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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
...inert status confirmed by the lack of a start codon and/or interruption by stop codons or frameshift mutations.Note that the mere presence of a homologous noncoding sequence in an outgroup is not sufficient to establish a de novo origin of the ORFan because it is possible that the outgroup sequence...
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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
...-specific population structure and selection history make it difficult to assess the impact of rare mutations. However, given the well-established role of rare variants in human disease, the field of canine genetics is beginning to focus on rare variant discovery and characterization (Halvorsen et al. 2021; Momozawa...
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Method: Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing
- Renato Salazar,
- Barbara Arbeithuber,
- Maja Ivankovic,
- Monika Heinzl,
- Sofia Moura,
- Ingrid Hartl,
- Theresa Mair,
- Angelika Lahnsteiner,
- Thomas Ebner,
- Omar Shebl,
- Johannes Pröll,
- and Irene Tiemann-Boege
Genome Res. March 2022 32: 499-511; Published in Advance February 24, 2022, doi:10.1101/gr.275695.121
...University Hospital, Johannes Kepler University, Linz, Austria 4020; 5Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria 5020 Corresponding author: irene.tiemann@jku.atAbstractDe novo mutations (DNMs) are important players in heritable diseases and evolution...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
..., multiple studies across many taxa showed that some novel genes arise de novo, that is, from previously noncoding DNA. To characterize the underlying mutations that allowed de novo gene emergence and their order of occurrence, homologous regions must be detected within noncoding sequences in closely related...
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Research: De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression
- Mark E. Gill,
- Alexia Rohmer,
- Serap Erkek-Ozhan,
- Ching-Yeu Liang,
- Sunwoo Chun,
- Evgeniy A. Ozonov,
- and Antoine H.F.M. Peters
Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
...line mutation rates (Xia et al. 2020), although a recent analysis of the types of mutations found in human germ cells suggests that this may not be a major driver (Moore et al. 2021).The catalog of transcripts known to be expressed during spermatogenesis reflects multiple historical features. Early...
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Method: De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens
- Taylor M. Weiskittel,
- Choong Y. Ung,
- Cristina Correia,
- Cheng Zhang,
- and Hu Li
Genome Res. January 2022 32: 124-134; Published in Advance December 7, 2021, doi:10.1101/gr.275889.121
...disease modules de novo, which enables us to elucidate the importance of mutated genes in specific patients and to understand the synthetic penetrance of these genes across patients. We reveal that importance of the notorious cancer drivers TP53 and PIK3CA fluctuate widely across breast cancers and peak...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
..., acetylation, and ADP-ribosylation (Wang et al. 2023).The de novo computational prediction of activating kinase mutations, which includes established drivers such as EGFR L858R and BRAF V600E, remains an ongoing challenge (Jordan et al. 2019). FunVar provides a novel protocol, based on CATH functional families...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...lessons reveal that properly assessed clinical presentations, coupled with genetic and biological awareness, can guide discovery of disease-causing unstable TRs. We highlight critical but underrecognized aspects of TR mutations. Repeat motifs may not be present in current reference s...
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Method: AIDE: annotation-assisted isoform discovery with high precision
- Wei Vivian Li,
- Shan Li,
- Xin Tong,
- Ling Deng,
- Hubing Shi,
- and Jingyi Jessica Li
Genome Res. December 2019 29: 2056-2072; Published in Advance November 6, 2019, doi:10.1101/gr.251108.119
...to the substantial information loss in RNA-seq experiments. Here, we introduce a novel statistical method, annotation-assisted isoform discovery (AIDE), the first approach that directly controls false isoform discoveries by implementing the testing-based model selection principle. Solving the isoform discovery...
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Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V. Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...expression (left) and hypertranscription (right) between elevated and overall indels. Confounders in somatic mutation ASE analysis Genome Research 5 www..org De novo driver indel detection in RNA-seq The inverse relationship between elevated AEV and purity (Fig. 2) may be exploited to recover...
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