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1. wtest: an R Package for Testing Main and Interaction Effect in Genotype Data with Binary Traits

Author

Sun, Rui, Chang, Billy, Zee, Benny Chung-Ying, and Wang, Maggie Haitian

Subjects
Statistics - Computation, Quantitative Biology - Quantitative Methods
Abstract

This R package evaluates main and pair-wise interaction effect of single nucleotide polymorphisms (SNPs) via the W-test, scalable to whole genome-wide data sets. The package provides fast and accurate p-value estimation of genetic markers, as well as diagnostic checking on the probability distributions. It allows flexible stage-wise or exhaustive association testing in a user-friendly interface. Availability: The package is available in CRAN, or from website: http://www2.ccrb.cuhk.edu.hk/wtest, Comment: 7 pages, 1 figure

Published
2016

2. Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data

Author

Abdallah, Kald, Aittokallio, Tero, Airola, Antti, Anghe, Catalina, Azima, Helia, Baertsch, Robert, Ballester, Pedro J, Bare, Chris, Bhandari, Vinayak, Bot, Brian M, Dang, Cuong C, Dunbar, Maria Bekker-Nielsen, Buchardt, Ann-Sophie, Buturovic, Ljubomir, Cao, Da, Chalise, Prabhakar, Cho, Junwoo, Chu, Tzu-Ming, Coley, R Yates, Conjeti, Sailesh, Correia, Sara, Costello, James C, Dai, Ziwei, Dai, Junqiang, Dargatz, Philip, Delavarkhan, Sam, Deng, Detian, Dhanik, Ankur, Du, Yu, Elangovan, Aparna, Ellis, Shellie, Elo, Laura L, Espiritu, Shadrielle M, Fan, Fan, Farshi, Ashkan B, Freitas, Ana, Fridley, Brooke, Friend, Stephen, Fuchs, Christiane, Gofer, Eyal, Peddinti, Gopalacharyulu, Graw, Stefan, Greiner, Russ, Guan, Yuanfang, Guinney, Justin, Guo, Jing, Gupta, Pankaj, Guyer, Anna I, Han, Jiawei, Hansen, Niels R, Chang, Billy HW, Hirvonen, Outi, Huang, Barbara, Huang, Chao, Hwang, Jinseub, Ibrahim, Joseph G, Jayaswa, Vivek, Jeon, Jouhyun, Ji, Zhicheng, Juvvadi, Deekshith, Jyrkkiö, Sirkku, Kanigel-Winner, Kimberly, Katouzian, Amin, Kazanov, Marat D, Khan, Suleiman A, Khayyer, Shahin, Kim, Dalho, Golinska, Agnieszka K, Koestler, Devin, Kokowicz, Fernanda, Kondofersky, Ivan, Krautenbacher, Norbert, Krstajic, Damjan, Kumar, Luke, Kurz, Christoph, Kyan, Matthew, Laajala, Teemu D, Laimighofer, Michael, Lee, Eunjee, Lesinski, Wojciech, Li, Miaozhu, Li, Ye, Lian, Qiuyu, Liang, Xiaotao, Lim, Minseong, Lin, Henry, Lin, Xihui, Lu, Jing, Mahmoudian, Mehrad, Manshaei, Roozbeh, Meier, Richard, Miljkovic, Dejan, Mirtti, Tuomas, Mnich, Krzysztof, Navab, Nassir, Neto, Elias C, Newton, Yulia, Norman, Thea, Pahikkala, Tapio, Pal, Subhabrata, Park, Byeongju, Patel, Jaykumar, Pathak, Swetabh, Pattin, Alejandrina, Ankerst, Donna P, Peng, Jian, Petersen, Anne H, Philip, Robin, Piccolo, Stephen R, Pölsterl, Sebastian, Polewko-Klim, Aneta, Rao, Karthik, Ren, Xiang, Rocha, Miguel, Rudnicki, Witold R., Ryan, Charles J, Ryu, Hyunnam, Sartor, Oliver, Scherb, Hagen, Sehgal, Raghav, Seyednasrollah, Fatemeh, Shang, Jingbo, Shao, Bin, Shen, Liji, Sher, Howard, Shiga, Motoki, Sokolov, Artem, Söllner, Julia F, Song, Lei, Soule, Howard, Stolovitzky, Gustavo, Stuart, Josh, Sun, Ren, Sweeney, Christopher J, Tahmasebi, Nazanin, Tan, Kar-Tong, Tomaziu, Lisbeth, Usset, Joseph, Vang, Yeeleng S, Vega, Roberto, Vieira, Vitor, Wang, David, Wang, Difei, Wang, Junmei, Wang, Lichao, Wang, Sheng, Wang, Tao, Wang, Yue, Wolfinger, Russ, Wong, Chris, Wu, Zhenke, Xiao, Jinfeng, Xie, Xiaohui, Xie, Yang, Xin, Doris, Yang, Hojin, Yu, Nancy, Yu, Thomas, Yu, Xiang, Zahedi, Sulmaz, Zanin, Massimiliano, Zhang, Chihao, Zhang, Jingwen, Zhang, Shihua, Zhang, Yanchun, Zhou, Fang Liz, Zhu, Hongtu, Zhu, Shanfeng, Zhu, Yuxin, Winner, Kimberly Kanigel, Bare, J Christopher, Neto, Elias Chaibub, Peddinti, Gopal, and Scher, Howard I

Published
2017
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4. Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

Author

Daneshjou, Roxana, Wang, Yanran, Bromberg, Yana, Bovo, Samuele, Martelli, Pier L, Babbi, Giulia, Lena, Pietro Di, Casadio, Rita, Edwards, Matthew, Gifford, David, Jones, David T, Sundaram, Laksshman, Bhat, Rajendra Rana, Li, Xiaolin, Pal, Lipika R., Kundu, Kunal, Yin, Yizhou, Moult, John, Jiang, Yuxiang, Pejaver, Vikas, Pagel, Kymberleigh A., Li, Biao, Mooney, Sean D., Radivojac, Predrag, Shah, Sohela, Carraro, Marco, Gasparini, Alessandra, Leonardi, Emanuela, Giollo, Manuel, Ferrari, Carlo, Tosatto, Silvio C E, Bachar, Eran, Azaria, Johnathan R., Ofran, Yanay, Unger, Ron, Niroula, Abhishek, Vihinen, Mauno, Chang, Billy, Wang, Maggie H, Franke, Andre, Petersen, Britt-Sabina, Pirooznia, Mehdi, Zandi, Peter, McCombie, Richard, Potash, James B., Altman, Russ B., Klein, Teri E., Hoskins, Roger A., Repo, Susanna, Brenner, Steven E., and Morgan, Alexander A.

Published
2017
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8. Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data

Author

Guinney, Justin, primary, Wang, Tao, additional, Laajala, Teemu D, additional, Winner, Kimberly Kanigel, additional, Bare, J Christopher, additional, Neto, Elias Chaibub, additional, Khan, Suleiman A, additional, Peddinti, Gopal, additional, Airola, Antti, additional, Pahikkala, Tapio, additional, Mirtti, Tuomas, additional, Yu, Thomas, additional, Bot, Brian M, additional, Shen, Liji, additional, Abdallah, Kald, additional, Norman, Thea, additional, Friend, Stephen, additional, Stolovitzky, Gustavo, additional, Soule, Howard, additional, Sweeney, Christopher J, additional, Ryan, Charles J, additional, Scher, Howard I, additional, Sartor, Oliver, additional, Xie, Yang, additional, Aittokallio, Tero, additional, Zhou, Fang Liz, additional, Costello, James C, additional, Anghe, Catalina, additional, Azima, Helia, additional, Baertsch, Robert, additional, Ballester, Pedro J, additional, Bare, Chris, additional, Bhandari, Vinayak, additional, Dang, Cuong C, additional, Dunbar, Maria Bekker-Nielsen, additional, Buchardt, Ann-Sophie, additional, Buturovic, Ljubomir, additional, Cao, Da, additional, Chalise, Prabhakar, additional, Cho, Junwoo, additional, Chu, Tzu-Ming, additional, Coley, R Yates, additional, Conjeti, Sailesh, additional, Correia, Sara, additional, Dai, Ziwei, additional, Dai, Junqiang, additional, Dargatz, Philip, additional, Delavarkhan, Sam, additional, Deng, Detian, additional, Dhanik, Ankur, additional, Du, Yu, additional, Elangovan, Aparna, additional, Ellis, Shellie, additional, Elo, Laura L, additional, Espiritu, Shadrielle M, additional, Fan, Fan, additional, Farshi, Ashkan B, additional, Freitas, Ana, additional, Fridley, Brooke, additional, Fuchs, Christiane, additional, Gofer, Eyal, additional, Peddinti, Gopalacharyulu, additional, Graw, Stefan, additional, Greiner, Russ, additional, Guan, Yuanfang, additional, Guinney, Justin, additional, Guo, Jing, additional, Gupta, Pankaj, additional, Guyer, Anna I, additional, Han, Jiawei, additional, Hansen, Niels R, additional, Chang, Billy HW, additional, Hirvonen, Outi, additional, Huang, Barbara, additional, Huang, Chao, additional, Hwang, Jinseub, additional, Ibrahim, Joseph G, additional, Jayaswa, Vivek, additional, Jeon, Jouhyun, additional, Ji, Zhicheng, additional, Juvvadi, Deekshith, additional, Jyrkkiö, Sirkku, additional, Kanigel-Winner, Kimberly, additional, Katouzian, Amin, additional, Kazanov, Marat D, additional, Khayyer, Shahin, additional, Kim, Dalho, additional, Golinska, Agnieszka K, additional, Koestler, Devin, additional, Kokowicz, Fernanda, additional, Kondofersky, Ivan, additional, Krautenbacher, Norbert, additional, Krstajic, Damjan, additional, Kumar, Luke, additional, Kurz, Christoph, additional, Kyan, Matthew, additional, Laimighofer, Michael, additional, Lee, Eunjee, additional, Lesinski, Wojciech, additional, Li, Miaozhu, additional, Li, Ye, additional, Lian, Qiuyu, additional, Liang, Xiaotao, additional, Lim, Minseong, additional, Lin, Henry, additional, Lin, Xihui, additional, Lu, Jing, additional, Mahmoudian, Mehrad, additional, Manshaei, Roozbeh, additional, Meier, Richard, additional, Miljkovic, Dejan, additional, Mnich, Krzysztof, additional, Navab, Nassir, additional, Neto, Elias C, additional, Newton, Yulia, additional, Pal, Subhabrata, additional, Park, Byeongju, additional, Patel, Jaykumar, additional, Pathak, Swetabh, additional, Pattin, Alejandrina, additional, Ankerst, Donna P, additional, Peng, Jian, additional, Petersen, Anne H, additional, Philip, Robin, additional, Piccolo, Stephen R, additional, Pölsterl, Sebastian, additional, Polewko-Klim, Aneta, additional, Rao, Karthik, additional, Ren, Xiang, additional, Rocha, Miguel, additional, Rudnicki, Witold R., additional, Ryu, Hyunnam, additional, Scherb, Hagen, additional, Sehgal, Raghav, additional, Seyednasrollah, Fatemeh, additional, Shang, Jingbo, additional, Shao, Bin, additional, Sher, Howard, additional, Shiga, Motoki, additional, Sokolov, Artem, additional, Söllner, Julia F, additional, Song, Lei, additional, Stuart, Josh, additional, Sun, Ren, additional, Tahmasebi, Nazanin, additional, Tan, Kar-Tong, additional, Tomaziu, Lisbeth, additional, Usset, Joseph, additional, Vang, Yeeleng S, additional, Vega, Roberto, additional, Vieira, Vitor, additional, Wang, David, additional, Wang, Difei, additional, Wang, Junmei, additional, Wang, Lichao, additional, Wang, Sheng, additional, Wang, Yue, additional, Wolfinger, Russ, additional, Wong, Chris, additional, Wu, Zhenke, additional, Xiao, Jinfeng, additional, Xie, Xiaohui, additional, Xin, Doris, additional, Yang, Hojin, additional, Yu, Nancy, additional, Yu, Xiang, additional, Zahedi, Sulmaz, additional, Zanin, Massimiliano, additional, Zhang, Chihao, additional, Zhang, Jingwen, additional, Zhang, Shihua, additional, Zhang, Yanchun, additional, Zhu, Hongtu, additional, Zhu, Shanfeng, additional, and Zhu, Yuxin, additional

Published
2017
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10. Addressing the Microvillus Inclusion Disease Knowledge Gap: A Comprehensive Case Analysis.

Author

Chang, Billy, Chang, Nelson, Patel, Ronak, McGrath, Christina, Kravtsov, Dmitry V., and Kvochina, Ludmila

Subjects
*KNOWLEDGE gap theory, *MICROVILLI, *CASE studies, *TREATMENT effectiveness, *GENETIC disorders
Abstract

Many children affected by the genetic intestinal disorder known as microvillus inclusion disease (MVID) may not live to see their third birthday. Given MVID's rarity, it can be difficult for doctors, researchers, and parents confronted with the devastating disease to locate necessary data related to the disorder, presenting challenges with research, diagnosis, and the development of treatment strategies. To address this knowledge gap, this paper summarizes data trends compiled from all known literature published globally on the disease and includes a comprehensive review of the outcome of treatment methods employed. [ABSTRACT FROM AUTHOR]

Published
2019

13. Zygosity Differences in Height and Body Mass Index of Twins From Infancy to Old Age: A Study of the CODATwins Project

Author

Jelenkovic, Aline, primary, Yokoyama, Yoshie, additional, Sund, Reijo, additional, Honda, Chika, additional, Bogl, Leonie H, additional, Aaltonen, Sari, additional, Ji, Fuling, additional, Ning, Feng, additional, Pang, Zengchang, additional, Ordoñana, Juan R., additional, Sánchez-Romera, Juan F., additional, Colodro-Conde, Lucia, additional, Burt, S. Alexandra, additional, Klump, Kelly L., additional, Medland, Sarah E., additional, Montgomery, Grant W., additional, Kandler, Christian, additional, McAdams, Tom A., additional, Eley, Thalia C., additional, Gregory, Alice M., additional, Saudino, Kimberly J., additional, Dubois, Lise, additional, Boivin, Michel, additional, Tarnoki, Adam D., additional, Tarnoki, David L., additional, Haworth, Claire M. A., additional, Plomin, Robert, additional, Öncel, Sevgi Y., additional, Aliev, Fazil, additional, Stazi, Maria A., additional, Fagnani, Corrado, additional, D’Ippolito, Cristina, additional, Craig, Jeffrey M., additional, Saffery, Richard, additional, Siribaddana, Sisira H., additional, Hotopf, Matthew, additional, Sumathipala, Athula, additional, Rijsdijk, Fruhling, additional, Spector, Timothy, additional, Mangino, Massimo, additional, Lachance, Genevieve, additional, Gatz, Margaret, additional, Butler, David A., additional, Bayasgalan, Gombojav, additional, Narandalai, Danshiitsoodol, additional, Freitas, Duarte L, additional, Maia, José Antonio, additional, Harden, K. Paige, additional, Tucker-Drob, Elliot M., additional, Kim, Bia, additional, Chong, Youngsook, additional, Hong, Changhee, additional, Shin, Hyun Jung, additional, Christensen, Kaare, additional, Skytthe, Axel, additional, Kyvik, Kirsten O., additional, Derom, Catherine A., additional, Vlietinck, Robert F., additional, Loos, Ruth J. F., additional, Cozen, Wendy, additional, Hwang, Amie E., additional, Mack, Thomas M., additional, He, Mingguang, additional, Ding, Xiaohu, additional, Chang, Billy, additional, Silberg, Judy L., additional, Eaves, Lindon J., additional, Maes, Hermine H., additional, Cutler, Tessa L., additional, Hopper, John L., additional, Aujard, Kelly, additional, Magnusson, Patrik K. E., additional, Pedersen, Nancy L., additional, Aslan, Anna K. Dahl, additional, Song, Yun-Mi, additional, Yang, Sarah, additional, Lee, Kayoung, additional, Baker, Laura A., additional, Tuvblad, Catherine, additional, Bjerregaard-Andersen, Morten, additional, Beck-Nielsen, Henning, additional, Sodemann, Morten, additional, Heikkilä, Kauko, additional, Tan, Qihua, additional, Zhang, Dongfeng, additional, Swan, Gary E., additional, Krasnow, Ruth, additional, Jang, Kerry L., additional, Knafo-Noam, Ariel, additional, Mankuta, David, additional, Abramson, Lior, additional, Lichtenstein, Paul, additional, Krueger, Robert F., additional, McGue, Matt, additional, Pahlen, Shandell, additional, Tynelius, Per, additional, Duncan, Glen E., additional, Buchwald, Dedra, additional, Corley, Robin P., additional, Huibregtse, Brooke M., additional, Nelson, Tracy L., additional, Whitfield, Keith E., additional, Franz, Carol E., additional, Kremen, William S., additional, Lyons, Michael J., additional, Ooki, Syuichi, additional, Brandt, Ingunn, additional, Nilsen, Thomas Sevenius, additional, Inui, Fujio, additional, Watanabe, Mikio, additional, Bartels, Meike, additional, van Beijsterveldt, Toos C. E. M., additional, Wardle, Jane, additional, Llewellyn, Clare H., additional, Fisher, Abigail, additional, Rebato, Esther, additional, Martin, Nicholas G., additional, Iwatani, Yoshinori, additional, Hayakawa, Kazuo, additional, Sung, Joohon, additional, Harris, Jennifer R., additional, Willemsen, Gonneke, additional, Busjahn, Andreas, additional, Goldberg, Jack H., additional, Rasmussen, Finn, additional, Hur, Yoon-Mi, additional, Boomsma, Dorret I., additional, Sørensen, Thorkild I. A., additional, Kaprio, Jaakko, additional, and Silventoinen, Karri, additional

Published
2015
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15. The CODATwins Project: The Cohort Description of Collaborative Project of Development of Anthropometrical Measures in Twins to Study Macro-Environmental Variation in Genetic and Environmental Effects on Anthropometric Traits

Author

Silventoinen, Karri, primary, Jelenkovic, Aline, additional, Sund, Reijo, additional, Honda, Chika, additional, Aaltonen, Sari, additional, Yokoyama, Yoshie, additional, Tarnoki, Adam D., additional, Tarnoki, David L., additional, Ning, Feng, additional, Ji, Fuling, additional, Pang, Zengchang, additional, Ordoñana, Juan R., additional, Sánchez-Romera, Juan F., additional, Colodro-Conde, Lucia, additional, Burt, S. Alexandra, additional, Klump, Kelly L., additional, Medland, Sarah E., additional, Montgomery, Grant W., additional, Kandler, Christian, additional, McAdams, Tom A., additional, Eley, Thalia C., additional, Gregory, Alice M., additional, Saudino, Kimberly J., additional, Dubois, Lise, additional, Boivin, Michel, additional, Haworth, Claire M. A., additional, Plomin, Robert, additional, Öncel, Sevgi Y., additional, Aliev, Fazil, additional, Stazi, Maria A., additional, Fagnani, Corrado, additional, D’Ippolito, Cristina, additional, Craig, Jeffrey M., additional, Saffery, Richard, additional, Siribaddana, Sisira H., additional, Hotopf, Matthew, additional, Sumathipala, Athula, additional, Spector, Timothy, additional, Mangino, Massimo, additional, Lachance, Genevieve, additional, Gatz, Margaret, additional, Butler, David A., additional, Bayasgalan, Gombojav, additional, Narandalai, Danshiitsoodol, additional, Freitas, Duarte L., additional, Maia, José Antonio, additional, Harden, K. Paige, additional, Tucker-Drob, Elliot M., additional, Christensen, Kaare, additional, Skytthe, Axel, additional, Kyvik, Kirsten O., additional, Hong, Changhee, additional, Chong, Youngsook, additional, Derom, Catherine A., additional, Vlietinck, Robert F., additional, Loos, Ruth J. F., additional, Cozen, Wendy, additional, Hwang, Amie E., additional, Mack, Thomas M., additional, He, Mingguang, additional, Ding, Xiaohu, additional, Chang, Billy, additional, Silberg, Judy L., additional, Eaves, Lindon J., additional, Maes, Hermine H., additional, Cutler, Tessa L., additional, Hopper, John L., additional, Aujard, Kelly, additional, Magnusson, Patrik K. E., additional, Pedersen, Nancy L., additional, Aslan, Anna K. Dahl, additional, Song, Yun-Mi, additional, Yang, Sarah, additional, Lee, Kayoung, additional, Baker, Laura A., additional, Tuvblad, Catherine, additional, Bjerregaard-Andersen, Morten, additional, Beck-Nielsen, Henning, additional, Sodemann, Morten, additional, Heikkilä, Kauko, additional, Tan, Qihua, additional, Zhang, Dongfeng, additional, Swan, Gary E., additional, Krasnow, Ruth, additional, Jang, Kerry L., additional, Knafo-Noam, Ariel, additional, Mankuta, David, additional, Abramson, Lior, additional, Lichtenstein, Paul, additional, Krueger, Robert F., additional, McGue, Matt, additional, Pahlen, Shandell, additional, Tynelius, Per, additional, Duncan, Glen E., additional, Buchwald, Dedra, additional, Corley, Robin P., additional, Huibregtse, Brooke M., additional, Nelson, Tracy L., additional, Whitfield, Keith E., additional, Franz, Carol E., additional, Kremen, William S., additional, Lyons, Michael J., additional, Ooki, Syuichi, additional, Brandt, Ingunn, additional, Nilsen, Thomas Sevenius, additional, Inui, Fujio, additional, Watanabe, Mikio, additional, Bartels, Meike, additional, van Beijsterveldt, Toos C. E. M., additional, Wardle, Jane, additional, Llewellyn, Clare H., additional, Fisher, Abigail, additional, Rebato, Esther, additional, Martin, Nicholas G., additional, Iwatani, Yoshinori, additional, Hayakawa, Kazuo, additional, Rasmussen, Finn, additional, Sung, Joohon, additional, Harris, Jennifer R., additional, Willemsen, Gonneke, additional, Busjahn, Andreas, additional, Goldberg, Jack H., additional, Boomsma, Dorret I., additional, Hur, Yoon-Mi, additional, Sørensen, Thorkild I. A., additional, and Kaprio, Jaakko, additional

Published
2015
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16. Trends in activities of daily living disability in a large sample of community-dwelling Chinese older adults in Hong Kong: an age-period-cohort analysis.

Author

Yu, Ruby, Wong, Moses, Chang, Billy, Xin Lai, Lum, C. M., WAuyeung, T., Lee, Jenny, Tsoi, Kelvin, Lee, Ruby, and Woo, Jean

Abstract

Background: To examine the trends in activities of daily living (ADL) disability in older Chinese adults in Hong Kong between 2001 and 2012. Methods: Using data from the Elderly Health Centres (EHCs) of the Department of Health comprising a total of 54 808 community-dwelling Chinese adults aged =65 years in 1 early cohort (1904-1917) and 10 3-year birth cohorts (1918-1920, 1921-1923, 1924-1926, 1927-1929, 1930-1932, 1933-1935, 1936-1938, 1939-1941, 1942-1944, 1945-1947), we examined trends in ADL disability by using age-period- cohort (APC) models. ADL disability was defined as being unable to perform at least 1 of 7 ADL activities (bathing, dressing, toileting, transferring, feeding, grooming, walking) independently. Cross-classified random-effects logistic regressions were performed for each of the APC trends with adjustment for age, period, cohort, sociodemographic, lifestyle, comorbidity and self-rated health. Results: The mean age of the cohort was 70.9±4.7 (range 65-99) years. The prevalence rate of ADL disability was 1.6%. ADL disability increased with age (p<0.001) and the gradient of the increase was steeper in the older age groups. At the same age, women (1.7%) were more likely to report ADL disability than men (1.4%, p=0.001). For both genders, there was an increase in ADL disability between 2003 and 2012; adjustment for age, cohort and other covariates has diminished the trends observed among men. There was no cohort effect in ADL disability. Conclusions: ADL disability in older adults has increased over the last decade. Further study is required to identify possible causes behind the disability trends. [ABSTRACT FROM AUTHOR]

Published
2016
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19. Case studies in data analysis.

Author

GIBBS, Alison L., KEEN, Kevin J., Liqun WANG, DEAN, C. B., PARISH, Roberta, CORMIER, Eric, Zheng SUN, SALAMH, Mustafa, BALSHAW, Robert F., COHEN FREUE, Gabriela V., Linghong LU, MANN, Rena K., SAAB, Rabih, STONE, Ryan, CHANG, Billy, DEMETRASHVILI, Nino, KOWGIER, Matthew, Qing GUO, Yalin CHEN, and Defen PENG

Subjects
CASE studies, PINE, PINACEAE, PROTEOMICS, BIOMARKERS
Abstract

The article describes two cases involving data analysis. The first case identifies the relevant factors for the growth of lodgepole pine trees using the nonparametric smoothing technique to determine a nonlinear relationship of the growth rate and the age of the trees. The second case examines the classification of disease status through proteomic biomarkers.

Published
2011
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20. Working towards precision medicine: predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

Author

Predrag Radivojac, Yanran Wang, Kunal Kundu, Maggie Haitian Wang, Laksshman Sundaram, Pier Luigi Martelli, Sohela Shah, Steven E. Brenner, Emanuela Leonardi, Yuxiang Jiang, Roxana Daneshjou, Mehdi Pirooznia, Marco Carraro, Rita Casadio, Biao Li, Giulia Babbi, Peter P. Zandi, John Moult, Silvio C. E. Tosatto, Andre Franke, Yanay Ofran, James B. Potash, David T. Jones, Mauno Vihinen, Billy Chang, Sean D. Mooney, Pietro Di Lena, Roger A. Hoskins, Russ B. Altman, David K. Gifford, Rajendra Rana Bhat, Kymberleigh A. Pagel, Carlo Ferrari, Yana Bromberg, Susanna Repo, Britt-Sabina Petersen, Xiaolin Li, Yizhou Yin, Alexander A. Morgan, Teri E. Klein, Lipika R. Pal, Ron Unger, Samuele Bovo, Abhishek Niroula, Richard W. McCombie, Vikas Pejaver, Eran Bachar, Matthew D. Edwards, Alessandra Gasparini, Johnathan Roy Azaria, Manuel Giollo, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Daneshjou, Roxana, Wang, Yanran, Bromberg, Yana, Bovo, Samuele, Martelli, Pier L, Babbi, Giulia, Pietro Di, Lena, Casadio, Rita, Edwards, Matthew, Gifford, David, Jones, David T, Sundaram, Laksshman, Bhat, Rajendra Rana, Xiaolin, Li, Pal, Lipika R., Kundu, Kunal, Yin, Yizhou, Moult, John, Jiang, Yuxiang, Pejaver, Vika, Pagel, Kymberleigh A., Biao, Li, Mooney, Sean D., Radivojac, Predrag, Shah, Sohela, Carraro, Marco, Gasparini, Alessandra, Leonardi, Emanuela, Giollo, Manuel, Ferrari, Carlo, Tosatto, Silvio C E, Bachar, Eran, Azaria, Johnathan R., Ofran, Yanay, Unger, Ron, Niroula, Abhishek, Vihinen, Mauno, Chang, Billy, Wang, Maggie H, Franke, Andre, Petersen, Britt-Sabina, Pirooznia, Mehdi, Zandi, Peter, Mccombie, Richard, Potash, James B., Altman, Russ B., Klein, Teri E., Hoskins, Roger A., Repo, Susanna, Brenner, Steven E., and Morgan, Alexander A.

Subjects
0301 basic medicine, Bipolar Disorder, Pharmacogenomic Variants, Information Dissemination, Disease, Biology, Bioinformatics, Genome, Whole Exome Sequencing, Article, 03 medical and health sciences, 0302 clinical medicine, Genetic, Crohn Disease, bipolar disorder, Crohn's disease, exomes, machine learning, phenotype prediction, warfarin, Genetics, Genetics (clinical), Databases, Genetic, Exome Sequencing, Humans, Genetic Predisposition to Disease, Precision Medicine, Exome, Exome sequencing, Interpretation (philosophy), Computational Biology, Precision medicine, Data science, Phenotype, 030104 developmental biology, Pharmacogenomic Variant, Warfarin, exome, 030217 neurology & neurosurgery, Human
Abstract

Precision medicine aims to predict a patient's disease risk and best therapeutic options by using that individual's genetic sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype–phenotype prediction challenges; participants build models, undergo assessment, and share key findings. For CAGI 4, three challenges involved using exome-sequencing data: Crohn's disease, bipolar disorder, and warfarin dosing. Previous CAGI challenges included prior versions of the Crohn's disease challenge. Here, we discuss the range of techniques used for phenotype prediction as well as the methods used for assessing predictive models. Additionally, we outline some of the difficulties associated with making predictions and evaluating them. The lessons learned from the exome challenges can be applied to both research and clinical efforts to improve phenotype prediction from genotype. In addition, these challenges serve as a vehicle for sharing clinical and research exome data in a secure manner with scientists who have a broad range of expertise, contributing to a collaborative effort to advance our understanding of genotype–phenotype relationships.

Published
2017

21. Association between body composition and retinal vascular caliber in children and adolescents.

Author

Xiao W, Gong W, Chen Q, Ding X, Chang B, and He M

Subjects
Adolescent, Blood Pressure, Child, Cross-Sectional Studies, Female, Follow-Up Studies, Humans, Male, Microvessels, Obesity physiopathology, Young Adult, Body Composition, Obesity pathology, Retinal Vessels pathology
Abstract

Purpose: To elucidate the relationship between body composition and retinal vascular caliber (RVC) in children and adolescents., Methods: Participants aged 7 to 19 years were recruited from the Guangzhou Twin Eye Study cohort. Retinal vascular caliber was measured cross-sectionally from retinal images using a computer-aided program. The data were expressed as the central retinal arteriolar equivalent (CRAE) and central retinal venular equivalent (CRVE). Triceps skinfold thickness (TSFT) was measured using a skinfold caliper. Body composition was obtained through bioelectrical impedance analysis, providing fat mass (FM), fat mass index (FMI), fat-free mass (FFM), fat-free mass index (FFMI), body water mass (BWM), body water percentage (BWP), basal metabolic rate (BMR), and trunk fat percentage (TFP)., Results: A total of 731 participants were included. Among the younger children (7-11 years), there was no significant association between body composition and RVC (all P > 0.05). However, for the older children (12-19 years), increasing FM, FMI, TFP, TSFT, and BMI were associated with CRAE negatively (β = -0.20, -0.68, -0.18, -0.17, and -0.48, respectively, all P < 0.05) and with CRVE positively (β = 0.47, 1.26, 0.34, 0.37, and 0.78, respectively, all P < 0.05), after adjusting for age, sex, axial length, mean arterial blood pressure, and the fellow vascular diameter. In contrast, increase in BWP was associated with larger CRAE (β = 0.33, P = 0.001) and smaller CRVE (β = -0.64, P < 0.001). Similar associations also were observed in the analyses when the body composition parameters were divided into quartiles (all P < 0.05)., Conclusions: In adolescents, greater body fat deposition is related to narrower retinal arterioles and wider retinal venules, and higher body water proportion is associated with retinal arterioles widening and retinal venules narrowing. Even during childhood, body composition might have an association with systemic microvasculature., (Copyright 2015 The Association for Research in Vision and Ophthalmology, Inc.)

Published
2015
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