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  1. When interpreting sequencing data from multiple spatial or longitudinal biopsies, detecting sample mix-ups is essential, yet more difficult than in studies of germline variation. In most genomic studies of tum...

    Authors: Brent S. Pedersen, Preetida J. Bhetariya, Joe Brown, Stephanie N. Kravitz, Gabor Marth, Randy L. Jensen, Mary P. Bronner, Hunter R. Underhill and Aaron R. Quinlan

    Citation: Genome Medicine 2020 12:62

    Content type: Software

    Published on:

  3. The molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear...

    Authors: Robert F. Hillary, Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, Sven Erik Ojavee, Qian Zhang, David C. Liewald, Craig W. Ritchie, Kathryn L. Evans, Elliot M. Tucker-Drob, Naomi R. Wray, Allan F. McRae, Peter M. Visscher…

    Citation: Genome Medicine 2020 12:60

    Content type: Research

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  4. Dietary glycans, widely used as food ingredients and not directly digested by humans, are of intense interest for their beneficial roles in human health through shaping the microbiome. Characterizing the consi...

    Authors: Richard Creswell, Jie Tan, Jonathan W. Leff, Brandon Brooks, Michael A. Mahowald, Ruth Thieroff-Ekerdt and Georg K. Gerber

    Citation: Genome Medicine 2020 12:59

    Content type: Research

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  6. COVID-19 (coronavirus disease 2019) has caused a major epidemic worldwide; however, much is yet to be known about the epidemiology and evolution of the virus partly due to the scarcity of full-length SARS-CoV-...

    Authors: Minfeng Xiao, Xiaoqing Liu, Jingkai Ji, Min Li, Jiandong Li, Lin Yang, Wanying Sun, Peidi Ren, Guifang Yang, Jincun Zhao, Tianzhu Liang, Huahui Ren, Tian Chen, Huanzi Zhong, Wenchen Song, Yanqun Wang…

    Citation: Genome Medicine 2020 12:57

    Content type: Research

    Published on:

  8. Traditionally, the transcriptomic and proteomic characterisation of CD4+ T cells at the single-cell level has been performed by two largely exclusive types of technologies: single-cell RNA sequencing (scRNA-seq) ...

    Authors: Dominik Trzupek, Melanie Dunstan, Antony J. Cutler, Mercede Lee, Leila Godfrey, Lorna Jarvis, Daniel B. Rainbow, Dominik Aschenbrenner, Joanne L. Jones, Holm H. Uhlig, Linda S. Wicker, John A. Todd and Ricardo C. Ferreira

    Citation: Genome Medicine 2020 12:55

    Content type: Research

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  9. Cell-free DNA (cfDNA) analysis has become essential in cancer diagnostics and prenatal testing. We present cfNOMe, a two-in-one method of measuring cfDNA cytosine methylation and nucleosome occupancy in a single ...

    Authors: Florian Erger, Deborah Nörling, Domenica Borchert, Esther Leenen, Sandra Habbig, Michael S. Wiesener, Malte P. Bartram, Andrea Wenzel, Christian Becker, Mohammad R. Toliat, Peter Nürnberg, Bodo B. Beck and Janine Altmüller

    Citation: Genome Medicine 2020 12:54

    Content type: Method

    Published on:

  10. The human plasma proteome is important for many biological processes and targets for diagnostics and therapy. It is therefore of great interest to understand the interplay of genetic and environmental factors ...

    Authors: Wen Zhong, Anders Gummesson, Abdellah Tebani, Max J. Karlsson, Mun-Gwan Hong, Jochen M. Schwenk, Fredrik Edfors, Göran Bergström, Linn Fagerberg and Mathias Uhlén

    Citation: Genome Medicine 2020 12:53

    Content type: Research

    Published on:

  11. Studies of cancer mutations have typically focused on identifying cancer driving mutations that confer growth advantage to cancer cells. However, cancer genomes accumulate a large number of passenger somatic m...

    Authors: Yoo-Ah Kim, Damian Wojtowicz, Rebecca Sarto Basso, Itay Sason, Welles Robinson, Dorit S. Hochbaum, Mark D. M. Leiserson, Roded Sharan, Fabio Vadin and Teresa M. Przytycka

    Citation: Genome Medicine 2020 12:52

    Content type: Research

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  12. Distinct prevalence of inherited genetic predisposition may partially explain the difference of cancer risks across ancestries. Ancestry-specific analyses of germline genomes are required to inform cancer gene...

    Authors: Ninad Oak, Andrew D. Cherniack, R. Jay Mashl, Fred R. Hirsch, Li Ding, Rameen Beroukhim, Zeynep H. Gümüş, Sharon E. Plon and Kuan-lin Huang

    Citation: Genome Medicine 2020 12:51

    Content type: Research

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  13. Populations of closely related microbial strains can be simultaneously present in bacterial communities such as the human gut microbiome. We recently developed a de novo genome assembly approach that uses read...

    Authors: Soumaya Zlitni, Alex Bishara, Eli L. Moss, Ekaterina Tkachenko, Joyce B. Kang, Rebecca N. Culver, Tessa M. Andermann, Ziming Weng, Christina Wood, Christine Handy, Hanlee P. Ji, Serafim Batzoglou and Ami S. Bhatt

    Citation: Genome Medicine 2020 12:50

    Content type: Research

    Published on:

  14. Mosaic mutations acquired during early embryogenesis can lead to severe early-onset genetic disorders and cancer predisposition, but are often undetectable in blood samples. The rate and mutational spectrum of...

    Authors: Francesc Muyas, Luis Zapata, Roderic Guigó and Stephan Ossowski

    Citation: Genome Medicine 2020 12:49

    Content type: Research

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  15. Clinical whole-genome sequencing (WGS) offers clear diagnostic benefits for patients with rare disease. However, there are barriers to its widespread adoption, including a lack of standards for clinical practi...

    Authors: Christian R. Marshall, David Bick, John W. Belmont, Stacie L. Taylor, Euan Ashley, David Dimmock, Vaidehi Jobanputra, Hutton M. Kearney, Shashikant Kulkarni and Heidi Rehm

    Citation: Genome Medicine 2020 12:48

    Content type: Comment

    Published on:

  16. Tumor cell-intrinsic mechanisms and complex interactions with the tumor microenvironment contribute to therapeutic failure via tumor evolution. It may be possible to overcome treatment resistance by developing...

    Authors: Hye Won Lee, Woosung Chung, Hae-Ock Lee, Da Eun Jeong, Areum Jo, Joung Eun Lim, Jeong Hee Hong, Do-Hyun Nam, Byong Chang Jeong, Se Hoon Park, Kyeung-Min Joo and Woong-Yang Park

    Citation: Genome Medicine 2020 12:47

    Content type: Research

    Published on:

  17. Hutchinson-Gilford progeria syndrome (HGPS) is a progeroid disease characterized by the early onset of age-related phenotypes including arthritis, loss of body fat and hair, and atherosclerosis. Cells from aff...

    Authors: Florian Köhler, Felix Bormann, Günter Raddatz, Julian Gutekunst, Samuel Corless, Tanja Musch, Anke S. Lonsdorf, Sylvia Erhardt, Frank Lyko and Manuel Rodríguez-Paredes

    Citation: Genome Medicine 2020 12:46

    Content type: Research

    Published on:

  18. Immune checkpoint blockade (ICB) with antibodies inhibiting cytotoxic T lymphocyte-associated protein-4 (CTLA-4) and programmed cell death protein-1 (PD-1) (or its ligand (PD-L1)) can stimulate immune response...

    Authors: Aaron M. Goodman, Andrea Castro, Rachel Marty Pyke, Ryosuke Okamura, Shumei Kato, Paul Riviere, Garrett Frampton, Ethan Sokol, Xinlian Zhang, Edward D. Ball, Hannah Carter and Razelle Kurzrock

    Citation: Genome Medicine 2020 12:45

    Content type: Research

    Published on:

  20. Cyclophosphamide, doxorubicin, vincristine, and prednisolone (CHOP)/CHOP-like chemotherapy is widely used in peripheral T cell lymphoma (PTCL). Here we conducted a phase 2, multicenter, randomized, controlled ...

    Authors: Ming-Ci Cai, Shu Cheng, Xin Wang, Jian-Da Hu, Yong-Ping Song, Yao-Hui Huang, Zi-Xun Yan, Yu-Jie Jiang, Xiao-Sheng Fang, Xiao-Yun Zheng, Li-Hua Dong, Meng-Meng Ji, Li Wang, Peng-Peng Xu and Wei-Li Zhao

    Citation: Genome Medicine 2020 12:41

    Content type: Research

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  22. The contribution of somatic mosaicism, or genetic mutations arising after oocyte fertilization, to congenital heart disease (CHD) is not well understood. Further, the relationship between mosaicism in blood an...

    Authors: Alexander Hsieh, Sarah U. Morton, Jon A. L. Willcox, Joshua M. Gorham, Angela C. Tai, Hongjian Qi, Steven DePalma, David McKean, Emily Griffin, Kathryn B. Manheimer, Daniel Bernstein, Richard W. Kim, Jane W. Newburger, George A. Porter Jr, Deepak Srivastava, Martin Tristani-Firouzi…

    Citation: Genome Medicine 2020 12:42

    Content type: Research

    Published on:

  23. Endogenous retroelements (EREs) constitute about 42% of the human genome and have been implicated in common human diseases such as autoimmunity and cancer. The dominant paradigm holds that EREs are expressed i...

    Authors: Jean-David Larouche, Assya Trofimov, Leslie Hesnard, Gregory Ehx, Qingchuan Zhao, Krystel Vincent, Chantal Durette, Patrick Gendron, Jean-Philippe Laverdure, Éric Bonneil, Caroline Côté, Sébastien Lemieux, Pierre Thibault and Claude Perreault

    Citation: Genome Medicine 2020 12:40

    Content type: Research

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  24. Large numbers of autosomal sites are found differentially methylated in the aging genome. Due to analytical difficulties in dealing with sex differences in X-chromosome content and X-inactivation (XCI) in fema...

    Authors: Shuxia Li, Jesper B. Lund, Kaare Christensen, Jan Baumbach, Jonas Mengel-From, Torben Kruse, Weilong Li, Afsaneh Mohammadnejad, Alison Pattie, Riccardo E. Marioni, Ian J. Deary and Qihua Tan

    Citation: Genome Medicine 2020 12:39

    Content type: Research

    Published on:

  25. Pancreatic neuroendocrine tumors (PANETs) are rare, slow growing cancers that often present with local and distant metastasis upon detection. PANETS contain distinct karyotypes, epigenetic dysregulation, and r...

    Authors: Rene Quevedo, Anna Spreafico, Jeff Bruce, Arnavaz Danesh, Samah El Ghamrasni, Amanda Giesler, Youstina Hanna, Cherry Have, Tiantian Li, S. Y. Cindy Yang, Tong Zhang, Sylvia L. Asa, Benjamin Haibe-Kains, Monika Krzyzanowska, Adam C. Smith, Simron Singh…

    Citation: Genome Medicine 2020 12:38

    Content type: Research

    Published on:

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

    Authors: Danuta R. Gawel, Jordi Serra-Musach, Sandra Lilja, Jesper Aagesen, Alex Arenas, Bengt Asking, Malin Bengnér, Janne Björkander, Sophie Biggs, Jan Ernerudh, Henrik Hjortswang, Jan-Erik Karlsson, Mattias Köpsen, Eun Jung Lee, Antonio Lentini, Xinxiu Li…

    Citation: Genome Medicine 2020 12:37

    Content type: Correction

    Published on:

    The original article was published in Genome Medicine 2019 11:47

  27. Clinical exome sequencing is frequently used to identify gene-disrupting variants in individuals with neurodevelopmental disorders. While splice-disrupting variants are known to contribute to these disorders, ...

    Authors: Stephan J. Sanders, Grace B. Schwartz and Kyle Kai-How Farh

    Citation: Genome Medicine 2020 12:36

    Content type: Comment

    Published on:

  28. Accurate lung cancer classification is crucial to guide therapeutic decisions. However, histological subtyping by pathologists requires tumor tissue—a necessity that is often intrinsically associated with proc...

    Authors: Lennart Raman, Malaïka Van der Linden, Kim Van der Eecken, Karim Vermaelen, Ingel Demedts, Veerle Surmont, Ulrike Himpe, Franceska Dedeurwaerdere, Liesbeth Ferdinande, Yolande Lievens, Kathleen Claes, Björn Menten and Jo Van Dorpe

    Citation: Genome Medicine 2020 12:35

    Content type: Research

    Published on:

  29. Reprogramming human induced pluripotent stem cells (iPSCs) from somatic cells and generating three-dimensional brain organoids from these iPSCs provide access to live human neuronal tissue with disease-specifi...

    Authors: Annie Kathuria, Kara Lopez-Lengowski, Magdalena Vater, Donna McPhie, Bruce M. Cohen and Rakesh Karmacharya

    Citation: Genome Medicine 2020 12:34

    Content type: Research

    Published on:

  30. Tumor mutational burden (TMB; the quantity of aberrant nucleotide sequences a given tumor may harbor) has been associated with response to immune checkpoint inhibitor therapy and is gaining broad acceptance as...

    Authors: Mary A. Wood, Benjamin R. Weeder, Julianne K. David, Abhinav Nellore and Reid F. Thompson

    Citation: Genome Medicine 2020 12:33

    Content type: Research

    Published on:

  31. Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of renal cancer. With currently available therapies, cure of advanced and metastatic ccRCC is achieved only in rare cases. Here, we developed a w...

    Authors: Anna Reustle, Moreno Di Marco, Carolin Meyerhoff, Annika Nelde, Juliane S. Walz, Stefan Winter, Siahei Kandabarau, Florian Büttner, Mathias Haag, Linus Backert, Daniel J. Kowalewski, Steffen Rausch, Jörg Hennenlotter, Viktoria Stühler, Marcus Scharpf, Falko Fend…

    Citation: Genome Medicine 2020 12:32

    Content type: Research

    Published on:

  33. Merkel cell carcinoma (MCC) is a highly aggressive neuroendocrine carcinoma of the skin caused by either the integration of Merkel cell polyomavirus (MCPyV) and expression of viral T antigens or by ultraviolet...

    Authors: Gabriel J. Starrett, Manisha Thakuria, Tianqi Chen, Christina Marcelus, Jingwei Cheng, Jason Nomburg, Aaron R. Thorner, Michael K. Slevin, Winslow Powers, Robert T. Burns, Caitlin Perry, Adriano Piris, Frank C. Kuo, Guilherme Rabinowits, Anita Giobbie-Hurder, Laura E. MacConaill…

    Citation: Genome Medicine 2020 12:30

    Content type: Research

    Published on:

  34. In cancer, normal epigenetic patterns are disturbed and contribute to gene expression changes, disease onset, and progression. The cancer epigenome is composed of the epigenetic patterns present in the tumor-i...

    Authors: Justyna A. Wierzbinska, Reka Toth, Naveed Ishaque, Karsten Rippe, Jan-Philipp Mallm, Lara C. Klett, Daniel Mertens, Thorsten Zenz, Thomas Hielscher, Marc Seifert, Ralf Küppers, Yassen Assenov, Pavlo Lutsik, Stephan Stilgenbauer, Philipp M. Roessner, Martina Seiffert…

    Citation: Genome Medicine 2020 12:29

    Content type: Research

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  35. Classifying pathogenicity of missense variants represents a major challenge in clinical practice during the diagnoses of rare and genetic heterogeneous neurodevelopmental disorders (NDDs). While orthologous ge...

    Authors: Dennis Lal, Patrick May, Eduardo Perez-Palma, Kaitlin E. Samocha, Jack A. Kosmicki, Elise B. Robinson, Rikke S. Møller, Roland Krause, Peter Nürnberg, Sarah Weckhuysen, Peter De Jonghe, Renzo Guerrini, Lisa M. Niestroj, Juliana Du, Carla Marini, James S. Ware…

    Citation: Genome Medicine 2020 12:28

    Content type: Research

    Published on:

  36. A comprehensive understanding of the pre-existing genetic variation in genes associated with antibiotic resistance in the Mycobacterium tuberculosis complex (MTBC) is needed to accurately interpret whole-genome s...

    Authors: Matthias Merker, Thomas A. Kohl, Ivan Barilar, Sönke Andres, Philip W. Fowler, Erja Chryssanthou, Kristian Ängeby, Pontus Jureen, Danesh Moradigaravand, Julian Parkhill, Sharon J. Peacock, Thomas Schön, Florian P. Maurer, Timothy Walker, Claudio Köser and Stefan Niemann

    Citation: Genome Medicine 2020 12:27

    Content type: Research

    Published on:

  37. Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated...

    Authors: Simon Kebede Merid, Alexei Novoloaca, Gemma C. Sharp, Leanne K. Küpers, Alvin T. Kho, Ritu Roy, Lu Gao, Isabella Annesi-Maesano, Pooja Jain, Michelle Plusquin, Manolis Kogevinas, Catherine Allard, Florianne O. Vehmeijer, Nabila Kazmi, Lucas A. Salas, Faisal I. Rezwan…

    Citation: Genome Medicine 2020 12:25

    Content type: Research

    Published on:

  38. Patient stratification based on molecular subtypes is an important strategy for cancer precision medicine. Deriving clinically informative cancer molecular subtypes from transcriptomic data generated on whole ...

    Authors: Li Wang, Robert P. Sebra, John P. Sfakianos, Kimaada Allette, Wenhui Wang, Seungyeul Yoo, Nina Bhardwaj, Eric E. Schadt, Xin Yao, Matthew D. Galsky and Jun Zhu

    Citation: Genome Medicine 2020 12:24

    Content type: Research

    Published on:

  39. Cell-free tumor-derived DNA (ctDNA) allows non-invasive monitoring of cancers, but its utility in renal cell cancer (RCC) has not been established.

    Authors: Christopher G. Smith, Tina Moser, Florent Mouliere, Johanna Field-Rayner, Matthew Eldridge, Anja L. Riediger, Dineika Chandrananda, Katrin Heider, Jonathan C. M. Wan, Anne Y. Warren, James Morris, Irena Hudecova, Wendy N. Cooper, Thomas J. Mitchell, Davina Gale, Andrea Ruiz-Valdepenas…

    Citation: Genome Medicine 2020 12:23

    Content type: Research

    Published on:

  40. T cells exhibit heterogeneous functional states in the tumor microenvironment. Immune checkpoint inhibitors (ICIs) can reinvigorate only the stem cell-like progenitor exhausted T cells, which suggests that inh...

    Authors: Kyungsoo Kim, Seyeon Park, Seong Yong Park, Gamin Kim, Su Myeong Park, Jae-Won Cho, Da Hee Kim, Young Min Park, Yoon Woo Koh, Hye Ryun Kim, Sang-Jun Ha and Insuk Lee

    Citation: Genome Medicine 2020 12:22

    Content type: Research

    Published on:

  41. Despite growing numbers of immune checkpoint blockade (ICB) trials with available omics data, it remains challenging to evaluate the robustness of ICB response and immune evasion mechanisms comprehensively. To...

    Authors: Jingxin Fu, Karen Li, Wubing Zhang, Changxin Wan, Jing Zhang, Peng Jiang and X. Shirley Liu

    Citation: Genome Medicine 2020 12:21

    Content type: Database

    Published on:

  42. Bevacizumab, a monoclonal antibody against soluble VEGFA, is an approved and commonly administered anti-angiogenic drug in patients with metastasized colorectal cancer (mCRC). The survival benefit of anti-VEGF...

    Authors: Qing Zhou, Samantha O. Perakis, Peter Ulz, Sumitra Mohan, Jakob M. Riedl, Emina Talakic, Sigurd Lax, Martin Tötsch, Gerald Hoefler, Thomas Bauernhofer, Martin Pichler, Armin Gerger, Jochen B. Geigl, Ellen Heitzer and Michael R. Speicher

    Citation: Genome Medicine 2020 12:20

    Content type: Research

    Published on:

  43. Midbrain dopaminergic neurons (MDN) represent 0.0005% of the brain’s neuronal population and mediate cognition, food intake, and metabolism. MDN are also posited to underlay the neurobiological dysfunction of ...

    Authors: Sergio Espeso-Gil, Tobias Halene, Jaroslav Bendl, Bibi Kassim, Gabriella Ben Hutta, Marina Iskhakova, Neda Shokrian, Pavan Auluck, Behnam Javidfar, Prashanth Rajarajan, Sandhya Chandrasekaran, Cyril J. Peter, Alanna Cote, Rebecca Birnbaum, Will Liao, Tyler Borrman…

    Citation: Genome Medicine 2020 12:19

    Content type: Research

    Published on:

  44. The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) aims to provide the conditions necessary for building a secure, flexible, and decentralized digital health infrast...

    Authors: F. M. Aarestrup, A. Albeyatti, W. J. Armitage, C. Auffray, L. Augello, R. Balling, N. Benhabiles, G. Bertolini, J. G. Bjaalie, M. Black, N. Blomberg, P. Bogaert, M. Bubak, B. Claerhout, L. Clarke, B. De Meulder…

    Citation: Genome Medicine 2020 12:18

    Content type: Opinion

    Published on:

  45. Gastric cancer is among the most lethal human malignancies. Previous studies have identified molecular aberrations that constitute dynamic biological networks and genomic complexities of gastric tumors. Howeve...

    Authors: Jason K. Sa, Jung Yong Hong, In-Kyoung Lee, Ju-sun Kim, Moon-Hee Sim, Ha Jung Kim, Ji Yeong An, Tae Sung Sohn, Joon Ho Lee, Jae Moon Bae, Sung Kim, Kyoung-Mee Kim, Seung Tae Kim, Se Hoon Park, Joon Oh Park, Ho Yeong Lim…

    Citation: Genome Medicine 2020 12:17

    Content type: Research

    Published on:

  47. While clinical factors such as age, grade, stage, and histological subtype provide physicians with information about patient prognosis, genomic data can further improve these predictions. Previous studies have...

    Authors: Ajay Chatrath, Roza Przanowska, Shashi Kiran, Zhangli Su, Shekhar Saha, Briana Wilson, Takaaki Tsunematsu, Ji-Hye Ahn, Kyung Yong Lee, Teressa Paulsen, Ewelina Sobierajska, Manjari Kiran, Xiwei Tang, Tianxi Li, Pankaj Kumar, Aakrosh Ratan…

    Citation: Genome Medicine 2020 12:15

    Content type: Research

    Published on:

  48. Exome sequencing (ES) is a first-tier diagnostic test for many suspected Mendelian disorders. While it is routine to detect small sequence variants, it is not a standard practice in clinical settings to detect...

    Authors: Ramakrishnan Rajagopalan, Jill R. Murrell, Minjie Luo and Laura K. Conlin

    Citation: Genome Medicine 2020 12:14

    Content type: Research

    Published on:

  49. For the majority of rare clinical missense variants, pathogenicity status cannot currently be classified. Classical homocystinuria, characterized by elevated homocysteine in plasma and urine, is caused by vari...

    Authors: Song Sun, Jochen Weile, Marta Verby, Yingzhou Wu, Yang Wang, Atina G. Cote, Iosifina Fotiadou, Julia Kitaygorodsky, Marc Vidal, Jasper Rine, Pavel Ješina, Viktor Kožich and Frederick P. Roth

    Citation: Genome Medicine 2020 12:13

    Content type: Research

    Published on:

  50. Cystic fibrosis is the most common autosomal recessive genetic disease in Caucasians. It is caused by mutations in the CFTR gene, leading to poor hydration of mucus and impairment of the respiratory, digestive, a...

    Authors: Gargi Dayama, Sambhawa Priya, David E. Niccum, Alexander Khoruts and Ran Blekhman

    Citation: Genome Medicine 2020 12:12

    Content type: Research

    Published on:

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