A method to build extended sequence context models of point mutations and indels
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-022-35596-5
Download full text from publisher
References listed on IDEAS
- D. G. MacArthur & T. A. Manolio & D. P. Dimmock & H. L. Rehm & J. Shendure & G. R. Abecasis & D. R. Adams & R. B. Altman & S. E. Antonarakis & E. A. Ashley & J. C. Barrett & L. G. Biesecker & D. F. Co, 2014. "Guidelines for investigating causality of sequence variants in human disease," Nature, Nature, vol. 508(7497), pages 469-476, April.
- Heng Li & Richard Durbin, 2011. "Inference of human population history from individual whole-genome sequences," Nature, Nature, vol. 475(7357), pages 493-496, July.
- Augustine Kong & Michael L. Frigge & Gisli Masson & Soren Besenbacher & Patrick Sulem & Gisli Magnusson & Sigurjon A. Gudjonsson & Asgeir Sigurdsson & Aslaug Jonasdottir & Adalbjorg Jonasdottir & Wend, 2012. "Rate of de novo mutations and the importance of father’s age to disease risk," Nature, Nature, vol. 488(7412), pages 471-475, August.
- Konrad J. Karczewski & Laurent C. Francioli & Grace Tiao & Beryl B. Cummings & Jessica Alföldi & Qingbo Wang & Ryan L. Collins & Kristen M. Laricchia & Andrea Ganna & Daniel P. Birnbaum & Laura D. Gau, 2020. "The mutational constraint spectrum quantified from variation in 141,456 humans," Nature, Nature, vol. 581(7809), pages 434-443, May.
- Jedidiah Carlson & Adam E. Locke & Matthew Flickinger & Matthew Zawistowski & Shawn Levy & Richard M. Myers & Michael Boehnke & Hyun Min Kang & Laura J. Scott & Jun Z. Li & Sebastian Zöllner, 2018. "Extremely rare variants reveal patterns of germline mutation rate heterogeneity in humans," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Yingying Zhang & Alden K. Leung & Jin Joo Kang & Yu Sun & Guanxi Wu & Le Li & Jiayang Sun & Lily Cheng & Tian Qiu & Junke Zhang & Shayne D. Wierbowski & Shagun Gupta & James G. Booth & Haiyuan Yu, 2025. "A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
- Matt C. Danzi & Maike F. Dohrn & Sarah Fazal & Danique Beijer & Adriana P. Rebelo & Vivian Cintra & Stephan Züchner, 2023. "Deep structured learning for variant prioritization in Mendelian diseases," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
- Kian Hong Kock & Patrick K. Kimes & Stephen S. Gisselbrecht & Sachi Inukai & Sabrina K. Phanor & James T. Anderson & Gayatri Ramakrishnan & Colin H. Lipper & Dongyuan Song & Jesse V. Kurland & Julia M, 2024. "DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Scott D. Findlay & Lindsay Romo & Christopher B. Burge, 2024. "Quantifying negative selection in human 3ʹ UTRs uncovers constrained targets of RNA-binding proteins," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Kelley Harris & Rasmus Nielsen, 2013. "Inferring Demographic History from a Spectrum of Shared Haplotype Lengths," PLOS Genetics, Public Library of Science, vol. 9(6), pages 1-20, June.
- Bian Li & Dan M. Roden & John A. Capra, 2022. "The 3D mutational constraint on amino acid sites in the human proteome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Laurent Excoffier & Isabelle Dupanloup & Emilia Huerta-Sánchez & Vitor C Sousa & Matthieu Foll, 2013. "Robust Demographic Inference from Genomic and SNP Data," PLOS Genetics, Public Library of Science, vol. 9(10), pages 1-17, October.
- Stephanie M. Bilinovich & Kristy Lewis & Barbara L. Thompson & Jeremy W. Prokop & Daniel B. Campbell, 2020. "Environmental Epigenetics of Diesel Particulate Matter Toxicogenomics," IJERPH, MDPI, vol. 17(20), pages 1-13, October.
- Vincent Michaud & Eulalie Lasseaux & David J. Green & Dave T. Gerrard & Claudio Plaisant & Tomas Fitzgerald & Ewan Birney & Benoît Arveiler & Graeme C. Black & Panagiotis I. Sergouniotis, 2022. "The contribution of common regulatory and protein-coding TYR variants to the genetic architecture of albinism," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
- Natalie DeForest & Yuqi Wang & Zhiyi Zhu & Jacqueline S. Dron & Ryan Koesterer & Pradeep Natarajan & Jason Flannick & Tiffany Amariuta & Gina M. Peloso & Amit R. Majithia, 2024. "Genome-wide discovery and integrative genomic characterization of insulin resistance loci using serum triglycerides to HDL-cholesterol ratio as a proxy," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Emily Olfson & Luis C. Farhat & Wenzhong Liu & Lawrence A. Vitulano & Gwyneth Zai & Monicke O. Lima & Justin Parent & Guilherme V. Polanczyk & Carolina Cappi & James L. Kennedy & Thomas V. Fernandez, 2024. "Rare de novo damaging DNA variants are enriched in attention-deficit/hyperactivity disorder and implicate risk genes," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
- Fiona A. Hagenbeek & Jana S. Hirzinger & Sophie Breunig & Susanne Bruins & Dmitry V. Kuznetsov & Kirsten Schut & Veronika V. Odintsova & Dorret I. Boomsma, 2023. "Maximizing the value of twin studies in health and behaviour," Nature Human Behaviour, Nature, vol. 7(6), pages 849-860, June.
- Alexendar R. Perez & Laura Sala & Richard K. Perez & Joana A. Vidigal, 2021. "CSC software corrects off-target mediated gRNA depletion in CRISPR-Cas9 essentiality screens," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
- Zhijie Liao & Kuldeep Kumar & Jakub Kopal & Guillaume Huguet & Zohra Saci & Martineau Jean-Louis & Zdenka Pausova & Igor Jurisica & Carrie E. Bearden & Sebastien Jacquemont & Tomas Paus, 2025. "Copy number variants and the tangential expansion of the cerebral cortex," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
- Matthew J. O’Neill & Tao Yang & Julie Laudeman & Maria E. Calandranis & M. Lorena Harvey & Joseph F. Solus & Dan M. Roden & Andrew M. Glazer, 2024. "ParSE-seq: a calibrated multiplexed assay to facilitate the clinical classification of putative splice-altering variants," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Iain Mathieson & David Reich, 2017. "Differences in the rare variant spectrum among human populations," PLOS Genetics, Public Library of Science, vol. 13(2), pages 1-17, February.
- Michel S. Naslavsky & Marilia O. Scliar & Guilherme L. Yamamoto & Jaqueline Yu Ting Wang & Stepanka Zverinova & Tatiana Karp & Kelly Nunes & José Ricardo Magliocco Ceroni & Diego Lima Carvalho & Carlo, 2022. "Whole-genome sequencing of 1,171 elderly admixed individuals from Brazil," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
- Ya-Mei Ding & Xiao-Xu Pang & Yu Cao & Wei-Ping Zhang & Susanne S. Renner & Da-Yong Zhang & Wei-Ning Bai, 2023. "Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Romain Fournier & Zoi Tsangalidou & David Reich & Pier Francesco Palamara, 2023. "Haplotype-based inference of recent effective population size in modern and ancient DNA samples," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Nicole Deflaux & Margaret Sunitha Selvaraj & Henry Robert Condon & Kelsey Mayo & Sara Haidermota & Melissa A. Basford & Chris Lunt & Anthony A. Philippakis & Dan M. Roden & Joshua C. Denny & Anjene Mu, 2023. "Demonstrating paths for unlocking the value of cloud genomics through cross cohort analysis," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-35596-5. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.