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  1. Lack of functional evidence hampers variant interpretation, leaving a large proportion of individuals with a suspected Mendelian disorder without genetic diagnosis after whole genome or whole exome sequencing ...

    Authors: Vicente A. Yépez, Mirjana Gusic, Robert Kopajtich, Christian Mertes, Nicholas H. Smith, Charlotte L. Alston, Rui Ban, Skadi Beblo, Riccardo Berutti, Holger Blessing, Elżbieta Ciara, Felix Distelmaier, Peter Freisinger, Johannes Häberle, Susan J. Hayflick, Maja Hempel…
    Citation: Genome Medicine 2022 14:38
  2. Carbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistanc...

    Authors: Rauf Salamzade, Abigail L. Manson, Bruce J. Walker, Thea Brennan-Krohn, Colin J. Worby, Peijun Ma, Lorrie L. He, Terrance P. Shea, James Qu, Sinéad B. Chapman, Whitney Howe, Sarah K. Young, Jenna I. Wurster, Mary L. Delaney, Sanjat Kanjilal, Andrew B. Onderdonk…
    Citation: Genome Medicine 2022 14:37
  3. Depression is a disabling and highly prevalent condition where genetic and epigenetic, such as DNA methylation (DNAm), differences contribute to disease risk. DNA methylation is influenced by genetic variation...

    Authors: Xueyi Shen, Doretta Caramaschi, Mark J. Adams, Rosie M. Walker, Josine L. Min, Alex Kwong, Gibran Hemani, Miruna C. Barbu, Heather C. Whalley, Sarah E. Harris, Ian J. Deary, Stewart W. Morris, Simon R. Cox, Caroline L. Relton, Riccardo E. Marioni, Kathryn L. Evans…
    Citation: Genome Medicine 2022 14:36
  4. Recent studies show that human gut microbial composition can determine whether a patient is a responder or non-responder to immunotherapy but have not identified a common microbial signal shared by responding ...

    Authors: Rachel C. Newsome, Raad Z. Gharaibeh, Christine M. Pierce, Wildson Vieira da Silva, Shirlene Paul, Stephanie R. Hogue, Qin Yu, Scott Antonia, Jose R. Conejo-Garcia, Lary A. Robinson and Christian Jobin
    Citation: Genome Medicine 2022 14:35
  5. Each year 3–6 million people develop life-threatening severe dengue (SD). Clinical warning signs for SD manifest late in the disease course and are nonspecific, leading to missed cases and excess hospital burd...

    Authors: Yiran E. Liu, Sirle Saul, Aditya Manohar Rao, Makeda Lucretia Robinson, Olga Lucia Agudelo Rojas, Ana Maria Sanz, Michelle Verghese, Daniel Solis, Mamdouh Sibai, Chun Hong Huang, Malaya Kumar Sahoo, Rosa Margarita Gelvez, Nathalia Bueno, Maria Isabel Estupiñan Cardenas, Luis Angel Villar Centeno, Elsa Marina Rojas Garrido…
    Citation: Genome Medicine 2022 14:33
  6. The All of Us Research Program (AoURP, “the program”) is an initiative, sponsored by the National Institutes of Health (NIH), that aims to enroll one million people (or more) across the USA. Through repeated enga...

    Authors: Eric Venner, Donna Muzny, Joshua D. Smith, Kimberly Walker, Cynthia L. Neben, Christina M. Lockwood, Phillip E. Empey, Ginger A. Metcalf, Chris Kachulis, Sana Mian, Anjene Musick, Heidi L. Rehm, Steven Harrison, Stacey Gabriel, Richard A. Gibbs, Deborah Nickerson…
    Citation: Genome Medicine 2022 14:34
  7. Increased epigenetic age acceleration (EAA) in survivors of childhood cancer is associated with specific treatment exposures, unfavorable health behaviors, and presence of certain chronic health conditions. To...

    Authors: Qian Dong, Nan Song, Na Qin, Cheng Chen, Zhenghong Li, Xiaojun Sun, John Easton, Heather Mulder, Emily Plyler, Geoffrey Neale, Emily Walker, Qian Li, Xiaotu Ma, Xiang Chen, I-Chan Huang, Yutaka Yasui…
    Citation: Genome Medicine 2022 14:32
  8. Identification of causal genes for polygenic human diseases has been extremely challenging, and our understanding of how physiological and pharmacological stimuli modulate genetic risk at disease-associated lo...

    Authors: Michael J. Gloudemans, Brunilda Balliu, Daniel Nachun, Theresia M. Schnurr, Matthew G. Durrant, Erik Ingelsson, Martin Wabitsch, Thomas Quertermous, Stephen B. Montgomery, Joshua W. Knowles and Ivan Carcamo-Orive
    Citation: Genome Medicine 2022 14:31
  9. The gut microbiota has been suggested to play a significant role in the development of overweight and obesity. However, the effects of calorie restriction on gut microbiota of overweight and obese adults, espe...

    Authors: Solomon A. Sowah, Alessio Milanese, Ruth Schübel, Jakob Wirbel, Ece Kartal, Theron S. Johnson, Frank Hirche, Mirja Grafetstätter, Tobias Nonnenmacher, Romy Kirsten, Marina López-Nogueroles, Agustín Lahoz, Kathrin V. Schwarz, Jürgen G. Okun, Cornelia M. Ulrich, Johanna Nattenmüller…
    Citation: Genome Medicine 2022 14:30
  10. Previous studies have linked the Mediterranean diet (MED) with improved cardiometabolic health, showing preliminary evidence for a mediating role of the gut microbiome. We recently suggested the Green-Mediterr...

    Authors: Ehud Rinott, Anat Yaskolka Meir, Gal Tsaban, Hila Zelicha, Alon Kaplan, Dan Knights, Kieran Tuohy, Matthias Uwe Scholz, Omry Koren, Meir J. Stampfer, Dong D. Wang, Iris Shai and Ilan Youngster
    Citation: Genome Medicine 2022 14:29
  11. Blood plasma proteins play an important role in immune defense against pathogens, including cytokine signaling, the complement system, and the acute-phase response. Recent large-scale studies have reported gen...

    Authors: Barthelemy Caron, Etienne Patin, Maxime Rotival, Bruno Charbit, Matthew L. Albert, Lluis Quintana-Murci, Darragh Duffy and Antonio Rausell
    Citation: Genome Medicine 2022 14:28
  12. The Colombian population, as well as those in other Latin American regions, arose from a recent tri-continental admixture among Native Americans, Spanish invaders, and enslaved Africans, all of whom passed thr...

    Authors: Juliana Acosta-Uribe, David Aguillón, J. Nicholas Cochran, Margarita Giraldo, Lucía Madrigal, Bradley W. Killingsworth, Rijul Singhal, Sarah Labib, Diana Alzate, Lina Velilla, Sonia Moreno, Gloria P. García, Amanda Saldarriaga, Francisco Piedrahita, Liliana Hincapié, Hugo E. López…
    Citation: Genome Medicine 2022 14:27
  13. The RNA profiles of tumor-educated platelets (TEPs) possess pathological features that could be used for early cancer detection. However, the utility of TEP RNA profiling in detecting early colorectal cancer (...

    Authors: Luming Xu, Xinbo Li, Xiangchun Li, Xingyue Wang, Qian Ma, Dan She, Xiaohuan Lu, Jiao Zhang, Qianqian Yang, Shijun Lei, Lin Wang and Zheng Wang
    Citation: Genome Medicine 2022 14:26
  14. Pancreatic neuroendocrine neoplasms (PanNENs) fall into two subclasses: the well-differentiated, low- to high-grade pancreatic neuroendocrine tumors (PanNETs), and the poorly-differentiated, high-grade pancrea...

    Authors: Tincy Simon, Pamela Riemer, Armin Jarosch, Katharina Detjen, Annunziata Di Domenico, Felix Bormann, Andrea Menne, Slim Khouja, Nanna Monjé, Liam H. Childs, Dido Lenze, Ulf Leser, Florian Rossner, Markus Morkel, Nils Blüthgen, Marianne Pavel…
    Citation: Genome Medicine 2022 14:24
  15. Cancer cells can proliferate indefinitely through telomere maintenance mechanisms. These mechanisms include telomerase-dependent elongation, mediated by TERT activation, and alternative lengthening of telomeres (...

    Authors: Radwa Sharaf, Meagan Montesion, Julia F. Hopkins, Jiarong Song, Garrett M. Frampton and Lee A. Albacker
    Citation: Genome Medicine 2022 14:25
  16. Identifying breast cancer patients with DNA repair pathway-related germline pathogenic variants (GPVs) is important for effectively employing systemic treatment strategies and risk-reducing interventions. Howe...

    Authors: Jiaqi Liu, Hengqiang Zhao, Yu Zheng, Lin Dong, Sen Zhao, Yukuan Huang, Shengkai Huang, Tianyi Qian, Jiali Zou, Shu Liu, Jun Li, Zihui Yan, Yalun Li, Shuo Zhang, Xin Huang, Wenyan Wang…
    Citation: Genome Medicine 2022 14:21
  17. Authors: Margo Diricks, Thomas A. Kohl, Nadja Käding, Vladislav Leshchinskiy, Susanne Hauswaldt, Omar Jiménez Vázquez, Christian Utpatel, Stefan Niemann, Jan Rupp and Matthias Merker
    Citation: Genome Medicine 2022 14:22

    The original article was published in Genome Medicine 2022 14:13

  18. Immune checkpoint inhibitor (ICI) therapy has revolutionized the treatment of many cancers. However, the limited population that benefits from ICI therapy makes it necessary to screen predictive biomarkers for...

    Authors: Junyu Long, Dongxu Wang, Anqiang Wang, Peipei Chen, Yu Lin, Jin Bian, Xu Yang, Mingjun Zheng, Haohai Zhang, Yongchang Zheng, Xinting Sang and Haitao Zhao
    Citation: Genome Medicine 2022 14:20
  19. While single-cell transcriptional profiling has greatly increased our capacity to interrogate biology, accurate cell classification within and between datasets is a key challenge. This is particularly so in pl...

    Authors: Sean B. Wilson, Sara E. Howden, Jessica M. Vanslambrouck, Aude Dorison, Jose Alquicira-Hernandez, Joseph E. Powell and Melissa H. Little
    Citation: Genome Medicine 2022 14:19
  20. Measuring host gene expression is a promising diagnostic strategy to discriminate bacterial and viral infections. Multiple signatures of varying size, complexity, and target populations have been described. Ho...

    Authors: Nicholas Bodkin, Melissa Ross, Micah T. McClain, Emily R. Ko, Christopher W. Woods, Geoffrey S. Ginsburg, Ricardo Henao and Ephraim L. Tsalik
    Citation: Genome Medicine 2022 14:18
  21. Alzheimer’s disease (AD) is characterized by robust microgliosis and phenotypic changes that accompany disease pathogenesis. Accumulating evidence from genetic studies suggests the importance of phospholipase ...

    Authors: Andy P. Tsai, Chuanpeng Dong, Peter Bor-Chian Lin, Evan J. Messenger, Brad T. Casali, Miguel Moutinho, Yunlong Liu, Adrian L. Oblak, Bruce T. Lamb, Gary E. Landreth, Stephanie J. Bissel and Kwangsik Nho
    Citation: Genome Medicine 2022 14:17
  22. Understanding the host genetic architecture and viral immunity contributes to the development of effective vaccines and therapeutics for controlling the COVID-19 pandemic. Alterations of immune responses in pe...

    Authors: Yunlong Ma, Fei Qiu, Chunyu Deng, Jingjing Li, Yukuan Huang, Zeyi Wu, Yijun Zhou, Yaru Zhang, Yichun Xiong, Yinghao Yao, Yigang Zhong, Jia Qu and Jianzhong Su
    Citation: Genome Medicine 2022 14:16
  23. Antimicrobial resistance (AMR) is a major global public health threat, which has been largely driven by the excessive use of antimicrobials. Control measures are urgently needed to slow the trajectory of AMR b...

    Authors: Claire Waddington, Megan E. Carey, Christine J. Boinett, Ellen Higginson, Balaji Veeraraghavan and Stephen Baker
    Citation: Genome Medicine 2022 14:15
  24. Bacteria belonging to the genus Haemophilus cause a wide range of diseases in humans. Recently, H. influenzae was classified by the WHO as priority pathogen due to the wide spread of ampicillin resistant strains....

    Authors: Margo Diricks, Thomas A. Kohl, Nadja Käding, Vladislav Leshchinskiy, Susanne Hauswaldt, Omar Jiménez Vázquez, Christian Utpatel, Stefan Niemann, Jan Rupp and Matthias Merker
    Citation: Genome Medicine 2022 14:13

    The Publisher Correction to this article has been published in Genome Medicine 2022 14:22

  25. Authors: Na Zhu, Michael W. Pauciulo, Carrie L. Welch, Katie A. Lutz, Anna W. Coleman, Claudia Gonzaga-Jauregui, Jiayao Wang, Joseph M. Grimes, Lisa J. Martin, Hua He, Yufeng Shen, Wendy K. Chung and William C. Nichols
    Citation: Genome Medicine 2022 14:12

    The original article was published in Genome Medicine 2019 11:69

  26. We propose DEGAS (Diagnostic Evidence GAuge of Single cells), a novel deep transfer learning framework, to transfer disease information from patients to cells. We call such transferrable information “impressions,...

    Authors: Travis S. Johnson, Christina Y. Yu, Zhi Huang, Siwen Xu, Tongxin Wang, Chuanpeng Dong, Wei Shao, Mohammad Abu Zaid, Xiaoqing Huang, Yijie Wang, Christopher Bartlett, Yan Zhang, Brian A. Walker, Yunlong Liu, Kun Huang and Jie Zhang
    Citation: Genome Medicine 2022 14:11
  27. The COVID-19 pandemic has resulted in 275 million infections and 5.4 million deaths as of December 2021. While effective vaccines are being administered globally, there is still a great need for antiviral ther...

    Authors: Marco Grodzki, Andrew P. Bluhm, Moritz Schaefer, Abderrahmane Tagmount, Max Russo, Amin Sobh, Roya Rafiee, Chris D. Vulpe, Stephanie M. Karst and Michael H. Norris
    Citation: Genome Medicine 2022 14:10
  28. With over 350,000 estimated deaths worldwide in 2018, prostate cancer (PCa) continues to be a major health concern and a significant cause of cancer-associated mortality among men. While cancer in general is c...

    Authors: Paul Vinu Salachan, Martin Rasmussen, Jacob Fredsøe, Benedicte Ulhøi, Michael Borre and Karina Dalsgaard Sørensen
    Citation: Genome Medicine 2022 14:9
  29. Circular RNAs (circRNAs) constitute a largely unexplored source for biomarker discovery in prostate cancer (PC). Here, we characterize the biomarker potential of circRNAs in PC, where the need for novel diagno...

    Authors: Emma Bollmann Hansen, Jacob Fredsøe, Trine Line Hauge Okholm, Benedicte Parm Ulhøi, Søren Klingenberg, Jørgen Bjerggaard Jensen, Jørgen Kjems, Kirsten Bouchelouche, Michael Borre, Christian Kroun Damgaard, Jakob Skou Pedersen, Lasse Sommer Kristensen and Karina Dalsgaard Sørensen
    Citation: Genome Medicine 2022 14:8
  30. Amyotrophic lateral sclerosis (ALS) is a complex, late-onset, neurodegenerative disease with a genetic contribution to disease liability. Genome-wide association studies (GWAS) have identified ten risk loci to...

    Authors: Restuadi Restuadi, Frederik J. Steyn, Edor Kabashi, Shyuan T. Ngo, Fei-Fei Cheng, Marta F. Nabais, Mike J. Thompson, Ting Qi, Yang Wu, Anjali K. Henders, Leanne Wallace, Chris R. Bye, Bradley J. Turner, Laura Ziser, Susan Mathers, Pamela A. McCombe…
    Citation: Genome Medicine 2022 14:7
  31. Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure ...

    Authors: Christine G. Preston, Matt W. Wright, Rao Madhavrao, Steven M. Harrison, Jennifer L. Goldstein, Xi Luo, Hannah Wand, Bryan Wulf, Gloria Cheung, Mark E. Mandell, Howard Tong, Shaung Cheng, Michael A. Iacocca, Arturo Lopez Pineda, Alice B. Popejoy, Karen Dalton…
    Citation: Genome Medicine 2022 14:6
  32. Lung adenocarcinoma, the most common type of lung cancer, has a high level of morphologic heterogeneity and is composed of tumor cells of multiple histological subtypes. It has been reported that immune cell i...

    Authors: Thinh T. Nguyen, Hyun-Sung Lee, Bryan M. Burt, Jia Wu, Jianjun Zhang, Christopher I. Amos and Chao Cheng
    Citation: Genome Medicine 2022 14:5
  33. Endometrial cancer (EC) is a major gynecological cancer with increasing incidence. It comprises four molecular subtypes with differing etiology, prognoses, and responses to chemotherapy. In the future, clinica...

    Authors: Vanessa F. Bonazzi, Olga Kondrashova, Deborah Smith, Katia Nones, Asmerom T. Sengal, Robert Ju, Leisl M. Packer, Lambros T. Koufariotis, Stephen H. Kazakoff, Aimee L. Davidson, Priya Ramarao-Milne, Vanessa Lakis, Felicity Newell, Rebecca Rogers, Claire Davies, James Nicklin…
    Citation: Genome Medicine 2022 14:3
  34. T and B cell receptor (TCR, BCR) repertoires constitute the foundation of adaptive immunity. Adaptive immune receptor repertoire sequencing (AIRR-seq) is a common approach to study immune system dynamics. Unde...

    Authors: Aviv Omer, Ayelet Peres, Oscar L Rodriguez, Corey T Watson, William Lees, Pazit Polak, Andrew M Collins and Gur Yaari
    Citation: Genome Medicine 2022 14:2
  35. A limited number of studies have characterized genomic properties of hepatocellular carcinoma (HCC) patients in response to anti-PD-1 immunotherapy.

    Authors: Jung Yong Hong, Hee Jin Cho, Jason K. Sa, Xiaoqiao Liu, Sang Yun Ha, Taehyang Lee, Hajung Kim, Wonseok Kang, Dong Hyun Sinn, Geum-Youn Gwak, Moon Seok Choi, Joon Hyeok Lee, Kwang Cheol Koh, Seung Woon Paik, Hee Chul Park, Tae Wook Kang…
    Citation: Genome Medicine 2022 14:1
  36. The human gut harbors trillions of microbes that play dynamic roles in health. While the microbiome contributes to many cardiometabolic traits by modulating host inflammation and metabolism, there is an incomp...

    Authors: Rebecca L. Walker, Hera Vlamakis, Jonathan Wei Jie Lee, Luke A. Besse, Vanessa Xanthakis, Ramachandran S. Vasan, Stanley Y. Shaw and Ramnik J. Xavier
    Citation: Genome Medicine 2021 13:188
  37. While understanding molecular heterogeneity across patients underpins precision oncology, there is increasing appreciation for taking intra-tumor heterogeneity into account. Based on large-scale analysis of ca...

    Authors: Chayaporn Suphavilai, Shumei Chia, Ankur Sharma, Lorna Tu, Rafael Peres Da Silva, Aanchal Mongia, Ramanuj DasGupta and Niranjan Nagarajan
    Citation: Genome Medicine 2021 13:189
  38. We present Beyondcell, a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq data and proposing cancer-specific treatments. Our method calcu...

    Authors: Coral Fustero-Torre, María José Jiménez-Santos, Santiago García-Martín, Carlos Carretero-Puche, Luis García-Jimeno, Vadym Ivanchuk, Tomás Di Domenico, Gonzalo Gómez-López and Fátima Al-Shahrour
    Citation: Genome Medicine 2021 13:187
  39. Familial ovarian cancer (OC) cases not harbouring pathogenic variants in either of the BRCA1 and BRCA2 OC-predisposing genes, which function in homologous recombination (HR) of DNA, could involve pathogenic varia...

    Authors: Caitlin T. Fierheller, Laure Guitton-Sert, Wejdan M. Alenezi, Timothée Revil, Kathleen K. Oros, Yuandi Gao, Karine Bedard, Suzanna L. Arcand, Corinne Serruya, Supriya Behl, Liliane Meunier, Hubert Fleury, Eleanor Fewings, Deepak N. Subramanian, Javad Nadaf, Jeffrey P. Bruce…
    Citation: Genome Medicine 2021 13:186
  40. Mutations in certain genes are known to increase breast cancer risk. We study the relevance of rare protein-truncating variants (PTVs) that may result in loss-of-function in breast cancer susceptibility genes ...

    Authors: Peh Joo Ho, Alexis J. Khng, Hui Wen Loh, Weang-Kee Ho, Cheng Har Yip, Nur Aishah Mohd-Taib, Veronique Kiak Mien Tan, Benita Kiat-Tee Tan, Su-Ming Tan, Ern Yu Tan, Swee Ho Lim, Suniza Jamaris, Yirong Sim, Fuh Yong Wong, Joanne Ngeow, Elaine Hsuen Lim…
    Citation: Genome Medicine 2021 13:185
  41. We discuss the current state of genomic medicine in Arab countries of the Middle East, a region with outsized contribution to Mendelian genetics due to inbreeding yet has poor representation in global variome ...

    Authors: Ahmad N. Abou Tayoun, Khalid A. Fakhro, Alawi Alsheikh-Ali and Fowzan S. Alkuraya
    Citation: Genome Medicine 2021 13:184
  42. N6-methyladenosine (m6A) is the most abundant modification of RNA in eukaryotic cells and play critical roles in cancer. While most related studies focus on m6A modifications in linear RNA, transcriptome-wide pro...

    Authors: Ying Ye, Weiyi Feng, Jialiang Zhang, Kaiyu Zhu, Xudong Huang, Ling Pan, Jiachun Su, Yanfen Zheng, Rui Li, Shuang Deng, Ruihong Bai, Lisha Zhuang, Lusheng Wei, Junge Deng, Mei Li, Rufu Chen…
    Citation: Genome Medicine 2021 13:183
  43. Clinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides add...

    Authors: Themoula Charalampous, Adela Alcolea-Medina, Luke B. Snell, Tom G. S. Williams, Rahul Batra, Christopher Alder, Andrea Telatin, Luigi Camporota, Christopher I. S. Meadows, Duncan Wyncoll, Nicholas A. Barrett, Carolyn J. Hemsley, Lisa Bryan, William Newsholme, Sara E. Boyd, Anna Green…
    Citation: Genome Medicine 2021 13:182
  44. Genetic studies have been tremendously successful in identifying genomic regions associated with a wide variety of phenotypes, although the success of these studies in identifying causal genes, their variants,...

    Authors: Jessy Carol Ntunzwenimana, Gabrielle Boucher, Jean Paquette, Hugues Gosselin, Azadeh Alikashani, Nicolas Morin, Claudine Beauchamp, Louise Thauvette, Marie-Ève Rivard, Frédérique Dupuis, Sonia Deschênes, Sylvain Foisy, Frédéric Latour, Geneviève Lavallée, Mark J. Daly, Ramnik J. Xavier…
    Citation: Genome Medicine 2021 13:181
  45. Cardiorespiratory fitness (CRF) and physical activity (PA) are well-established predictors of morbidity and all-cause mortality. However, CRF is not routinely measured and PA not routinely prescribed as part o...

    Authors: Ken B. Hanscombe, Elodie Persyn, Matthew Traylor, Kylie P. Glanville, Mark Hamer, Jonathan R. I. Coleman and Cathryn M. Lewis
    Citation: Genome Medicine 2021 13:180
  46. Targeted therapies in oncology are promising but variants of uncertain significance (VUS) limit their use for clinical management and necessitate functional testing in vitro. Using BRCA1 and BRCA2 variants, which...

    Authors: Amandine Billaud, Louise-Marie Chevalier, Paule Augereau, Jean-Sebastien Frenel, Christophe Passot, Mario Campone and Alain Morel
    Citation: Genome Medicine 2021 13:174
  47. Ensuring accordance with principles of healthcare ethics requires improved communication of pathogen genomic data. This could include educating healthcare professionals in communicating pathogen genomic inform...

    Authors: Angeline S Ferdinand, Jane S Hocking, Justin T. Denholm, Benjamin P. Howden and Deborah A. Williamson
    Citation: Genome Medicine 2021 13:178
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