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Method: Three-dimensional missense tolerance ratio analysis
- Riley E. Perszyk,
- Anders S. Kristensen,
- Polina Lyuboslavsky,
- and Stephen F. Traynelis
Genome Res. August 2021 31: 1447-1461; Published in Advance July 22, 2021, doi:10.1101/gr.275528.121
...in the healthy population and is a hotspot for disease-associated variants.Despite providing insight into critical regions of a protein that are tolerant or intolerant to change, the MTR algorithm could still become a more accurate in silico predictor for pathogenicity of variants identified in patients...
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Perspective: Human genomic disease variants: A neutral evolutionary explanation
- Joel T. Dudley,
- Yuseob Kim,
- Li Liu,
- Glenn J. Markov,
- Kristyn Gerold,
- Rong Chen,
- Atul J. Butte,
- and Sudhir Kumar
Genome Res. August 2012 22: 1383-1394; Published in Advance June 4, 2012, doi:10.1101/gr.133702.111
...neutral evolutionary origins (previously neutral), with a relatively smaller fraction exhibiting adaptive evolutionary origins (previously adaptive). This pattern is expected to hold true for common as well as rare disease variants. Ultimately, a neutral evolutionary perspective will provide medicine...
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Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...development may also contribute to psychiatric disease risk.Most genes have been associated with at least one regulatory eQTL. However, protein-coding mutations are relatively rare. We reasoned that genes harboring rare deleterious coding mutations might also be regulated by common variants...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...to the Undiagnosed Diseases Network patient data set, Watershed-SV identified more disease-relevant rare SV candidates than CADD-SV, offering valuable insights into gene disruption mechanisms. These evolving tools promote a more comprehensive and accurate evaluation of variant effects. While these tools help...
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Research: Identification and validation of supervariants reveal novel loci associated with human white matter microstructure
- Shiying Wang,
- Ting Li,
- Bingxin Zhao,
- Wei Dai,
- Yisha Yao,
- Cai Li,
- Tengfei Li,
- Hongtu Zhu,
- and Heping Zhang
Genome Res. January 2024 34: 20-33; Published in Advance December 12, 2023, doi:10.1101/gr.277905.123
...genetic variants located in genes that have been related to brain structures, cognitive functions, and neuropsychiatric diseases. Our findings provide a better understanding of the genetic architecture underlying white matter microstructure.White matter, as an essential part of the central nervous system...
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Research: Growth disrupting mutations in epigenetic regulatory molecules are associated with abnormalities of epigenetic aging
- Aaron R. Jeffries,
- Reza Maroofian,
- Claire G. Salter,
- Barry A. Chioza,
- Harold E. Cross,
- Michael A. Patton,
- Emma Dempster,
- I. Karen Temple,
- Deborah J.G. Mackay,
- Faisal I. Rezwan,
- Lise Aksglaede,
- Diana Baralle,
- Tabib Dabir,
- Matthew F. Hunter,
- Arveen Kamath,
- Ajith Kumar,
- Ruth Newbury-Ecob,
- Angelo Selicorni,
- Amanda Springer,
- Lionel Van Maldergem,
- Vinod Varghese,
- Naomi Yachelevich,
- Katrina Tatton-Brown,
- Jonathan Mill,
- Andrew H. Crosby,
- and Emma L. Baple
Genome Res. July 2019 29: 1057-1066; Published in Advance June 3, 2019, doi:10.1101/gr.243584.118
...are not strongly influenced by cell-type variation. We used DMRcate (Peters et al. 2015) to identify spatially correlated regions of differential DNA methylation significantly associated with the DNMT3A c.2312G > A; p.(Arg771Gln) variant, identifying 388 autosomal differentially methylated regions (DMRs) (for...
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Research: Genome-wide analysis of differential RNA editing in epilepsy
- Prashant Kumar Srivastava,
- Marta Bagnati,
- Andree Delahaye-Duriez,
- Jeong-Hun Ko,
- Maxime Rotival,
- Sarah R. Langley,
- Kirill Shkura,
- Manuela Mazzuferi,
- Bénédicte Danis,
- Jonathan van Eyll,
- Patrik Foerch,
- Jacques Behmoaras,
- Rafal M. Kaminski,
- Enrico Petretto,
- and Michael R. Johnson
Genome Res. March 2017 27: 440-450; doi:10.1101/gr.210740.116
...(Hauser et al. 1993; Prinz 2008). Epilepsy can develop following brain injury or as a consequence of genetic predisposition (Speed et al. 2014). Large-scale mapping of common and rare gene variants has identified several genes that confer risk for genetic epilepsy (Allen et al. 2013; Euro...
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Research: Integrative analysis of the melanoma transcriptome
- Michael F. Berger,
- Joshua Z. Levin,
- Krishna Vijayendran,
- Andrey Sivachenko,
- Xian Adiconis,
- Jared Maguire,
- Laura A. Johnson,
- James Robinson,
- Roel G. Verhaak,
- Carrie Sougnez,
- Robert C. Onofrio,
- Liuda Ziaugra,
- Kristian Cibulskis,
- Elisabeth Laine,
- Jordi Barretina,
- Wendy Winckler,
- David E. Fisher,
- Gad Getz,
- Matthew Meyerson,
- David B. Jaffe,
- Stacey B. Gabriel,
- Eric S. Lander,
- Reinhard Dummer,
- Andreas Gnirke,
- Chad Nusbaum,
- and Levi A. Garraway
Genome Res. April 2010 20: 413-427; Published in Advance February 23, 2010, doi:10.1101/gr.103697.109
...high quality variant calls.We estimated that the sensitivity for detecting variant sequences is ;75% of that for calling reference genotypes. These variants identified by comparison to the human reference sequence are expected to consist of (in descending order of frequency) inherited polymorphisms...
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