Advances and challenges in quantitative delineation of the genetic architecture of complex traits

被引:0
作者
Tang, Hua [1 ]
He, Zihuai [2 ,3 ]
机构
[1] Stanford Univ, Dept Genet, Stanford, CA 94305 USA
[2] Stanford Univ, Dept Neurol & Neurol Sci, Stanford, CA 94305 USA
[3] Stanford Univ, Dept Med, Quantitat Sci Unit, Stanford, CA 94305 USA
关键词
genome-wide association study; heritability; rare variants; biobank; colocalization; eQTL; polygenic risk scores; transcriptome-wide association study; GENOME-WIDE ASSOCIATION; LEVERAGING MULTIETHNIC EVIDENCE; MIXED-MODEL ANALYSIS; COMMON DISEASE; PARTITIONING HERITABILITY; GENOTYPE IMPUTATION; RARE VARIANTS; SEQUENCE; GWAS; TRANSCRIPTOME;
D O I
10.15302/J-QB-021-0249
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Background: Genome-wide association studies (GWAS) have been widely adopted in studies of human complex traits and diseases. Results: This review surveys areas of active research: quantifying and partitioning trait heritability, fine mapping functional variants and integrative analysis, genetic risk prediction of phenotypes, and the analysis of sequencing studies that have identified millions of rare variants. Current challenges and opportunities are highlighted. Conclusion: GWAS have fundamentally transformed the field of human complex trait genetics. Novel statistical and computational methods have expanded the scope of GWAS and have provided valuable insights on the genetic architecture underlying complex phenotypes.
引用
收藏
页码:168 / 184
页数:17
相关论文
共 155 条
[1]   A method and server for predicting damaging missense mutations [J].
Adzhubei, Ivan A. ;
Schmidt, Steffen ;
Peshkin, Leonid ;
Ramensky, Vasily E. ;
Gerasimova, Anna ;
Bork, Peer ;
Kondrashov, Alexey S. ;
Sunyaev, Shamil R. .
NATURE METHODS, 2010, 7 (04) :248-249
[2]   Genetic effects on gene expression across human tissues [J].
Aguet, Francois ;
Brown, Andrew A. ;
Castel, Stephane E. ;
Davis, Joe R. ;
He, Yuan ;
Jo, Brian ;
Mohammadi, Pejman ;
Park, Yoson ;
Parsana, Princy ;
Segre, Ayellet V. ;
Strober, Benjamin J. ;
Zappala, Zachary ;
Cummings, Beryl B. ;
Gelfand, Ellen T. ;
Hadley, Kane ;
Huang, Katherine H. ;
Lek, Monkol ;
Li, Xiao ;
Nedzel, Jared L. ;
Nguyen, Duyen Y. ;
Noble, Michael S. ;
Sullivan, Timothy J. ;
Tukiainen, Taru ;
MacArthur, Daniel G. ;
Getz, Gad ;
Management, Nih Program ;
Addington, Anjene ;
Guan, Ping ;
Koester, Susan ;
Little, A. Roger ;
Lockhart, Nicole C. ;
Moore, Helen M. ;
Rao, Abhi ;
Struewing, Jeffery P. ;
Volpi, Simona ;
Collection, Biospecimen ;
Brigham, Lori E. ;
Hasz, Richard ;
Hunter, Marcus ;
Johns, Christopher ;
Johnson, Mark ;
Kopen, Gene ;
Leinweber, William F. ;
Lonsdale, John T. ;
McDonald, Alisa ;
Mestichelli, Bernadette ;
Myer, Kevin ;
Roe, Bryan ;
Salvatore, Michael ;
Shad, Saboor .
NATURE, 2017, 550 (7675) :204-+
[3]   Genetic Mapping in Human Disease [J].
Altshuler, David ;
Daly, Mark J. ;
Lander, Eric S. .
SCIENCE, 2008, 322 (5903) :881-888
[4]   A global reference for human genetic variation [J].
Altshuler, David M. ;
Durbin, Richard M. ;
Abecasis, Goncalo R. ;
Bentley, David R. ;
Chakravarti, Aravinda ;
Clark, Andrew G. ;
Donnelly, Peter ;
Eichler, Evan E. ;
Flicek, Paul ;
Gabriel, Stacey B. ;
Gibbs, Richard A. ;
Green, Eric D. ;
Hurles, Matthew E. ;
Knoppers, Bartha M. ;
Korbel, Jan O. ;
Lander, Eric S. ;
Lee, Charles ;
Lehrach, Hans ;
Mardis, Elaine R. ;
Marth, Gabor T. ;
McVean, Gil A. ;
Nickerson, Deborah A. ;
Wang, Jun ;
Wilson, Richard K. ;
Boerwinkle, Eric ;
Doddapaneni, Harsha ;
Han, Yi ;
Korchina, Viktoriya ;
Kovar, Christie ;
Lee, Sandra ;
Muzny, Donna ;
Reid, Jeffrey G. ;
Zhu, Yiming ;
Chang, Yuqi ;
Feng, Qiang ;
Fang, Xiaodong ;
Guo, Xiaosen ;
Jian, Min ;
Jiang, Hui ;
Jin, Xin ;
Lan, Tianming ;
Li, Guoqing ;
Li, Jingxiang ;
Li, Yingrui ;
Liu, Shengmao ;
Liu, Xiao ;
Lu, Yao ;
Ma, Xuedi ;
Tang, Meifang ;
Wang, Bo .
NATURE, 2015, 526 (7571) :68-+
[5]   Integrating common and rare genetic variation in diverse human populations [J].
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 ;
Chang, Kyle ;
Hawes, Alicia ;
Lewis, Lora R. ;
Ren, Yanru ;
Wheeler, David ;
Muzny, Donna Marie ;
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 ;
Anttila, Verneri ;
Brodeur, Wendy ;
Daly, Mark J. ;
Leslie, Stephen ;
McVean, Gil ;
Moutsianas, Loukas ;
Nguyen, Huy ;
Zhang, Qingrun ;
Ghori, Mohammed J. R. ;
McGinnis, Ralph ;
McLaren, William ;
Takeuchi, Fumihiko ;
Grossman, Sharon R. .
NATURE, 2010, 467 (7311) :52-58
[6]   The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans [J].
Ardlie, Kristin G. ;
DeLuca, David S. ;
Segre, Ayellet V. ;
Sullivan, Timothy J. ;
Young, Taylor R. ;
Gelfand, Ellen T. ;
Trowbridge, Casandra A. ;
Maller, Julian B. ;
Tukiainen, Taru ;
Lek, Monkol ;
Ward, Lucas D. ;
Kheradpour, Pouya ;
Iriarte, Benjamin ;
Meng, Yan ;
Palmer, Cameron D. ;
Esko, Tonu ;
Winckler, Wendy ;
Hirschhorn, Joel N. ;
Kellis, Manolis ;
MacArthur, Daniel G. ;
Getz, Gad ;
Shabalin, Andrey A. ;
Li, Gen ;
Zhou, Yi-Hui ;
Nobel, Andrew B. ;
Rusyn, Ivan ;
Wright, Fred A. ;
Lappalainen, Tuuli ;
Ferreira, Pedro G. ;
Ongen, Halit ;
Rivas, Manuel A. ;
Battle, Alexis ;
Mostafavi, Sara ;
Monlong, Jean ;
Sammeth, Michael ;
Mele, Marta ;
Reverter, Ferran ;
Goldmann, Jakob M. ;
Koller, Daphne ;
Guigo, Roderic ;
McCarthy, Mark I. ;
Dermitzakis, Emmanouil T. ;
Gamazon, Eric R. ;
Im, Hae Kyung ;
Konkashbaev, Anuar ;
Nicolae, Dan L. ;
Cox, Nancy J. ;
Flutre, Timothee ;
Wen, Xiaoquan ;
Stephens, Matthew .
SCIENCE, 2015, 348 (6235) :648-660
[7]   The power of genomic control [J].
Bacanu, SA ;
Devlin, B ;
Roeder, K .
AMERICAN JOURNAL OF HUMAN GENETICS, 2000, 66 (06) :1933-1944
[8]   Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort [J].
Banda, Yambazi ;
Kvale, Mark N. ;
Hoffmann, Thomas J. ;
Hesselson, Stephanie E. ;
Ranatunga, Dilrini ;
Tang, Hua ;
Sabatti, Chiara ;
Croen, Lisa A. ;
Dispensa, Brad P. ;
Henderson, Mary ;
Iribarren, Carlos ;
Jorgenson, Eric ;
Kushi, Lawrence H. ;
Ludwig, Dana ;
Olberg, Diane ;
Quesenberry, Charles P., Jr. ;
Rowell, Sarah ;
Sadler, Marianne ;
Sakoda, Lori C. ;
Sciortino, Stanley ;
Shen, Ling ;
Smethurst, David ;
Somkin, Carol P. ;
Van Den Eeden, Stephen K. ;
Walter, Lawrence ;
Whitmer, Rachel A. ;
Kwok, Pui-Yan ;
Schaefer, Catherine ;
Risch, Neil .
GENETICS, 2015, 200 (04) :1285-+
[9]   Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics [J].
Barbeira, Alvaro N. ;
Dickinson, Scott P. ;
Bonazzola, Rodrigo ;
Zheng, Jiamao ;
Wheeler, Heather E. ;
Torres, Jason M. ;
Torstenson, Eric S. ;
Shah, Kaanan P. ;
Garcia, Tzintzuni ;
Edwards, Todd L. ;
Stahl, Eli A. ;
Huckins, Laura M. ;
Nicolae, Dan L. ;
Cox, Nancy J. ;
Im, Hae Kyung .
NATURE COMMUNICATIONS, 2018, 9
[10]   A Quarter Century of APOE and Alzheimer's Disease: Progress to Date and the Path Forward [J].
Belloy, Michael E. ;
Napolioni, Valerio ;
Greicius, Michael D. .
NEURON, 2019, 101 (05) :820-838