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  1. 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
  2. Extension of prostate cancer beyond the primary site by local invasion or nodal metastasis is associated with poor prognosis. Despite significant research on tumour evolution in prostate cancer metastasis, the...

    Authors: Srinivasa Rao, Clare Verrill, Lucia Cerundolo, Nasullah Khalid Alham, Zeynep Kaya, Miriam O’Hanlon, Alicia Hayes, Adam Lambert, Martha James, Iain D. C. Tullis, Jane Niederer, Shelagh Lovell, Altan Omer, Francisco Lopez, Tom Leslie, Francesca Buffa…
    Citation: Genome Medicine 2024 16:35
  3. Drug resistance in tuberculosis (TB) poses a major ongoing challenge to public health. The recent inclusion of bedaquiline into TB drug regimens has improved treatment outcomes, but this advance is threatened ...

    Authors: Camus Nimmo, Arturo Torres Ortiz, Cedric C. S. Tan, Juanita Pang, Mislav Acman, James Millard, Nesri Padayatchi, Alison D. Grant, Max O’Donnell, Alex Pym, Ola B. Brynildsrud, Vegard Eldholm, Louis Grandjean, Xavier Didelot, François Balloux and Lucy van Dorp
    Citation: Genome Medicine 2024 16:34
  4. 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
  5. To diagnose the full spectrum of hereditary and congenital diseases, genetic laboratories use many different workflows, ranging from karyotyping to exome sequencing. A single generic high-throughput workflow w...

    Authors: Gaby Schobers, Ronny Derks, Amber den Ouden, Hilde Swinkels, Jeroen van Reeuwijk, Ermanno Bosgoed, Dorien Lugtenberg, Su Ming Sun, Jordi Corominas Galbany, Marjan Weiss, Marinus J. Blok, Richelle A. C. M. Olde Keizer, Tom Hofste, Debby Hellebrekers, Nicole de Leeuw, Alexander Stegmann…
    Citation: Genome Medicine 2024 16:32
  6. Population screening for risk of type 1 diabetes (T1D) has been proposed to identify those with islet autoimmunity (presence of islet autoantibodies). As islet autoantibodies can be transient, screening with a...

    Authors: Kristin A. Guertin, David R. Repaske, Julia F. Taylor, Eli S. Williams, Suna Onengut-Gumuscu, Wei-Min Chen, Sarah R. Boggs, Liping Yu, Luke Allen, Lacey Botteon, Louis Daniel, Katherine G. Keating, Mika K. Labergerie, Tyler S. Lienhart, Jorge A. Gonzalez-Mejia, Matt J. Starnowski…
    Citation: Genome Medicine 2024 16:31
  7. Biological processes are controlled by groups of genes acting in concert. Investigating gene–gene interactions within different cell types can help researchers understand the regulatory mechanisms behind human...

    Authors: Zekun Li, Gerui Liu, Xiaoxiao Yang, Meng Shu, Wen Jin, Yang Tong, Xiaochuan Liu, Yuting Wang, Jiapei Yuan and Yang Yang
    Citation: Genome Medicine 2024 16:30
  8. Chronic kidney disease (CKD) is highly prevalent among Indigenous Australians, especially those in remote regions. The Tiwi population has been isolated from mainland Australia for millennia and exhibits uniqu...

    Authors: Vignesh Arunachalam, Rodney Lea, Wendy Hoy, Simon Lee, Susan Mott, Judith Savige, John D. Mathews, Brendan J. McMorran and Shivashankar H. Nagaraj
    Citation: Genome Medicine 2024 16:29
  9. Children with relapsed central nervous system (CNS tumors), neuroblastoma, sarcomas, and other rare solid tumors face poor outcomes. This prospective clinical trial examined the feasibility of combining genomi...

    Authors: Giselle L. Saulnier Sholler, Genevieve Bergendahl, Elizabeth C. Lewis, Jacqueline Kraveka, William Ferguson, Abhinav B. Nagulapally, Karl Dykema, Valerie I. Brown, Michael S. Isakoff, Joseph Junewick, Deanna Mitchell, Jawhar Rawwas, William Roberts, Don Eslin, Javier Oesterheld, Randal K. Wada…
    Citation: Genome Medicine 2024 16:28
  10. Interactions between the gut microbiota, diet, and host metabolism contribute to the development of cardiovascular disease, but a firm link between disease-specific gut microbiota alterations and circulating m...

    Authors: Sajan C. Raju, Antonio Molinaro, Ayodeji Awoyemi, Silje F. Jørgensen, Peder R. Braadland, Andraz Nendl, Ingebjørg Seljeflot, Per M. Ueland, Adrian McCann, Pål Aukrust, Beate Vestad, Cristiane Mayerhofer, Kaspar Broch, Lars Gullestad, Knut T. Lappegård, Bente Halvorsen…
    Citation: Genome Medicine 2024 16:27
  11. Evolutionary models of breast cancer progression differ on the extent to which metastatic potential is pre-encoded within primary tumors. Although metastatic recurrences often harbor putative driver mutations ...

    Authors: Matthew R. Lawrence-Paul, Tien-chi Pan, Dhruv K. Pant, Natalie N. C. Shih, Yan Chen, George K. Belka, Michael Feldman, Angela DeMichele and Lewis A. Chodosh
    Citation: Genome Medicine 2024 16:26
  12. African ancestry populations have the highest burden of stroke worldwide, yet the genetic basis of stroke in these populations is obscure. The Stroke Investigative Research and Educational Network (SIREN) is a...

    Authors: Rufus O. Akinyemi, Hemant K. Tiwari, Vinodh Srinivasasainagendra, Onoja Akpa, Fred S. Sarfo, Albert Akpalu, Kolawole Wahab, Reginald Obiako, Morenikeji Komolafe, Lukman Owolabi, Godwin O. Osaigbovo, Olga A. Mamaeva, Brian A. Halloran, Joshua Akinyemi, Daniel Lackland, Olugbo Y. Obiabo…
    Citation: Genome Medicine 2024 16:25
  13. The Lentivirus human immunodeficiency virus (HIV) causes chronic inflammation and AIDS in humans, with variable rates of disease progression between individuals driven by both host and viral factors. Similarly, s...

    Authors: Aaron J. Wilk, Joshua O. Marceau, Samuel W. Kazer, Ira Fleming, Vincent N. Miao, Jennyfer Galvez-Reyes, Jason T. Kimata, Alex K. Shalek, Susan Holmes, Julie Overbaugh and Catherine A. Blish
    Citation: Genome Medicine 2024 16:24
  14. Few methicillin-resistant Staphylococcus aureus (MRSA) from the early years of its global emergence have been sequenced. Knowledge about evolutionary factors promoting the success of specific MRSA multi-locus seq...

    Authors: Vanni Benvenga, Aline Cuénod, Srinithi Purushothaman, Gottfried Dasen, Maja Weisser, Stefano Bassetti, Tim Roloff, Martin Siegemund, Ulrich Heininger, Julia Bielicki, Marianne Wehrli, Paul Friderich, Reno Frei, Andreas Widmer, Kathrin Herzog, Hans Fankhauser…
    Citation: Genome Medicine 2024 16:23
  15. Although polygenic risk score (PRS) has emerged as a promising tool for predicting cancer risk from genome-wide association studies (GWAS), the individual-level accuracy of lung cancer PRS and the extent to wh...

    Authors: Xinan Wang, Ziwei Zhang, Yi Ding, Tony Chen, Lorelei Mucci, Demetrios Albanes, Maria Teresa Landi, Neil E. Caporaso, Stephen Lam, Adonina Tardon, Chu Chen, Stig E. Bojesen, Mattias Johansson, Angela Risch, Heike Bickeböller, H-Erich Wichmann…
    Citation: Genome Medicine 2024 16:22
  16. The immune system has a central role in preventing carcinogenesis. Alteration of systemic immune cell levels may increase cancer risk. However, the extent to which common genetic variation influences blood tra...

    Authors: Miguel Angel Pardo-Cea, Xavier Farré, Anna Esteve, Joanna Palade, Roderic Espín, Francesca Mateo, Eric Alsop, Marc Alorda, Natalia Blay, Alexandra Baiges, Arzoo Shabbir, Francesc Comellas, Antonio Gómez, Montserrat Arnan, Alex Teulé, Monica Salinas…
    Citation: Genome Medicine 2024 16:21
  17. Recent studies using single-cell transcriptomic analysis have reported several distinct clusters of neoplastic epithelial cells and cancer-associated fibroblasts in the pancreatic cancer tumor microenvironment...

    Authors: Seongryong Kim, Galam Leem, Junjeong Choi, Yongjun Koh, Suho Lee, Sang-Hee Nam, Jin Su Kim, Chan Hee Park, Ho Kyoung Hwang, Kyoung Il Min, Jung Hyun Jo, Hee Seung Lee, Moon Jae Chung, Jeong Youp Park, Seung Woo Park, Si Young Song…
    Citation: Genome Medicine 2024 16:20
  18. Age and obesity are dominant risk factors for several common cardiometabolic disorders, and both are known to impair adipose tissue function. However, the underlying cellular and genetic factors linking aging ...

    Authors: Asha Kar, Marcus Alvarez, Kristina M. Garske, Huiling Huang, Seung Hyuk T. Lee, Milena Deal, Sankha Subhra Das, Amogha Koka, Zoeb Jamal, Karen L. Mohlke, Markku Laakso, Sini Heinonen, Kirsi H. Pietiläinen and Päivi Pajukanta
    Citation: Genome Medicine 2024 16:19
  19. Despite therapeutic advances, once a cancer has metastasized to the bone, it represents a highly morbid and lethal disease. One third of patients with advanced clear cell renal cell carcinoma (ccRCC) present w...

    Authors: Shenglin Mei, Adele M. Alchahin, Ioanna Tsea, Youmna Kfoury, Taghreed Hirz, Nathan Elias Jeffries, Ting Zhao, Yanxin Xu, Hanyu Zhang, Hirak Sarkar, Shulin Wu, Alexander O. Subtelny, John Inge Johnsen, Yida Zhang, Keyan Salari, Chin-Lee Wu…
    Citation: Genome Medicine 2024 16:1
  20. Despite advancements in the successful use of immunotherapy in treating a variety of solid tumors, applications in treating brain tumors have lagged considerably. This is due, at least in part, to the lack of ...

    Authors: Vrunda Trivedi, Changlin Yang, Kelena Klippel, Oleg Yegorov, Christina von Roemeling, Lan Hoang-Minh, Graeme Fenton, Elizabeth Ogando-Rivas, Paul Castillo, Ginger Moore, Kaytora Long-James, Kyle Dyson, Bently Doonan, Catherine Flores and Duane A. Mitchell
    Citation: Genome Medicine 2024 16:17
  21. The impact of the gut microbiome on the initiation and intensity of immune-related adverse events (irAEs) prompted by immune checkpoint inhibitors (ICIs) is widely acknowledged. Nevertheless, there is inconsis...

    Authors: Muni Hu, Xiaolin Lin, Tiantian Sun, Xiaoyan Shao, Xiaowen Huang, Weiwei Du, Mengzhe Guo, Xiaoqiang Zhu, Yilu Zhou, Tianying Tong, Fangfang Guo, Ting Han, Xiuqi Wu, Yi Shi, Xiuying Xiao, Youwei Zhang…
    Citation: Genome Medicine 2024 16:16
  22. Immunotherapy based on checkpoint inhibitors is highly effective in mismatch repair deficient (MMRd) colorectal cancer (CRC). These tumors carry a high number of mutations, which are predicted to translate int...

    Authors: Giuseppe Rospo, Rosaria Chilà, Vittoria Matafora, Veronica Basso, Simona Lamba, Alice Bartolini, Angela Bachi, Federica Di Nicolantonio, Anna Mondino, Giovanni Germano and Alberto Bardelli
    Citation: Genome Medicine 2024 16:15
  23. Sudden unexpected death in children is a tragic event. Understanding the genetics of sudden death in the young (SDY) enables family counseling and cascade screening. The objective of this study was to characte...

    Authors: Megan J. Puckelwartz, Lorenzo L. Pesce, Edgar J. Hernandez, Gregory Webster, Lisa M. Dellefave-Castillo, Mark W. Russell, Sarah S. Geisler, Samuel D. Kearns, Felix Karthik, Susan P. Etheridge, Tanner O. Monroe, Tess D. Pottinger, Prince J. Kannankeril, M. Benjamin Shoemaker, Darlene Fountain, Dan M. Roden…
    Citation: Genome Medicine 2024 16:13
  24. Detecting human cancers through cell-free DNA (cfDNA) in blood is a sensitive and non-invasive option. However, capturing multiple forms of epigenetic information remains a technical and financial challenge.

    Authors: Yumei Li, Jianfeng Xu, Chaorong Chen, Zhenhai Lu, Desen Wan, Diange Li, Jason S. Li, Allison J. Sorg, Curt C. Roberts, Shivani Mahajan, Maxime A. Gallant, Itai Pinkoviezky, Ya Cui, David J. Taggart and Wei Li
    Citation: Genome Medicine 2024 16:9
  25. Optimal integration of transcriptomics data and associated spatial information is essential towards fully exploiting spatial transcriptomics to dissect tissue heterogeneity and map out inter-cellular communica...

    Authors: Hang Xu, Huazhu Fu, Yahui Long, Kok Siong Ang, Raman Sethi, Kelvin Chong, Mengwei Li, Rom Uddamvathanak, Hong Kai Lee, Jingjing Ling, Ao Chen, Ling Shao, Longqi Liu and Jinmiao Chen
    Citation: Genome Medicine 2024 16:12
  26. Neoadjuvant chemotherapy (NAC) has become a standard treatment strategy for breast cancer (BC). However, owing to the high heterogeneity of these tumors, it is unclear which patient population most likely bene...

    Authors: Gengshen Yin, Liyuan Liu, Ting Yu, Lixiang Yu, Man Feng, Chengjun Zhou, Xiaoying Wang, Guoxin Teng, Zhongbing Ma, Wenzhong Zhou, Chunmiao Ye, Jialin Zhang, Changhua Ji, Linfeng Zhao, Peng Zhou, Yaxun Guo…
    Citation: Genome Medicine 2024 16:11
  27. Type 2 diabetes (T2D) is a heterogeneous and polygenic disease. Previous studies have leveraged the highly polygenic and pleiotropic nature of T2D variants to partition the heterogeneity of T2D, in order to st...

    Authors: Samuel Ghatan, Jeroen van Rooij, Mandy van Hoek, Cindy G. Boer, Janine F. Felix, Maryam Kavousi, Vincent W. Jaddoe, Eric J. G. Sijbrands, Carolina Medina-Gomez, Fernando Rivadeneira and Ling Oei
    Citation: Genome Medicine 2024 16:10
  28. As normal cells transform into cancers, their cell state changes, which may drive cancer cells into a stem-like or more primordial, foetal, or embryonic cell state. The transcriptomic profile of this final sta...

    Authors: Gerda Kildisiute, Maria Kalyva, Rasa Elmentaite, Stijn van Dongen, Christine Thevanesan, Alice Piapi, Kirsty Ambridge, Elena Prigmore, Muzlifah Haniffa, Sarah A. Teichmann, Karin Straathof, Isidro Cortés-Ciriano, Sam Behjati and Matthew D. Young
    Citation: Genome Medicine 2024 16:8
  29. Copy-number variations (CNVs) have been associated with rare and debilitating genomic disorders (GDs) but their impact on health later in life in the general population remains poorly described.

    Authors: Chiara Auwerx, Maarja Jõeloo, Marie C. Sadler, Nicolò Tesio, Sven Ojavee, Charlie J. Clark, Reedik Mägi, Alexandre Reymond and Zoltán Kutalik
    Citation: Genome Medicine 2024 16:5
  30. 5’ untranslated regions (5’UTRs) are essential modulators of protein translation. Predicting the impact of 5’UTR variants is challenging and rarely performed in routine diagnostics. Here, we present a combined...

    Authors: Alfredo Dueñas Rey, Marta del Pozo Valero, Manon Bouckaert, Katherine A Wood, Filip Van den Broeck, Malena Daich Varela, Huw B Thomas, Mattias Van Heetvelde, Marieke De Bruyne, Stijn Van de Sompele, Miriam Bauwens, Hanne Lenaerts, Quinten Mahieu, Dragana Josifova, Carlo Rivolta, Raymond T O’Keefe…
    Citation: Genome Medicine 2024 16:7
  31. Authors: Daniela Matuozzo, Estelle Talouarn, Astrid Marchal, Peng Zhang, Jeremy Manry, Yoann Seeleuthner, Yu Zhang, Alexandre Bolze, Matthieu Chaldebas, Baptiste Milisavljevic, Adrian Gervais, Paul Bastard, Takaki Asano, Lucy Bizien, Federica Barzaghi, Hassan Abolhassani…
    Citation: Genome Medicine 2024 16:6

    The original article was published in Genome Medicine 2023 15:22

  32. Next-generation sequencing (NGS) has significantly transformed the landscape of identifying disease-causing genes associated with genetic disorders. However, a substantial portion of sequenced patients remains...

    Authors: Christina Canavati, Dana Sherill-Rofe, Lara Kamal, Idit Bloch, Fouad Zahdeh, Elad Sharon, Batel Terespolsky, Islam Abu Allan, Grace Rabie, Mariana Kawas, Hanin Kassem, Karen B. Avraham, Paul Renbaum, Ephrat Levy-Lahad, Moien Kanaan and Yuval Tabach
    Citation: Genome Medicine 2024 16:4
  33. Pituitary neuroendocrine tumors (PitNETs) are one of the most common types of intracranial tumors. Currently, the cellular characteristics of normal pituitary and various other types of PitNETs are still not c...

    Authors: Nan Yan, Weiyan Xie, Dongfang Wang, Qiuyue Fang, Jing Guo, Yiyuan Chen, Xinqi Li, Lei Gong, Jialin Wang, Wenbo Guo, Xuegong Zhang, Yazhuo Zhang, Jin Gu and Chuzhong Li
    Citation: Genome Medicine 2024 16:2
  34. Despite the acceleration of somatic driver gene discovery facilitated by recent large-scale tumor sequencing data, the contribution of inherited variants remains largely unexplored, primarily focusing on previ...

    Authors: Seulki Song, Youngil Koh, Seokhyeon Kim, Sang Mi Lee, Hyun Uk Kim, Jung Min Ko, Se-Hoon Lee, Sung-Soo Yoon and Solip Park
    Citation: Genome Medicine 2023 15:107
  35. The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines recommend using variant enrichment among cases as "strong" evidence for pathogenicity per the P...

    Authors: Sihan Liu, Mingjun Zhong, Yu Huang, Qian Zhang, Ting Chen, Xiaofei Xu, Wan Peng, Xiaolu Wang, Xiaoshu Feng, Lu Kang, Yu Lu, Jing Cheng, Fengxiao Bu and Huijun Yuan
    Citation: Genome Medicine 2023 15:116
  36. Identifying expressed somatic mutations from single-cell RNA sequencing data de novo is challenging but highly valuable. We propose RESA – Recurrently Expressed SNV Analysis, a computational framework to ident...

    Authors: Tianyun Zhang, Hanying Jia, Tairan Song, Lin Lv, Doga C. Gulhan, Haishuai Wang, Wei Guo, Ruibin Xi, Hongshan Guo and Ning Shen
    Citation: Genome Medicine 2023 15:115
  37. Long-read whole genome sequencing (lrWGS) has the potential to address the technical limitations of exome sequencing in ways not possible by short-read WGS. However, its utility in autosomal recessive Mendelia...

    Authors: Lama AlAbdi, Hanan E. Shamseldin, Ebtissal Khouj, Rana Helaby, Bayan Aljamal, Mashael Alqahtani, Aisha Almulhim, Halima Hamid, Mais O. Hashem, Firdous Abdulwahab, Omar Abouyousef, Amal Jaafar, Tarfa Alshidi, Mohammed Al-Owain, Amal Alhashem, Saeed Al Tala…
    Citation: Genome Medicine 2023 15:114
  38. In China, ~1,072,100 small for gestational age (SGA) births occur annually. These SGA newborns are a high-risk population of developmental delay. Our study aimed to evaluate the genetic profile of SGA newborns...

    Authors: Hui Xiao, Huiyao Chen, Xiang Chen, Yulan Lu, Bingbing Wu, Huijun Wang, Yun Cao, Liyuan Hu, Xinran Dong, Wenhao Zhou and Lin Yang
    Citation: Genome Medicine 2023 15:112
  39. Clonal hematopoiesis (CH) frequently progresses after chemotherapy or radiotherapy. We evaluated the clinical impact of preoperative CH on the survival outcomes of patients with non-small cell lung cancer (NSC...

    Authors: Jae Kwang Yun, Sugyeong Kim, Hongyul An, Geun Dong Lee, Hyeong Ryul Kim, Yong-Hee Kim, Dong Kwan Kim, Seung-Il Park, Sehoon Choi and Youngil Koh
    Citation: Genome Medicine 2023 15:111
  40. Damage in the ischemic core and penumbra after stroke affects patient prognosis. Microglia immediately respond to ischemic insult and initiate immune inflammation, playing an important role in the cellular inj...

    Authors: Huiya Li, Pinyi Liu, Bing Zhang, Zengqiang Yuan, Mengdi Guo, Xinxin Zou, Yi Qian, Shiji Deng, Liwen Zhu, Xiang Cao, Tao Tao, Shengnan Xia, Xinyu Bao and Yun Xu
    Citation: Genome Medicine 2023 15:109
  41. Normal cell BRCA1 epimutations have been associated with increased risk of triple-negative breast cancer (TNBC). However, the fraction of TNBCs that may have BRCA1 epimutations as their underlying cause is unknow...

    Authors: Oleksii Nikolaienko, Hans P. Eikesdal, Elisabet Ognedal, Bjørnar Gilje, Steinar Lundgren, Egil S. Blix, Helge Espelid, Jürgen Geisler, Stephanie Geisler, Emiel A. M. Janssen, Synnøve Yndestad, Laura Minsaas, Beryl Leirvaag, Reidun Lillestøl, Stian Knappskog and Per E. Lønning
    Citation: Genome Medicine 2023 15:104
  42. In vitro and in vivo studies have shown that certain cytokines and hormones may play a role in the development and progression of type 2 diabetes (T2D). However, studies on their role in T2D in humans are scar...

    Authors: Karlijn A. C. Meeks, Amy R. Bentley, Themistocles L. Assimes, Nora Franceschini, Adebowale A. Adeyemo, Charles N. Rotimi and Ayo P. Doumatey
    Citation: Genome Medicine 2023 15:108
  43. Klebsiella pneumoniae is a notorious clinical pathogen and frequently carries various plasmids, which are the main carriers of antimicrobial resistance and virulence genes. In comparison to self-transmissible co...

    Authors: Jianfeng Zhang, Yanping Xu, Meng Wang, Xiaobin Li, Zhiyuan Liu, Dai Kuang, Zixin Deng, Hong-Yu Ou and Jieming Qu
    Citation: Genome Medicine 2023 15:106
  44. The precise characterization of individual tumors and immune microenvironments using transcriptome sequencing has provided a great opportunity for successful personalized cancer treatment. However, the cancer ...

    Authors: Chen Tang, Shaliu Fu, Xuan Jin, Wannian Li, Feiyang Xing, Bin Duan, Xiaojie Cheng, Xiaohan Chen, Shuguang Wang, Chenyu Zhu, Gaoyang Li, Guohui Chuai, Yayi He, Ping Wang and Qi Liu
    Citation: Genome Medicine 2023 15:105

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