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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...of ancestral breeds and the specific ancestral breeds of the hybrid population. Input*: The purebred and classifier I are derived from the “feature SNP screening” output. Simulated hybrids are generated based on the inputs of “feature SNP screening” (purebred data). HITSNP extracts feature SNP information from...
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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
...expression and 10x Genomics multiome combines transcriptome with chromatin accessibility data (Stoeckius et al. 2017). Our single-cell Rapid Capture Hybridization sequencing (scRaCH-seq) method enables the capture of multiple transcripts from preindexed and stored cDNA independent of the 10x Genomics kit...
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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...Chromosome-level sub-aware de novo assembly provides insight into Saccharomyces bayanus divergence after hybridization Cory Gardner1,2,5, Junhao Chen3,5, Christina Hadfield2, Zhaolian Lu3, David Debruin2, Yu Zhan3, Maureen J. Donlin2,4, Tae-Hyuk Ahn1,2 and Zhenguo Lin2,3 1Department of Computer...
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Research: Reactivation of transposable elements following hybridization in fission yeast
- Sergio Tusso,
- Fang Suo,
- Yue Liang,
- Li-Lin Du,
- and Jochen B.W. Wolf
Genome Res. February 2022 32: 324-336; Published in Advance December 14, 2021, doi:10.1101/gr.276056.121
...families. These results are consistent with full-length elements being mostly of young age and solo LTRs being of much older origin.In the S. pombe reference strain, ∼70% of Tf2 mobilization events involve homologous recombination between newly synthesized cDNA and a pre-existing copy of Tf2; the remaining...
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Research: Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations
- Yasine Malki,
- Guannan Kang,
- W.K. Jacky Lam,
- Qing Zhou,
- Suk Hang Cheng,
- Peter P.H. Cheung,
- Jinyue Bai,
- Ming Lok Chan,
- Chui Ting Lee,
- Wenlei Peng,
- Yiqiong Zhang,
- Wanxia Gai,
- Winsome W.S. Wong,
- Mary-Jane L. Ma,
- Wenshuo Li,
- Xinzhou Xu,
- Zhuoran Gao,
- Irene O.L. Tse,
- Huimin Shang,
- L.Y. Lois Choy,
- Peiyong Jiang,
- K.C. Allen Chan,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 31-42; Published in Advance November 27, 2024, doi:10.1101/gr.279667.124
...enrichment of viral DNA molecules from the total pool of plasma DNA, as it improves the positive predictive value of NPC detection (Lam et al. 2018). Enrichment in the screening study was performed using a hybridization-based capture with probes that cover the entire EBV and selected human autosomal DNA...
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Research: Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes
- Suleyman Gulsuner,
- Amal AbuRayyan,
- Jessica B. Mandell,
- Ming K. Lee,
- Greta V. Bernier,
- Barbara M. Norquist,
- Sarah B. Pierce,
- Mary-Claire King,
- and Tom Walsh
Genome Res. November 2024 34: 1825-1831; Published in Advance September 13, 2024, doi:10.1101/gr.279158.124
...encountered frequently. Of the 120 families in this series, 88 families, or 73%, harbored at least one rare or private deep intronic variant in a breast cancer gene. To scale deep intronic screening from 120 families to thousands of families, it is important to prioritize the many genomic variants for cDNA...
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Research: The human ribosomal DNA array is composed of highly homogenized tandem clusters
- Yutaro Hori,
- Akira Shimamoto,
- and Takehiko Kobayashi
Genome Res. November 2021 31: 1971-1982; Published in Advance August 18, 2021, doi:10.1101/gr.275838.121
...at 4°C. DNA concentration was measured with a Qubit assay kit (Invitrogen).Construction of the Cas9-enriched Oxford Nanopore libraryThe published protocol (Gilpatrick et al. 2020) was modified specifically for rDNA, which consists of hundreds of copies. First, Cas9 RNP was assembled as described...
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Research: Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement
- Peter A. Audano and
- Christine R. Beck
Genome Res. January 2024 34: 7-19; Published in Advance January 4, 2024, doi:10.1101/gr.278203.123
...confirm that SNP and indel polymorphisms are enriched at shifted breakpoints and are also absent from variant callsets. Breakpoint homology increases the likelihood of imprecise SV calls and the distance they are shifted, and tandem duplications are the most heavily affected SVs. Because graph methods...
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Research: Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance
- Mathieu Hénault,
- Souhir Marsit,
- Guillaume Charron,
- and Christian R. Landry
Genome Res. November/December 2022 32: 2043-2056; Published in Advance November 9, 2022, doi:10.1101/gr.276885.122
...leakage or de novo mutations. mtDNA integrity and the resolution of heteroplasmy have important implications, notably for mitochondrial genetic disorders, speciation, and evolution in hybrids. However, the impact of genetic variation on the transition to homoplasmy from initially heteroplasmic backgrounds...
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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
..., Germany Corresponding authors: pnavarro@pasteur.fr, job.dekker@umassmed.eduAbstractMitotic chromosomes are considered to be universally folded as loop arrays across species and cell types. However, some studies suggest that features of mitotic chromosomes might be cell type– or species-specific. We...
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