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23 results on '"Sohi, Harkirat"'

1. Admixture mapping implicates 13q33.3 as ancestry-of-origin locus for Alzheimer disease in Hispanic and Latino populations

Author

Horimoto, Andrea R.V.R., Boyken, Lisa A., Blue, Elizabeth E., Grinde, Kelsey E., Nafikov, Rafael A., Sohi, Harkirat K., Nato, Alejandro Q., Jr., Bis, Joshua C., Brusco, Luis I., Morelli, Laura, Ramirez, Alfredo, Dalmasso, Maria Carolina, Temple, Seth, Satizabal, Claudia, Browning, Sharon R., Seshadri, Sudha, Wijsman, Ellen M., and Thornton, Timothy A.

Published
2023
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2. Human whole-exome genotype data for Alzheimer’s disease

Author

Leung, Yuk Yee, Naj, Adam C., Chou, Yi Fan, Valladares, Otto, Schmidt, Michael, Hamilton-Nelson, Kara, Wheeler, Nicholas, Lin, Honghuang, Gangadharan, Prabhakaran, Qu, Liming, Clark, Kaylyn, Kuzma, Amanda B., Lee, Wan Ping, Cantwell, Laura, Nicaretta, Heather, van der Lee, Sven, English, Adam, Kalra, Divya, Muzny, Donna, Skinner, Evette, Doddapeneni, Harsha, Dinh, Huyen, Hu, Jianhong, Santibanez, Jireh, Jayaseelan, Joy, Worley, Kim, Gibbs, Richard A., Lee, Sandra, Dugan-Perez, Shannon, Korchina, Viktoriya, Nasser, Waleed, Liu, Xiuping, Han, Yi, Zhu, Yiming, Liu, Yue, Khan, Ziad, Zhu, Congcong, Sun, Fangui Jenny, Jun, Gyungah R., Chung, Jaeyoon, Farrell, John, Zhang, Xiaoling, Banks, Eric, Gupta, Namrata, Gabriel, Stacey, Butkiewicz, Mariusz, Benchek, Penelope, Smieszek, Sandra, Song, Yeunjoo, Vardarajan, Badri, Reitz, Christiane, Reyes-Dumeyer, Dolly, Tosto, Giuseppe, De Jager, Phillip L., Barral, Sandra, Ma, Yiyi, Beiser, Alexa, Liu, Ching Ti, Dupuis, Josee, Lunetta, Kathy, Cupples, L. Adrienne, Choi, Seung Hoan, Chen, Yuning, Mez, Jesse, Vanderspek, Ashley, Ikram, M. Arfan, Ahmad, Shahzad, Faber, Kelley, Foroud, Tatiana, Mlynarski, Elisabeth, Schmidt, Helena, Schmidt, Reinhold, Kunkle, Brian, Rajabli, Farid, Beecham, Gary, Vance, Jeffrey M., Adams, Larry D., Cuccaro, Michael, Mena, Pedro, Booth, Briana M., Renton, Alan, Goate, Alison, Marcora, Edoardo, Stine, Adam, Feolo, Michael, Launer, Lenore J., Koboldt, Daniel C., Wilson, Richard K., van Duijn, Cornelia, Amin, Najaf, Kapoor, Manav, Salerno, William, Bennett, David A., Xia, Li Charlie, Malamon, John, Mosley, Thomas H., Satizabal, Claudia, Jan Bressler, Bressler, Jian, Xueqiu, Nato, Alejandro Q., Horimoto, Andrea R., Wang, Bowen, Psaty, Bruce, Witten, Daniela, Tsuang, Debby, Blue, Elizabeth, Wijsman, Ellen, Sohi, Harkirat, Nguyen, Hiep, Bis, Joshua C., Rice, Kenneth, Brown, Lisa, Dorschner, Michael, Saad, Mohamad, Navas, Pat, Nafikov, Rafael, Thornton, Timothy, Day, Tyler, Haut, Jacob, Sha, Jin, Zhang, Nancy, Iqbal, Taha, Zhao, Yi, Below, Jennifer E., Larson, David E., Appelbaum, Elizabeth, Waligorski, Jason, Antonacci-Fulton, Lucinda, Fulton, Robert S., Haines, Jonathan, Farrer, Lindsay, Seshadri, Sudha, Brkanac, Zoran, Cruchaga, Carlos, Pericak-Vance, Margaret, Mayeux, Richard P., Bush, William S., Destefano, Anita, Martin, Eden, Schellenberg, Gerard D., Wang, Li San, Leung, Yuk Yee, Naj, Adam C., Chou, Yi Fan, Valladares, Otto, Schmidt, Michael, Hamilton-Nelson, Kara, Wheeler, Nicholas, Lin, Honghuang, Gangadharan, Prabhakaran, Qu, Liming, Clark, Kaylyn, Kuzma, Amanda B., Lee, Wan Ping, Cantwell, Laura, Nicaretta, Heather, van der Lee, Sven, English, Adam, Kalra, Divya, Muzny, Donna, Skinner, Evette, Doddapeneni, Harsha, Dinh, Huyen, Hu, Jianhong, Santibanez, Jireh, Jayaseelan, Joy, Worley, Kim, Gibbs, Richard A., Lee, Sandra, Dugan-Perez, Shannon, Korchina, Viktoriya, Nasser, Waleed, Liu, Xiuping, Han, Yi, Zhu, Yiming, Liu, Yue, Khan, Ziad, Zhu, Congcong, Sun, Fangui Jenny, Jun, Gyungah R., Chung, Jaeyoon, Farrell, John, Zhang, Xiaoling, Banks, Eric, Gupta, Namrata, Gabriel, Stacey, Butkiewicz, Mariusz, Benchek, Penelope, Smieszek, Sandra, Song, Yeunjoo, Vardarajan, Badri, Reitz, Christiane, Reyes-Dumeyer, Dolly, Tosto, Giuseppe, De Jager, Phillip L., Barral, Sandra, Ma, Yiyi, Beiser, Alexa, Liu, Ching Ti, Dupuis, Josee, Lunetta, Kathy, Cupples, L. Adrienne, Choi, Seung Hoan, Chen, Yuning, Mez, Jesse, Vanderspek, Ashley, Ikram, M. Arfan, Ahmad, Shahzad, Faber, Kelley, Foroud, Tatiana, Mlynarski, Elisabeth, Schmidt, Helena, Schmidt, Reinhold, Kunkle, Brian, Rajabli, Farid, Beecham, Gary, Vance, Jeffrey M., Adams, Larry D., Cuccaro, Michael, Mena, Pedro, Booth, Briana M., Renton, Alan, Goate, Alison, Marcora, Edoardo, Stine, Adam, Feolo, Michael, Launer, Lenore J., Koboldt, Daniel C., Wilson, Richard K., van Duijn, Cornelia, Amin, Najaf, Kapoor, Manav, Salerno, William, Bennett, David A., Xia, Li Charlie, Malamon, John, Mosley, Thomas H., Satizabal, Claudia, Jan Bressler, Bressler, Jian, Xueqiu, Nato, Alejandro Q., Horimoto, Andrea R., Wang, Bowen, Psaty, Bruce, Witten, Daniela, Tsuang, Debby, Blue, Elizabeth, Wijsman, Ellen, Sohi, Harkirat, Nguyen, Hiep, Bis, Joshua C., Rice, Kenneth, Brown, Lisa, Dorschner, Michael, Saad, Mohamad, Navas, Pat, Nafikov, Rafael, Thornton, Timothy, Day, Tyler, Haut, Jacob, Sha, Jin, Zhang, Nancy, Iqbal, Taha, Zhao, Yi, Below, Jennifer E., Larson, David E., Appelbaum, Elizabeth, Waligorski, Jason, Antonacci-Fulton, Lucinda, Fulton, Robert S., Haines, Jonathan, Farrer, Lindsay, Seshadri, Sudha, Brkanac, Zoran, Cruchaga, Carlos, Pericak-Vance, Margaret, Mayeux, Richard P., Bush, William S., Destefano, Anita, Martin, Eden, Schellenberg, Gerard D., and Wang, Li San

Abstract

The heterogeneity of the whole-exome sequencing (WES) data generation methods present a challenge to a joint analysis. Here we present a bioinformatics strategy for joint-calling 20,504 WES samples collected across nine studies and sequenced using ten capture kits in fourteen sequencing centers in the Alzheimer’s Disease Sequencing Project. The joint-genotype called variant-called format (VCF) file contains only positions within the union of capture kits. The VCF was then processed specifically to account for the batch effects arising from the use of different capture kits from different studies. We identified 8.2 million autosomal variants. 96.82% of the variants are high-quality, and are located in 28,579 Ensembl transcripts. 41% of the variants are intronic and 1.8% of the variants are with CADD > 30, indicating they are of high predicted pathogenicity. Here we show our new strategy can generate high-quality data from processing these diversely generated WES samples. The improved ability to combine data sequenced in different batches benefits the whole genomics research community.

Published
2024

3. Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project

Author

Naj, Adam C., Lin, Honghuang, Vardarajan, Badri N., White, Simon, Lancour, Daniel, Ma, Yiyi, Schmidt, Michael, Sun, Fangui, Butkiewicz, Mariusz, Bush, William S., Kunkle, Brian W., Malamon, John, Amin, Najaf, Choi, Seung Hoan, Hamilton-Nelson, Kara L., van der Lee, Sven J., Gupta, Namrata, Koboldt, Daniel C., Saad, Mohamad, Wang, Bowen, Nato, Alejandro Q., Jr., Sohi, Harkirat K., Kuzma, Amanda, Wang, Li-San, Cupples, L. Adrienne, van Duijn, Cornelia, Seshadri, Sudha, Schellenberg, Gerard D., Boerwinkle, Eric, Bis, Joshua C., Dupuis, Josée, Salerno, William J., Wijsman, Ellen M., Martin, Eden R., and DeStefano, Anita L.

Published
2019
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4. A rare missense variant of CASP7 is associated with familial late-onset Alzheimer's disease

Author

Bellair, Michelle, Dinh, Huyen, Doddapeneni, Harsha, Dugan-Perez, Shannon, English, Adam, Gibbs, Richard A., Han, Yi, Hu, Jianhong, Jayaseelan, Joy, Kalra, Divya, Khan, Ziad, Korchina, Viktoriya, Lee, Sandra, Liu, Yue, Liu, Xiuping, Muzny, Donna, Nasser, Waleed, Salerno, William, Santibanez, Jireh, Skinner, Evette, White, Simon, Worley, Kim, Zhu, Yiming, Beiser, Alexa, Chen, Yuning, Chung, Jaeyoon, Cupples, L. Adrienne, DeStefano, Anita, Dupuis, Josee, Farrell, John, Farrer, Lindsay, Lancour, Daniel, Lin, Honghuang, Liu, Ching Ti, Lunetta, Kathy, Ma, Yiyi, Patel, Devanshi, Sarnowski, Chloe, Satizabal, Claudia, Seshadri, Sudha, Sun, Fangui Jenny, Zhang, Xiaoling, Choi, Seung Hoan, Banks, Eric, Gabriel, Stacey, Gupta, Namrata, Bush, William, Butkiewicz, Mariusz, Haines, Jonathan, Smieszek, Sandra, Song, Yeunjoo, Barral, Sandra, De Jager, Phillip L., Mayeux, Richard, Reitz, Christiane, Reyes, Dolly, Tosto, Giuseppe, Vardarajan, Badri, Amad, Shahzad, Amin, Najaf, Ikram, M. Afran, van der Lee, Sven, van Duijn, Cornelia, Vanderspek, Ashley, Schmidt, Helena, Schmidt, Reinhold, Goate, Alison, Kapoor, Manav, Marcora, Edoardo, Renton, Alan, Faber, Kelley, Foroud, Tatiana, Feolo, Michael, Stine, Adam, Launer, Lenore J., Bennett, David A., Xia, Li Charlie, Beecham, Gary, Hamilton-Nelson, Kara, Jaworski, James, Kunkle, Brian, Martin, Eden, Pericak-Vance, Margaret, Rajabli, Farid, Schmidt, Michael, Mosley, Thomas H., Cantwell, Laura, Childress, Micah, Chou, Yi-Fan, Cweibel, Rebecca, Gangadharan, Prabhakaran, Kuzma, Amanda, Leung, Yuk Yee, Lin, Han-Jen, Malamon, John, Mlynarski, Elisabeth, Naj, Adam, Qu, Liming, Schellenberg, Gerard, Valladares, Otto, Wang, Li-San, Wang, Weixin, Zhang, Nancy, Below, Jennifer E., Boerwinkle, Eric, Bressler, Jan, Fornage, Myriam, Jian, Xueqiu, Liu, Xiaoming, Bis, Joshua C., Blue, Elizabeth, Brown, Lisa, Day, Tyler, Dorschner, Michael, Horimoto, Andrea R., Nafikov, Rafael, Nato, Alejandro Q., Jr., Navas, Pat, Nguyen, Hiep, Psaty, Bruce, Rice, Kenneth, Saad, Mohamad, Sohi, Harkirat, Thornton, Timothy, Tsuang, Debby, Wang, Bowen, Wijsman, Ellen, Witten, Daniela, Antonacci-Fulton, Lucinda, Appelbaum, Elizabeth, Cruchaga, Carlos, Fulton, Robert S., Koboldt, Daniel C., Larson, David E., Waligorski, Jason, Wilson, Richard K., Zhu, Congcong, Vardarajan, Badri N., Farrell, John J., Haines, Jonathan L., Schellenberg, Gerard D., Pericak-Vance, Margaret A., Lunetta, Kathryn L., and Farrer, Lindsay A.

Published
2019
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5. The Milky Way Tomography with SDSS: II. Stellar Metallicity

Author

Ivezic, Zeljko, Sesar, Branimir, Juric, Mario, Bond, Nicholas, Dalcanton, Julianne, Rockosi, Constance M., Yanny, Brian, Newberg, Heidi J., Beers, Timothy C., Prieto, Carlos Allende, Wilhelm, Ron, Lee, Young Sun, Sivarani, Thirupathi, Norris, John E., Bailer-Jones, Coryn A. L., Fiorentin, Paola Re, Schlegel, David, Uomoto, Alan, Lupton, Robert H., Knapp, Gillian R., Gunn, James E., Covey, Kevin R., Smith, J. Allyn, Miknaitis, Gajus, Doi, Mamoru, Tanaka, Masayuki, Fukugita, Masataka, Kent, Steve, Finkbeiner, Douglas, Munn, Jeffrey A., Pier, Jeffrey R., Quinn, Tom, Hawley, Suzanne, Anderson, Scott, Kiuchi, Furea, Chen, Alex, Bushong, James, Sohi, Harkirat, Haggard, Daryl, Kimball, Amy, Barentine, John, Brewington, Howard, Harvanek, Mike, Kleinman, Scott, Krzesinski, Jurek, Long, Dan, Nitta, Atsuko, Snedden, Stephanie, Lee, Brian, Harris, Hugh, Brinkmann, Jonathan, Schneider, Donald P., and York, Donald G.

Subjects
Astrophysics
Abstract

Using effective temperature and metallicity derived from SDSS spectra for ~60,000 F and G type main sequence stars (0.2

Published
2008
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7. Cognitively defined Alzheimer's dementia subgroups have distinct atrophy patterns.

Author

Crane, Paul K., Groot, Colin, Ossenkoppele, Rik, Mukherjee, Shubhabrata, Choi, Seo‐Eun, Lee, Michael, Scollard, Phoebe, Gibbons, Laura E., Sanders, R. Elizabeth, Trittschuh, Emily, Saykin, Andrew J., Mez, Jesse, Nakano, Connie, Donald, Christine Mac, Sohi, Harkirat, and Risacher, Shannon

Abstract

INTRODUCTION: We sought to determine structural magnetic resonance imaging (MRI) characteristics across subgroups defined based on relative cognitive domain impairments using data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and to compare cognitively defined to imaging‐defined subgroups. METHODS: We used data from 584 people with Alzheimer's disease (AD) (461 amyloid positive, 123 unknown amyloid status) and 118 amyloid‐negative controls. We used voxel‐based morphometry to compare gray matter volume (GMV) for each group compared to controls and to AD‐Memory. RESULTS: There was pronounced bilateral lower medial temporal lobe atrophy with relative cortical sparing for AD‐Memory, lower left hemisphere GMV for AD‐Language, anterior lower GMV for AD‐Executive, and posterior lower GMV for AD‐Visuospatial. Formal asymmetry comparisons showed substantially more asymmetry in the AD‐Language group than any other group (p = 1.15 × 10−10). For overlap between imaging‐defined and cognitively defined subgroups, AD‐Memory matched up with an imaging‐defined limbic predominant group. DISCUSSION: MRI findings differ across cognitively defined AD subgroups. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Rare genetic variation implicated in non-Hispanic white families with Alzheimer disease

Author

Beecham, Gary W., Vardarajan, Badri, Blue, Elizabeth, Bush, William, Jaworski, James, Barral, Sandra, DeStefano, Anita, Hamilton-Nelson, Kara, Kunkle, Brian, Martin, Eden R., Naj, Adam, Rajabli, Farid, Reitz, Christiane, Thornton, Timothy, van Duijn, Cornelia, Goate, Allison, Seshadri, Sudha, Farrer, Lindsay A., Boerwinkle, Eric, Schellenberg, Gerard, Haines, Jonathan L., Wijsman, Ellen, Mayeux, Richard, Pericak-Vance, Margaret A., English, Adam, Kalra, Divya, Muzny, Donna, Skinner, Evette, Doddapeneni, Harsha, Dinh, Huyen, Hu, Jianhong, Santibanez, Jireh, Jayaseelan, Joy, Worley, Kim, Bellair, Michelle, Gibbs, Richard A., Lee, Sandra, Dugan-Perez, Shannon, White, Simon, Korchina, Viktoriya, Nasser, Waleed, Salerno, William, Liu, Xiuping, Han, Yi, Zhu, Yiming, Liu, Yue, Khan, Ziad, Cupples, Adrienne, Beiser, Alexa, DeStefanos, Anita, Liu, Ching Ti, Sarnowski, Chloe, Satizabal, Claudia, Lancour, Dan, Patel, Devanshi, Sun, Fangui Jenny, Lin, Honghuang, Chung, Jaeyoon, Farrell, John, Dupuis, Josee, Lunetta, Kathy, Farrer, Lindsay, Seshadri, Sudha, Zhang, Xiaoling, Ma, Yiyi, Chen, Yuning, Banks, Eric, Gupta, Namrata, Choi, Seung Hoan, Gabriel, Stacey, Haines, Jonathan, Butkiewicz, Mariusz, Smieszek, Sandra, Bush, Will, Song, Yeunjoo, Vardarajan, Badri, Reitz, Christiane, Reyes, Dolly, Tosto, Giuseppe, De Jager, Phillip L, Mayeux, Richard, Barral, Sandra, Vanderspek, Ashley, van Duijn, Cornelia, Ikram, M Afran, Amin, Najaf, Amad, Shahzad, van der Lee, Sven, Faber, Kelley, Foroud, Tatiana, Schmidt, Helena, Schmidt, Reinhold, Renton, Alan, Goate, Alison, Marcora, Edoardo, Kapoor, Manav, Stine, Adam, Feolo, Michael, Launer, Lenore J., Bennett, David A, Xia, Li Charlie, Kunkle, Brian, Martin, Eden, Rajabli, Farid, Beecham, Gary, Jaworski, James, Hamilton-Nelson, Kara, Pericak-Vance, Margaret, Schmidt, Michael, Mosley, Thomas H., Kuzma, Amanda, Lin, Han-Jen, Qu, Liming, Wang, Micah Childress, Li-San, Valladares, Otto, Gangadharan, Prabhakaran, Cweibel, Rebecca, Zhao, Yi, Chou, Yi-Fan, Naj, Adam, Mlynarski, Elisabeth, Schellenberg, Gerard, Malamon, John, Cantwell, Laura, Zhang, Nancy, Wang, Weixin, Leung, Yuk Yee, Boerwinkle, Eric, Bressler, Jan, Below, Jennifer E., Fornage, Myriam, Liu, Xiaoming, Jian, Xueqiu, Nato, Alejandro Q, Jr., Horimoto, Andrea R, Wang, Bowen, Psaty, Bruce, Witten, Daniela, Tsuang, Debby, Blue, Elizabeth, Wijsman, Ellen, Sohi, Harkirat, Nguyen, Hiep, Bis, Joshua C., Rice, Kenneth, Brown, Lisa, Dorschner, Michael, Saad, Mohamad, Navas, Pat, Nafikov, Rafael, Thornton, Timothy, Day, Tyler, Cruchaga, Carlos, Koboldt, Daniel C., Larson, David E., Appelbaum, Elizabeth, Waligorski, Jason, Antonacci-Fulton, Lucinda, Wilson, Richard K., and Fulton, Robert S.

Published
2018
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11. P1-335: FUNCTIONAL CONNECTIVITY PATTERNS ACROSS COGNITIVELY-DEFINED ALZHEIMER'S DISEASE SUBTYPES IN THE ALZHEIMER'S DISEASE NEUROIMAGING INITIATIVE

Author

Lee, Briana E., primary, Crane, Paul K., additional, Risacher, Shannon L., additional, Groot, Colin, additional, Mez, Jesse, additional, Saykin, Andrew J., additional, Trittschuh, Emily H., additional, MacDonald, Christine, additional, Ossenkoppele, Rik, additional, Gibbons, Laura E., additional, Sanders, R. Elizabeth, additional, Choi, Seo-Eun, additional, Mukherjee, Shubhabrata, additional, Sohi, Harkirat, additional, Gennari, John, additional, and Madhyastha, Tara, additional

Published
2019
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12. P1-361: REGIONAL DIFFERENCES IN CORTICAL THICKNESS ACROSS COGNITIVELY DEFINED ALZHEIMER'S DISEASE SUBGROUPS

Author

Sohi, Harkirat, primary, Gennari, John, additional, Madhyastha, Tara, additional, Lee, Briana E., additional, Risacher, Shannon L., additional, MacDonald, Christine, additional, Groot, Colin, additional, Ossenkoppele, Rik, additional, Mez, Jesse, additional, Trittschuh, Emily H., additional, Saykin, Andrew J., additional, Mukherjee, Shubhabrata, additional, Gibbons, Laura E., additional, Sanders, R. Elizabeth, additional, Choi, Seo-Eun, additional, and Crane, Paul K., additional

Published
2019
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13. Analysis of pedigree data in populations with multiple ancestries: Strategies for dealing with admixture in Caribbean Hispanic families from the ADSP

Author

Nafikov, Rafael A., primary, Nato, Alejandro Q., additional, Sohi, Harkirat, additional, Wang, Bowen, additional, Brown, Lisa, additional, Horimoto, Andrea R., additional, Vardarajan, Badri N., additional, Barral, Sandra M., additional, Tosto, Giuseppe, additional, Mayeux, Richard P., additional, Thornton, Timothy A., additional, Blue, Elizabeth, additional, and Wijsman, Ellen M., additional

Published
2018
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14. Solving Interoperability in Translational Health

Author

Turner, Anne, additional, Facelli, Julio, additional, Jaspers, Monique, additional, Wetter, Thomas, additional, Pfeifer, Daniel, additional, Gatewood, Laël Cranmer, additional, Adam, Terry, additional, Li, YuChuan, additional, Lin, Ming-Chin, additional, Evans, R. Scott, additional, Beukenhorst, Anna, additional, Theodoore van Mens, Hugo Johan, additional, Tensen, Esmée, additional, Bock, Christian, additional, Fendrich, Laura, additional, Seitz, Peter, additional, Suleder, Julian, additional, Aldekhyyel, Ranyah, additional, Bridgeman, Kent, additional, Hu, Zhen, additional, Sattler, Aaron, additional, Guo, Shin-Yi, additional, Mohaimenul, Islam Md., additional, Anggraini Ningrum, Dina Nur, additional, Tung, Hsin-Ru, additional, Bian, Jiantao, additional, Plasek, Joseph, additional, Rommel, Casey, additional, Burke, Juandalyn, additional, and Sohi, Harkirat, additional

Published
2017
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19. THE MILKY WAY TOMOGRAPHY WITH SDSS. III. STELLAR KINEMATICS

Author

Bond, Nicholas A., primary, Ivezić, Željko, additional, Sesar, Branimir, additional, Jurić, Mario, additional, Munn, Jeffrey A., additional, Kowalski, Adam, additional, Loebman, Sarah, additional, Roškar, Rok, additional, Beers, Timothy C., additional, Dalcanton, Julianne, additional, Rockosi, Constance M., additional, Yanny, Brian, additional, Newberg, Heidi J., additional, Allende Prieto, Carlos, additional, Wilhelm, Ron, additional, Lee, Young Sun, additional, Sivarani, Thirupathi, additional, Majewski, Steven R., additional, Norris, John E., additional, Bailer-Jones, Coryn A. L., additional, Fiorentin, Paola Re, additional, Schlegel, David, additional, Uomoto, Alan, additional, Lupton, Robert H., additional, Knapp, Gillian R., additional, Gunn, James E., additional, Covey, Kevin R., additional, Smith, J. Allyn, additional, Miknaitis, Gajus, additional, Doi, Mamoru, additional, Tanaka, Masayuki, additional, Fukugita, Masataka, additional, Kent, Steve, additional, Finkbeiner, Douglas, additional, Quinn, Tom R., additional, Hawley, Suzanne, additional, Anderson, Scott, additional, Kiuchi, Furea, additional, Chen, Alex, additional, Bushong, James, additional, Sohi, Harkirat, additional, Haggard, Daryl, additional, Kimball, Amy, additional, McGurk, Rosalie, additional, Barentine, John, additional, Brewington, Howard, additional, Harvanek, Mike, additional, Kleinman, Scott, additional, Krzesinski, Jurek, additional, Long, Dan, additional, Nitta, Atsuko, additional, Snedden, Stephanie, additional, Lee, Brian, additional, Pier, Jeffrey R., additional, Harris, Hugh, additional, Brinkmann, Jonathan, additional, and Schneider, Donald P., additional

Published
2010
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20. The Milky Way Tomography with SDSS. II. Stellar Metallicity

Author

Ivezić, Željko, primary, Sesar, Branimir, additional, Jurić, Mario, additional, Bond, Nicholas, additional, Dalcanton, Julianne, additional, Rockosi, Constance M., additional, Yanny, Brian, additional, Newberg, Heidi J., additional, Beers, Timothy C., additional, Allende Prieto, Carlos, additional, Wilhelm, Ron, additional, Lee, Young Sun, additional, Sivarani, Thirupathi, additional, Norris, John E., additional, Bailer‐Jones, Coryn A. L., additional, Re Fiorentin, Paola, additional, Schlegel, David, additional, Uomoto, Alan, additional, Lupton, Robert H., additional, Knapp, Gillian R., additional, Gunn, James E., additional, Covey, Kevin R., additional, Smith, J. Allyn, additional, Miknaitis, Gajus, additional, Doi, Mamoru, additional, Tanaka, Masayuki, additional, Fukugita, Masataka, additional, Kent, Steve, additional, Finkbeiner, Douglas, additional, Munn, Jeffrey A., additional, Pier, Jeffrey R., additional, Quinn, Tom, additional, Hawley, Suzanne, additional, Anderson, Scott, additional, Kiuchi, Furea, additional, Chen, Alex, additional, Bushong, James, additional, Sohi, Harkirat, additional, Haggard, Daryl, additional, Kimball, Amy, additional, Barentine, John, additional, Brewington, Howard, additional, Harvanek, Mike, additional, Kleinman, Scott, additional, Krzesinski, Jurek, additional, Long, Dan, additional, Nitta, Atsuko, additional, Snedden, Stephanie, additional, Lee, Brian, additional, Harris, Hugh, additional, Brinkmann, Jonathan, additional, Schneider, Donald P., additional, and York, Donald G., additional

Published
2008
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21. Analysis of individual families implicates noncoding DNA variation and multiple biological pathways in Alzheimer's disease risk: Genetics/genetic factors of Alzheimer's disease.

Author

Wijsman, Ellen M., Day, Tyler R., Thornton, Timothy A., Horimoto, Andrea R., Blue, Elizabeth E., Bis, Josh C., Sohi, Harkirat K., Nato, Alejandro Q., Nafikov, Rafael A., Navas, Patrick, Saad, Mohamad, Tsuang, Debby W., Barral, Sandra, Vardarajan, Badri N., Beecham, Gary W., Martin, Eden R., van Duijn, Cornelia M., Pericak‐Vance, Margaret A., and Mayeux, Richard

Abstract

Background: Late‐onset Alzheimer's disease (AD) is a complex disorder with multiple genetic risk factors. Linkage and association analysis have mapped dozens of loci in pooled analysis of many pedigrees or large numbers of unrelated cases and controls. Identification of the underlying DNA risk variants in the regions of interest (ROIs) has been complicated by both the genetic heterogeneity and the cost, until recently, of comprehensive DNA sequencing in ROIs. The known loci also leave much heritability unexplained. Method: We used the families in the AD Sequencing Project (ADSP) discovery family sample to identify variants of interest from whole genome sequences (WGS), and through the variants, genes implicated in risk. We used SNP‐based multipoint linkage analysis to identify ROIs with rare VOIs, carrying out analysis without trimming pedigrees. We pursued all ROIs with family‐specific lodmax scores >1.9, reducing the variants of interest by several filters. We carried out pedigree‐based genotype imputation from the available WGS data, followed by family‐based association analysis, filtered for low population minor allele frequency. We prioritized genes with a low false‐discovery rate for association of single‐cell transcription in brain with AD disease state (PMID:31209304), and genes with high expression in bulk brain (PMID: 24309898). Result: We obtained 46 distinct ROIs representing lodmax1.9‐3.5 per ROI in each of 26 of the 110 ADSP discovery families analyzed. 29 ROIs further investigated in 16 of the families yielded 59 prioritized genes, with 1‐11 genes/ROI. Only 4 out of 321 variants that passed all filters in these genes were in exons, with minimal overlap with genes identified in AD GWASs. Only one ROI occurred in two families, with evidence for a shared‐haplotype between these families, implicating FBXO2 and FBXO44. Both genes are implicated in ubiquitination, while FBXO2 interacts with BACE1. Multiple pathways, both known and new, are implicated, including the ubiquitin‐proteasome system, neural development and maintenance, and mitochondrial functions. Conclusion: This analysis underscores the evidence for extensive genetic heterogeneity and rare variants underlying AD risk, along with multiple potential mechanisms. The preponderance of prioritize non‐coding variants suggests alterations in gene regulation and/or expression as an aspect of AD genetic risk. [ABSTRACT FROM AUTHOR]

Published
2020
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22. Cognitively defined Alzheimer's dementia subgroups have distinct atrophy patterns.

Author

Crane PK, Groot C, Ossenkoppele R, Mukherjee S, Choi SE, Lee M, Scollard P, Gibbons LE, Sanders RE, Trittschuh E, Saykin AJ, Mez J, Nakano C, Donald CM, Sohi H, and Risacher S

Subjects
Humans, Brain diagnostic imaging, Brain pathology, Neuroimaging methods, Magnetic Resonance Imaging, Atrophy pathology, Alzheimer Disease pathology, Cognitive Dysfunction diagnostic imaging, Cognitive Dysfunction pathology
Abstract

Introduction: We sought to determine structural magnetic resonance imaging (MRI) characteristics across subgroups defined based on relative cognitive domain impairments using data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and to compare cognitively defined to imaging-defined subgroups., Methods: We used data from 584 people with Alzheimer's disease (AD) (461 amyloid positive, 123 unknown amyloid status) and 118 amyloid-negative controls. We used voxel-based morphometry to compare gray matter volume (GMV) for each group compared to controls and to AD-Memory., Results: There was pronounced bilateral lower medial temporal lobe atrophy with relative cortical sparing for AD-Memory, lower left hemisphere GMV for AD-Language, anterior lower GMV for AD-Executive, and posterior lower GMV for AD-Visuospatial. Formal asymmetry comparisons showed substantially more asymmetry in the AD-Language group than any other group (p = 1.15 × 10 -10 ). For overlap between imaging-defined and cognitively defined subgroups, AD-Memory matched up with an imaging-defined limbic predominant group., Discussion: MRI findings differ across cognitively defined AD subgroups., (© 2023 The Authors. Alzheimer's & Dementia published by Wiley Periodicals LLC on behalf of Alzheimer's Association.)

Published
2024
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23. Genetic Variation in Genes Underlying Diverse Dementias May Explain a Small Proportion of Cases in the Alzheimer's Disease Sequencing Project.

Author

Blue EE, Bis JC, Dorschner MO, Tsuang DW, Barral SM, Beecham G, Below JE, Bush WS, Butkiewicz M, Cruchaga C, DeStefano A, Farrer LA, Goate A, Haines J, Jaworski J, Jun G, Kunkle B, Kuzma A, Lee JJ, Lunetta KL, Ma Y, Martin E, Naj A, Nato AQ, Navas P, Nguyen H, Reitz C, Reyes D, Salerno W, Schellenberg GD, Seshadri S, Sohi H, Thornton TA, Valadares O, van Duijn C, Vardarajan BN, Wang LS, Boerwinkle E, Dupuis J, Pericak-Vance MA, Mayeux R, and Wijsman EM

Subjects
Aged, Aged, 80 and over, Alzheimer Disease epidemiology, Case-Control Studies, Cohort Studies, Dementia epidemiology, Female, Genetic Variation, Genome-Wide Association Study, Humans, Male, Polymorphism, Single Nucleotide, Prevalence, Sequence Analysis, DNA, Alzheimer Disease genetics, Dementia genetics, Nerve Tissue Proteins genetics
Abstract

Background/aims: The Alzheimer's Disease Sequencing Project (ADSP) aims to identify novel genes influencing Alzheimer's disease (AD). Variants within genes known to cause dementias other than AD have previously been associated with AD risk. We describe evidence of co-segregation and associations between variants in dementia genes and clinically diagnosed AD within the ADSP., Methods: We summarize the properties of known pathogenic variants within dementia genes, describe the co-segregation of variants annotated as "pathogenic" in ClinVar and new candidates observed in ADSP families, and test for associations between rare variants in dementia genes in the ADSP case-control study. The participants were clinically evaluated for AD, and they represent European, Caribbean Hispanic, and isolate Dutch populations., Results/conclusions: Pathogenic variants in dementia genes were predominantly rare and conserved coding changes. Pathogenic variants within ARSA, CSF1R, and GRN were observed, and candidate variants in GRN and CHMP2B were nominated in ADSP families. An independent case-control study provided evidence of an association between variants in TREM2, APOE, ARSA, CSF1R, PSEN1, and MAPT and risk of AD. Variants in genes which cause dementing disorders may influence the clinical diagnosis of AD in a small proportion of cases within the ADSP., (© 2018 S. Karger AG, Basel.)

Published
2018
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