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  1. Drawing genotype-to-phenotype maps in tumors is of paramount importance for understanding tumor heterogeneity. Assignment of single cells to their tumor clones of origin can be approached by matching the genot...

    Authors: Shadi Darvish Shafighi, Szymon M. Kiełbasa, Julieta Sepúlveda-Yáñez, Ramin Monajemi, Davy Cats, Hailiang Mei, Roberta Menafra, Susan Kloet, Hendrik Veelken, Cornelis A.M. van Bergen and Ewa Szczurek
    Citation: Genome Medicine 2021 13:45
  2. 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
  3. Prognosis evaluation of advanced breast cancer and therapeutic strategy are mostly based on clinical features of advanced disease and molecular profiling of the primary tumor. Very few studies have evaluated t...

    Authors: Céline Callens, Keltouma Driouch, Anaïs Boulai, Zakia Tariq, Aurélie Comte, Frédérique Berger, Lisa Belin, Ivan Bièche, Vincent Servois, Patricia Legoix, Virginie Bernard, Sylvain Baulande, Walid Chemlali, François-Clément Bidard, Virginie Fourchotte, Anne Vincent- Salomon…
    Citation: Genome Medicine 2021 13:44
  4. ChAdOx1 nCoV-19 is a recombinant adenovirus vaccine against SARS-CoV-2 that has passed phase III clinical trials and is now in use across the globe. Although replication-defective in normal cells, 28 kbp of ad...

    Authors: Abdulaziz Almuqrin, Andrew D. Davidson, Maia Kavanagh Williamson, Philip A. Lewis, Kate J. Heesom, Susan Morris, Sarah C. Gilbert and David A. Matthews
    Citation: Genome Medicine 2021 13:43
  5. Contemporary deep learning approaches show cutting-edge performance in a variety of complex prediction tasks. Nonetheless, the application of deep learning in healthcare remains limited since deep learning met...

    Authors: Hryhorii Chereda, Annalen Bleckmann, Kerstin Menck, Júlia Perera-Bel, Philip Stegmaier, Florian Auer, Frank Kramer, Andreas Leha and Tim Beißbarth
    Citation: Genome Medicine 2021 13:42
  6. Macular telangiectasia type 2 (MacTel) is a rare, heritable and largely untreatable retinal disorder, often comorbid with diabetes. Genetic risk loci subtend retinal vascular calibre and glycine/serine/threoni...

    Authors: Roberto Bonelli, Brendan R. E. Ansell, Luca Lotta, Thomas Scerri, Traci E. Clemons, Irene Leung, Tunde Peto, Alan C. Bird, Ferenc B. Sallo, Claudia Langenberg and Melanie Bahlo
    Citation: Genome Medicine 2021 13:39
  7. Whether elevated blood pressure (BP) is a modifiable risk factor for atrial fibrillation (AF) is not established. We tested (1) whether the association between BP and risk of AF is causal, (2) whether it varie...

    Authors: Milad Nazarzadeh, Ana-Catarina Pinho-Gomes, Zeinab Bidel, Dexter Canoy, Abbas Dehghan, Karl Smith Byrne, Derrick A. Bennett, George Davey Smith and Kazem Rahimi
    Citation: Genome Medicine 2021 13:38
  8. Type 2 diabetes (T2D), a multifactorial disease influenced by host genetics and environmental factors, is the most common endocrine disease. Several studies have shown that the gut microbiota as a close-up env...

    Authors: Camila Alvarez-Silva, Alireza Kashani, Tue Haldor Hansen, Nishal Kumar Pinna, Ranjit Mohan Anjana, Anirban Dutta, Shruti Saxena, Julie Støy, Ulla Kampmann, Trine Nielsen, Torben Jørgensen, Visvanathan Gnanaprakash, Rameshkumar Gnanavadivel, Aswath Sukumaran, Coimbatore Subramanian Shanthi Rani, Kristine Færch…
    Citation: Genome Medicine 2021 13:37
  9. Recent studies have indicated an association of gut microbiota and microbial metabolites with type 2 diabetes mellitus (T2D). However, large-scale investigation of the gut microbiota of “prediabetic” (PD) subj...

    Authors: Nishal Kumar Pinna, Ranjit Mohan Anjana, Shruti Saxena, Anirban Dutta, Visvanathan Gnanaprakash, Gnanavadivel Rameshkumar, Sukumaran Aswath, Srividhya Raghavan, Coimbatore Subramanian Shanthi Rani, Venkatesan Radha, Muthuswamy Balasubramanyam, Archana Pant, Trine Nielsen, Torben Jørgensen, Kristine Færch, Alireza Kashani…
    Citation: Genome Medicine 2021 13:36
  10. Immunoglobulin G4-related disease (IgG4-RD) and systemic sclerosis (SSc) are rare autoimmune diseases characterized by the presence of CD4+ cytotoxic T cells in the blood as well as inflammation and fibrosis i...

    Authors: Damian R. Plichta, Juhi Somani, Matthieu Pichaud, Zachary S. Wallace, Ana D. Fernandes, Cory A. Perugino, Harri Lähdesmäki, John H. Stone, Hera Vlamakis, Daniel C. Chung, Dinesh Khanna, Shiv Pillai and Ramnik J. Xavier
    Citation: Genome Medicine 2021 13:35
  11. 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
  12. Clinical-grade whole-genome sequencing (cWGS) has the potential to become the standard of care within the clinic because of its breadth of coverage and lack of bias towards certain regions of the genome. Color...

    Authors: Agata Stodolna, Miao He, Mahesh Vasipalli, Zoya Kingsbury, Jennifer Becq, Joanne D. Stockton, Mark P. Dilworth, Jonathan James, Toju Sillo, Daniel Blakeway, Stephen T. Ward, Tariq Ismail, Mark T. Ross and Andrew D. Beggs
    Citation: Genome Medicine 2021 13:33
  13. Whole genome sequencing (WGS) has the potential to outperform clinical microarrays for the detection of structural variants (SV) including copy number variants (CNVs), but has been challenged by high false pos...

    Authors: Andre E. Minoche, Ben Lundie, Greg B. Peters, Thomas Ohnesorg, Mark Pinese, David M. Thomas, Andreas Zankl, Tony Roscioli, Nicole Schonrock, Sarah Kummerfeld, Leslie Burnett, Marcel E. Dinger and Mark J. Cowley
    Citation: Genome Medicine 2021 13:32
  14. Splicing of genomic exons into mRNAs is a critical prerequisite for the accurate synthesis of human proteins. Genetic variants impacting splicing underlie a substantial proportion of genetic disease, but are c...

    Authors: Philipp Rentzsch, Max Schubach, Jay Shendure and Martin Kircher
    Citation: Genome Medicine 2021 13:31
  15. 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
  16. 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
  17. Once antibiotic-resistant bacteria become established within the gut microbiota, they can cause infections in the host and be transmitted to other people and the environment. Currently, there are no effective ...

    Authors: Amy Langdon, Drew J. Schwartz, Christopher Bulow, Xiaoqing Sun, Tiffany Hink, Kimberly A. Reske, Courtney Jones, Carey-Ann D. Burnham, Erik R. Dubberke and Gautam Dantas
    Citation: Genome Medicine 2021 13:28
  18. The incidence of colorectal cancer (CRC) is increasing in developing countries, yet limited research on the CRC- associated microbiota has been conducted in these areas, in part due to scarce resources, facili...

    Authors: Caroline Young, Henry M. Wood, Ramakrishnan Ayloor Seshadri, Pham Van Nang, Carlos Vaccaro, Luis Contreras Melendez, Mayilvahanan Bose, Mai Van Doi, Tamara Alejandra Piñero, Camilo Tapia Valladares, Julieta Arguero, Alba Fuentes Balaguer, Kelsey N. Thompson, Yan Yan, Curtis Huttenhower and Philip Quirke
    Citation: Genome Medicine 2021 13:27
  19. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Cheng-Cao Sun, Wei Zhu, Shu-Jun Li, Wei Hu, Jian Zhang, Yue Zhuo, Han Zhang, Juan Wang, Yu Zhang, Shao-Xin Huang, Qi-Qiang He and De-Jia Li
    Citation: Genome Medicine 2021 13:25

    The original article was published in Genome Medicine 2020 12:77

  20. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Tonći Šuštić, Sake van Wageningen, Evert Bosdriesz, Robert J. D. Reid, John Dittmar, Cor Lieftink, Roderick L. Beijersbergen, Lodewyk F. A. Wessels, Rodney Rothstein and René Bernards
    Citation: Genome Medicine 2021 13:24

    The original article was published in Genome Medicine 2018 10:90

  21. 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
  22. tRNA-derived small RNAs (tDRs), which are widely distributed in human tissues including blood and urine, play an important role in the progression of cancer. However, the expression of tDRs in colorectal cance...

    Authors: Yingmin Wu, Xiangling Yang, Guanmin Jiang, Haisheng Zhang, Lichen Ge, Feng Chen, Jiexin Li, Huanliang Liu and Hongsheng Wang
    Citation: Genome Medicine 2021 13:20
  23. Basal cell carcinoma (BCC) of the skin is the most common form of human cancer, with more than 90% of tumours presenting with clear genetic activation of the Hedgehog pathway. However, polygenic risk factors a...

    Authors: Christelle Adolphe, Angli Xue, Atefeh Taherian Fard, Laura A. Genovesi, Jian Yang and Brandon J. Wainwright
    Citation: Genome Medicine 2021 13:19
  24. Noninvasive prenatal testing (NIPT) of recessive monogenic diseases depends heavily on knowing the correct parental haplotypes. However, the currently used family-based haplotyping method requires pedigrees, a...

    Authors: Chao Chen, Ru Li, Jun Sun, Yaping Zhu, Lu Jiang, Jian Li, Fang Fu, Junhui Wan, Fengyu Guo, Xiaoying An, Yaoshen Wang, Linlin Fan, Yan Sun, Xiaosen Guo, Sumin Zhao, Wanyang Wang…
    Citation: Genome Medicine 2021 13:18
  25. 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
  26. Accurately quantifying the risk of osteoporotic fracture is important for directing appropriate clinical interventions. While skeletal measures such as heel quantitative speed of sound (SOS) and dual-energy X-...

    Authors: Tianyuan Lu, Vincenzo Forgetta, Julyan Keller-Baruch, Maria Nethander, Derrick Bennett, Marie Forest, Sahir Bhatnagar, Robin G. Walters, Kuang Lin, Zhengming Chen, Liming Li, Magnus Karlsson, Dan Mellström, Eric Orwoll, Eugene V. McCloskey, John A. Kanis…
    Citation: Genome Medicine 2021 13:16
  27. Pancreatic cancer (PC) is a complex disease in which both non-genetic and genetic factors interplay. To date, 40 GWAS hits have been associated with PC risk in individuals of European descent, explaining 4.1% ...

    Authors: Evangelina López de Maturana, Juan Antonio Rodríguez, Lola Alonso, Oscar Lao, Esther Molina-Montes, Isabel Adoración Martín-Antoniano, Paulina Gómez-Rubio, Rita Lawlor, Alfredo Carrato, Manuel Hidalgo, Mar Iglesias, Xavier Molero, Matthias Löhr, Christopher Michalski, José Perea, Michael O’Rorke…
    Citation: Genome Medicine 2021 13:15
  28. Identifying the complete repertoire of genes that drive cancer in individual patients is crucial for precision oncology. Most established methods identify driver genes that are recurrently altered across patie...

    Authors: Joel Nulsen, Hrvoje Misetic, Christopher Yau and Francesca D. Ciccarelli
    Citation: Genome Medicine 2021 13:12
  29. 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
  30. Gastric cancer (GC) is a heterogenous disease consisted of several subtypes with distinct molecular traits. The clinical implication of molecular classification has been limited especially in association with ...

    Authors: Seung Tae Kim, Jason K. Sa, Sung Yong Oh, Kyung Kim, Jung Yong Hong, Won Ki Kang, Kyoung-Mee Kim and Jeeyun Lee
    Citation: Genome Medicine 2021 13:11
  31. Personalised dietary modulation of the gut microbiota may be key to disease management. Current investigations provide a broad understanding of the impact of diet on the composition and activity of the gut mic...

    Authors: Emily R. Leeming, Panayiotis Louca, Rachel Gibson, Cristina Menni, Tim D. Spector and Caroline I. Le Roy
    Citation: Genome Medicine 2021 13:10
  32. 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
  33. 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
  34. 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
  35. 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
  36. Ebola virus disease (EVD) is an often-fatal infection where the effectiveness of medical countermeasures is uncertain. During the West African outbreak (2013–2016), several patients were treated with different...

    Authors: Andrew Bosworth, Natasha Y. Rickett, Xiaofeng Dong, Lisa F. P. Ng, Isabel García-Dorival, David A. Matthews, Tom Fletcher, Michael Jacobs, Emma C. Thomson, Miles W. Carroll and Julian A. Hiscox
    Citation: Genome Medicine 2021 13:5
  37. During COVID-19, diagnostic serological tools and vaccines have been developed. To inform control activities in a post-vaccine surveillance setting, we have developed an online “immuno-analytics” resource that...

    Authors: Daniel Ward, Matthew Higgins, Jody E. Phelan, Martin L. Hibberd, Susana Campino and Taane G. Clark
    Citation: Genome Medicine 2021 13:4
  38. 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

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

  39. The apolipoprotein E (APOE) ε4 allele is the strongest genetic risk factor for late onset Alzheimer’s disease, whilst the ε2 allele confers protection. Previous studies report differential DNA methylation of APOE

    Authors: Rosie M. Walker, Kadi Vaher, Mairead L. Bermingham, Stewart W. Morris, Andrew D. Bretherick, Yanni Zeng, Konrad Rawlik, Carmen Amador, Archie Campbell, Chris S. Haley, Caroline Hayward, David J. Porteous, Andrew M. McIntosh, Riccardo E. Marioni and Kathryn L. Evans
    Citation: Genome Medicine 2021 13:1
  40. The identification of genetic variation that directly impacts infection susceptibility to SARS-CoV-2 and disease severity of COVID-19 is an important step towards risk stratification, personalized treatment pl...

    Authors: Yu-Chung Lin, Jennifer D. Brooks, Shelley B. Bull, France Gagnon, Celia M. T. Greenwood, Rayjean J. Hung, Jerald Lawless, Andrew D. Paterson, Lei Sun and Lisa J. Strug
    Citation: Genome Medicine 2020 12:115
  41. 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
  42. Antibiotic-resistant Klebsiella pneumoniae are a major cause of hospital- and community-acquired infections, including sepsis, liver abscess, and pneumonia, driven mainly by the emergence of successful high-risk ...

    Authors: Stefan E. Heiden, Nils-Olaf Hübner, Jürgen A. Bohnert, Claus-Dieter Heidecke, Axel Kramer, Veronika Balau, Wolfgang Gierer, Stephan Schaefer, Tim Eckmanns, Sören Gatermann, Elias Eger, Sebastian Guenther, Karsten Becker and Katharina Schaufler
    Citation: Genome Medicine 2020 12:113
  43. The recent emergence and dissemination of high-level mobile tigecycline resistance Tet(X) challenge the clinical effectiveness of tigecycline, one of the last-resort therapeutic options for complicated infecti...

    Authors: Chong Chen, Chao-Yue Cui, Jun-Jun Yu, Qian He, Xiao-Ting Wu, Yu-Zhang He, Ze-Hua Cui, Cang Li, Qiu-Lin Jia, Xiang-Guang Shen, Ruan-Yang Sun, Xi-Ran Wang, Min-Ge Wang, Tian Tang, Yan Zhang, Xiao-Ping Liao…
    Citation: Genome Medicine 2020 12:111
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