Literature DB >> 25371374

Genetic simulation tools for post-genome wide association studies of complex diseases.

Huann-Sheng Chen1, Carolyn M Hutter2, Leah E Mechanic3, Elizabeth M Gillanders3, Eric J Feuer1, Christopher I Amos4, Vineet Bafna5, Elizabeth R Hauser6, Ryan D Hernandez7, Chun Li8, David A Liberles9, Kimberly McAllister10, Jason H Moore11, Dina N Paltoo12, George J Papanicolaou13, Bo Peng14, Marylyn D Ritchie15, Gabriel Rosenfeld1, John S Witte16.   

Abstract

Genetic simulation programs are used to model data under specified assumptions to facilitate the understanding and study of complex genetic systems. Standardized data sets generated using genetic simulation are essential for the development and application of novel analytical tools in genetic epidemiology studies. With continuing advances in high-throughput genomic technologies and generation and analysis of larger, more complex data sets, there is a need for updating current approaches in genetic simulation modeling. To provide a forum to address current and emerging challenges in this area, the National Cancer Institute (NCI) sponsored a workshop, entitled "Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases" at the National Institutes of Health (NIH) in Bethesda, Maryland on March 11-12, 2014. The goals of the workshop were to (1) identify opportunities, challenges, and resource needs for the development and application of genetic simulation models; (2) improve the integration of tools for modeling and analysis of simulated data; and (3) foster collaborations to facilitate development and applications of genetic simulation. During the course of the meeting, the group identified challenges and opportunities for the science of simulation, software and methods development, and collaboration. This paper summarizes key discussions at the meeting, and highlights important challenges and opportunities to advance the field of genetic simulation.
© 2014 WILEY PERIODICALS, INC.

Entities:  

Keywords:  complex phenotypes; computational resources; genetic simulation; next-generation sequencing; rare variants

Mesh:

Year:  2014        PMID: 25371374      PMCID: PMC4270837          DOI: 10.1002/gepi.21870

Source DB:  PubMed          Journal:  Genet Epidemiol        ISSN: 0741-0395            Impact factor:   2.135


  38 in total

1.  Approximate Bayesian computation in population genetics.

Authors:  Mark A Beaumont; Wenyang Zhang; David J Balding
Journal:  Genetics       Date:  2002-12       Impact factor: 4.562

2.  A rare nonsynonymous sequence variant in C3 is associated with high risk of age-related macular degeneration.

Authors:  Hannes Helgason; Patrick Sulem; Maheswara R Duvvari; Hongrong Luo; Gudmar Thorleifsson; Hreinn Stefansson; Ingileif Jonsdottir; Gisli Masson; Daniel F Gudbjartsson; G Bragi Walters; Olafur Th Magnusson; Augustine Kong; Thorunn Rafnar; Lambertus A Kiemeney; Frederieke E Schoenmaker-Koller; Ling Zhao; Camiel J F Boon; Yaojun Song; Sascha Fauser; Michelle Pei; Tina Ristau; Shirrina Patel; Sandra Liakopoulos; Johannes P H van de Ven; Carel B Hoyng; Henry Ferreyra; Yaou Duan; Paul S Bernstein; Asbjorg Geirsdottir; Gudleif Helgadottir; Einar Stefansson; Anneke I den Hollander; Kang Zhang; Fridbert Jonasson; Haraldur Sigurdsson; Unnur Thorsteinsdottir; Kari Stefansson
Journal:  Nat Genet       Date:  2013-09-15       Impact factor: 38.330

Review 3.  Genetic architecture of cancer and other complex diseases: lessons learned and future directions.

Authors:  Lucia A Hindorff; Elizabeth M Gillanders; Teri A Manolio
Journal:  Carcinogenesis       Date:  2011-03-31       Impact factor: 4.944

Review 4.  Genome simulation approaches for synthesizing in silico datasets for human genomics.

Authors:  Marylyn D Ritchie; William S Bush
Journal:  Adv Genet       Date:  2010       Impact factor: 1.944

5.  Evolution and functional impact of rare coding variation from deep sequencing of human exomes.

Authors:  Jacob A Tennessen; Abigail W Bigham; Timothy D O'Connor; Wenqing Fu; Eimear E Kenny; Simon Gravel; Sean McGee; Ron Do; Xiaoming Liu; Goo Jun; Hyun Min Kang; Daniel Jordan; Suzanne M Leal; Stacey Gabriel; Mark J Rieder; Goncalo Abecasis; David Altshuler; Deborah A Nickerson; Eric Boerwinkle; Shamil Sunyaev; Carlos D Bustamante; Michael J Bamshad; Joshua M Akey
Journal:  Science       Date:  2012-05-17       Impact factor: 47.728

6.  Genetic data simulators and their applications: an overview.

Authors:  Bo Peng; Huann-Sheng Chen; Leah E Mechanic; Ben Racine; John Clarke; Elizabeth Gillanders; Eric J Feuer
Journal:  Genet Epidemiol       Date:  2014-12-13       Impact factor: 2.135

7.  Properties and modeling of GWAS when complex disease risk is due to non-complementing, deleterious mutations in genes of large effect.

Authors:  Kevin R Thornton; Andrew J Foran; Anthony D Long
Journal:  PLoS Genet       Date:  2013-02-21       Impact factor: 5.917

8.  On the need for mechanistic models in computational genomics and metagenomics.

Authors:  David A Liberles; Ashley I Teufel; Liang Liu; Tanja Stadler
Journal:  Genome Biol Evol       Date:  2013       Impact factor: 3.416

9.  The impact of population demography and selection on the genetic architecture of complex traits.

Authors:  Kirk E Lohmueller
Journal:  PLoS Genet       Date:  2014-05-29       Impact factor: 5.917

10.  HuPSON: the human physiology simulation ontology.

Authors:  Michaela Gündel; Erfan Younesi; Ashutosh Malhotra; Jiali Wang; Hui Li; Bijun Zhang; Bernard de Bono; Heinz-Theodor Mevissen; Martin Hofmann-Apitius
Journal:  J Biomed Semantics       Date:  2013-11-22
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  10 in total

1.  Genetic Simulation Resources and the GSR Certification Program.

Authors:  Bo Peng; Man Chong Leong; Huann-Sheng Chen; Melissa Rotunno; Katy R Brignole; John Clarke; Leah E Mechanic
Journal:  Bioinformatics       Date:  2019-02-15       Impact factor: 6.937

2.  Population genetic simulations of complex phenotypes with implications for rare variant association tests.

Authors:  Lawrence H Uricchio; Raul Torres; John S Witte; Ryan D Hernandez
Journal:  Genet Epidemiol       Date:  2014-11-21       Impact factor: 2.135

3.  Genetic data simulators and their applications: an overview.

Authors:  Bo Peng; Huann-Sheng Chen; Leah E Mechanic; Ben Racine; John Clarke; Elizabeth Gillanders; Eric J Feuer
Journal:  Genet Epidemiol       Date:  2014-12-13       Impact factor: 2.135

4.  Machine learning and data mining in complex genomic data--a review on the lessons learned in Genetic Analysis Workshop 19.

Authors:  Inke R König; Jonathan Auerbach; Damian Gola; Elizabeth Held; Emily R Holzinger; Marc-André Legault; Rui Sun; Nathan Tintle; Hsin-Chou Yang
Journal:  BMC Genet       Date:  2016-02-03       Impact factor: 2.797

5.  GESDB: a platform of simulation resources for genetic epidemiology studies.

Authors:  Po-Ju Yao; Ren-Hua Chung
Journal:  Database (Oxford)       Date:  2016-05-30       Impact factor: 3.451

6.  A Model of Compound Heterozygous, Loss-of-Function Alleles Is Broadly Consistent with Observations from Complex-Disease GWAS Datasets.

Authors:  Jaleal S Sanjak; Anthony D Long; Kevin R Thornton
Journal:  PLoS Genet       Date:  2017-01-19       Impact factor: 5.917

7.  Presidential address: Six open questions to genetic epidemiologists.

Authors:  Inke R König
Journal:  Genet Epidemiol       Date:  2019-01-19       Impact factor: 2.135

8.  Analysis validation has been neglected in the Age of Reproducibility.

Authors:  Kathleen E Lotterhos; Jason H Moore; Ann E Stapleton
Journal:  PLoS Biol       Date:  2018-12-10       Impact factor: 8.029

Review 9.  Host and Microbiome Genome-Wide Association Studies: Current State and Challenges.

Authors:  Denis Awany; Imane Allali; Shareefa Dalvie; Sian Hemmings; Kilaza S Mwaikono; Nicholas E Thomford; Andres Gomez; Nicola Mulder; Emile R Chimusa
Journal:  Front Genet       Date:  2019-01-22       Impact factor: 4.599

10.  Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases.

Authors:  Kimberly McAllister; Leah E Mechanic; Christopher Amos; Hugues Aschard; Ian A Blair; Nilanjan Chatterjee; David Conti; W James Gauderman; Li Hsu; Carolyn M Hutter; Marta M Jankowska; Jacqueline Kerr; Peter Kraft; Stephen B Montgomery; Bhramar Mukherjee; George J Papanicolaou; Chirag J Patel; Marylyn D Ritchie; Beate R Ritz; Duncan C Thomas; Peng Wei; John S Witte
Journal:  Am J Epidemiol       Date:  2017-10-01       Impact factor: 5.363

  10 in total

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