Searching journal content for articles similar to Spielmann et al. 26 (2): 183.

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Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- Joo Hye Yeo,
- Hyongbum Henry Kim,
- Sang Ho Oh,
- and Jinu Lee
Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
.... 50 51 INTRODUCTION 52 Homology-directed repair (HDR) is a widely used pathway for precise editing, 53 employing CRISPR–Cas9, which enables the accurate insertion or correction of specific 54 DNA sequences at defined genomic loci. HDR-mediated editing is broadly applied in 55 biomedical research...
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Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
- Maureen Pittman,
- Kihyun Lee,
- Franco Felix,
- Yu Huang,
- Adrienne Lam,
- Mauro W. Costa,
- Deepak Srivastava,
- and Katherine S. Pollard
Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
.... Corresponding authors: deepak.srivastava@gladstone.ucsf.edu, kpollard@gladstone.ucsf.eduAbstractExome sequencing of thousands of families has revealed many risk genes for congenital heart defects (CHDs), yet most cases cannot be explained by a single causal mutation. Even within the same family, individuals...
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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. April 2026 36: 661-670; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...and atypical CNVs from family and population sequencing. Genome Res 21: 974–984. doi:10.1101/gr.114876.110 ↵Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A. 2015. OMIM.org: online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders. Nucleic Acids Res 43: D...
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Research: Optical genome mapping identifies rare structural variants in neural tube defects
- Nikhil S. Sahajpal,
- Jane Dean,
- Benjamin Hilton,
- Timothy Fee,
- Cindy Skinner,
- Alex Hastie,
- Barbara R. DuPont,
- Alka Chaubey,
- Michael J. Friez,
- and Roger E. Stevenson
Genome Res. April 2025 35: 798-809; Published in Advance March 19, 2025, doi:10.1101/gr.279318.124
..., Dionne-Laporte A, Spiegelman D, Henrion É, Diallo O, Audibert F, Michaud JL, et al. 2019. Whole exome sequencing identifies novel predisposing genes in neural tube defects. Mol Genet Genomic Med 7: e00467. doi:10.1002/mgg3.467 ↵Levy-Sakin M, Pastor S, Mostovoy Y, Li L, Leung AKY, McCaffrey J, Young E...
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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...the transcriptome (Eisenberg and Levanon 2018; Duan 2025). Editing events taking place in coding sequences (CDSs)might alter the genomically encoded amino acid and lead to nonsynonymous changes, namely, “recoding” (Alon et al. 2015). Genome-wide profiling of RNA editing sites has been performed in several metazoans...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...and Keightley 2009; Bergeron et al. 2022). This has enabled mutation rates to be estimated in a wide range of taxa (Lynch et al. 2023; Wang and Obbard 2023), including humans and mice (Ohno 2019). However, the most widely available short-read sequencing technologies only allow inference of the rate and spectrum...
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Research: A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia
- Haloom Rafehi,
- Liam G. Fearnley,
- Justin Read,
- Penny Snell,
- Kayli C. Davies,
- Liam Scott,
- Greta Gillies,
- Genevieve C. Thompson,
- Tess A. Field,
- Aleena Eldo,
- Simon Bodek,
- Ernest Butler,
- Luke Chen,
- John Drago,
- Himanshu Goel,
- Anna Hackett,
- G. Michael Halmagyi,
- Andrew Hannaford,
- Katya Kotschet,
- Kishore R. Kumar,
- Smitha Kumble,
- Matthew Lee-Archer,
- Abhishek Malhotra,
- Mark Paine,
- Michael Poon,
- Kate Pope,
- Katrina Reardon,
- Steven Ring,
- Anne Ronan,
- Matthew Silsby,
- Renee Smyth,
- Chloe Stutterd,
- Mathew Wallis,
- John Waterston,
- Thomas Wellings,
- Kirsty West,
- Christine Wools,
- Kathy H.C. Wu,
- David J. Szmulewicz,
- Martin B. Delatycki,
- Melanie Bahlo,
- and Paul J. Lockhart
Genome Res. April 2025 35: 769-785; Published in Advance February 27, 2025, doi:10.1101/gr.279634.124
...pathogenic RE. Alternative physical enrichment technologies that do not require PCR amplification have been developed, including CRISPR–Cas9 enrichment. However, these enrichment approaches are bespoke, difficult to multiplex, and are limited to ∼50 targets per library preparation. Recently, the development...
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Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
- Shuangxi Ji,
- Tong Zhu,
- Ankit Sethia,
- and Wenyi Wang
Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
..., Miller CA, Mardis ER, Ding L, Wilson RK. 2012. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22: 568–576. doi:10.1101/gr.129684.111 ↵Köster J, Rahmann S. 2012. Snakemake: a scalable bioinformatics workflow engine. Bioinformatics 28: 2520...
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Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
- Hongke Peng,
- Jafar S. Jabbari,
- Luyi Tian,
- Changqing Wang,
- Yupei You,
- Chong Chyn Chua,
- Natasha S. Anstee,
- Noorul Amin,
- Andrew H. Wei,
- Nadia M. Davidson,
- Andrew W. Roberts,
- David C.S. Huang,
- Matthew E. Ritchie,
- and Rachel Thijssen
Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
...treated with venetoclax, SF3B1 mutation was detected in five samples by whole exome sequencing (WES) (Thijssen et al. 2022) which was used as a ground truth to validate the scRaCH-seq data. For the identification of SF3B1 mutations, we aggregated the scRaCH-seq data from all the samples, revealing many SF...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
...eliminate tens of thousands of DNA sequences from a germline copy. Recently, we showed that the chromatin remodeler ISWI1 is required for somatic development in the ciliate Paramecium tetraurelia. Here, we describe two high similarity paralogous proteins, ICOPa and ICOPb, essential for their editing. ICOPa...
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