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Non-human and non-rodent vertebrate genomics

Section edited by Shane Burgess and Jacqueline Smith

This section covers all aspects of the genomics of vertebrates, excluding humans, primates and rodents, including livestock species.

Page 1 of 18

  1. Content type: Research article

    The comparison of expression QTL (eQTL) maps obtained in different tissues is an essential step to understand how gene expression is genetically regulated in a context-dependent manner. In the current work, we...

    Authors: Rayner González-Prendes, Emilio Mármol-Sánchez, Raquel Quintanilla, Anna Castelló, Ali Zidi, Yuliaxis Ramayo-Caldas, Tainã Figueiredo Cardoso, Arianna Manunza, Ángela Cánovas and Marcel Amills

    Citation: BMC Genomics 2019 20:518

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  2. Content type: Research article

    Long non-coding RNAs (lncRNAs) perform crucial roles in biological process involving complex mechanisms. However, information regarding their abundance, characteristics and potential functions linked to fish s...

    Authors: Mingkun Luo, Lanmei Wang, Haoran Yin, Wenbin Zhu, Jianjun Fu and Zaijie Dong

    Citation: BMC Genomics 2019 20:515

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  3. Content type: Research article

    Dermal papilla cells (DPCs), the “signaling center” of hair follicle (HF), delicately master continual growth of hair in mammals including cashmere, the fine fiber annually produced by secondary HF embedded in...

    Authors: Sen Ma, Ying Wang, Guangxian Zhou, Yi Ding, Yuxin Yang, Xiaolong Wang, Enping Zhang and Yulin Chen

    Citation: BMC Genomics 2019 20:512

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  4. Content type: Research article

    In female mammals, the initiation of puberty, coupling with the dramatically morphological changes in ovaries, indicates the sexual and follicular maturation. Previous studies have suggested that the disrupted...

    Authors: Xiaolong Yuan, Shaopan Ye, Zitao Chen, Xiangchun Pan, Shuwen Huang, Zhonghui Li, Yuyi Zhong, Ning Gao, Hao Zhang, Jiaqi Li and Zhe Zhang

    Citation: BMC Genomics 2019 20:510

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  5. Content type: Research article

    Livestock production aims to provide meats of high and consistent eating quality. Insufficient intramuscular (IM) fat and excessive subcutaneous (SC) fat are paramount pork quality challenges. IM fat and SC fa...

    Authors: Wenjing Wu, Dawei Zhang, Yajun Yin, Miao Ji, Ke Xu, Xin Huang, Yongjia Peng and Jin Zhang

    Citation: BMC Genomics 2019 20:509

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  6. Content type: Research article

    We present results from a computational analysis developed to integrate transcriptome and metabolomic data in order to explore the heat stress response in the liver of the modern broiler chicken. Heat stress i...

    Authors: Allen H. Hubbard, Xiaoke Zhang, Sara Jastrebski, Abhyudai Singh and Carl Schmidt

    Citation: BMC Genomics 2019 20:502

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  7. Content type: Research article

    Understanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one of the most essential tasks to develop appropriate genetic improvement programs.

    Authors: Lingyang Xu, Liu Yang, Bo Zhu, Wengang Zhang, Zezhao Wang, Yan Chen, Lupei Zhang, Xue Gao, Huijiang Gao, George E. Liu and Junya Li

    Citation: BMC Genomics 2019 20:494

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  8. Content type: Research article

    Epigenetic variation may result from selection for complex traits related to metabolic processes or appear in the course of adaptation to mediate responses to exogenous stressors. Moreover epigenetic marks, in...

    Authors: Siriluck Ponsuksili, Nares Trakooljul, Sajjanar Basavaraj, Frieder Hadlich, Eduard Murani and Klaus Wimmers

    Citation: BMC Genomics 2019 20:492

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  9. Content type: Research article

    Mycobacterium avium subsp. paratuberculosis (MAP), the etiologic agent of Johne’s disease is spread between cattle via the fecal-oral route, yet the functional changes in the salivary gland associated with infect...

    Authors: Sanjay Mallikarjunappa, Mounir Adnane, Paul Cormican, Niel A. Karrow and Kieran G. Meade

    Citation: BMC Genomics 2019 20:491

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  10. Content type: Research article

    Global biodiversity is decreasing at an alarming rate and amphibians are at the forefront of this crisis. Understanding the factors that negatively impact amphibian populations and effectively monitoring their...

    Authors: Timothy A. Clay, Michael A. Steffen, Michael L. Treglia, Carolyn D. Torres, Ana Lilia Trujano-Alvarez and Ronald M. Bonett

    Citation: BMC Genomics 2019 20:482

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  11. Content type: Research article

    When puberty starts before males reach harvest size, animal welfare and sustainability issues occur in Atlantic salmon (Salmo salar) aquaculture. Hallmarks of male puberty are an increased proliferation activity ...

    Authors: Diego Crespo, Jan Bogerd, Elisabeth Sambroni, Florence LeGac, Eva Andersson, Rolf B. Edvardsen, Elisabeth Jönsson Bergman, Björn Thrandur Björnsson, Geir Lasse Taranger and Rüdiger W. Schulz

    Citation: BMC Genomics 2019 20:475

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  12. Content type: Research article

    The improvement of feed efficiency is a key economic goal within the pig production industry. The objective of this study was to examine transcriptomic differences in both the liver and muscle of pigs divergen...

    Authors: Stafford Vigors, John V. O’Doherty, Kenneth Bryan and Torres Sweeney

    Citation: BMC Genomics 2019 20:461

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  13. Content type: Research article

    Hibernation is a physiological state exploited by many animals exposed to prolonged adverse environmental conditions associated with winter. Large changes in metabolism and cellular function occur, with many s...

    Authors: Alexander Capraro, Denis O’Meally, Shafagh A. Waters, Hardip R. Patel, Arthur Georges and Paul D. Waters

    Citation: BMC Genomics 2019 20:460

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  14. Content type: Research article

    Recent advances in genomics have greatly increased research opportunities for non-model species. For wildlife, a growing availability of reference genomes means that population genetics is no longer restricted...

    Authors: Belinda Wright, Katherine A. Farquharson, Elspeth A. McLennan, Katherine Belov, Carolyn J. Hogg and Catherine E. Grueber

    Citation: BMC Genomics 2019 20:453

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  15. Content type: Research article

    Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be ident...

    Authors: Octávio Augusto Costa Almeida, Gabriel Costa Monteiro Moreira, Fernanda Marcondes Rezende, Clarissa Boschiero, Jane de Oliveira Peixoto, Adriana Mercia Guaratini Ibelli, Mônica Corrêa Ledur, Francisco José de Novais and Luiz Lehmann Coutinho

    Citation: BMC Genomics 2019 20:449

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  16. Content type: Research article

    Under caged conditions, birds are affected more severely by environmental stressors such as dietary structure, activity space, human disturbances, and pathogens, which may be reflected in the gene expression i...

    Authors: Yu Wang, Jinxin Guo, Lin Wang, Hengjiu Tian and Jinling Sui

    Citation: BMC Genomics 2019 20:447

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  17. Content type: Research article

    Accompanied with rapid growth and high density aquaculture, gibel carp has been seriously threatened by Carassius auratus herpesvirus (CaHV) since 2012. In previous study, distinct CaHV resistances and immune res...

    Authors: Wei-Jia Lu, Fan-Xiang Gao, Yang Wang, Qi-Ya Zhang, Zhi Li, Xiao-Juan Zhang, Li Zhou and Jian-Fang Gui

    Citation: BMC Genomics 2019 20:432

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  18. Content type: Research article

    To control the osmotic pressure in the body, physiological adjustments to salinity fluctuations require the fish to regulate body fluid homeostasis in relation to environmental change via osmoregulation. Previ...

    Authors: Maoliang Su, Jianan Zhou, Zhengyu Duan and Junbin Zhang

    Citation: BMC Genomics 2019 20:418

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  19. Content type: Research article

    Immediately after birth, the porcine intestine rapidly develops morphologically, functionally, and immunologically. The jejunum, the second part of the small intestine, is of importance for nutrient uptake and...

    Authors: Dirkjan Schokker, Ina Hulsegge, Henri Woelders and Johanna M. J. Rebel

    Citation: BMC Genomics 2019 20:414

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  20. Content type: Methodology article

    China has the richest local chicken breeding resources in the world and is the world’s second largest producer of meat-type chickens. Development of a moderate-density SNP array for genetic analysis of chicken...

    Authors: Ranran Liu, Siyuan Xing, Jie Wang, Maiqing Zheng, Huanxian Cui, Richard P. M. A. Crooijmans, Qinghe Li, Guiping Zhao and Jie Wen

    Citation: BMC Genomics 2019 20:410

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  21. Content type: Research article

    Overfeeding reduces laying performance in broiler breeder hens, which is associated with obesity, hepatic steatosis and systemic inflammation. To unravel the underlying mechanisms governing the effect of feedi...

    Authors: Zehui Wei, Pengcheng Li, Sijia Huang, Purevsuren Lkhagvagarav, Mengqi Zhu, Chuanyu Liang and Cunling Jia

    Citation: BMC Genomics 2019 20:408

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  22. Content type: Research article

    Fertility in dairy cows depends on ovarian cyclicity and on uterine involution. Ovarian cyclicity and uterine involution are delayed when there is uterine dysbiosis (overgrowth of pathogenic bacteria). Fertili...

    Authors: Stephen G. Moore, Aaron C. Ericsson, Susanta K. Behura, William R. Lamberson, Timothy J. Evans, Matthew S. McCabe, Scott E. Poock and Matthew C. Lucy

    Citation: BMC Genomics 2019 20:405

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  23. Content type: Research article

    Human milk oligosaccharides (OS) play a key role in brain and gut microbiota development of the neonate, but the underlying biosynthetic steps of OS in the mammary gland are still largely unknown. As bovine mi...

    Authors: Nina A. Poulsen, Randall C. Robinson, Daniela Barile, Lotte B. Larsen and Bart Buitenhuis

    Citation: BMC Genomics 2019 20:404

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  24. Content type: Research article

    Through precise implementation of distinct cell type specification programs, differentially regulated in both space and time, complex patterns emerge during organogenesis. Thanks to its easy experimental acces...

    Authors: Christian Feregrino, Fabio Sacher, Oren Parnas and Patrick Tschopp

    Citation: BMC Genomics 2019 20:401

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  25. Content type: Research article

    Adenovirus protein, Gam1, triggers the proteolytic destruction of the E1 SUMO-activating enzyme. Microinjection of an empirically determined amount of Gam1 mRNA into one-cell Xenopus embryos can reduce SUMOylatio...

    Authors: Michelle M. Bertke, Kyle M. Dubiak, Laura Cronin, Erliang Zeng and Paul W. Huber

    Citation: BMC Genomics 2019 20:386

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  26. Content type: Research article

    Copy number variations (CNVs), which are genetic variations present throughout mammalian genomes, are a vital source of phenotypic variation that can lead to the development of unique traits. In this study we ...

    Authors: Congjun Jia, Hongbo Wang, Chen Li, Xiaoyun Wu, Linsen Zan, Xuezhi Ding, Xian Guo, Pengjia Bao, Jie Pei, Min Chu, Chunnian Liang and Ping Yan

    Citation: BMC Genomics 2019 20:376

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  27. Content type: Research article

    Dysregulation of adipogenesis causes metabolic diseases, like obesity and fatty liver. Migratory birds such as geese have a high tolerance of massive energy intake and exhibit little pathological development. ...

    Authors: Guosong Wang, Long Jin, Yan Li, Qianzi Tang, Silu Hu, Hengyong Xu, Clare A. Gill, Mingzhou Li and Jiwen Wang

    Citation: BMC Genomics 2019 20:372

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  28. Content type: Research article

    Palatoschisis or cleft palate is a known anomaly in pigs resulting in their death. However, little is known about its aetiology. A detailed description of the phenotype was derived from necropsy and by compute...

    Authors: Alexander Grahofer, Anna Letko, Irene Monika Häfliger, Vidhya Jagannathan, Alain Ducos, Olivia Richard, Vanessa Peter, Heiko Nathues and Cord Drögemüller

    Citation: BMC Genomics 2019 20:349

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  29. Content type: Research article

    Our understanding of the pig transcriptome is limited. RNA transcript diversity among nine tissues was assessed using poly(A) selected single-molecule long-read isoform sequencing (Iso-seq) and Illumina RNA se...

    Authors: H. Beiki, H. Liu, J. Huang, N. Manchanda, D. Nonneman, T. P. L. Smith, J. M. Reecy and C. K. Tuggle

    Citation: BMC Genomics 2019 20:344

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  30. Content type: Research article

    Elevated water temperature, as is expected through climate change, leads to masculinization in fish species with sexual plasticity, resulting in changes in population dynamics. These changes are one important ...

    Authors: Shahrbanou Hosseini, Ngoc-Thuy Ha, Henner Simianer, Clemens Falker-Gieske, Bertram Brenig, Andre Franke, Gabriele Hörstgen-Schwark, Jens Tetens, Sebastian Herzog and Ahmad Reza Sharifi

    Citation: BMC Genomics 2019 20:341

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  31. Content type: Research article

    Artificial induction of mutagenesis is effective for genetic resource innovation and breeding. However, the traditional mutation methods for fish breeding are not convenient or safe for daily use. Hence, devel...

    Authors: Hou Ji-Lun, Zhang Xiao-Yan, Wang Gui-Xing, Sun Zhao-Hui, Du Wei, Zhao Ya-Xian, Si Fei, Wang Li-Yan, Xing Xin-Hui and Wang Yu-Fen

    Citation: BMC Genomics 2019 20:323

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  32. Content type: Research article

    In this study we integrated the CNV (copy number variation) and WssGWAS (weighted single-step approach for genome-wide association) analyses to increase the knowledge about number of piglets born alive, an eco...

    Authors: Nedenia Bonvino Stafuzza, Rafael Medeiros de Oliveira Silva, Breno de Oliveira Fragomeni, Yutaka Masuda, Yijian Huang, Kent Gray and Daniela A. Lino Lourenco

    Citation: BMC Genomics 2019 20:321

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  33. Content type: Research article

    Though intensive genetic selection has led to extraordinary advances in growth rate and feed efficiency in production of meat-type chickens, endocrine processes controlling these traits are still poorly unders...

    Authors: Laura E. Ellestad, Larry A. Cogburn, Jean Simon, Elisabeth Le Bihan-Duval, Samuel E. Aggrey, Mardi S. Byerly, Michel J. Duclos and Tom E. Porter

    Citation: BMC Genomics 2019 20:316

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  34. Content type: Research article

    Early development of an oviparous organism is based on maternally stocked structural, nutritional and regulatory components. These components influence the future developmental potential of an embryo, which is...

    Authors: Teshome Tilahun Bizuayehu, Maren Mommens, Arvind Y. M. Sundaram, Anusha K. S. Dhanasiri and Igor Babiak

    Citation: BMC Genomics 2019 20:315

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  35. Content type: Research article

    Cattle populations are highly amenable to the genetic mapping of male reproductive traits because longitudinal data on ejaculate quality and dense microarray-derived genotypes are available for thousands of ar...

    Authors: Terhi Iso-Touru, Christine Wurmser, Heli Venhoranta, Maya Hiltpold, Tujia Savolainen, Anu Sironen, Konrad Fischer, Krzysztof Flisikowski, Ruedi Fries, Alejandro Vicente-Carrillo, Manuel Alvarez-Rodriguez, Szabolcs Nagy, Mervi Mutikainen, Jaana Peippo, Juhani Taponen, Goutam Sahana…

    Citation: BMC Genomics 2019 20:286

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  36. Content type: Research article

    The interferon-induced transmembrane (IFITM) protein family comprises a class of restriction factors widely characterised in humans for their potent antiviral activity. Their biological activity is well docume...

    Authors: Irene Bassano, Swee Hoe Ong, Maximo Sanz-Hernandez, Michal Vinkler, Adebabay Kebede, Olivier Hanotte, Ebele Onuigbo, Mark Fife and Paul Kellam

    Citation: BMC Genomics 2019 20:272

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  37. Content type: Research article

    The Russian White is a gene pool breed, registered in 1953 after crossing White Leghorns with local populations and, for 50 years, selected for cold tolerance and high egg production (EL). The breed has great ...

    Authors: Andrei A. Kudinov, Natalia V. Dementieva, Olga V. Mitrofanova, Olga I. Stanishevskaya, Elena S. Fedorova, Tatiana A. Larkina, Arina I. Mishina, Kirill V. Plemyashov, Darren K. Griffin and Michael N. Romanov

    Citation: BMC Genomics 2019 20:270

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  38. Content type: Research article

    Fertility is among the most important economic traits in dairy cattle. Genomic prediction for cow fertility has received much attention in the last decade, while bull fertility has been largely overlooked. The...

    Authors: Juan Pablo Nani, Fernanda M. Rezende and Francisco Peñagaricano

    Citation: BMC Genomics 2019 20:258

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  39. Content type: Research article

    An unfavorable genetic correlation between milk production and fertility makes simultaneous improvement of milk production and fertility difficult in cattle breeding. Rapid genetic improvement in milk producti...

    Authors: Zexi Cai, Bernt Guldbrandtsen, Mogens Sandø Lund and Goutam Sahana

    Citation: BMC Genomics 2019 20:255

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  40. Content type: Research article

    Placental efficiency (PE) describes the relationship between placental and fetal weights (fetal wt/placental wt). Within litters, PE can vary drastically, resulting in similarly sized pigs associated with diff...

    Authors: Shanice K. Krombeen, Vijay Shankar, Rooksana E. Noorai, Christopher A. Saski, Julia L. Sharp, Matthew E. Wilson and Tiffany A. Wilmoth

    Citation: BMC Genomics 2019 20:254

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  41. Content type: Research article

    Marek’s disease virus (MDV) is an oncogenic herpesvirus that can cause T-cell lymphomas in chicken. Long noncoding RNA (lncRNA) is strongly associated with various cancers and many other diseases. In chickens,...

    Authors: Zhen You, Qinghe Zhang, Changjun Liu, Jiuzhou Song, Ning Yang and Ling Lian

    Citation: BMC Genomics 2019 20:245

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  42. Content type: Research article

    Lactation and associated metabolic stresses during the post-partum period have been shown to impair fertility in dairy cows. The oviduct plays key roles in embryo development and the establishment of pregnancy...

    Authors: Yann Locatelli, Niamh Forde, Helmut Blum, Alexander Graf, Benoît Piégu, Pascal Mermillod, Eckhard Wolf, Patrick Lonergan and Marie Saint-Dizier

    Citation: BMC Genomics 2019 20:233

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  43. Content type: Research article

    Monogenean flatworms are the main fish ectoparasites inflicting serious economic losses in aquaculture. The polyopisthocotylean Sparicotyle chrysophrii parasitizes the gills of gilthead sea bream (GSB, Sparus aur...

    Authors: M. Carla Piazzon, Ivona Mladineo, Fernando Naya-Català, Ron P. Dirks, Susanne Jong-Raadsen, Anamarija Vrbatović, Jerko Hrabar, Jaume Pérez-Sánchez and Ariadna Sitjà-Bobadilla

    Citation: BMC Genomics 2019 20:200

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  44. Content type: Research article

    Copy number variations (CNVs) are structural variants consisting of large-scale insertions and deletions of genomic fragments. Exploring CNVs and estimating their effects on phenotypes are useful for genome se...

    Authors: Mei Liu, Lingzhao Fang, Shuli Liu, Michael G. Pan, Eyal Seroussi, John B. Cole, Li Ma, Hong Chen and George E. Liu

    Citation: BMC Genomics 2019 20:181

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  45. Content type: Research article

    The power of genome-wide association studies (GWAS) is often limited by the sample size available for the analysis. Milk fatty acid (FA) traits are scarcely recorded due to expensive and time-consuming analyti...

    Authors: G. Gebreyesus, A. J. Buitenhuis, N. A. Poulsen, M. H. P. W. Visker, Q. Zhang, H. J. F. van Valenberg, D. Sun and H. Bovenhuis

    Citation: BMC Genomics 2019 20:178

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  46. Content type: Research article

    With the unprecedented rapid growth rate (up to 2.75 cm/day), velvet antler is an invaluable model for the identification of potent growth factors and signaling networks for extremely fast growing tissues, mai...

    Authors: Hengxing Ba, Datao Wang, Tung On Yau, Yudong Shang and Chunyi Li

    Citation: BMC Genomics 2019 20:173

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