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Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
- Jonas de Tribolet-Hardy,
- Christian W. Thorball,
- Romain Forey,
- Evarist Planet,
- Julien Duc,
- Alexandre Coudray,
- Bara Khubieh,
- Sandra Offner,
- Cyril Pulver,
- Jacques Fellay,
- Michael Imbeault,
- Priscilla Turelli,
- and Didier Trono
Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
...selection in terms of dN/dS across the nine primate species listed above was obtained with PAML (v4.4) as previously described (McLaren et al. 2015).Human genetic variation dataHuman genetic exome and whole sequencing data were obtained from The Genome Aggregation Database (gnomAD) (Lek et al. 2016...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...basenji dog (Canis lupus familiaris) . BMC Genomics 22: 188. doi:10.1186/s12864-021-07493-6 ↵Elvers I, Turner-Maier J, Swofford R, Koltookian M, Johnson J, Stewart C, Zhang CZ, Schumacher SE, Beroukhim R, Rosenberg M, et al. 2015. Exome sequencing of lymphomas from three dog breeds reveals somatic...
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Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
- Luis Ferrández-Peral,
- Xiaoyu Zhan,
- Marina Alvarez-Estape,
- Cristina Chiva,
- Paula Esteller-Cucala,
- Raquel García-Pérez,
- Eva Julià,
- Esther Lizano,
- Òscar Fornas,
- Eduard Sabidó,
- Qiye Li,
- Tomàs Marquès-Bonet,
- David Juan,
- and Guojie Zhang
Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
...–related genes and cell proliferation genes are preferential targets of evolutionary innovations. Moreover, the convergent accumulation of these innovations and their occurrence in genes under positive selection in primates highlight the strength of the evolutionary pressures suffered by the immune response...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 2023 33: 463-477; Published in Advance April 3, 2023, doi:10.1101/gr.277372.12
...cohorts in order to associate SVs with more traits. The results suggest that population-scale long-read sequencing will give a new dimension to our understanding of SV prevalence and their impact on phenotypes. Logically, it may allow an effective implementation of precise genomic selection on the basis...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 27, 2023 ; Published in Advance March 27, 2023, doi:10.1101/gr.277372.122
...implementation of precise genomic selection on the basis of SVs. Methods Sample collection and PacBio sequencing Samples were selected to form an optimal representation of the diversity of European and Asian sheep breeds. The sampling information is provided in Supplemental Tables S2 and S17. High...
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Research: A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci
- Elisabeth J. van Bree,
- Rita L.F.P. Guimarães,
- Mischa Lundberg,
- Elena R. Blujdea,
- Jimi L. Rosenkrantz,
- Fred T.G. White,
- Josse Poppinga,
- Paula Ferrer-Raventós,
- Anne-Fleur E. Schneider,
- Isabella Clayton,
- David Haussler,
- Marcel J.T. Reinders,
- Henne Holstege,
- Adam D. Ewing,
- Colette Moses,
- and Frank M.J. Jacobs
Genome Res. April 2022 32: 656-670; Published in Advance March 24, 2022, doi:10.1101/gr.275515.121
...were sequenced by MAD: Dutch Genomics Service & Support Provider of the University of Amsterdam using a NextSeq 550 Illumina sequencer.RNA CaptureSeqSamples of CD2AP-SVA KO and unedited control were used for RNA CaptureSeq. RNA isolation of cortical organoids and library preparation were performed...
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Research: Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background
- Ingegerd Elvers,
- Jason Turner-Maier,
- Ross Swofford,
- Michele Koltookian,
- Jeremy Johnson,
- Chip Stewart,
- Cheng-Zhong Zhang,
- Steven E. Schumacher,
- Rameen Beroukhim,
- Mara Rosenberg,
- Rachael Thomas,
- Evan Mauceli,
- Gad Getz,
- Federica Di Palma,
- Jaime F. Modiano,
- Matthew Breen,
- Kerstin Lindblad-Toh,
- and Jessica Alföldi
Genome Res. November 2015 25: 1634-1645; Published in Advance September 16, 2015, doi:10.1101/gr.194449.115
...Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background Ingegerd Elvers 1 , 2 , Jason Turner-Maier 1 , Ross Swofford 1 , Michele Koltookian 1 , Jeremy Johnson 1 , Chip Stewart...
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Research: Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection
- PingHsun Hsieh,
- Krishna R. Veeramah,
- Joseph Lachance,
- Sarah A. Tishkoff,
- Jeffrey D. Wall,
- Michael F. Hammer,
- and Ryan N. Gutenkunst
Genome Res. March 2016 26: 279-290; Published in Advance February 17, 2016, doi:10.1101/gr.192971.115
...Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection PingHsun Hsieh 1 , Krishna R. Veeramah 2 , 3 , Joseph Lachance 4 , 5...
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Method: BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations
- Antonio Nappi,
- Liubov Shilova,
- Theofanis Karaletsos,
- Na Cai,
- and Francesco Paolo Casale
Genome Res. December 2025 35: 2682-2690; Published in Advance October 24, 2025, doi:10.1101/gr.280689.125
...components (PCs), selecting individuals within seven standard deviations from the first six PCs, and filtered to self-reported ethnicities, specifically “white-British,” “Irish,” or “White.” To account for batch effects in whole-exome sequencing, we followed a similar approach to Karczewski et al. (2022...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...breeds (<10 kg), thus highlighting the importance of allelic heterogeneity in selection for breed traits. Most variants prioritized in this analysis are not associated with genomic signatures for breed differentiation, as these regions are enriched for constrained genes intolerant to nonsynonymous...
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