@article{Venter2001c,
abstract = {A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90{\%} of the genome is in scaffold assemblies of 100,000 bp or more, and 25{\%} of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1{\%} of the genome is spanned by exons, whereas 24{\%} is in introns, with 75{\%} of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1{\%} of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.},
author = {Venter, J C and Et al.},
doi = {10.1126/science.1058040},
journal = {Science},
keywords = {*Genome, Human,*Human Genome Project,*Sequence Analysis, DNA/methods,Algorithms,Animal,Chromosome Banding,Chromosome Mapping,Chromosomes, Artificial, Bacterial,Computational Biology,Consensus Sequence,CpG Islands,DNA, Intergenic,Databases, Factual,Evolution, Molecular,Exons,Female,Gene Duplication,Genes,Human,Introns,Male,Phenotype,Physical Chromosome Mapping,Polymorphism, Single Nucleotide,Proteins/genetics/physiology,Pseudogenes,Repetitive Sequences, Nucleic Acid,Retroelements,Species Specificity,Support, Non-U.S. Gov't,Variation (Genetics)},
number = {5507},
pages = {1304--1351},
title = {{The sequence of the human genome}},
url = {http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/referer?http://www.ncbi.nlm.nih.gov/htbin-post/Omim/getmim?field=medline{\_}uid{\&}search=11181995},
volume = {291},
year = {2001}
}
@misc{Visscher2012a,
abstract = {The past five years have seen many scientific and biological discoveries made through the experimental design of genome-wide association studies (GWASs). These studies were aimed at detecting variants at genomic loci that are associated with complex traits in the population and, in particular, at detecting associations between common single-nucleotide polymorphisms (SNPs) and common diseases such as heart disease, diabetes, auto-immune diseases, and psychiatric disorders. We start by giving a number of quotes from scientists and journalists about perceived problems with GWASs. We will then briefly give the history of GWASs and focus on the discoveries made through this experimental design, what those discoveries tell us and do not tell us about the genetics and biology of complex traits, and what immediate utility has come out of these studies. Rather than giving an exhaustive review of all reported findings for all diseases and other complex traits, we focus on the results for auto-immune diseases and metabolic diseases. We return to the perceived failure or disappointment about GWASs in the concluding section. {\textcopyright} 2012 The American Society of Human Genetics.},
author = {Visscher, Peter M. and Brown, Matthew A. and McCarthy, Mark I. and Yang, Jian},
booktitle = {American Journal of Human Genetics},
doi = {10.1016/j.ajhg.2011.11.029},
isbn = {1537-6605 (Electronic)$\backslash$r0002-9297 (Linking)},
issn = {00029297},
number = {1},
pages = {7--24},
pmid = {22243964},
title = {{Five years of GWAS discovery}},
volume = {90},
year = {2012}
}
@article{Durbin2010,
abstract = {This issue of Nature contains the first publication from The 1000 Genomes Project, an international collaboration that will produce an extensive public catalogue of human genetic variation. The plan, in fact, is to sequence about 2,000 unidentified individuals from 20 populations around the world. This first paper presents the results from the project's pilot phase, testing three different strategies for genome-wide sequencing with high-throughput platforms: low-coverage whole-genome sequencing of 179 individuals in three population groups, high-coverage sequencing of two motherfatherchild trios, and exon-targeted sequencing of 697 individuals from seven populations.},
author = {Durbin, Richard M. and Altshuler, David L. and Durbin, Richard M. and Abecasis, Gon{\c{c}}alo R. and Bentley, David R. and Chakravarti, Aravinda and Clark, Andrew G. and Collins, Francis S. and {De La Vega}, Francisco M. and Donnelly, Peter and Egholm, Michael and Flicek, Paul and Gabriel, Stacey B. and Gibbs, Richard A. and Knoppers, Bartha M. and Lander, Eric S. and Lehrach, Hans and Mardis, Elaine R. and McVean, Gil A. and Nickerson, Debbie A. and Peltonen, Leena and Schafer, Alan J. and Sherry, Stephen T. and Wang, Jun and Wilson, Richard K. and Gibbs, Richard A. and Deiros, David and Metzker, Mike and Muzny, Donna and Reid, Jeff and Wheeler, David and Wang, Jun and Li, Jingxiang and Jian, Min and Li, Guoqing and Li, Ruiqiang and Liang, Huiqing and Tian, Geng and Wang, Bo and Wang, Jian and Wang, Wei and Yang, Huanming and Zhang, Xiuqing and Zheng, Huisong and Lander, Eric S. and Altshuler, David L. and Ambrogio, Lauren and Bloom, Toby and Cibulskis, Kristian and Fennell, Tim J. and Gabriel, Stacey B. and Jaffe, David B. and Shefler, Erica and Sougnez, Carrie L. and Bentley, David R. and Gormley, Niall and Humphray, Sean and Kingsbury, Zoya and Koko-Gonzales, Paula and Stone, Jennifer and McKernan, Kevin J. and Costa, Gina L. and Ichikawa, Jeffry K. and Lee, Clarence C. and Sudbrak, Ralf and Lehrach, Hans and Borodina, Tatiana A. and Dahl, Andreas and Davydov, Alexey N. and Marquardt, Peter and Mertes, Florian and Nietfeld, Wilfiried and Rosenstiel, Philip and Schreiber, Stefan and Soldatov, Aleksey V. and Timmermann, Bernd and Tolzmann, Marius and Egholm, Michael and Affourtit, Jason and Ashworth, Dana and Attiya, Said and Bachorski, Melissa and Buglione, Eli and Burke, Adam and Caprio, Amanda and Celone, Christopher and Clark, Shauna and Conners, David and Desany, Brian and Gu, Lisa and Guccione, Lorri and Kao, Kalvin and Kebbel, Andrew and Knowlton, Jennifer and Labrecque, Matthew and McDade, Louise and Mealmaker, Craig and Minderman, Melissa and Nawrocki, Anne and Niazi, Faheem and Pareja, Kristen and Ramenani, Ravi and Riches, David and Song, Wanmin and Turcotte, Cynthia and Wang, Shally and Mardis, Elaine R. and Wilson, Richard K. and Dooling, David and Fulton, Lucinda and Fulton, Robert and Weinstock, George and Durbin, Richard M. and Burton, John and Carter, David M. and Churcher, Carol and Coffey, Alison and Cox, Anthony and Palotie, Aarno and Quail, Michael and Skelly, Tom and Stalker, James and Swerdlow, Harold P. and Turner, Daniel and {De Witte}, Anniek and Giles, Shane and Gibbs, Richard A. and Wheeler, David and Bainbridge, Matthew and Challis, Danny and Sabo, Aniko and Yu, Fuli and Yu, Jin and Wang, Jun and Fang, Xiaodong and Guo, Xiaosen and Li, Ruiqiang and Li, Yingrui and Luo, Ruibang and Tai, Shuaishuai and Wu, Honglong and Zheng, Hancheng and Zheng, Xiaole and Zhou, Yan and Li, Guoqing and Wang, Jian and Yang, Huanming and Marth, Gabor T. and Garrison, Erik P. and Huang, Weichun and Indap, Amit and Kural, Deniz and Lee, Wan-Ping and {Fung Leong}, Wen and Quinlan, Aaron R. and Stewart, Chip and Stromberg, Michael P. and Ward, Alistair N. and Wu, Jiantao and Lee, Charles and Mills, Ryan E. and Shi, Xinghua and Daly, Mark J. and DePristo, Mark A. and Altshuler, David L. and Ball, Aaron D. and Banks, Eric and Bloom, Toby and Browning, Brian L. and Cibulskis, Kristian and Fennell, Tim J. and Garimella, Kiran V. and Grossman, Sharon R. and Handsaker, Robert E. and Hanna, Matt and Hartl, Chris and Jaffe, David B. and Kernytsky, Andrew M. and Korn, Joshua M. and Li, Heng and Maguire, Jared R. and McCarroll, Steven A. and McKenna, Aaron and Nemesh, James C. and Philippakis, Anthony A. and Poplin, Ryan E. and Price, Alkes and Rivas, Manuel A. and Sabeti, Pardis C. and Schaffner, Stephen F. and Shefler, Erica and Shlyakhter, Ilya A. and Cooper, David N. and Ball, Edward V. and Mort, Matthew and Phillips, Andrew D. and Stenson, Peter D. and Sebat, Jonathan and Makarov, Vladimir and Ye, Kenny and Yoon, Seungtai C. and Bustamante, Carlos D. and Clark, Andrew G. and Boyko, Adam and Degenhardt, Jeremiah and Gravel, Simon and Gutenkunst, Ryan N. and Kaganovich, Mark and Keinan, Alon and Lacroute, Phil and Ma, Xin and Reynolds, Andy and Clarke, Laura and Flicek, Paul and Cunningham, Fiona and Herrero, Javier and Keenen, Stephen and Kulesha, Eugene and Leinonen, Rasko and McLaren, William M. and Radhakrishnan, Rajesh and Smith, Richard E. and Zalunin, Vadim and Zheng-Bradley, Xiangqun and Korbel, Jan O. and St{\"{u}}tz, Adrian M. and Humphray, Sean and Bauer, Markus and {Keira Cheetham}, R. and Cox, Tony and Eberle, Michael and James, Terena and Kahn, Scott and Murray, Lisa and Chakravarti, Aravinda and Ye, Kai and {De La Vega}, Francisco M. and Fu, Yutao and Hyland, Fiona C. L. and Manning, Jonathan M. and McLaughlin, Stephen F. and Peckham, Heather E. and Sakarya, Onur and Sun, Yongming A. and Tsung, Eric F. and Batzer, Mark A. and Konkel, Miriam K. and Walker, Jerilyn A. and Sudbrak, Ralf and Albrecht, Marcus W. and Amstislavskiy, Vyacheslav S. and Herwig, Ralf and Parkhomchuk, Dimitri V. and Sherry, Stephen T. and Agarwala, Richa and Khouri, Hoda M. and Morgulis, Aleksandr O. and Paschall, Justin E. and Phan, Lon D. and Rotmistrovsky, Kirill E. and Sanders, Robert D. and Shumway, Martin F. and Xiao, Chunlin and McVean, Gil A. and Auton, Adam and Iqbal, Zamin and Lunter, Gerton and Marchini, Jonathan L. and Moutsianas, Loukas and Myers, Simon and Tumian, Afidalina and Desany, Brian and Knight, James and Winer, Roger and Craig, David W. and Beckstrom-Sternberg, Steve M. and Christoforides, Alexis and Kurdoglu, Ahmet A. and Pearson, John V. and Sinari, Shripad A. and Tembe, Waibhav D. and Haussler, David and Hinrichs, Angie S. and Katzman, Sol J. and Kern, Andrew and Kuhn, Robert M. and Przeworski, Molly and Hernandez, Ryan D. and Howie, Bryan and Kelley, Joanna L. and {Cord Melton}, S. and Abecasis, Gon{\c{c}}alo R. and Li, Yun and Anderson, Paul and Blackwell, Tom and Chen, Wei and Cookson, William O. and Ding, Jun and {Min Kang}, Hyun and Lathrop, Mark and Liang, Liming and Moffatt, Miriam F. and Scheet, Paul and Sidore, Carlo and Snyder, Matthew and Zhan, Xiaowei and Z{\"{o}}llner, Sebastian and Awadalla, Philip and Casals, Ferran and Idaghdour, Youssef and Keebler, John and Stone, Eric A. and Zilversmit, Martine and Jorde, Lynn and Xing, Jinchuan and Eichler, Evan E. and Aksay, Gozde and Alkan, Can and Hajirasouliha, Iman and Hormozdiari, Fereydoun and Kidd, Jeffrey M. and {Cenk Sahinalp}, S. and Sudmant, Peter H. and Mardis, Elaine R. and Chen, Ken and Chinwalla, Asif and Ding, Li and Koboldt, Daniel C. and McLellan, Mike D. and Dooling, David and Weinstock, George and Wallis, John W. and Wendl, Michael C. and Zhang, Qunyuan and Durbin, Richard M. and Albers, Cornelis A. and Ayub, Qasim and Balasubramaniam, Senduran and Barrett, Jeffrey C. and Carter, David M. and Chen, Yuan and Conrad, Donald F. and Danecek, Petr and Dermitzakis, Emmanouil T. and Hu, Min and Huang, Ni and Hurles, Matt E. and Jin, Hanjun and Jostins, Luke and Keane, Thomas M. and {Quang Le}, Si and Lindsay, Sarah and Long, Quan and MacArthur, Daniel G. and Montgomery, Stephen B. and Parts, Leopold and Stalker, James and Tyler-Smith, Chris and Walter, Klaudia and Zhang, Yujun and Gerstein, Mark B. and Snyder, Michael and Abyzov, Alexej and Balasubramanian, Suganthi and Bjornson, Robert and Du, Jiang and Grubert, Fabian and Habegger, Lukas and Haraksingh, Rajini and Jee, Justin and Khurana, Ekta and Lam, Hugo Y. K. and Leng, Jing and {Jasmine Mu}, Xinmeng and Urban, Alexander E. and Zhang, Zhengdong and Li, Yingrui and Luo, Ruibang and Marth, Gabor T. and Garrison, Erik P. and Kural, Deniz and Quinlan, Aaron R. and Stewart, Chip and Stromberg, Michael P. and Ward, Alistair N. and Wu, Jiantao and Lee, Charles and Mills, Ryan E. and Shi, Xinghua and McCarroll, Steven A. and Banks, Eric and DePristo, Mark A. and Handsaker, Robert E. and Hartl, Chris and Korn, Joshua M. and Li, Heng and Nemesh, James C. and Sebat, Jonathan and Makarov, Vladimir and Ye, Kenny and Yoon, Seungtai C. and Degenhardt, Jeremiah and Kaganovich, Mark and Clarke, Laura and Smith, Richard E. and Zheng-Bradley, Xiangqun and Korbel, Jan O. and Humphray, Sean and {Keira Cheetham}, R. and Eberle, Michael and Kahn, Scott and Murray, Lisa and Ye, Kai and {De La Vega}, Francisco M. and Fu, Yutao and Peckham, Heather E. and Sun, Yongming A. and Batzer, Mark A. and Konkel, Miriam K. and Walker, Jerilyn A. and Xiao, Chunlin and Iqbal, Zamin and Desany, Brian and Blackwell, Tom and Snyder, Matthew and Xing, Jinchuan and Eichler, Evan E. and Aksay, Gozde and Alkan, Can and Hajirasouliha, Iman and Hormozdiari, Fereydoun and Kidd, Jeffrey M. and Chen, Ken and Chinwalla, Asif and Ding, Li and McLellan, Mike D. and Wallis, John W. and Hurles, Matt E. and Conrad, Donald F. and Walter, Klaudia and Zhang, Yujun and Gerstein, Mark B. and Snyder, Michael and Abyzov, Alexej and Du, Jiang and Grubert, Fabian and Haraksingh, Rajini and Jee, Justin and Khurana, Ekta and Lam, Hugo Y. K. and Leng, Jing and {Jasmine Mu}, Xinmeng and Urban, Alexander E. and Zhang, Zhengdong and Gibbs, Richard A. and Bainbridge, Matthew and Challis, Danny and Coafra, Cristian and Dinh, Huyen and Kovar, Christie and Lee, Sandy and Muzny, Donna and Nazareth, Lynne and Reid, Jeff and Sabo, Aniko and Yu, Fuli and Yu, Jin and Marth, Gabor T. and Garrison, Erik P. and Indap, Amit and {Fung Leong}, Wen and Quinlan, Aaron R. and Stewart, Chip and Ward, Alistair N. and Wu, Jiantao and Cibulskis, Kristian and Fennell, Tim J. and Gabriel, Stacey B. and Garimella, Kiran V. and Hartl, Chris and Shefler, Erica and Sougnez, Carrie L. and Wilkinson, Jane and Clark, Andrew G. and Gravel, Simon and Grubert, Fabian and Clarke, Laura and Flicek, Paul and Smith, Richard E. and Zheng-Bradley, Xiangqun and Sherry, Stephen T. and Khouri, Hoda M. and Paschall, Justin E. and Shumway, Martin F. and Xiao, Chunlin and McVean, Gil A. and Katzman, Sol J. and Abecasis, Gon{\c{c}}alo R. and Blackwell, Tom and Mardis, Elaine R. and Dooling, David and Fulton, Lucinda and Fulton, Robert and Koboldt, Daniel C. and Durbin, Richard M. and Balasubramaniam, Senduran and Coffey, Allison and Keane, Thomas M. and MacArthur, Daniel G. and Palotie, Aarno and Scott, Carol and Stalker, James and Tyler-Smith, Chris and Gerstein, Mark B. and Balasubramanian, Suganthi and Chakravarti, Aravinda and Knoppers, Bartha M. and Abecasis, Gon{\c{c}}alo R. and Bustamante, Carlos D. and Gharani, Neda and Gibbs, Richard A. and Jorde, Lynn and Kaye, Jane S. and Kent, Alastair and Li, Taosha and McGuire, Amy L. and McVean, Gil A. and Ossorio, Pilar N. and Rotimi, Charles N. and Su, Yeyang and Toji, Lorraine H. and Tyler-Smith, Chris and Brooks, Lisa D. and Felsenfeld, Adam L. and McEwen, Jean E. and Abdallah, Assya and Juenger, Christopher R. and Clemm, Nicholas C. and Collins, Francis S. and Duncanson, Audrey and Green, Eric D. and Guyer, Mark S. and Peterson, Jane L. and Schafer, Alan J. and Abecasis, Gon{\c{c}}alo R. and Altshuler, David L. and Auton, Adam and Brooks, Lisa D. and Durbin, Richard M. and Gibbs, Richard A. and Hurles, Matt E. and McVean, Gil A.},
doi = {10.1038/nature09534},
issn = {0028-0836},
journal = {Nature},
keywords = {1000-genomes,Genome,Population genetics,Structural variation,wide association studies},
mendeley-tags = {1000-genomes},
month = {oct},
number = {7319},
pages = {1061--1073},
publisher = {Nature Publishing Group},
title = {{A map of human genome variation from population-scale sequencing}},
url = {http://www.nature.com/doifinder/10.1038/nature09534},
volume = {467},
year = {2010}
}
@article{Liu2019,
abstract = {Early genome-wide association studies (GWASs) led to the surprising discovery that, for typical complex traits, most of the heritability is due to huge numbers of common variants with tiny effect sizes. Previously, we argued that new models are needed to understand these patterns. Here, we provide a formal model in which genetic contributions to complex traits are partitioned into direct effects from core genes and indirect effects from peripheral genes acting in trans. We propose that most heritability is driven by weak trans-eQTL SNPs, whose effects are mediated through peripheral genes to impact the expression of core genes. In particular, if the core genes for a trait tend to be co-regulated, then the effects of peripheral variation can be amplified such that nearly all of the genetic variance is driven by weak trans effects. Thus, our model proposes a framework for understanding key features of the architecture of complex traits. Development of the “omnigenic” model to encompass specific effects on gene expression provides a defined framework for testing how variants in core and peripheral genes reflect genetic heritability.},
author = {Liu, Xuanyao and Li, Yang I. and Pritchard, Jonathan K.},
doi = {10.1016/j.cell.2019.04.014},
issn = {10974172},
journal = {Cell},
keywords = {cis-eQTLs,complex traits,core genes,genetic architecture,heritability,omnigenic model,polygenic model,trans-eQTLs},
month = {may},
number = {4},
pages = {1022--1034.e6},
publisher = {Cell Press},
title = {{Trans Effects on Gene Expression Can Drive Omnigenic Inheritance}},
volume = {177},
year = {2019}
}
@article{Gamazon2015a,
abstract = {Genome-wide association studies (GWAS) have identified thousands of variants robustly associated with complex traits. However, the biological mechanisms underlying these associations are, in general, not well understood. We propose a gene-based association method called PrediXcan that directly tests the molecular mechanisms through which genetic variation affects phenotype. The approach estimates the component of gene expression determined by an individual's genetic profile and correlates 'imputed' gene expression with the phenotype under investigation to identify genes involved in the etiology of the phenotype. Genetically regulated gene expression is estimated using whole-genome tissue-dependent prediction models trained with reference transcriptome data sets. PrediXcan enjoys the benefits of gene-based approaches such as reduced multiple-testing burden and a principled approach to the design of follow-up experiments. Our results demonstrate that PrediXcan can detect known and new genes associated with disease traits and provide insights into the mechanism of these associations.},
author = {Gamazon, Eric R and Wheeler, Heather E and Shah, Kaanan P and Mozaffari, Sahar V and Aquino-Michaels, Keston and Carroll, Robert J and Eyler, Anne E and Denny, Joshua C and Nicolae, Dan L and Cox, Nancy J and Im, Hae Kyung},
doi = {10.1038/ng.3367},
isbn = {1061-4036},
issn = {15461718},
journal = {Nature Genetics},
keywords = {twas},
mendeley-tags = {twas},
month = {sep},
number = {9},
pages = {1091--1098},
pmid = {26258848},
title = {{A gene-based association method for mapping traits using reference transcriptome data}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26258848 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4552594 http://www.nature.com/articles/ng.3367},
volume = {47},
year = {2015}
}
@article{Nagpal2019,
abstract = {The transcriptome-wide association studies (TWASs) that test for association between the study trait and the imputed gene expression levels from cis-acting expression quantitative trait loci (cis-eQTL) genotypes have successfully enhanced the discovery of genetic risk loci for complex traits. By using the gene expression imputation models fitted from reference datasets that have both genetic and transcriptomic data, TWASs facilitate gene-based tests with GWAS data while accounting for the reference transcriptomic data. The existing TWAS tools like PrediXcan and FUSION use parametric imputation models that have limitations for modeling the complex genetic architecture of transcriptomic data. Therefore, to improve on this, we employ a nonparametric Bayesian method that was originally proposed for genetic prediction of complex traits, which assumes a data-driven nonparametric prior for cis-eQTL effect sizes. The nonparametric Bayesian method is flexible and general because it includes both of the parametric imputation models used by PrediXcan and FUSION as special cases. Our simulation studies showed that the nonparametric Bayesian model improved both imputation R2 for transcriptomic data and the TWAS power over PrediXcan when ≥1{\%} cis-SNPs co-regulate gene expression and gene expression heritability ≤0.2. In real applications, the nonparametric Bayesian method fitted transcriptomic imputation models for 57.8{\%} more genes over PrediXcan, thus improving the power of follow-up TWASs. We implement both parametric PrediXcan and nonparametric Bayesian methods in a convenient software tool “TIGAR” (Transcriptome-Integrated Genetic Association Resource), which imputes transcriptomic data and performs subsequent TWASs using individual-level or summary-level GWAS data.},
author = {Nagpal, Sini and Meng, Xiaoran and Epstein, Michael P. and Tsoi, L. C. and Patrick, Matthew and Gibson, Greg and {De Jager}, Philip L. and Bennett, David A. and Wingo, Aliza P. and Wingo, Thomas S. and Yang, Jingjing},
doi = {10.1016/j.ajhg.2019.05.018},
issn = {15376605},
journal = {American Journal of Human Genetics},
keywords = {TIGAR,gene expression imputation,gene mapping,genetically regulated gene expression,nonparametric Bayesian method,transcriptome-wide association studies},
title = {{TIGAR: An Improved Bayesian Tool for Transcriptomic Data Imputation Enhances Gene Mapping of Complex Traits}},
year = {2019}
}
@misc{Lonsdale2013a,
abstract = {Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not correlated with protein-coding changes, suggesting that polymorphisms in regulatory regions probably contribute to many disease phenotypes. Here we describe the Genotype-Tissue Expression (GTEx) project, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues.},
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Lonsdale, John and Thomas, Jeffrey and Salvatore, Mike and Phillips, Rebecca and Lo, Edmund and Shad, Saboor and Hasz, Richard and Walters, Gary and Garcia, Fernando and Young, Nancy and Foster, Barbara and Moser, Mike and Karasik, Ellen and Gillard, Bryan and Ramsey, Kimberley and Sullivan, Susan and Bridge, Jason and Magazine, Harold and Syron, John and Fleming, Johnelle and Siminoff, Laura and Traino, Heather and Mosavel, Maghboeba and Barker, Laura and Jewell, Scott and Rohrer, Dan and Maxim, Dan and Filkins, Dana and Harbach, Philip and Cortadillo, Eddie and Berghuis, Bree and Turner, Lisa and Hudson, Eric and Feenstra, Kristin and Sobin, Leslie and Robb, James and Branton, Phillip and Korzeniewski, Greg and Shive, Charles and Tabor, David and Qi, Liqun and Groch, Kevin and Nampally, Sreenath and Buia, Steve and Zimmerman, Angela and Smith, Anna and Burges, Robin and Robinson, Karna and Valentino, Kim and Bradbury, Deborah and Cosentino, Mark and Diaz-Mayoral, Norma and Kennedy, Mary and Engel, Theresa and Williams, Penelope and Erickson, Kenyon and Ardlie, Kristin and Winckler, Wendy and Getz, Gad and DeLuca, David and {Daniel MacArthur} and Kellis, Manolis and Thomson, Alexander and Young, Taylor and Gelfand, Ellen and Donovan, Molly and Meng, Yan and Grant, George and Mash, Deborah and Marcus, Yvonne and Basile, Margaret and Liu, Jun and Zhu, Jun and Tu, Zhidong and Cox, Nancy J. and Nicolae, Dan L. and Gamazon, Eric R. and Im, Hae Kyung and Konkashbaev, Anuar and Pritchard, Jonathan and Stevens, Matthew and Flutre, Timoth{\`{e}}e and Wen, Xiaoquan and Dermitzakis, Emmanouil T. and Lappalainen, Tuuli and Guigo, Roderic and Monlong, Jean and Sammeth, Michael and Koller, Daphne and Battle, Alexis and Mostafavi, Sara and McCarthy, Mark and Rivas, Manual and Maller, Julian and Rusyn, Ivan and Nobel, Andrew and Wright, Fred and Shabalin, Andrey and Feolo, Mike and Sharopova, Nataliya and Sturcke, Anne and Paschal, Justin and Anderson, James M. and Wilder, Elizabeth L. and Derr, Leslie K. and Green, Eric D. and Struewing, Jeffery P. and Temple, Gary and Volpi, Simona and Boyer, Joy T. and Thomson, Elizabeth J. and Guyer, Mark S. and Ng, Cathy and Abdallah, Assya and Colantuoni, Deborah and Insel, Thomas R. and Koester, Susan E. and {A Roger Little} and Bender, Patrick K. and Lehner, Thomas and Yao, Yin and Compton, Carolyn C. and Vaught, Jimmie B. and Sawyer, Sherilyn and Lockhart, Nicole C. and Demchok, Joanne and Moore, Helen F.},
booktitle = {Nature Genetics},
doi = {10.1038/ng.2653},
eprint = {NIHMS150003},
isbn = {1061-4036},
issn = {10614036},
number = {6},
pages = {580--585},
pmid = {23715323},
title = {{The Genotype-Tissue Expression (GTEx) project}},
volume = {45},
year = {2013}
}
@article{Lander2001a,
abstract = {The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.},
archivePrefix = {arXiv},
arxivId = {11237011},
author = {Lander, Eric S. and Linton, Lauren M. and Birren, Bruce and Nusbaum, Chad and Zody, Michael C. and Baldwin, Jennifer and Devon, Keri and Dewar, Ken and Doyle, Michael and Fitzhugh, William and Funke, Roel and Gage, Diane and Harris, Katrina and Heaford, Andrew and Howland, John and Kann, Lisa and Lehoczky, Jessica and Levine, Rosie and McEwan, Paul and McKernan, Kevin and Meldrim, James and Mesirov, Jill P. and Miranda, Cher and Morris, William and Naylor, Jerome and Raymond, Christina and Rosetti, Mark and Santos, Ralph and Sheridan, Andrew and Sougnez, Carrie and Stange-Thomann, Nicole and Stojanovic, Nikola and Subramanian, Aravind and Wyman, Dudley and Rogers, Jane and Sulston, John and Ainscough, Rachael and Beck, Stephan and Bentley, David and Burton, John and Clee, Christopher and Carter, Nigel and Coulson, Alan and Deadman, Rebecca and Deloukas, Panos and Dunham, Andrew and Dunham, Ian and Durbin, Richard and French, Lisa and Grafham, Darren and Gregory, Simon and Hubbard, Tim and Humphray, Sean and Hunt, Adrienne and Jones, Matthew and Lloyd, Christine and McMurray, Amanda and Matthews, Lucy and Mercer, Simon and Milne, Sarah and Mullikin, James C. and Mungall, Andrew and Plumb, Robert and Ross, Mark and Shownkeen, Ratna and Sims, Sarah and Waterston, Robert H. and Wilson, Richard K. and Hillier, Ladeana W. and McPherson, John D. and Marra, Marco A. and Mardis, Elaine R. and Fulton, Lucinda A. and Chinwalla, Asif T. and Pepin, Kymberlie H. and Gish, Warren R. and Chissoe, Stephanie L. and Wendl, Michael C. and Delehaunty, Kim D. and Miner, Tracie L. and Delehaunty, Andrew and Kramer, Jason B. and Cook, Lisa L. and Fulton, Robert S. and Johnson, Douglas L. and Minx, Patrick J. and Clifton, Sandra W. and Hawkins, Trevor and Branscomb, Elbert and Predki, Paul and Richardson, Paul and Wenning, Sarah and Slezak, Tom and Doggett, Norman and Cheng, Jan Fang and Olsen, Anne and Lucas, Susan and Elkin, Christopher and Uberbacher, Edward and Frazier, Marvin and Gibbs, Richard A. and Muzny, Donna M. and Scherer, Steven E. and Bouck, John B. and Sodergren, Erica J. and Worley, Kim C. and Rives, Catherine M. and Gorrell, James H. and Metzker, Michael L. and Naylor, Susan L. and Kucherlapati, Raju S. and Nelson, David L. and Weinstock, George M. and Sakaki, Yoshiyuki and Fujiyama, Asao and Hattori, Masahira and Yada, Tetsushi and Toyoda, Atsushi and Itoh, Takehiko and Kawagoe, Chiharu and Watanabe, Hidemi and Totoki, Yasushi and Taylor, Todd and Weissenbach, Jean and Heilig, Roland and Saurin, William and Artiguenave, Francois and Brottier, Philippe and Bruls, Thomas and Pelletier, Eric and Robert, Catherine and Wincker, Patrick and Rosenthal, Andr{\'{e}} and Platzer, Matthias and Nyakatura, Gerald and Taudien, Stefan and Rump, Andreas and Smith, Douglas R. and Doucette-Stamm, Lynn and Rubenfield, Marc and Weinstock, Keith and Hong, Mei Lee and Dubois, Joann and Yang, Huanming and Yu, Jun and Wang, Jian and Huang, Guyang and Gu, Jun and Hood, Leroy and Rowen, Lee and Madan, Anup and Qin, Shizen and Davis, Ronald W. and Federspiel, Nancy A. and Abola, A. Pia and Proctor, Michael J. and Roe, Bruce A. and Chen, Feng and Pan, Huaqin and Ramser, Juliane and Lehrach, Hans and Reinhardt, Richard and McCombie, W. Richard and {De La Bastide}, Melissa and Dedhia, Neilay and Bl{\"{o}}cker, Helmut and Hornischer, Klaus and Nordsiek, Gabriele and Agarwala, Richa and Aravind, L. and Bailey, Jeffrey A. and Bateman, Alex and Batzoglou, Serafim and Birney, Ewan and Bork, Peer and Brown, Daniel G. and Burge, Christopher B. and Cerutti, Lorenzo and Chen, Hsiu Chuan and Church, Deanna and Clamp, Michele and Copley, Richard R. and Doerks, Tobias and Eddy, Sean R. and Eichler, Evan E. and Furey, Terrence S. and Galagan, James and Gilbert, James G.R. and Harmon, Cyrus and Hayashizaki, Yoshihide and Haussler, David and Hermjakob, Henning and Hokamp, Karsten and Jang, Wonhee and Johnson, L. Steven and Jones, Thomas A. and Kasif, Simon and Kaspryzk, Arek and Kennedy, Scot and Kent, W. James and Kitts, Paul and Koonin, Eugene V. and Korf, Ian and Kulp, David and Lancet, Doron and Lowe, Todd M. and McLysaght, Aoife and Mikkelsen, Tarjei and Moran, John V. and Mulder, Nicola and Pollara, Victor J. and Ponting, Chris P. and Schuler, Greg and Schultz, J{\"{o}}rg and Slater, Guy and Smit, Arian F.A. and Stupka, Elia and Szustakowki, Joseph and Thierry-Mieg, Danielle and Thierry-Mieg, Jean and Wagner, Lukas and Wallis, John and Wheeler, Raymond and Williams, Alan and Wolf, Yuri I. and Wolfe, Kenneth H. and Yang, Shiaw Pyng and Yeh, Ru Fang and Collins, Francis and Guyer, Mark S. and Peterson, Jane and Felsenfeld, Adam and Wetterstrand, Kris A. and Myers, Richard M. and Schmutz, Jeremy and Dickson, Mark and Grimwood, Jane and Cox, David R. and Olson, Maynard V. and Kaul, Rajinder and Raymond, Christopher and Shimizu, Nobuyoshi and Kawasaki, Kazuhiko and Minoshima, Shinsei and Evans, Glen A. and Athanasiou, Maria and Schultz, Roger and Patrinos, Aristides and Morgan, Michael J.},
doi = {10.1038/35057062},
eprint = {11237011},
isbn = {0028-0836 (Print)$\backslash$r0028-0836 (Linking)},
issn = {00280836},
journal = {Nature},
keywords = {Animals,Chromosome Mapping,Conserved Sequence,CpG Islands,DNA,DNA Transposable Elements,DNA: methods,Databases,Drug Industry,Evolution,Factual,Forecasting,GC Rich Sequence,Gene Duplication,Genes,Genetic Diseases,Genetics,Genome,Human,Human Genome Project,Humans,Inborn,Medical,Molecular,Mutation,Nucleic Acid,Private Sector,Proteins,Proteins: genetics,Proteome,Public Sector,RNA,RNA: genetics,Repetitive Sequences,Sequence Analysis,Species Specificity},
number = {6822},
pages = {860--921},
pmid = {11237011},
title = {{Initial sequencing and analysis of the human genome}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11237011},
volume = {409},
year = {2001}
}
@article{Mortazavi2008,
abstract = {We have mapped and quantified mouse transcriptomes by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq). This provides a digital measure of the presence and prevalence of transcripts from known and previously unknown genes. We report reference measurements composed of 41-52 million mapped 25-base-pair reads for poly(A)-selected RNA from adult mouse brain, liver and skeletal muscle tissues. We used RNA standards to quantify transcript prevalence and to test the linear range of transcript detection, which spanned five orders of magnitude. Although {\textgreater}90{\%} of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3′ untranscribed regions, as well as new candidate microRNA precursors. RNA splice events, which are not readily measured by standard gene expression microarray or serial analysis of gene expression methods, were detected directly by mapping splice-crossing sequence reads. We observed 1.45 × 105 distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices.},
author = {Mortazavi, Ali and Williams, Brian A. and McCue, Kenneth and Schaeffer, Lorian and Wold, Barbara},
doi = {10.1038/nmeth.1226},
issn = {15487091},
journal = {Nature Methods},
month = {jul},
number = {7},
pages = {621--628},
pmid = {18516045},
title = {{Mapping and quantifying mammalian transcriptomes by RNA-Seq}},
volume = {5},
year = {2008}
}
@article{Zerbino2018,
abstract = {The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. Large amounts of raw data are thus transformed into knowledge, which is made available via a multitude of channels, in particular our browser (http://www.ensembl.org). Over time, we have expanded in multiple directions. First, our resources describe multiple fields of genomics, in particular gene annotation, comparative genomics, genetics and epigenomics. Second, we cover a growing number of genome assemblies; Ensembl Release 90 contains exactly 100. Third, our databases feed simultaneously into an array of services designed around different use cases, ranging from quick browsing to genome-wide bioinformatic analysis. We present here the latest developments of the Ensembl project, with a focus on managing an increasing number of assemblies, supporting efforts in genome interpretation and improving our browser.},
author = {Zerbino, Daniel R and Achuthan, Premanand and Akanni, Wasiu and Amode, M Ridwan and Barrell, Daniel and Bhai, Jyothish and Billis, Konstantinos and Cummins, Carla and Gall, Astrid and Gir{\'{o}}n, Carlos Garc{\'{i}}a and Gil, Laurent and Gordon, Leo and Haggerty, Leanne and Haskell, Erin and Hourlier, Thibaut and Izuogu, Osagie G and Janacek, Sophie H and Juettemann, Thomas and To, Jimmy Kiang and Laird, Matthew R and Lavidas, Ilias and Liu, Zhicheng and Loveland, Jane E and Maurel, Thomas and McLaren, William and Moore, Benjamin and Mudge, Jonathan and Murphy, Daniel N and Newman, Victoria and Nuhn, Michael and Ogeh, Denye and Ong, Chuang Kee and Parker, Anne and Patricio, Mateus and Riat, Harpreet Singh and Schuilenburg, Helen and Sheppard, Dan and Sparrow, Helen and Taylor, Kieron and Thormann, Anja and Vullo, Alessandro and Walts, Brandon and Zadissa, Amonida and Frankish, Adam and Hunt, Sarah E and Kostadima, Myrto and Langridge, Nicholas and Martin, Fergal J and Muffato, Matthieu and Perry, Emily and Ruffier, Magali and Staines, Dan M and Trevanion, Stephen J and Aken, Bronwen L and Cunningham, Fiona and Yates, Andrew and Flicek, Paul},
doi = {10.1093/nar/gkx1098},
issn = {13624962},
journal = {Nucleic Acids Research},
month = {jan},
number = {D1},
pages = {D754--D761},
title = {{Ensembl 2018}},
url = {http://academic.oup.com/nar/article/46/D1/D754/4634002},
volume = {46},
year = {2018}
}
@article{Molineris2011a,
abstract = {Changes in gene regulation are believed to play an important role in the evolution of animals. It has been suggested that changes in cis-regulatory regions are responsible for many or most of the anatomical and behavioral differences between humans and apes. However, the study of the evolution of cis-regulatory regions is made problematic by the degeneracy of transcription factor (TF) binding sites and the shuffling of their positions. In this work, we use the predicted total affinity of a promoter for a large collection of TFs as the basis for studying the evolution of cis-regulatory regions in mammals. We introduce the human specificity of a promoter, measuring the divergence between the affinity profile of a human promoter and its orthologous promoters in other mammals. The promoters of genes involved in functional categories such as neural processes and signal transduction, among others, have higher human specificity compared with the rest of the genome. Clustering of the human-specific affinities (HSAs) of neural genes reveals patterns of promoter evolution associated with functional categories such as synaptic transmission and brain development and to diseases such as bipolar disorder and autism. {\textcopyright} 2011 The Author Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.},
author = {Molineris, Ivan and Grassi, Elena and Ala, Ugo and {Di Cunto}, Ferdinando and Provero, Paolo},
doi = {10.1093/molbev/msr027},
issn = {07374038},
journal = {Molecular Biology and Evolution},
keywords = {adaptive evolution,regulatory evolution,transcriptional regulation},
month = {aug},
number = {8},
pages = {2173--2183},
title = {{Evolution of promoter affinity for transcription factors in the human lineage}},
url = {https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msr027},
volume = {28},
year = {2011}
}
@book{James2013a,
abstract = {... But ESL is intended for individuals with ad- vanced training in the mathematical sciences. An Introduction to Statistical Learning (ISL) arose from the perceived need for a broader and less tech- nical treatment of these topics. ... $\backslash$n},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {James, Gareth and Witten, Daniela and Hastie, Trevor and Tibshirani, Robert},
booktitle = {An Introduction to Statistical Learning},
doi = {10.1007/978-1-4614-7138-7},
eprint = {arXiv:1011.1669v3},
isbn = {978-1-4614-7137-0},
issn = {01621459},
pmid = {10911016},
title = {{An Introduction to Statistical Learning}},
url = {http://link.springer.com/content/pdf/10.1007/978-1-4614-7138-7.pdf{\%}5Cnhttp://link.springer.com/10.1007/978-1-4614-7138-7},
year = {2013}
}
@article{Danecek2011,
abstract = {Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. {\textcopyright} The Author(s) 2011. Published by Oxford University Press.},
author = {Danecek, Petr and Auton, Adam and Abecasis, Goncalo and Albers, Cornelis A. and Banks, Eric and DePristo, Mark A. and Handsaker, Robert E. and Lunter, Gerton and Marth, Gabor T. and Sherry, Stephen T. and McVean, Gilean and Durbin, Richard},
doi = {10.1093/bioinformatics/btr330},
issn = {13674803},
journal = {Bioinformatics},
month = {aug},
number = {15},
pages = {2156--2158},
pmid = {21653522},
title = {{The variant call format and VCFtools}},
volume = {27},
year = {2011}
}
@book{Hastie2009,
abstract = {During the past decade there has been an explosion in computation and information technology. With it have come vast amounts of data in a variety of fields such as medicine, biology, finance, and marketing. The challenge of understanding these data has led to the development of new tools in the field of statistics, and spawned new areas such as data mining, machine learning, and bioinformatics. Many of these tools have common underpinnings but are often expressed with different terminology. This book describes the important ideas in these areas in a common conceptual framework. While the approach is statistical, the emphasis is on concepts rather than mathematics. Many examples are given, with a liberal use of color graphics. It is a valuable resource for statisticians and anyone interested in data mining in science or industry. The book's coverage is broad, from supervised learning (prediction) to unsupervised learning. The many topics include neural networks, support vector machines, classification trees and boosting---the first comprehensive treatment of this topic in any book.},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Hastie, Trevor and Tibshirani, Robert and Friedman, Jerome},
booktitle = {Springer series in statistics},
doi = {10.1007/978-0-387-84858-7},
eprint = {arXiv:1011.1669v3},
isbn = {978-0-387-84858-7},
issn = {00111287},
keywords = {Data Mining,Inference,Neural Nets,Prediction,Statistical Learning},
pages = {282},
pmid = {12377617},
title = {{The Elements of Statistical Learning The Elements of Statistical LearningData Mining, Inference, and Prediction, Second Edition}},
url = {http://www.worldcat.org/oclc/405547558{\%}5CnHastie, Tibshirani et al - The elements of statistical learning.pdf{\%}5Cnhttp://www.springer.com.libproxy1.nus.edu.sg/statistics/statistical+theory+and+methods/book/978-0-387-84857-0{\%}5Cnhttp://statweb.stanford.edu/{~}tibs/E},
year = {2009}
}
