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Genomic epidemiology

This section considers studies of the association of genetic factors or variations in the human genome with human health and disease, their prevalence within families and populations, their interactions with environmental factors, and their contribution to disease risk.

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  1. Oxidative stress has been related to type 2 diabetes (T2D) and cardiovascular disease (CVD), the leading global cause of death. Contributions of environmental factors such as oxidative stress on complex traits...

    Authors: Åsa K. Hedman, Mihkel Zilmer, Johan Sundström, Lars Lind and Erik Ingelsson

    Citation: BMC Medical Genomics 2016 9:72

    Content type: Research article

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  2. DNA methylation levels will be important for detection of epigenetic effects. However, there are few reports showing sex-related differences in the sensitivity to DNA methylation. To evaluate their sex-related...

    Authors: Mikio Watanabe, Chika Honda, Yoshinori Iwatani, Shiro Yorifuji, Hiroyasu Iso, Kei Kamide, Jun Hatazawa, Shinji Kihara, Norio Sakai, Hiroko Watanabe, Kiyoko Makimoto, Mikio Watanabe, Chika Honda and Yoshinori Iwatani

    Citation: BMC Medical Genomics 2016 9:55

    Content type: Research article

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  3. Based on age of presentation, celiac disease (CD) is categorised as pediatric CD and adult CD. It however remains unclear if these are genetically and/or phenotypically distinct disorders or just different spe...

    Authors: Sabyasachi Senapati, Ajit Sood, Vandana Midha, Neena Sood, Suresh Sharma, Lalit Kumar and B. K. Thelma

    Citation: BMC Medical Genomics 2016 9:44

    Content type: Research article

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  4. Neurodevelopment is orchestrated by a wide range of genes, and the genetic causes of neurodevelopmental disorders are thus heterogeneous. We applied whole exome sequencing (WES) for molecular diagnosis and in sil...

    Authors: Wu-Lin Charng, Ender Karaca, Zeynep Coban Akdemir, Tomasz Gambin, Mehmed M. Atik, Shen Gu, Jennifer E. Posey, Shalini N. Jhangiani, Donna M. Muzny, Harsha Doddapaneni, Jianhong Hu, Eric Boerwinkle, Richard A. Gibbs, Jill A. Rosenfeld, Hong Cui, Fan Xia…

    Citation: BMC Medical Genomics 2016 9:42

    Content type: Research article

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  5. Genetic screening to identify carriers of autosomal recessive diseases has become an integral part of routine prenatal care. In spite of the rapid growth of known mutations, most current screening programs inc...

    Authors: Moran Gal, Khen Khermesh, Michal Barak, Min Lin, Hadas Lahat, Haike Reznik Wolf, Michael Lin, Elon Pras and Erez Y. Levanon

    Citation: BMC Medical Genomics 2016 9:24

    Content type: Research article

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  6. MicroRNAs (miRNAs) have been implicated in the incidence and progression of cancer. It has been proposed that single nucleotide polymorphisms (SNPs) influence cancer risk due to their position within genes inv...

    Authors: Lila E. Mullany, Jennifer S. Herrick, Roger K. Wolff, Matthew F. Buas and Martha L. Slattery

    Citation: BMC Medical Genomics 2016 9:21

    Content type: Research article

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  7. Recent genome-wide association studies (GWAS) have shown that single nucleotide polymorphisms (SNPs) in the Chr9p21 region are associated with coronary artery disease (CAD). Most of the SNPs identified in this...

    Authors: Wei Zhao, Jennifer A Smith, Guangmei Mao, Myriam Fornage, Patricia A Peyser, Yan V Sun, Stephen T Turner and Sharon LR Kardia

    Citation: BMC Medical Genomics 2015 8:21

    Content type: Research article

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  8. Given the growing use of whole-exome sequencing (WES) for clinical diagnostics of complex human disorders, we evaluated coverage of clinically relevant cardiac genes on WES and factors influencing uniformity a...

    Authors: Dorin Manase, Lisa CA D’Alessandro, Ashok Kumar Manickaraj, Saeed Al Turki, Matthew E Hurles and Seema Mital

    Citation: BMC Medical Genomics 2014 7:67

    Content type: Research article

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  9. Dramatic improvements in DNA-sequencing technologies and computational analyses have led to wide use of whole exome sequencing (WES) to identify the genetic basis of Mendelian disorders. More than 180 novel ra...

    Authors: Casper Shyr, Maja Tarailo-Graovac, Michael Gottlieb, Jessica JY Lee, Clara van Karnebeek and Wyeth W Wasserman

    Citation: BMC Medical Genomics 2014 7:64

    Content type: Research article

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    The Correction to this article has been published in BMC Medical Genomics 2017 10:69

  10. Bicuspid aortic valve (BAV) is the most common type of congenital heart disease with a population prevalence of 1-2%. While BAV is known to be highly heritable, mutations in single genes (such as GATA5 and NOTCH1

    Authors: Elizabeth M Bonachea, Gloria Zender, Peter White, Don Corsmeier, David Newsom, Sara Fitzgerald-Butt, Vidu Garg and Kim L McBride

    Citation: BMC Medical Genomics 2014 7:56

    Content type: Research article

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  11. Allergic rhinitis is a common disease whose genetic basis is incompletely explained. We report an integrated genomic analysis of allergic rhinitis.

    Authors: Supinda Bunyavanich, Eric E Schadt, Blanca E Himes, Jessica Lasky-Su, Weiliang Qiu, Ross Lazarus, John P Ziniti, Ariella Cohain, Michael Linderman, Dara G Torgerson, Celeste S Eng, Maria Pino-Yanes, Badri Padhukasahasram, James J Yang, Rasika A Mathias, Terri H Beaty…

    Citation: BMC Medical Genomics 2014 7:48

    Content type: Research article

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  12. Genome-wide interrogation of DNA methylation (DNAm) in blood-derived leukocytes has become feasible with the advent of CpG genotyping arrays. In epithelial ovarian cancer (EOC), one report found substantial DN...

    Authors: Brooke L Fridley, Sebastian M Armasu, Mine S Cicek, Melissa C Larson, Chen Wang, Stacey J Winham, Kimberly R Kalli, Devin C Koestler, David N Rider, Viji Shridhar, Janet E Olson, Julie M Cunningham and Ellen L Goode

    Citation: BMC Medical Genomics 2014 7:21

    Content type: Research article

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  13. GWAS have consistently revealed that LDLR locus variability influences LDL-cholesterol in general population. Severe LDLR mutations are responsible for familial hypercholesterolemia (FH). However, most primary hy...

    Authors: Isabel De Castro-Orós, Javier Pérez-López, Rocio Mateo-Gallego, Soraya Rebollar, Marta Ledesma, Montserrat León, Montserrat Cofán, Jose A Casasnovas, Emilio Ros, Jose C Rodríguez-Rey, Fernando Civeira and Miguel Pocoví

    Citation: BMC Medical Genomics 2014 7:17

    Content type: Research article

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  14. The purpose of this manuscript is to describe the PhenX RISING network and the site experiences in the implementation of PhenX measures into ongoing population-based genomic studies.

    Authors: Catherine A McCarty, Wayne Huggins, Allison E Aiello, Robert M Bilder, Ahmad Hariri, Terry L Jernigan, Erik Newman, Dharambir K Sanghera, Timothy J Strauman, Yi Zeng, Erin M Ramos and Heather A Junkins

    Citation: BMC Medical Genomics 2014 7:16

    Content type: Research article

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  15. Childhood abuse is associated with increased adult disease risk, suggesting that processes acting over the long-term, such as epigenetic regulation of gene activity, may be involved. DNA methylation is a criti...

    Authors: Matthew Suderman, Nada Borghol, Jane J Pappas, Snehal M Pinto Pereira, Marcus Pembrey, Clyde Hertzman, Chris Power and Moshe Szyf

    Citation: BMC Medical Genomics 2014 7:13

    Content type: Research article

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  16. Variable responses to the Hepatitis B Virus (HBV) vaccine have recently been reported as strongly dependent on genetic causes. Yet, the details on such mechanisms of action are still unknown. In parallel, alte...

    Authors: Youtao Lu, Yi Cheng, Weili Yan and Christine Nardini

    Citation: BMC Medical Genomics 2014 7:12

    Content type: Research article

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  17. Uric acid (UA) is a complex phenotype influenced by both genetic and environmental factors as well as their interactions. Current genome-wide association studies (GWASs) have identified a variety of genetic de...

    Authors: Binyao Yang, Zengnan Mo, Chen Wu, Handong Yang, Xiaobo Yang, Yunfeng He, Lixuan Gui, Li Zhou, Huan Guo, Xiaomin Zhang, Jing Yuan, Xiayun Dai, Jun Li, Gaokun Qiu, Suli Huang, Qifei Deng…

    Citation: BMC Medical Genomics 2014 7:10

    Content type: Research article

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  18. Both genetic and epigenetic factors influence the development and progression of epithelial ovarian cancer (EOC). However, there is an incomplete understanding of the interrelationship between these factors an...

    Authors: Devin C Koestler, Prabhakar Chalise, Mine S Cicek, Julie M Cunningham, Sebastian Armasu, Melissa C Larson, Jeremy Chien, Matthew Block, Kimberly R Kalli, Thomas A Sellers, Brooke L Fridley and Ellen L Goode

    Citation: BMC Medical Genomics 2014 7:8

    Content type: Research article

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  19. The purpose of this paper is to describe the data collection efforts and validation of PhenX measures in the Personalized Medicine Research Project (PMRP) cohort.

    Authors: Catherine A McCarty, Richard Berg, Carla M Rottscheit, Carol J Waudby, Terrie Kitchner, Murray Brilliant and Marylyn D Ritchie

    Citation: BMC Medical Genomics 2014 7:3

    Content type: Research article

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  20. Non-small cell lung cancer (NSCLC), a leading cause of cancer deaths, represents a heterogeneous group of neoplasms, mostly comprising squamous cell carcinoma (SCC), adenocarcinoma (AC) and large-cell carcinom...

    Authors: Vladimir Lazar, Chen Suo, Cedric Orear, Joost van den Oord, Zsofia Balogh, Justine Guegan, Bastien Job, Guillaume Meurice, Hugues Ripoche, Stefano Calza, Johanna Hasmats, Joakim Lundeberg, Ludovic Lacroix, Philippe Vielh, Fabienne Dufour, Janne Lehtiö…

    Citation: BMC Medical Genomics 2013 6:53

    Content type: Research article

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  21. Massively parallel sequencing (MPS) has revolutionised biomedical research and offers enormous capacity for clinical application. We previously reported Hi-Plex, a streamlined highly-multiplexed PCR-MPS approa...

    Authors: Tú Nguyen-Dumont, Zhi L Teo, Bernard J Pope, Fleur Hammet, Maryam Mahmoodi, Helen Tsimiklis, Nelly Sabbaghian, Marc Tischkowitz, William D Foulkes, Graham G Giles, John L Hopper, Melissa C Southey and Daniel J Park

    Citation: BMC Medical Genomics 2013 6:48

    Content type: Research article

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  22. Obstructive sleep apnea (OSA) is associated with adverse and interdependent cognitive and cardiovascular consequences. Increasing evidence suggests that nitric oxide synthase (NOS) and endothelin family (EDN) gen...

    Authors: Siriporn Chatsuriyawong, David Gozal, Leila Kheirandish-Gozal, Rakesh Bhattacharjee, Ahamed A Khalyfa, Yang Wang, Wasana Sukhumsirichart and Abdelnaby Khalyfa

    Citation: BMC Medical Genomics 2013 6:29

    Content type: Research article

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  23. The collection of viable DNA samples is an essential element of any genetics research programme. Biological samples for DNA purification are now routinely collected in many studies with a variety of sampling m...

    Authors: David J Pulford, Michael Mosteller, J David Briley, Kelley W Johansson and Anita J Nelsen

    Citation: BMC Medical Genomics 2013 6:20

    Content type: Research article

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  24. Genotype-Driven Recruitment (GDR) is a research design that recruits research participants based on genotype rather than based on the presence or absence of a particular condition or clinical outcome. Analyses...

    Authors: Isabelle Budin-Ljøsne, Kaitlin J Soye, Anne Marie Tassé, Bartha Maria Knoppers and Jennifer R Harris

    Citation: BMC Medical Genomics 2013 6:19

    Content type: Debate

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  25. Metabolic syndrome (MetS) is an aberration associated with increased risk for cancer and inflammation. Adiponectin, an adipocyte-produced abundant protein hormone, has countering effect on the diabetogenic and...

    Authors: Yi Zhang, Jack W Kent Jr, Michael Olivier, Omar Ali, Diana Cerjak, Ulrich Broeckel, Reham M Abdou, Thomas D Dyer, Anthony Comuzzie, Joanne E Curran, Melanie A Carless, David L Rainwater, Harald H H Göring, John Blangero and Ahmed H Kissebah

    Citation: BMC Medical Genomics 2013 6:14

    Content type: Research article

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  26. Fatty acid-binding proteins (FABPs) play regulatory roles at the nexus of lipid metabolism and signaling. Dyslipidemia in clinical manifestation frequently co-occurs with obesity, insulin resistance and hypert...

    Authors: Yi Zhang, Jack W Kent, Adam Lee, Diana Cerjak, Omar Ali, Robert Diasio, Michael Olivier, John Blangero, Melanie A Carless and Ahmed H Kissebah

    Citation: BMC Medical Genomics 2013 6:9

    Content type: Research article

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  27. The SH2B1 gene (Src-homology 2B adaptor protein 1 gene) is a solid candidate gene for obesity. Large scale GWAS studies depicted markers in the vicinity of the gene; animal models suggest a potential relevance fo...

    Authors: Anna-Lena Volckmar, Florian Bolze, Ivonne Jarick, Nadja Knoll, André Scherag, Thomas Reinehr, Thomas Illig, Harald Grallert, Heinz-Erich Wichmann, Susanna Wiegand, Heike Biebermann, Heiko Krude, Pamela Fischer-Posovszky, Winfried Rief, Martin Wabitsch, Martin Klingenspor…

    Citation: BMC Medical Genomics 2012 5:65

    Content type: Research article

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  28. Next-generation DNA sequencing is opening new avenues for genetic association studies in common diseases that, like deep vein thrombosis (DVT), have a strong genetic predisposition still largely unexplained by...

    Authors: Luca A Lotta, Mark Wang, Jin Yu, Ida Martinelli, Fuli Yu, Serena M Passamonti, Dario Consonni, Emanuela Pappalardo, Marzia Menegatti, Steven E Scherer, Lora L Lewis, Humeira Akbar, Yuanqing Wu, Matthew N Bainbridge, Donna M Muzny, Pier M Mannucci…

    Citation: BMC Medical Genomics 2012 5:7

    Content type: Research article

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  29. Glioblastoma multiforme (GBM) tends to occur between the ages of 45 and 70. This relatively early onset and its poor prognosis make the impact of GBM on public health far greater than would be suggested by its...

    Authors: Tun-Hsiang Yang, Mark Kon, Jui-Hung Hung and Charles DeLisi

    Citation: BMC Medical Genomics 2011 4:63

    Content type: Research article

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  30. Hepatocellular carcinoma (HCC) is a worldwide malignant liver tumor with high incidence in China. Subchromosomal amplifications and deletions accounted for major genomic alterations occurred in HCC. Digital ka...

    Authors: Hui Dong, Hongyi Zhang, Jianping Liang, Huadong Yan, Yangyi Chen, Yan Shen, Yalin Kong, Shengyue Wang, Guoping Zhao and Weirong Jin

    Citation: BMC Medical Genomics 2011 4:60

    Content type: Research article

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  31. Recent genome-wide association (GWA) analyses have identified common single nucleotide polymorphisms (SNPs) that are associated with obesity. However, the reported genetic variation in obesity explains only a ...

    Authors: Hong Jiao, Peter Arner, Johan Hoffstedt, David Brodin, Beatrice Dubern, Sébastien Czernichow, Ferdinand van't Hooft, Tomas Axelsson, Oluf Pedersen, Torben Hansen, Thorkild IA Sørensen, Johannes Hebebrand, Juha Kere, Karin Dahlman-Wright, Anders Hamsten, Karine Clement…

    Citation: BMC Medical Genomics 2011 4:51

    Content type: Research article

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  32. We performed a genome-wide scan of 27,578 CpG loci covering 14,475 genes to identify differentially methylated loci (DML) in colorectal carcinoma (CRC).

    Authors: Muhammad G Kibriya, Maruf Raza, Farzana Jasmine, Shantanu Roy, Rachelle Paul-Brutus, Ronald Rahaman, Charlotte Dodsworth, Muhammad Rakibuz-Zaman, Mohammed Kamal and Habibul Ahsan

    Citation: BMC Medical Genomics 2011 4:50

    Content type: Research article

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  33. Cancer is a disease of genome alterations that arise through the acquisition of multiple somatic DNA sequence mutations. Some of these mutations can be critical for the development of a tumor and can be useful...

    Authors: Jan Küntzer, Daniela Maisel, Hans-Peter Lenhof, Stefan Klostermann and Helmut Burtscher

    Citation: BMC Medical Genomics 2011 4:43

    Content type: Database

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  34. Diabetic retinopathy (DR) is a leading cause of blindness in working age adults. Approximately 95% of patients with Type 1 diabetes develop some degree of retinopathy within 25 years of diagnosis despite norma...

    Authors: Georgina V Bixler, Heather D VanGuilder, Robert M Brucklacher, Scot R Kimball, Sarah K Bronson and Willard M Freeman

    Citation: BMC Medical Genomics 2011 4:40

    Content type: Research article

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  35. The gene CHEK2 encodes a checkpoint kinase playing a key role in the DNA damage pathway. Though CHEK2 has been identified as an intermediate breast cancer susceptibility gene, only a small proportion of high-risk...

    Authors: Tú Nguyen-Dumont, Lars P Jordheim, Jocelyne Michelon, Nathalie Forey, Sandrine McKay-Chopin, Olga Sinilnikova, Florence Le Calvez-Kelm, Melissa C Southey, Sean V Tavtigian and Fabienne Lesueur

    Citation: BMC Medical Genomics 2011 4:39

    Content type: Research article

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  36. Uric acid is the primary byproduct of purine metabolism. Hyperuricemia is associated with body mass index (BMI), sex, and multiple complex diseases including gout, hypertension (HTN), renal disease, and type 2 di...

    Authors: Bashira A Charles, Daniel Shriner, Ayo Doumatey, Guanjie Chen, Jie Zhou, Hanxia Huang, Alan Herbert, Norman P Gerry, Michael F Christman, Adebowale Adeyemo and Charles N Rotimi

    Citation: BMC Medical Genomics 2011 4:17

    Content type: Research article

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  37. Infection with H. pylori is important in the etiology of gastric cancer. Gastric cancer is infrequent in Africa, despite high frequencies of H. pylori infection, referred to as the African enigma. Variation in en...

    Authors: Tineke E Buffart, Melanie Louw, Nicole CT van Grieken, Marianne Tijssen, Beatriz Carvalho, Bauke Ylstra, Heike Grabsch, Chris JJ Mulder, Cornelis JH van de Velde, Schalk W van der Merwe and Gerrit A Meijer

    Citation: BMC Medical Genomics 2011 4:7

    Content type: Research article

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  38. Aortic root diameter is a clinically relevant trait due to its known relationship with the pathogenesis of aortic regurgitation and risk for aortic dissection. African Americans are an understudied population ...

    Authors: Nathan E Wineinger, Amit Patki, Kristin J Meyers, Ulrich Broeckel, Charles C Gu, DC Rao, Richard B Devereux, Donna K Arnett and Hemant K Tiwari

    Citation: BMC Medical Genomics 2011 4:4

    Content type: Research article

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  39. The onset of birth in humans, like other apes, differs from non-primate mammals in its endocrine physiology. We hypothesize that higher primate-specific gene evolution may lead to these differences and target ...

    Authors: Jevon Plunkett, Scott Doniger, Thomas Morgan, Ritva Haataja, Mikko Hallman, Hilkka Puttonen, Ramkumar Menon, Edward Kuczynski, Errol Norwitz, Victoria Snegovskikh, Aarno Palotie, Leena Peltonen, Vineta Fellman, Emily A DeFranco, Bimal P Chaudhari, John Oates…

    Citation: BMC Medical Genomics 2010 3:62

    Content type: Research article

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  40. Obesity results from an imbalance between food intake and energy expenditure, which leads to an excess of adipose tissue. The excess of adipose tissue and adipocyte dysfunction associated with obesity are link...

    Authors: Sara Rodríguez-Acebes, Nuria Palacios, José I Botella-Carretero, Nuria Olea, Lorena Crespo, Roberto Peromingo, Diego Gómez-Coronado, Miguel A Lasunción, Clotilde Vázquez and Javier Martínez-Botas

    Citation: BMC Medical Genomics 2010 3:61

    Content type: Research article

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  41. Disease-specific genetic information has been increasing at rapid rates as a consequence of recent improvements and massive cost reductions in sequencing technologies. Numerous systems designed to capture and ...

    Authors: Dennis P Wall, Rimma Pivovarov, Mark Tong, Jae-Yoon Jung, Vincent A Fusaro, Todd F DeLuca and Peter J Tonellato

    Citation: BMC Medical Genomics 2010 3:50

    Content type: Software

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