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  1. Chronic kidney disease (CKD) is a progressive disease for which there is no effective cure. We aimed to identify potential drug targets for CKD and kidney function by integrating plasma proteome and transcript...

    Authors: Shucheng Si, Hongyan Liu, Lu Xu and Siyan Zhan
    Citation: Genome Medicine 2024 16:84
  2. Somatic copy number alterations are a hallmark of cancer that offer unique opportunities for therapeutic exploitation. Here, we focused on the identification of specific vulnerabilities for tumors harboring ch...

    Authors: Stephan Krieg, Thomas Rohde, Tobias Rausch, Luise Butthof, Lena Wendler-Link, Christoph Eckert, Kai Breuhahn, Bruno Galy, Jan Korbel, Maximilian Billmann, Marco Breinig and Darjus F. Tschaharganeh
    Citation: Genome Medicine 2024 16:83
  3. Genome-wide functional screening using the CRISPR-Cas9 system is a powerful tool to uncover tumor-specific and common genetic dependencies across cancer cell lines. Current CRISPR-Cas9 knockout libraries, howe...

    Authors: Daniel J. Merk, Linda Paul, Foteini Tsiami, Helen Hohenthanner, Ghazal Mohseni Kouchesfahani, Lara A. Haeusser, Bianca Walter, Adam Brown, Nicole S. Persky, David E. Root and Ghazaleh Tabatabai
    Citation: Genome Medicine 2024 16:82
  4. Early detection of colorectal neoplasms can reduce the colorectal cancer (CRC) burden by timely intervention for high-risk individuals. However, effective risk prediction models are lacking for personalized CR...

    Authors: Jianbo Tian, Ming Zhang, Fuwei Zhang, Kai Gao, Zequn Lu, Yimin Cai, Can Chen, Caibo Ning, Yanmin Li, Sangni Qian, Hao Bai, Yizhuo Liu, Heng Zhang, Shuoni Chen, Xiangpan Li, Yongchang Wei…
    Citation: Genome Medicine 2024 16:81
  5. Gastric cancer is the fifth most common cancer type. Most patients are diagnosed at advanced stages with poor prognosis. A non-invasive assay for the detection of early-stage gastric cancer is highly desirable...

    Authors: Pengfei Yu, Ping Chen, Min Wu, Guangyu Ding, Hua Bao, Yian Du, Zhiyuan Xu, Litao Yang, Jingquan Fang, Xingmao Huang, Qian Lai, Jia Wei, Junrong Yan, Shanshan Yang, Peng He, Xue Wu…
    Citation: Genome Medicine 2024 16:79
  6. Antimicrobial resistance (AMR) is an intensifying threat that requires urgent mitigation to avoid a post-antibiotic era. Pseudomonas aeruginosa represents one of the greatest AMR concerns due to increasing multi-...

    Authors: Danielle E. Madden, Timothy Baird, Scott C. Bell, Kate L. McCarthy, Erin P. Price and Derek S. Sarovich
    Citation: Genome Medicine 2024 16:78
  7. Colorectal cancer (CRC) arises from complex interactions between host and environment, which include the gut and tissue microbiome. It is hypothesized that epigenetic regulation by gut microbiota is a fundamen...

    Authors: Zhi Liu, Qingqing Zhang, Hong Zhang, Zhongyuan Yi, Huihui Ma, Xiaoyi Wang, Jingjing Wang, Yang Liu, Yi Zheng, Weijia Fang, Ping Huang and Xingyin Liu
    Citation: Genome Medicine 2024 16:77
  8. Congenital hypopituitarism (CH) and its associated syndromes, septo-optic dysplasia (SOD) and holoprosencephaly (HPE), are midline defects that cause significant morbidity for affected people. Variants in 67 g...

    Authors: Julian Martinez-Mayer, Michelle L. Brinkmeier, Sean P. O’Connell, Arnold Ukagwu, Marcelo A. Marti, Mirta Miras, Maria V. Forclaz, Maria G. Benzrihen, Leonard Y. M. Cheung, Sally A. Camper, Buffy S. Ellsworth, Lori T. Raetzman, Maria I. Pérez-Millán and Shannon W. Davis
    Citation: Genome Medicine 2024 16:75
  9. Polygenic prediction studies in continental Africans are scarce. Africa’s genetic and environmental diversity pose a challenge that limits the generalizability of polygenic risk scores (PRS) for body mass inde...

    Authors: Tinashe Chikowore, Kristi Läll, Lisa K. Micklesfield, Zane Lombard, Julia H. Goedecke, Segun Fatumo, Shane A. Norris, Reedik Magi, Michele Ramsay, Paul W. Franks, Guillaume Pare and Andrew P. Morris
    Citation: Genome Medicine 2024 16:74
  10. KCNE1 encodes a 129-residue cardiac potassium channel (IKs) subunit. KCNE1 variants are associated with long QT syndrome and atrial fibrillation. However, most variants have insufficient evidence of clinical con...

    Authors: Ayesha Muhammad, Maria E. Calandranis, Bian Li, Tao Yang, Daniel J. Blackwell, M. Lorena Harvey, Jeremy E. Smith, Zerubabell A. Daniel, Ashli E. Chew, John A. Capra, Kenneth A. Matreyek, Douglas M. Fowler, Dan M. Roden and Andrew M. Glazer
    Citation: Genome Medicine 2024 16:73
  11. We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney, caused by de novo variants in the degron of...

    Authors: Sissy Bassani, Jacqueline Chrast, Giovanna Ambrosini, Norine Voisin, Frédéric Schütz, Alfredo Brusco, Fabio Sirchia, Lydia Turban, Susanna Schubert, Rami Abou Jamra, Jan-Ulrich Schlump, Desiree DeMille, Pinar Bayrak-Toydemir, Gary Rex Nelson, Kristen Nicole Wong, Laura Duncan…
    Citation: Genome Medicine 2024 16:72
  12. The role of metabolism in the variation of age at menarche (AAM) and age at natural menopause (ANM) in the female population is not entirely known. We aimed to investigate the causal role of circulating metabo...

    Authors: Mojgan Yazdanpanah, Nahid Yazdanpanah, Isabel Gamache, Ken Ong, John R. B. Perry and Despoina Manousaki
    Citation: Genome Medicine 2024 16:69
  13. Disease prevalence and mean phenotype values differ between many populations, including Inuit and Europeans. Whether these differences are partly explained by genetic differences or solely due to differences i...

    Authors: Long Lin, Mette K. Andersen, Frederik Filip Stæger, Zilong Li, Kristian Hanghøj, Allan Linneberg, Niels Grarup, Marit Eika Jørgensen, Torben Hansen, Ida Moltke and Anders Albrechtsen
    Citation: Genome Medicine 2024 16:71
  14. Rare oncogenic driver events, particularly affecting the expression or splicing of driver genes, are suspected to substantially contribute to the large heterogeneity of hematologic malignancies. However, their...

    Authors: Xueqi Cao, Sandra Huber, Ata Jadid Ahari, Franziska R. Traube, Marc Seifert, Christopher C. Oakes, Polina Secheyko, Sergey Vilov, Ines F. Scheller, Nils Wagner, Vicente A. Yépez, Piers Blombery, Torsten Haferlach, Matthias Heinig, Leonhard Wachutka, Stephan Hutter…
    Citation: Genome Medicine 2024 16:70
  15. Inflammatory bowel disease (IBD) and Parkinson’s disease (PD) are chronic disorders that have been suggested to share common pathophysiological processes. LRRK2 has been implicated as playing a role in both disea...

    Authors: Meltem Ece Kars, Yiming Wu, Peter D. Stenson, David N. Cooper, Johan Burisch, Inga Peter and Yuval Itan
    Citation: Genome Medicine 2024 16:66
  16. Infections caused by multidrug-resistant gram-negative bacteria present a severe threat to global public health. The WHO defines drug-resistant Klebsiella pneumoniae as a priority pathogen for which alternative t...

    Authors: Eva Heinz, Oliver Pearse, Allan Zuza, Sithembile Bilima, Chisomo Msefula, Patrick Musicha, Patriciah Siyabu, Edith Tewesa, Fabrice E. Graf, Rebecca Lester, Samantha Lissauer, Jennifer Cornick, Joseph M. Lewis, Kondwani Kawaza, Nicholas R. Thomson and Nicholas A. Feasey
    Citation: Genome Medicine 2024 16:67
  17. Using computational tools, bulk transcriptomics can be deconvoluted to estimate the abundance of constituent cell types. However, existing deconvolution methods are conditioned on the assumption that the whole...

    Authors: Guanqun Meng, Yue Pan, Wen Tang, Lijun Zhang, Ying Cui, Fredrick R. Schumacher, Ming Wang, Rui Wang, Sijia He, Jeffrey Krischer, Qian Li and Hao Feng
    Citation: Genome Medicine 2024 16:65
  18. Genetic variants that severely alter protein products (e.g. nonsense, frameshift) are often associated with disease. For some genes, these predicted loss-of-function variants (pLoFs) are observed throughout th...

    Authors: Robin N. Beaumont, Gareth Hawkes, Adam C. Gunning and Caroline F. Wright
    Citation: Genome Medicine 2024 16:64
  19. The clinical utility of genetic information for type 2 diabetes (T2D) prediction with polygenic scores (PGS) in ancestrally diverse, real-world US healthcare systems is unclear, especially for those at low cli...

    Authors: Ravi Mandla, Philip Schroeder, Bianca Porneala, Jose C. Florez, James B. Meigs, Josep M. Mercader and Aaron Leong
    Citation: Genome Medicine 2024 16:63
  20. The "missing" heritability of complex traits may be partly explained by genetic variants interacting with other genes or environments that are difficult to specify, observe, and detect. We propose a new kernel...

    Authors: Andrew J. Bass, Shijia Bian, Aliza P. Wingo, Thomas S. Wingo, David J. Cutler and Michael P. Epstein
    Citation: Genome Medicine 2024 16:62
  21. Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have prev...

    Authors: João Dourado Santos, Daniel Sobral, Miguel Pinheiro, Joana Isidro, Carlijn Bogaardt, Miguel Pinto, Rodrigo Eusébio, André Santos, Rafael Mamede, Daniel L. Horton, João Paulo Gomes and Vítor Borges
    Citation: Genome Medicine 2024 16:61
  22. Pituitary neuroendocrine tumors (PitNETs) are common gland neoplasms demonstrating distinctive transcription factors. Although the role of immune cells in PitNETs has been widely recognized, the precise immuno...

    Authors: Shaojian Lin, Yuting Dai, Changxi Han, Tianyi Han, Linfeng Zhao, Renyan Wu, Jianyue Liu, Bo Zhang, Ning Huang, Yanting Liu, Shujing Lai, Jintong Shi, Yu Wang, Meiqing Lou, Jing Xie, Yijun Cheng…
    Citation: Genome Medicine 2024 16:60
  23. Gut dysbiosis has been linked with both HIV infection and diabetes, but its interplay with metabolic and inflammatory responses in diabetes, particularly in the context of HIV infection, remains unclear.

    Authors: Kai Luo, Brandilyn A. Peters, Jee-Young Moon, Xiaonan Xue, Zheng Wang, Mykhaylo Usyk, David B. Hanna, Alan L. Landay, Michael F. Schneider, Deborah Gustafson, Kathleen M. Weber, Audrey French, Anjali Sharma, Kathryn Anastos, Tao Wang, Todd Brown…
    Citation: Genome Medicine 2024 16:59
  24. Klebsiella pneumoniae is a major bacterial and opportunistic human pathogen, increasingly recognized as a healthcare burden globally. The convergence of resistance and virulence in K. pneumoniae strains has led t...

    Authors: Sharif Hala, Mohammed Malaikah, Jiayi Huang, Wesam Bahitham, Omniya Fallatah, Samer Zakri, Chakkiath Paul Antony, Mohammed Alshehri, Raeece Naeem Ghazzali, Fathia Ben-Rached, Abdullah Alsahafi, Asim Alsaedi, Ghadeer AlAhmadi, Mai Kaaki, Meshari Alazmi, Baraa AlhajHussein…
    Citation: Genome Medicine 2024 16:58
  25. Carbapenem-resistant Escherichia coli (CREC) has been considered as WHO priority pathogens, causing a great public health concern globally. While CREC from patients has been thoroughly investigated, the prevalenc...

    Authors: Yan Li, Yanyan Zhang, Xinran Sun, Yuchen Wu, Zelin Yan, Xiaoyang Ju, Yonglu Huang, Hongwei Zhou, Zhiqiang Wang, Shaolin Wang, Rong Zhang and Ruichao Li
    Citation: Genome Medicine 2024 16:57
  26. Despite the abundance of genotype-phenotype association studies, the resulting association outcomes often lack robustness and interpretations. To address these challenges, we introduce PheSeq, a Bayesian deep ...

    Authors: Xinzhi Yao, Sizhuo Ouyang, Yulong Lian, Qianqian Peng, Xionghui Zhou, Feier Huang, Xuehai Hu, Feng Shi and Jingbo Xia
    Citation: Genome Medicine 2024 16:56
  27. Most primary Triple Negative Breast Cancers (TNBCs) show amplification of the Epidermal Growth Factor Receptor (EGFR) gene, leading to increased protein expression. However, unlike other EGFR-driven cancers, t...

    Authors: Simona Pellecchia, Melania Franchini, Gaetano Viscido, Riccardo Arnese and Gennaro Gambardella
    Citation: Genome Medicine 2024 16:55
  28. Lung cancer is the leading cause of cancer-related death in the world. In contrast to many other cancers, a direct connection to modifiable lifestyle risk in the form of tobacco smoke has long been establishe...

    Authors: Maria Stella de Biase, Florian Massip, Tzu-Ting Wei, Federico M. Giorgi, Rory Stark, Amanda Stone, Amy Gladwell, Martin O’Reilly, Daniel Schütte, Ines de Santiago, Kerstin B. Meyer, Florian Markowetz, Bruce A. J. Ponder, Robert C. Rintoul and Roland F. Schwarz
    Citation: Genome Medicine 2024 16:54
  29. Genome sequencing of large biobanks from under-represented ancestries provides a valuable resource for the interrogation of Mendelian disease burden at world population level, complementing small-scale familia...

    Authors: Waleed Aamer, Aljazi Al-Maraghi, Najeeb Syed, Geethanjali Devadoss Gandhi, Elbay Aliyev, Alya A. Al-Kurbi, Omayma Al-Saei, Muhammad Kohailan, Navaneethakrishnan Krishnamoorthy, Sasirekha Palaniswamy, Khulod Al-Malki, Saleha Abbasi, Nourhen Agrebi, Fatemeh Abbaszadeh, Ammira S. Al-Shabeeb Akil, Ramin Badii…
    Citation: Genome Medicine 2024 16:46
  30. NODAL signaling plays a critical role in embryonic patterning and heart development in vertebrates. Genetic variants resulting in perturbations of the TGF-β/NODAL signaling pathway have reproducibly been shown...

    Authors: Zain Dardas, Jawid M. Fatih, Angad Jolly, Moez Dawood, Haowei Du, Christopher M. Grochowski, Edward G. Jones, Shalini N. Jhangiani, Xander H. T. Wehrens, Pengfei Liu, Weimin Bi, Eric Boerwinkle, Jennifer E. Posey, Donna M. Muzny, Richard A. Gibbs, James R. Lupski…
    Citation: Genome Medicine 2024 16:53
  31. Prostate cancer is a significant health concern, particularly among African American (AA) men who exhibit higher incidence and mortality compared to European American (EA) men. Understanding the molecular mech...

    Authors: Swathi Ramakrishnan, Eduardo Cortes-Gomez, Sarah R. Athans, Kristopher M. Attwood, Spencer R. Rosario, Se Jin Kim, Donald E. Mager, Emily G. Isenhart, Qiang Hu, Jianmin Wang and Anna Woloszynska
    Citation: Genome Medicine 2024 16:52
  32. A major contributing factor to glioblastoma (GBM) development and progression is its ability to evade the immune system by creating an immune-suppressive environment, where GBM-associated myeloid cells, includ...

    Authors: Yahaya A. Yabo, Pilar M. Moreno-Sanchez, Yolanda Pires-Afonso, Tony Kaoma, Bakhtiyor Nosirov, Andrea Scafidi, Luca Ermini, Anuja Lipsa, Anaïs Oudin, Dimitrios Kyriakis, Kamil Grzyb, Suresh K. Poovathingal, Aurélie Poli, Arnaud Muller, Reka Toth, Barbara Klink…
    Citation: Genome Medicine 2024 16:51
  33. Mitochondria play essential roles in tumorigenesis; however, little is known about the contribution of mitochondrial DNA (mtDNA) to esophageal squamous cell carcinoma (ESCC). Whole-genome sequencing (WGS) is b...

    Authors: Xuehan Zhuang, Rui Ye, Yong Zhou, Matthew Yibo Cheng, Heyang Cui, Longlong Wang, Shuangping Zhang, Shubin Wang, Yongping Cui and Weimin Zhang
    Citation: Genome Medicine 2024 16:50
  34. The efficacy of neoadjuvant chemo-immunotherapy (NAT) in esophageal squamous cell carcinoma (ESCC) is challenged by the intricate interplay within the tumor microenvironment (TME). Unveiling the immune landsca...

    Authors: Gang Ji, Qi Yang, Song Wang, Xiaolong Yan, Qiuxiang Ou, Li Gong, Jinbo Zhao, Yongan Zhou, Feng Tian, Jie Lei, Xiaorong Mu, Jian Wang, Tao Wang, Xiaoping Wang, Jianyong Sun, Jipeng Zhang…
    Citation: Genome Medicine 2024 16:49
  35. Natural killer/T cell lymphoma (NKTCL) is a clinically and genetically heterogeneous disease with poor prognosis. Genome sequencing and mutation characterization provides a powerful approach for patient strati...

    Authors: Zegeng Chen, He Huang, Huangming Hong, Huageng Huang, Huawei Weng, Le Yu, Jian Xiao, Zhao Wang, Xiaojie Fang, Yuyi Yao, Jia-Xing Yue and Tongyu Lin
    Citation: Genome Medicine 2024 16:48
  36. Aberrant DNA methylation is a major characteristic of cancer genomes. It remains unclear which biological processes determine epigenetic reprogramming and how these processes influence the variants in the canc...

    Authors: Qingqing Qin, Ying Zhou, Jintao Guo, Qinwei Chen, Weiwei Tang, Yuchen Li, Jun You and Qiyuan Li
    Citation: Genome Medicine 2024 16:47
  37. Type 1 diabetes mellitus (T1DM) is a prototypic endocrine autoimmune disease resulting from an immune-mediated destruction of pancreatic insulin-secreting http://static-content.springer.com/image/art%3A10.1186%2Fs13073-024-01300-z/13073_2024_1300_Article_IEq1.gif ...

    Authors: Mohammad Amin Honardoost, Andreas Adinatha, Florian Schmidt, Bobby Ranjan, Maryam Ghaeidamini, Nirmala Arul Rayan, Michelle Gek Liang Lim, Ignasius Joanito, Quy Xiao Xuan Lin, Deepa Rajagopalan, Shi Qi Mok, You Yi Hwang, Anis Larbi, Chiea Chuen Khor, Roger Foo, Bernhard Otto Boehm…
    Citation: Genome Medicine 2024 16:45
  38. Histopathology and genomic profiling are cornerstones of precision oncology and are routinely obtained for patients with cancer. Traditionally, histopathology slides are manually reviewed by highly trained pat...

    Authors: Michaela Unger and Jakob Nikolas Kather
    Citation: Genome Medicine 2024 16:44
  39. Limited understanding of the diversity of variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene across ancestries hampers efforts to advance molecular diagnosis of cystic fibrosis (CF). ...

    Authors: Justin E. Ideozu, Mengzhen Liu, Bridget M. Riley-Gillis, Sri R. Paladugu, Fedik Rahimov, Preethi Krishnan, Rakesh Tripathi, Patrick Dorr, Hara Levy, Ashvani Singh, Jeffrey F. Waring and Aparna Vasanthakumar
    Citation: Genome Medicine 2024 16:43
  40. Ineffective drug treatment is a major problem for many patients with immune-mediated inflammatory diseases (IMIDs). Important reasons are the lack of systematic solutions for drug prioritisation and repurposin...

    Authors: Samuel Schäfer, Martin Smelik, Oleg Sysoev, Yelin Zhao, Desiré Eklund, Sandra Lilja, Mika Gustafsson, Holger Heyn, Antonio Julia, István A. Kovács, Joseph Loscalzo, Sara Marsal, Huan Zhang, Xinxiu Li, Danuta Gawel, Hui Wang…
    Citation: Genome Medicine 2024 16:42
  41. The occurrence of metabolic syndrome (MetS) and the gut microbiota composition are known to differ across ethnicities yet how these three factors are interwoven is unknown. Also, it is unknown what the relativ...

    Authors: Manon Balvers, Marcus de Goffau, Natal van Riel, Bert-Jan van den Born, Henrike Galenkamp, Koos Zwinderman, Max Nieuwdorp and Evgeni Levin
    Citation: Genome Medicine 2024 16:41
  42. The presence of coronary plaques with high-risk characteristics is strongly associated with adverse cardiac events beyond the identification of coronary stenosis. Testing by coronary computed tomography angiog...

    Authors: Peter Loof Møller, Palle Duun Rohde, Jonathan Nørtoft Dahl, Laust Dupont Rasmussen, Louise Nissen, Samuel Emil Schmidt, Victoria McGilligan, Daniel F. Gudbjartsson, Kari Stefansson, Hilma Holm, Jacob Fog Bentzon, Morten Bøttcher, Simon Winther and Mette Nyegaard
    Citation: Genome Medicine 2024 16:40
  43. In the accompanying study, Nimmo and colleagues estimated the dates of emergence of mutations in mmpR5 (Rv0678), the most important resistance gene to the anti-tuberculosis drug bedaquiline, in over 3500 geograph...

    Authors: Paolo Miotto, Daniela M. Cirillo, Thomas Schön and Claudio U. Köser
    Citation: Genome Medicine 2024 16:39

    The Research to this article has been published in Genome Medicine 2024 16:34

  44. Type 2 diabetes (T2D) has reached epidemic proportions globally, including in Africa. However, molecular studies to understand the pathophysiology of T2D remain scarce outside Europe and North America. The aim...

    Authors: Ayo P. Doumatey, Daniel Shriner, Jie Zhou, Lin Lei, Guanjie Chen, Omolara Oluwasola-Taiwo, Susan Nkem, Adela Ogundeji, Sally N. Adebamowo, Amy R. Bentley, Mateus H. Gouveia, Karlijn A. C. Meeks, Clement A. Adebamowo, Adebowale A. Adeyemo and Charles N. Rotimi
    Citation: Genome Medicine 2024 16:38
  45. Multidrug-resistant (MDR) bacteria are a growing global threat, especially in healthcare facilities. Faecal microbiota transplantation (FMT) is an effective prevention strategy for recurrences of Clostridioides d...

    Authors: Sam Nooij, Karuna E. W. Vendrik, Romy D. Zwittink, Quinten R. Ducarmon, Josbert J. Keller, Ed J. Kuijper and Elisabeth M. Terveer
    Citation: Genome Medicine 2024 16:37
  46. Polygenic scores (PGS) can be used for risk stratification by quantifying individuals’ genetic predisposition to disease, and many potentially clinically useful applications have been proposed. Here, we review...

    Authors: Ruidong Xiang, Martin Kelemen, Yu Xu, Laura W. Harris, Helen Parkinson, Michael Inouye and Samuel A. Lambert
    Citation: Genome Medicine 2024 16:33

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