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The impact of genomics on precision public health

Guest editors: Muin Khoury and Kathryn Holt

New Content Item (1)Genome Medicine is pleased to present a special issue on ‘The impact of genomics on precision public health', guest edited by Dr Muin Khoury from the US Centers for Disease Control and Prevention and by Dr Kathryn Holt from Monash University and the London School of Hygiene and Tropical Medicine. The emergence of pathogen and human genome sequencing in clinical and public health practice provides opportunities and challenges for using genomics to improve population health. Human and pathogen genomics are at the leading edge of the application of new technologies to public health practice. Research efforts in this area are contributing to a new era of 'precision public health', an emerging multidisciplinary field that uses genomics, other big data and artificial intelligence to predict risk and outcomes, and to improve population health. This special issue aims to capture recent insights and advances in our understanding of how to use pathogen and human genomics in public health approaches to prevent and control diseases, as well as to enhance health promotion and reduce health disparities.  

This collection of articles has not been sponsored and articles will undergo the journal’s standard peer-review process. The Guest Editors declare that they have no competing interests. The Guest Editors serve an advisory role to guide the scope of the special issue and commissioned content; final editorial decisions lie with the Editor.

  1. Multidrug-resistant Mycobacterium tuberculosis (Mtb) is a significant global public health threat. Genotypic resistance prediction from Mtb DNA sequences offers an alternative to laboratory-based drug-susceptibil...

    Authors: Matthias I. Gröschel, Martin Owens, Luca Freschi, Roger Vargas Jr, Maximilian G. Marin, Jody Phelan, Zamin Iqbal, Avika Dixit and Maha R. Farhat

    Citation: Genome Medicine 2021 13:138

    Content type: Software

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  2. Pathogen whole genome sequencing (WGS) is being incorporated into public health surveillance and disease control systems worldwide and has the potential to make significant contributions to infectious disease ...

    Authors: Angeline S. Ferdinand, Margaret Kelaher, Courtney R. Lane, Anders Gonçalves da Silva, Norelle L. Sherry, Susan A. Ballard, Patiyan Andersson, Tuyet Hoang, Justin T. Denholm, Marion Easton, Benjamin P. Howden and Deborah A. Williamson

    Citation: Genome Medicine 2021 13:121

    Content type: Research

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  3. Precision public health is a relatively new field that integrates components of precision medicine, such as human genomics research, with public health concepts to help improve population health. Despite inter...

    Authors: Megan C. Roberts, Alison E. Fohner, Latrice Landry, Dana Lee Olstad, Amelia K. Smit, Erin Turbitt and Caitlin G. Allen

    Citation: Genome Medicine 2021 13:97

    Content type: Opinion

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  4. DNA methylation (DNAm) is associated with gene regulation and estimated glomerular filtration rate (eGFR), a measure of kidney function. Decreased eGFR is more common among US Hispanics and African Americans. ...

    Authors: Charles E. Breeze, Anna Batorsky, Mi Kyeong Lee, Mindy D. Szeto, Xiaoguang Xu, Daniel L. McCartney, Rong Jiang, Amit Patki, Holly J. Kramer, James M. Eales, Laura Raffield, Leslie Lange, Ethan Lange, Peter Durda, Yongmei Liu, Russ P. Tracy…

    Citation: Genome Medicine 2021 13:74

    Content type: Research

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  5. Antimicrobial-resistant (AMR) Neisseria gonorrhoeae is an urgent threat to public health, as strains resistant to at least one of the two last-line antibiotics used in empiric therapy of gonorrhoea, ceftriaxone a...

    Authors: Leonor Sánchez-Busó, Corin A. Yeats, Benjamin Taylor, Richard J. Goater, Anthony Underwood, Khalil Abudahab, Silvia Argimón, Kevin C. Ma, Tatum D. Mortimer, Daniel Golparian, Michelle J. Cole, Yonatan H. Grad, Irene Martin, Brian H. Raphael, William M. Shafer, Katy Town…

    Citation: Genome Medicine 2021 13:61

    Content type: Research

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  6. Newborn screening aims to identify individual patients who could benefit from early management, treatment, and/or surveillance practices. As sequencing technologies have progressed and we move into the era of ...

    Authors: Daniela M. DeCristo, Laura V. Milko, Julianne M. O’Daniel, Ann Katherine M. Foreman, Lonna F. Mollison, Bradford C. Powell, Cynthia M. Powell and Jonathan S. Berg

    Citation: Genome Medicine 2021 13:50

    Content type: Research

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  7. Childhood obesity is reported to be associated with the risk of many diseases in adulthood. However, observational studies cannot fully account for confounding factors. We aimed to systematically assess the ca...

    Authors: Shan-Shan Dong, Kun Zhang, Yan Guo, Jing-Miao Ding, Yu Rong, Jun-Cheng Feng, Shi Yao, Ruo-Han Hao, Feng Jiang, Jia-Bin Chen, Hao Wu, Xiao-Feng Chen and Tie-Lin Yang

    Citation: Genome Medicine 2021 13:48

    Content type: Research

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  8. We report the findings from 4437 individuals (3219 patients and 1218 relatives) who have been analyzed by whole genome sequencing (WGS) at the Genomic Medicine Center Karolinska-Rare Diseases (GMCK-RD) since m...

    Authors: Henrik Stranneheim, Kristina Lagerstedt-Robinson, Måns Magnusson, Malin Kvarnung, Daniel Nilsson, Nicole Lesko, Martin Engvall, Britt-Marie Anderlid, Henrik Arnell, Carolina Backman Johansson, Michela Barbaro, Erik Björck, Helene Bruhn, Jesper Eisfeldt, Christoph Freyer, Giedre Grigelioniene…

    Citation: Genome Medicine 2021 13:40

    Content type: Research

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  9. Coat protein complex 1 (COPI) is integral in the sorting and retrograde trafficking of proteins and lipids from the Golgi apparatus to the endoplasmic reticulum (ER). In recent years, coat proteins have been i...

    Authors: William L. Macken, Annie Godwin, Gabrielle Wheway, Karen Stals, Liliya Nazlamova, Sian Ellard, Ahmed Alfares, Taghrid Aloraini, Lamia AlSubaie, Majid Alfadhel, Sulaiman Alajaji, Htoo A. Wai, Jay Self, Andrew G. L. Douglas, Alexander P. Kao, Matthew Guille…

    Citation: Genome Medicine 2021 13:34

    Content type: Research

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  10. Since early February 2021, the causative agent of COVID-19, SARS-CoV-2, has infected over 104 million people with more than 2 million deaths according to official reports. The key to understanding the biology ...

    Authors: Yanqun Wang, Daxi Wang, Lu Zhang, Wanying Sun, Zhaoyong Zhang, Weijun Chen, Airu Zhu, Yongbo Huang, Fei Xiao, Jinxiu Yao, Mian Gan, Fang Li, Ling Luo, Xiaofang Huang, Yanjun Zhang, Sook-san Wong…

    Citation: Genome Medicine 2021 13:30

    Content type: Research

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  11. The clinical utility of personal genomic information in identifying individuals at increased risks for dyslipidemia and cardiovascular diseases remains unclear.

    Authors: Claudia H. T. Tam, Cadmon K. P. Lim, Andrea O. Y. Luk, Alex C. W. Ng, Heung-man Lee, Guozhi Jiang, Eric S. H. Lau, Baoqi Fan, Raymond Wan, Alice P. S. Kong, Wing-hung Tam, Risa Ozaki, Elaine Y. K. Chow, Ka-fai Lee, Shing-chung Siu, Grace Hui…

    Citation: Genome Medicine 2021 13:29

    Content type: Research

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  12. We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or > 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic...

    Authors: Dave J. Baker, Alp Aydin, Thanh Le-Viet, Gemma L. Kay, Steven Rudder, Leonardo de Oliveira Martins, Ana P. Tedim, Anastasia Kolyva, Maria Diaz, Nabil-Fareed Alikhan, Lizzie Meadows, Andrew Bell, Ana Victoria Gutierrez, Alexander J. Trotter, Nicholas M. Thomson, Rachel Gilroy…

    Citation: Genome Medicine 2021 13:21

    Content type: Method

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  13. Population-based genomic screening has the predicted ability to reduce morbidity and mortality associated with medically actionable conditions. However, much research is needed to develop standards for genomic...

    Authors: Noura S. Abul-Husn, Emily R. Soper, Giovanna T. Braganza, Jessica E. Rodriguez, Natasha Zeid, Sinead Cullina, Dean Bobo, Arden Moscati, Amanda Merkelson, Ruth J. F. Loos, Judy H. Cho, Gillian M. Belbin, Sabrina A. Suckiel and Eimear E. Kenny

    Citation: Genome Medicine 2021 13:17

    Content type: Research

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  14. Several polygenic risk scores (PRS) have been developed for cardiovascular risk prediction, but the additive value of including PRS together with conventional risk factors for risk prediction is questionable. ...

    Authors: Monica Isgut, Jimeng Sun, Arshed A. Quyyumi and Greg Gibson

    Citation: Genome Medicine 2021 13:13

    Content type: Research

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  15. Enterococcus faecium is a commensal of the gastrointestinal tract of animals and humans but also a causative agent of hospital-acquired infections. Resistance against glycopeptides and to vancomycin has motivated...

    Authors: Sergio Arredondo-Alonso, Janetta Top, Jukka Corander, Rob J. L. Willems and Anita C. Schürch

    Citation: Genome Medicine 2021 13:9

    Content type: Research

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  16. Shigella is a major diarrheal pathogen for which there is presently no vaccine. Whole genome sequencing provides the ability to predict and derive novel antigens for use as vaccines. Here, we aimed to identify no...

    Authors: Ruklanthi de Alwis, Li Liang, Omid Taghavian, Emma Werner, Hao Chung The, Trang Nguyen Hoang Thu, Vu Thuy Duong, D. Huw Davies, Philip L. Felgner and Stephen Baker

    Citation: Genome Medicine 2021 13:8

    Content type: Research

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  17. The SARS-CoV-2 pandemic is currently leading to increasing numbers of COVID-19 patients all over the world. Clinical presentations range from asymptomatic, mild respiratory tract infection, to severe cases wit...

    Authors: Anna C. Aschenbrenner, Maria Mouktaroudi, Benjamin Krämer, Marie Oestreich, Nikolaos Antonakos, Melanie Nuesch-Germano, Konstantina Gkizeli, Lorenzo Bonaguro, Nico Reusch, Kevin Baßler, Maria Saridaki, Rainer Knoll, Tal Pecht, Theodore S. Kapellos, Sarandia Doulou, Charlotte Kröger…

    Citation: Genome Medicine 2021 13:7

    Content type: Research

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  18. Clinical laboratory (lab) tests are used in clinical practice to diagnose, treat, and monitor disease conditions. Test results are stored in electronic health records (EHRs), and a growing number of EHRs are l...

    Authors: Jessica K. Dennis, Julia M. Sealock, Peter Straub, Younga H. Lee, Donald Hucks, Ky’Era Actkins, Annika Faucon, Yen-Chen Anne Feng, Tian Ge, Slavina B. Goleva, Maria Niarchou, Kritika Singh, Theodore Morley, Jordan W. Smoller, Douglas M. Ruderfer, Jonathan D. Mosley…

    Citation: Genome Medicine 2021 13:6

    Content type: Research

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  19. Family history has traditionally been an essential part of clinical care to assess health risks. However, declining sequencing costs have precipitated a shift towards genomics-first approaches in population sc...

    Authors: Yasmin Bylstra, Weng Khong Lim, Sylvia Kam, Koei Wan Tham, R. Ryanne Wu, Jing Xian Teo, Sonia Davila, Jyn Ling Kuan, Sock Hoai Chan, Nicolas Bertin, Cheng Xi Yang, Steve Rozen, Bin Tean Teh, Khung Keong Yeo, Stuart Alexander Cook, Saumya Shekhar Jamuar…

    Citation: Genome Medicine 2021 13:3

    Content type: Research

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    The Correction to this article has been published in Genome Medicine 2021 13:109

  20. Tuberculosis, caused by bacteria in the Mycobacterium tuberculosis complex (MTBC), is a major global public health burden. Strain-specific genomic diversity in the known lineages of MTBC is an important factor in...

    Authors: Gary Napier, Susana Campino, Yared Merid, Markos Abebe, Yimtubezinash Woldeamanuel, Abraham Aseffa, Martin L. Hibberd, Jody Phelan and Taane G. Clark

    Citation: Genome Medicine 2020 12:114

    Content type: Research

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  21. DNA methylation has been shown to be associated with adiposity in adulthood. However, whether similar DNA methylation patterns are associated with childhood and adolescent body mass index (BMI) is largely unkn...

    Authors: Florianne O. L. Vehmeijer, Leanne K. Küpers, Gemma C. Sharp, Lucas A. Salas, Samantha Lent, Dereje D. Jima, Gwen Tindula, Sarah Reese, Cancan Qi, Olena Gruzieva, Christian Page, Faisal I. Rezwan, Philip E. Melton, Ellen Nohr, Geòrgia Escaramís, Peter Rzehak…

    Citation: Genome Medicine 2020 12:105

    Content type: Research

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  22. Multidrug-resistant (MDR) Mycobacterium tuberculosis complex strains not detected by commercial molecular drug susceptibility testing (mDST) assays due to the RpoB I491F resistance mutation are threatening the co...

    Authors: Patrick Beckert, Elisabeth Sanchez-Padilla, Matthias Merker, Viola Dreyer, Thomas A. Kohl, Christian Utpatel, Claudio U. Köser, Ivan Barilar, Nazir Ismail, Shaheed Vally Omar, Marisa Klopper, Robin M. Warren, Harald Hoffmann, Gugu Maphalala, Elisa Ardizzoni, Bouke C. de Jong…

    Citation: Genome Medicine 2020 12:104

    Content type: Research

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  23. Polygenic risk scores (PRSs) are a summarization of an individual’s genetic risk for a disease or trait. These scores are being generated in research and commercial settings to study how they may be used to gu...

    Authors: Shang-Fu Chen, Raquel Dias, Doug Evans, Elias L. Salfati, Shuchen Liu, Nathan E. Wineinger and Ali Torkamani

    Citation: Genome Medicine 2020 12:100

    Content type: Research

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  24. Whole-genome sequencing (WGS) is increasingly used to map the spread of bacterial and viral pathogens in nosocomial settings. A limiting factor for more widespread adoption of WGS for hospital infection preven...

    Authors: Ana Berbel Caban, Theodore R. Pak, Ajay Obla, Amy C. Dupper, Kieran I. Chacko, Lindsey Fox, Alexandra Mills, Brianne Ciferri, Irina Oussenko, Colleen Beckford, Marilyn Chung, Robert Sebra, Melissa Smith, Sarah Conolly, Gopi Patel, Andrew Kasarskis…

    Citation: Genome Medicine 2020 12:96

    Content type: Research

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  25. Genomic studies of patients with COVID-19, or exposed to it, are underway to delineate host factors associated with variability in susceptibility, infectivity, and disease severity. Here, we highlight the ethi...

    Authors: Gail Geller, Priya Duggal, Chloe L. Thio, Debra Mathews, Jeffrey P. Kahn, Lisa L. Maragakis and Brian T. Garibaldi

    Citation: Genome Medicine 2020 12:95

    Content type: Comment

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  26. Humans and viruses have co-evolved for millennia resulting in a complex host genetic architecture. Understanding the genetic mechanisms of immune response to viral infection provides insight into disease etiol...

    Authors: Linda Kachuri, Stephen S. Francis, Maike L. Morrison, George A. Wendt, Yohan Bossé, Taylor B. Cavazos, Sara R. Rashkin, Elad Ziv and John S. Witte

    Citation: Genome Medicine 2020 12:93

    Content type: Research

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