Laurence N, Le Marchand, Loic, Riba, Laura, Ordóñez-Sánchez, María Luisa, Rodríguez-Guillén, Rosario, Cruz-Bautista, Ivette, Rodríguez-Torres, Maribel, Muñoz-Hernández, Linda Liliana, Sáenz, Tamara, Gómez, Donají, Alvirde, Ulices, Onofrio, Robert C, Brodeur, Wendy M, Gage, Diane, Murphy, Jacquelyn, Franklin, Jennifer, Mahan, Scott, Ardlie, Kristin, Crenshaw, Andrew T, Winckler, Wendy, Prüfer, Kay, Shunkov, Michael V, Sawyer, Susanna, Stenzel, Udo, Kelso, Janet, Lek, Monkol, Sankararaman, Sriram, MacArthur, Daniel G, Derevianko, Anatoli P, Pääbo, Svante, Gopal, Shuba, Grammatikos, James A, Smith, Ian C, Bullock, Kevin H, Deik, Amy A, Souza, Amanda L, Pierce, Kerry A, Clish, Clary B, Fennell, Timothy, and Farjoun, Yossi

Subjects
Nutrition, Diabetes, Prevention, Genetics, 2.1 Biological and endogenous factors, Aetiology, Metabolic and endocrine, Alleles, Animals, Asian People, Black People, Cohort Studies, Diabetes Mellitus, Type 2, Endoplasmic Reticulum, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Haplotypes, HeLa Cells, Humans, Indians, North American, Lipid Metabolism, Liver, Male, Mexico, Monocarboxylic Acid Transporters, Neanderthals, Polymorphism, Single Nucleotide, RNA, Messenger, Triglycerides, White People, SIGMA Type 2 Diabetes Consortium, Hela Cells, General Science & Technology
Abstract

Performing genetic studies in multiple human populations can identify disease risk alleles that are common in one population but rare in others, with the potential to illuminate pathophysiology, health disparities, and the population genetic origins of disease alleles. Here we analysed 9.2 million single nucleotide polymorphisms (SNPs) in each of 8,214 Mexicans and other Latin Americans: 3,848 with type 2 diabetes and 4,366 non-diabetic controls. In addition to replicating previous findings, we identified a novel locus associated with type 2 diabetes at genome-wide significance spanning the solute carriers SLC16A11 and SLC16A13 (P = 3.9 × 10(-13); odds ratio (OR) = 1.29). The association was stronger in younger, leaner people with type 2 diabetes, and replicated in independent samples (P = 1.1 × 10(-4); OR = 1.20). The risk haplotype carries four amino acid substitutions, all in SLC16A11; it is present at ~50% frequency in Native American samples and ~10% in east Asian, but is rare in European and African samples. Analysis of an archaic genome sequence indicated that the risk haplotype introgressed into modern humans via admixture with Neanderthals. The SLC16A11 messenger RNA is expressed in liver, and V5-tagged SLC16A11 protein localizes to the endoplasmic reticulum. Expression of SLC16A11 in heterologous cells alters lipid metabolism, most notably causing an increase in intracellular triacylglycerol levels. Despite type 2 diabetes having been well studied by genome-wide association studies in other populations, analysis in Mexican and Latin American individuals identified SLC16A11 as a novel candidate gene for type 2 diabetes with a possible role in triacylglycerol metabolism.

Published
2014

5. Common Variants at 9p21 and 8q22 Are Associated with Increased Susceptibility to Optic Nerve Degeneration in Glaucoma

Author

Wiggs, Janey L, Yaspan, Brian L, Hauser, Michael A, Kang, Jae H, Allingham, R Rand, Olson, Lana M, Abdrabou, Wael, Fan, Bao J, Wang, Dan Y, Brodeur, Wendy, Budenz, Donald L, Caprioli, Joseph, Crenshaw, Andrew, Crooks, Kristy, DelBono, Elizabeth, Doheny, Kimberly F, Friedman, David S, Gaasterland, Douglas, Gaasterland, Terry, Laurie, Cathy, Lee, Richard K, Lichter, Paul R, Loomis, Stephanie, Liu, Yutao, Medeiros, Felipe A, McCarty, Cathy, Mirel, Daniel, Moroi, Sayoko E, Musch, David C, Realini, Anthony, Rozsa, Frank W, Schuman, Joel S, Scott, Kathleen, Singh, Kuldev, Stein, Joshua D, Trager, Edward H, VanVeldhuisen, Paul, Vollrath, Douglas, Wollstein, Gadi, Yoneyama, Sachiko, Zhang, Kang, Weinreb, Robert N, Ernst, Jason, Kellis, Manolis, Masuda, Tomohiro, Zack, Don, Richards, Julia E, Pericak-Vance, Margaret, Pasquale, Louis R, and Haines, Jonathan L

Subjects
Biological Sciences, Genetics, Clinical Research, Neurosciences, Eye Disease and Disorders of Vision, Neurodegenerative, Aging, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Eye, Alleles, Chromosomes, Human, Pair 8, Chromosomes, Human, Pair 9, Exfoliation Syndrome, Genome-Wide Association Study, Glaucoma, Open-Angle, Homeodomain Proteins, Humans, Nerve Degeneration, Optic Nerve, Polymorphism, Single Nucleotide, RNA, Long Noncoding, RNA, Untranslated, Transforming Growth Factor beta, Developmental Biology
Abstract

Optic nerve degeneration caused by glaucoma is a leading cause of blindness worldwide. Patients affected by the normal-pressure form of glaucoma are more likely to harbor risk alleles for glaucoma-related optic nerve disease. We have performed a meta-analysis of two independent genome-wide association studies for primary open angle glaucoma (POAG) followed by a normal-pressure glaucoma (NPG, defined by intraocular pressure (IOP) less than 22 mmHg) subgroup analysis. The single-nucleotide polymorphisms that showed the most significant associations were tested for association with a second form of glaucoma, exfoliation-syndrome glaucoma. The overall meta-analysis of the GLAUGEN and NEIGHBOR dataset results (3,146 cases and 3,487 controls) identified significant associations between two loci and POAG: the CDKN2BAS region on 9p21 (rs2157719 [G], OR = 0.69 [95%CI 0.63-0.75], p = 1.86×10⁻¹⁸), and the SIX1/SIX6 region on chromosome 14q23 (rs10483727 [A], OR = 1.32 [95%CI 1.21-1.43], p = 3.87×10⁻¹¹). In sub-group analysis two loci were significantly associated with NPG: 9p21 containing the CDKN2BAS gene (rs2157719 [G], OR = 0.58 [95% CI 0.50-0.67], p = 1.17×10⁻¹²) and a probable regulatory region on 8q22 (rs284489 [G], OR = 0.62 [95% CI 0.53-0.72], p = 8.88×10⁻¹⁰). Both NPG loci were also nominally associated with a second type of glaucoma, exfoliation syndrome glaucoma (rs2157719 [G], OR = 0.59 [95% CI 0.41-0.87], p = 0.004 and rs284489 [G], OR = 0.76 [95% CI 0.54-1.06], p = 0.021), suggesting that these loci might contribute more generally to optic nerve degeneration in glaucoma. Because both loci influence transforming growth factor beta (TGF-beta) signaling, we performed a genomic pathway analysis that showed an association between the TGF-beta pathway and NPG (permuted p = 0.009). These results suggest that neuro-protective therapies targeting TGF-beta signaling could be effective for multiple forms of glaucoma.

Published
2012

8. Integrating common and rare genetic variation in diverse human populations

Author

Altshuler, David M., Gibbs, Richard A., Peltonen, Leena, Dermitzakis, Emmanouil, Schaffner, Stephen F., Yu, Fuli, Bonnen, Penelope E., de Bakker, Paul I. W., Deloukas, Panos, Gabriel, Stacey B., Gwilliam, Rhian, Hunt, Sarah, Inouye, Michael, Jia, Xiaoming, Palotie, Aarno, Parkin, Melissa, Whittaker, Pamela, Yu, Fuli, Chang, Kyle, Hawes, Alicia, Lewis, Lora R., Ren, Yanru, Wheeler, David, Marie Muzny, Donna, Barnes, Chris, Darvishi, Katayoon, Hurles, Matthew, Korn, Joshua M., Kristiansson, Kati, Lee, Charles, McCarroll, Steven A., Nemesh, James, Keinan, Alon, Montgomery, Stephen B., Pollack, Samuela, Price, Alkes L., Soranzo, Nicole, Gonzaga-Jauregui, Claudia, Keinan, Alon, Anttila, Verneri, Brodeur, Wendy, Daly, Mark J., Leslie, Stephen, McVean, Gil, Moutsianas, Loukas, Nguyen, Huy, Schaffner, Stephen F., Zhang, Qingrun, Ghori, Mohammed J. R., McGinnis, Ralph, McLaren, William, Price, Alkes L., Schaffner, Stephen F., Takeuchi, Fumihiko, Grossman, Sharon R., Shlyakhter, Ilya, Hostetter, Elizabeth B., Sabeti, Pardis C., Adebamowo, Clement A., Foster, Morris W., Gordon, Deborah R., Licinio, Julio, Cristina Manca, Maria, Marshall, Patricia A., Matsuda, Ichiro, Ngare, Duncan, Ota Wang, Vivian, Reddy, Deepa, Rotimi, Charles N., Royal, Charmaine D., Sharp, Richard R., Zeng, Changqing, Brooks, Lisa D., and McEwen, Jean E.

Published
2010
Full Text
View/download PDF

9. Additional file 3: of Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

Author

Costello, Maura, Fleharty, Mark, Abreu, Justin, Farjoun, Yossi, Ferriera, Steven, Holmes, Laurie, Granger, Brian, Green, Lisa, Howd, Tom, Mason, Tamara, Vicente, Gina, Dasilva, Michael, Brodeur, Wendy, DeSmet, Timothy, Dodge, Sheila, Lennon, Niall, and Gabriel, Stacey

Abstract

Suggested guidelines for designing robust indexes for Illumina sequencing. (DOCX 129Â kb)

Published
2018
Full Text
View/download PDF

10. Additional file 1: of Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

Author

Costello, Maura, Fleharty, Mark, Abreu, Justin, Farjoun, Yossi, Ferriera, Steven, Holmes, Laurie, Granger, Brian, Green, Lisa, Howd, Tom, Mason, Tamara, Vicente, Gina, Dasilva, Michael, Brodeur, Wendy, DeSmet, Timothy, Dodge, Sheila, Lennon, Niall, and Gabriel, Stacey

Abstract

Figure S1. Initial testing of single vs dual indexed sequencing on HiSeq. Figure S2. Previous experience with index swapping during exome capture library preparation (previously unpublished data). (DOCX 1113Â kb)

Published
2018
Full Text
View/download PDF

11. Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

Author

Costello, Maura, primary, Fleharty, Mark, additional, Abreu, Justin, additional, Farjoun, Yossi, additional, Ferriera, Steven, additional, Holmes, Laurie, additional, Howd, Tom, additional, Mason, Tamara, additional, Vicente, Gina, additional, Dasilva, Michael, additional, Brodeur, Wendy, additional, DeSmet, Timothy, additional, Dodge, Sheila, additional, Lennon, Niall J., additional, and Gabriel, Stacey, additional

Published
2017
Full Text
View/download PDF

12. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

Author

Srivastava, Gyan, Lunnon, Katie, Burgess, Jeremy, Yu, Lei, Ernst, Jason, McCabe, Cristin, Tang, Anna, Raj, Towfique, Replogle, Joseph, Brodeur, Wendy, Gabriel, Stacey, Younkin, Curtis, Zou, Fanggeng, Szyf, Moshe, Meissner, Alexander, Ertekin-Taner, Nilufer, Kellis, Manolis, Mill, Jonathan, De Jager, Philip L., Schalkwyk, Leonard C., Eaton, Matthew Lucas, Eaton, Matthew L., Keenan, Brendan T., Chai, High S., Younkin, Steven G., Epstein, Charles B., Schneider, Julie A., Bernstein, Bradley E., Chibnik, Lori B., Bennett, David A., Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Eaton, Matthew Lucas, Ernst, Jason, Meissner, Alexander, and Kellis, Manolis

Subjects
Male, Aging, Genome-wide association study, Neurodegenerative, Alzheimer's Disease, 80 and over, 2.1 Biological and endogenous factors, Psychology, Protein Interaction Maps, Aetiology, Epigenomics, Genetics, Aged, 80 and over, General Neuroscience, Intracellular Signaling Peptides and Proteins, Brain, Adaptor Proteins, Nuclear Proteins, Methylation, Amyloidosis, Middle Aged, 3. Good health, CpG site, Neurological, DNA methylation, Female, Cognitive Sciences, Alzheimer's disease, Ankyrins, and over, Biology, Article, Alzheimer Disease, Acquired Cognitive Impairment, medicine, Humans, Genetic Predisposition to Disease, Gene, Adaptor Proteins, Signal Transducing, Aged, Neurology & Neurosurgery, Tumor Suppressor Proteins, Human Genome, Signal Transducing, Neurosciences, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), DNA Methylation, medicine.disease, Brain Disorders, Differentially methylated regions, Dementia, CpG Islands, Carrier Proteins, Genome-Wide Association Study
Abstract

We used a collection of 708 prospectively collected autopsied brains to assess the methylation state of the brain's DNA in relation to Alzheimer's disease (AD). We found that the level of methylation at 71 of the 415,848 interrogated CpGs was significantly associated with the burden of AD pathology, including CpGs in the ABCA7 and BIN1 regions, which harbor known AD susceptibility variants. We validated 11 of the differentially methylated regions in an independent set of 117 subjects. Furthermore, we functionally validated these CpG associations and identified the nearby genes whose RNA expression was altered in AD: ANK1, CDH23, DIP2A, RHBDF2, RPL13, SERPINF1 and SERPINF2. Our analyses suggest that these DNA methylation changes may have a role in the onset of AD given that we observed them in presymptomatic subjects and that six of the validated genes connect to a known AD susceptibility gene network., National Institutes of Health (U.S.) (Grant R01 AG036042), National Institutes of Health (U.S.) (Grant R01AG036836), National Institutes of Health (U.S.) (Grant R01 AG17917), National Institutes of Health (U.S.) (Grant R01AG15819), National Institutes of Health (U.S.) (Grant R01 AG032990), National Institutes of Health (U.S.) (Grant R01 AG18023), National Institutes of Health (U.S.) (Grant RC2 AG036547), National Institutes of Health (U.S.) (Grant P30 AG10161), National Institutes of Health (U.S.) (Grant P50 AG016574), National Institutes of Health (U.S.) (Grant U01 ES017155), National Institutes of Health (U.S.) (Grant KL2 RR024151), National Institutes of Health (U.S.) (Grant K25 AG041906-01)

Published
2014

13. Genome-Wide Association Analysis Identifies Loci for Type 2 Diabetes and Triglyceride Levels

Author

Saxena, Richa, primary, Voight, Benjamin F., additional, Lyssenko, Valeriya, additional, Burtt, Noël P., additional, de Bakker, Paul I. W., additional, Chen, Hong, additional, Roix, Jeffrey J., additional, Kathiresan, Sekar, additional, Hirschhorn, Joel N., additional, Daly, Mark J., additional, Hughes, Thomas E., additional, Groop, Leif, additional, Altshuler, David, additional, Almgren, Peter, additional, Florez, Jose C., additional, Meyer, Joanne, additional, Ardlie, Kristin, additional, Bengtsson Boström, Kristina, additional, Isomaa, Bo, additional, Lettre, Guillaume, additional, Lindblad, Ulf, additional, Lyon, Helen N., additional, Melander, Olle, additional, Newton-Cheh, Christopher, additional, Nilsson, Peter, additional, Orho-Melander, Marju, additional, Råstam, Lennart, additional, Speliotes, Elizabeth K., additional, Taskinen, Marja-Riitta, additional, Tuomi, Tiinamaija, additional, Guiducci, Candace, additional, Berglund, Anna, additional, Carlson, Joyce, additional, Gianniny, Lauren, additional, Hackett, Rachel, additional, Hall, Liselotte, additional, Holmkvist, Johan, additional, Laurila, Esa, additional, Sjögren, Marketa, additional, Sterner, Maria, additional, Surti, Aarti, additional, Svensson, Margareta, additional, Svensson, Malin, additional, Tewhey, Ryan, additional, Blumenstiel, Brendan, additional, Parkin, Melissa, additional, DeFelice, Matthew, additional, Barry, Rachel, additional, Brodeur, Wendy, additional, Camarata, Jody, additional, Chia, Nancy, additional, Fava, Mary, additional, Gibbons, John, additional, Handsaker, Bob, additional, Healy, Claire, additional, Nguyen, Kieu, additional, Gates, Casey, additional, Sougnez, Carrie, additional, Gage, Diane, additional, Nizzari, Marcia, additional, Gabriel, Stacey B., additional, Chirn, Gung-Wei, additional, Ma, Qicheng, additional, Parikh, Hemang, additional, Richardson, Delwood, additional, Ricke, Darrell, additional, and Purcell, Shaun, additional

Published
2007
Full Text
View/download PDF

14. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

Author

De Jager, Philip Lawrence, Srivastava, Gyan, Lunnon, Katie, Burgess, Jeremy, Schalkwyk, Leonard C, Yu, Lei, Eaton, Matthew L, Keenan, Brendan T, Ernst, Jason, McCabe, Cristin, Tang, Anna, Raj, Towfique, Replogle, Joseph, Brodeur, Wendy, Gabriel, Stacey, Chai, High S, Younkin, Curtis, Younkin, Steven G, Zou, Fanggeng, Szyf, Moshe, Epstein, Charles B, Schneider, Julie A, Bernstein, Bradley E., Meissner, Alexander, Ertekin-Taner, Nilufer, Chibnik, Lori, Kellis, Manolis, Mill, Jonathan, and Bennett, David A

Abstract

We used a collection of 708 prospectively collected autopsied brains to assess the methylation state of the brain's DNA in relation to Alzheimer's disease (AD). We found that the level of methylation at 71 of the 415,848 interrogated CpGs was significantly associated with the burden of AD pathology, including CpGs in the ABCA7 and BIN1 regions, which harbor known AD susceptibility variants. We validated 11 of the differentially methylated regions in an independent set of 117 subjects. Furthermore, we functionally validated these CpG associations and identified the nearby genes whose RNA expression was altered in AD: ANK1, CDH23, DIP2A, RHBDF2, RPL13, SERPINF1 and SERPINF2. Our analyses suggest that these DNA methylation changes may have a role in the onset of AD given that we observed them in presymptomatic subjects and that six of the validated genes connect to a known AD susceptibility gene network., Stem Cell and Regenerative Biology

Published
2014
Full Text
View/download PDF

15. Common Variants at 9p21 and 8q22 Are Associated with Increased Susceptibility to Optic Nerve Degeneration in Glaucoma

Author

Yaspan, Brian L., Hauser, Michael A., Allingham, R. Rand, Olson, Lana M., Abdrabou, Wael, Brodeur, Wendy, Budenz, Donald L., Caprioli, Joseph, Crenshaw, Andrew, Crooks, Kristy, DelBono, Elizabeth, Doheny, Kimberly F., Gaasterland, Douglas, Gaasterland, Terry, Laurie, Cathy, Lichter, Paul R., Loomis, Stephanie, Liu, Yutao, Medeiros, Felipe A., McCarty, Cathy, Mirel, Daniel, Moroi, Sayoko E., Musch, David C., Realini, Anthony, Rozsa, Frank W., Schuman, Joel S., Scott, Kathleen, Singh, Kuldev, Trager, Edward H., VanVeldhuisen, Paul, Vollrath, Douglas, Wollstein, Gadi, Yoneyama, Sachiko, Zhang, Kang, Weinreb, Robert N., Ernst, Jason, Masuda, Tomohiro, Zack, Don, Richards, Julia E., Pericak-Vance, Margaret, Haines, Jonathan L., Wiggs, Janey Lee, Kang, Jae Hee Hee, Fan, Baojian, Wang, Danyi, Friedman, David S., Lee, Richard K., Stein, Joshua D., Kellis, Manolis, and Pasquale, Louis

Subjects
Medicine, Ophthalmology, Glaucoma, Inherited Eye Disorders
Abstract

Optic nerve degeneration caused by glaucoma is a leading cause of blindness worldwide. Patients affected by the normal-pressure form of glaucoma are more likely to harbor risk alleles for glaucoma-related optic nerve disease. We have performed a meta-analysis of two independent genome-wide association studies for primary open angle glaucoma (POAG) followed by a normal-pressure glaucoma (NPG, defined by intraocular pressure (IOP) less than 22 mmHg) subgroup analysis. The single-nucleotide polymorphisms that showed the most significant associations were tested for association with a second form of glaucoma, exfoliation-syndrome glaucoma. The overall meta-analysis of the GLAUGEN and NEIGHBOR dataset results (3,146 cases and 3,487 controls) identified significant associations between two loci and POAG: the CDKN2BAS region on 9p21 (rs2157719 [G], OR = 0.69 [95%CI 0.63–0.75], p = 1.86×10\(^{−18}\)), and the SIX1/SIX6 region on chromosome 14q23 (rs10483727 [A], OR = 1.32 [95%CI 1.21–1.43], p = 3.87×10\(^{−11}\)). In sub-group analysis two loci were significantly associated with NPG: 9p21 containing the CDKN2BAS gene (rs2157719 [G], OR = 0.58 [95% CI 0.50–0.67], p = 1.17×10\(^{−12}\)) and a probable regulatory region on 8q22 (rs284489 [G], OR = 0.62 [95% CI 0.53–0.72], p = 8.88×10\(^{−10}\)). Both NPG loci were also nominally associated with a second type of glaucoma, exfoliation syndrome glaucoma (rs2157719 [G], OR = 0.59 [95% CI 0.41–0.87], p = 0.004 and rs284489 [G], OR = 0.76 [95% CI 0.54–1.06], p = 0.021), suggesting that these loci might contribute more generally to optic nerve degeneration in glaucoma. Because both loci influence transforming growth factor beta (TGF-beta) signaling, we performed a genomic pathway analysis that showed an association between the TGF-beta pathway and NPG (permuted p = 0.009). These results suggest that neuro-protective therapies targeting TGF-beta signaling could be effective for multiple forms of glaucoma.

Published
2012
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results