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Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
- Hao Zhu,
- Jiao Zhang,
- Soumya Rao,
- Matthew D. Durbin,
- Ying Li,
- Ruirui Lang,
- Jiqiang Liu,
- Baichuan Xiao,
- Hailin Shan,
- Ziqiu Meng,
- Jinmo Wang,
- Xiaokai Tang,
- Zhenni Shi,
- Liza L. Cox,
- Shouqin Zhao,
- Stephanie M. Ware,
- Tiong Y. Tan,
- Michelle de Silva,
- Lyndon Gallacher,
- Ting Liu,
- Jie Mi,
- Changqing Zeng,
- Hou-Feng Zheng,
- Qingguo Zhang,
- Stylianos E. Antonarakis,
- Timothy C. Cox,
- and Yong-Biao Zhang
Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
...). Multiple factors affect the penetrance of P/LP variants, including genetic variants such as eQTLs regulating the expression of the trans-alleles, cis regulatory variation (cis eQTLs), genetic modifiers unlinked with the causative gene, polygenic risk, imprinting, epigenetic regulation, and environmental...
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Research: The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome
- Young-Lim Lee,
- Aniek C. Bouwman,
- Chad Harland,
- Mirte Bosse,
- Gabriel Costa Monteiro Moreira,
- Roel F. Veerkamp,
- Erik Mullaart,
- Nadine Cambisano,
- Martien A.M. Groenen,
- Latifa Karim,
- Wouter Coppieters,
- Michel Georges,
- and Carole Charlier
Genome Res. September 2023 33: 1455-1464; Published in Advance October 4, 2023, doi:10.1101/gr.277884.123
...: 667–679. doi:10.1016/j.ajhg.2016.02.018 ↵Brandler WM, Antaki D, Gujral M, Kleiber ML, Whitney J, Maile MS, Hong O, Chapman TR, Tan S, Tandon P, et al. 2018. Paternally inherited cis-regulatory structural variants are associated with autism. Science 360: 327–331. doi:10.1126/science.aan2261 ↵Collins RL...
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Research: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
- Angelo A. Ruggieri,
- Luca Livraghi,
- James J. Lewis,
- Elizabeth Evans,
- Francesco Cicconardi,
- Laura Hebberecht,
- Yadira Ortiz-Ruiz,
- Stephen H. Montgomery,
- Alfredo Ghezzi,
- José Arcadio Rodriguez-Martinez,
- Chris D. Jiggins,
- W. Owen McMillan,
- Brian A. Counterman,
- Riccardo Papa,
- and Steven M. Van Belleghem
Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122
...the and their overall distribution was similarly affected by linked selection as single nucleotide substitutions. Using chromatin accessibility profiles (i.e., ATAC-seq) of head tissue in caterpillars to identify sequences with potential cis-regulatory function, we found that out of the 31,066 identified differences...
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Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
- Benjamin J. Auerbach,
- Jian Hu,
- Muredach P. Reilly,
- and Mingyao Li
Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
...to be a promising approach toward modeling the role of genomic variants in cis regulatory logic. In particular, CNNs have already shown great promise in modeling the contribution of promoter genetic variation on mean gene expression levels. Agarwal and Shendure (2020) first introduced their algorithm, Xpresso...
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Methods: Localization of a long-range cis-regulatory element of IL13 by allelic transcript ratio mapping
- Julian T. Forton,
- Irina A. Udalova,
- Susana Campino,
- Kirk A. Rockett,
- Jeremy Hull,
- and Dominic P. Kwiatkowski
Genome Res. January 2007 17: 82-87; Published in Advance November 29, 2006, doi:10.1101/gr.5663007
...by locating a highly significant cis -regulatory element operating on IL13 at long range from a position 250 kb upstream from the gene ( P = 2 × 10 −6 ). As this method is unaffected by other sources of variation, such as environmental and trans -acting genetic factors, it provides a tractable approach...
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Research: Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes
- Eric R. Lucas,
- Alistair Miles,
- Nicholas J. Harding,
- Chris S. Clarkson,
- Mara K.N. Lawniczak,
- Dominic P. Kwiatkowski,
- David Weetman,
- Martin J. Donnelly,
- and The Anopheles gambiae 1000 Genomes Consortium
Genome Res. August 2019 29: 1250-1261; Published in Advance July 25, 2019, doi:10.1101/gr.245795.118
...countries intensifies and as the operational deployment of next-generation bed nets targeting metabolic resistance gathers pace. Our detailed descriptions of CNVs found across the species range provide the tools to do so.Copy number variants (CNVs) are a form of genetic variation that occur when a genomic...
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LETTER: Long-range DNase I hypersensitivity mapping reveals the imprinted Igf2r and Air promoters share cis-regulatory elements
- Florian M. Pauler,
- Stefan H. Stricker,
- Katarzyna E. Warczok,
- and Denise P. Barlow
Genome Res. October 2005 15: 1379-1387; doi:10.1101/gr.3783805
...Long-range DNase I hypersensitivity mapping reveals the imprinted Igf2r and Air promoters share cis -regulatory elements Florian M. Pauler , Stefan H. Stricker , Katarzyna E. Warczok , and Denise P. Barlow 1 CeMM Research Center...
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Method: A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening
- Yarui Diao,
- Bin Li,
- Zhipeng Meng,
- Inkyung Jung,
- Ah Young Lee,
- Jesse Dixon,
- Lenka Maliskova,
- Kun-liang Guan,
- Yin Shen,
- and Bing Ren
Genome Res. March 2016 26: 397-405; Published in Advance January 26, 2016, doi:10.1101/gr.197152.115
...to common human diseases (Maurano et al. 2012; Roadmap Epigenomics Consortium et al. 2015). A major bottleneck in advancing this hypothesis is a lack of high-throughputmeans to functionally characterize the large number of predicted cis-regulatory elements with regard to their contributions to target gene...
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Method: Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort
- Christopher M. Vockley,
- Cong Guo,
- William H. Majoros,
- Michael Nodzenski,
- Denise M. Scholtens,
- M. Geoffrey Hayes,
- William L. Lowe, Jr.,
- and Timothy E. Reddy
Genome Res. August 2015 25: 1206-1214; Published in Advance June 17, 2015, doi:10.1101/gr.190090.115
..., Gutierrez-Arcelus M, Panousis NI, et al. 2013. Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science 342: 744–747. ↵Kwasnieski JC, Mogno I, Myers CA, Corbo JC, Cohen BA. 2012. Complex effects of nucleotide variants in a mammalian cis-regulatory element...
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Resource: Mapping DNA structural variation in dogs
- Wei-Kang Chen,
- Joshua D. Swartz,
- Laura J. Rush,
- and Carlos E. Alvarez
Genome Res. March 2009 19: 500-509; Published in Advance November 17, 2008, doi:10.1101/gr.083741.108
...predisposes to Crohn disease of the colon . Am. J. Hum. Genet. 79 : 439 – 448 . ↵ Ferretti, V. , Poitras, C. , Bergeron, D. , Coulombe, B. , Robert, F. , Blanchette, M. ( 2007 ) PReMod: A database of -wide mammalian cis -regulatory module predictions . Nucleic Acids Res. 35 : D122 – D126 . ↵ Freeman, J...

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