Searching journal content for articles similar to Shang et al. 31 (1): 121.

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  1. 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
    ...level per copy in tumor relative to normal, and nonsense-mediated decay (NMD) efficiency were used to model the VAF ratio of RNA to DNA (i.e., VAFRNA/VAFDNA), which is termed allelic expression variation (AEV). Theoretical and simulation studies were conducted to identify conditions for AEV >1 (elevated...
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  2. Method: A HIT-trapping strategy for rapid generation of reversible and conditional alleles using a universal donor
    • Hengxing Lu,
    • Jun Liu,
    • Tao Feng,
    • Zihang Guo,
    • Yunjun Yin,
    • Fei Gao,
    • Gengsheng Cao,
    • Xuguang Du,
    • and Sen Wu
    Genome Res. May 2021 31: 900-909; Published in Advance April 1, 2021, doi:10.1101/gr.271312.120
    ...one-step generation of reversible and conditional alleles in a single experiment. As a proof of concept, we successfully created mutant alleles for 21 disease-related genes in primary porcine fibroblasts with an average knock-in frequency of 53.2%, a great improvement over previous approaches...
  3. Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
    • Sheila Lutz,
    • Megan Lawler,
    • Samuel Amidon,
    • and Frank W Albert
    Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
    ...to the telomere (Fig. 1, Step 1). 159 We then induced SPA of the W303 chromosomes by activating conditional GAL1 promoters at 160 each centromere (Fig. 1, Step 2). Transcription from the GAL1 promoters leads to centromere 161 instability and loss of the W303 chromosomes during mitotic division (Reid et al. 2008...
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  4. Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
    • Yali Zhang,
    • Yayi Zhou,
    • Yangyang Chen,
    • Xueyu Wang,
    • Boyan Hu,
    • Shahid Siddique,
    • Romnick A. Latina,
    • Veronica I. Casey,
    • Dexin Bo,
    • Yucheng Liao,
    • Min Zhang,
    • Ming Sun,
    • Fengjuan Zhang,
    • and Dadong Dai
    Genome Res. March 23, 2026 ; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
    ...the haplotypes. Expression levels of alleles were measured across each developmental stage and condition, allowing us to identify differentially expressed alleles (DEAs). Specifically, we detected 2642, 3004, 4329, 5396, 4924, 4713, and 3615 DEAs in the J2, J3/J4, male, female, mixed stage, drought stress, and 4...
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  5. Method: Single-step capture and sequencing of natural DNA for detection of BRCA1 mutations
    • John F. Thompson,
    • Jeffrey G. Reifenberger,
    • Eldar Giladi,
    • Kristen Kerouac,
    • Jaime Gill,
    • Erik Hansen,
    • Avak Kahvejian,
    • Philipp Kapranov,
    • Travis Knope,
    • Doron Lipson,
    • Kathleen E. Steinmann,
    • and Patrice M. Milos
    Genome Res. February 2012 22: 340-345; Published in Advance July 15, 2011, doi:10.1101/gr.122192.111
    ...positions that differ from the reference in a statistically significant fashion are flagged. The next stage identifies the most likely alleles at each candidate location and realigns the reads to the candidate alleles. This step reduces alignment errors substantially in locations with true sequence variants...
  6. Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
    • Michael K.B. Ford,
    • Ananth Hari,
    • Meredith Yeager,
    • Lisa Mirabello,
    • Stephen Chanock,
    • Ibrahim Numanagić,
    • COVNET Consortium,
    • and S. Cenk Sahinalp
    Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
    ...alleles grows. This methodological framework, demonstrated here with COVID-19, establishes a foundation for investigating the role of immune receptor genetic variation in a broad spectrum of diseases. Particularly promising candidates for future studies include autoimmune conditions in which germline...
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  7. Method: Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR
    • Artem Mikelov,
    • George Nefediev,
    • Alexander Tashkeev,
    • Oscar L. Rodriguez,
    • Diego Aguilar Ortmans,
    • Valeriia Skatova,
    • Mark Izraelson,
    • Alexey N. Davydov,
    • Stanislav Poslavsky,
    • Souad Rahmouni,
    • Corey T. Watson,
    • Dmitriy Chudakov,
    • Scott D. Boyd,
    • and Dmitry Bolotin
    Genome Res. December 2024 34: 2293-2303; Published in Advance October 21, 2024, doi:10.1101/gr.278775.123
    ...of information. Further, some alleles exhibit low usage levels, precluding their detection with AIRR-seq. Despite these limitations, AIRR-seq data remain valuable for applications focused on functional adaptive immune repertoires and their fluctuations in different conditions.The ability to precisely call known...
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  8. Review: The superpowers of imprinting control regions
    • Bertille Montibus,
    • Franck Court,
    • and Philippe Arnaud
    Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
    ...presenting with methylation defects, primarily losses, at multiple imprinted loci, a condition known as multilocus imprinting disturbance (MLID) (Touati et al. 2019; Eggermann et al. 2022).The involvement of KRAB-ZFP proteins in the critical maintenance step that defines gDMRs/ICRs aligns with the hypothesis...
  9. Method: Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End
    • Lucinda C. Xiao,
    • Ayush Semwal,
    • Brianna St John,
    • Kathleen Zeglinski,
    • Shian Su,
    • James Lancaster,
    • Shifeng Xue,
    • Bruno Reversade,
    • Matthew E. Ritchie,
    • Frédérique Magdinier,
    • Marnie E. Blewitt,
    • and Quentin Gouil
    Genome Res. March 23, 2026 ; Published in Advance March 23, 2026, doi:10.1101/gr.280907.125
    ...guideline updates highlight the need for more accurate and comprehensive diagnostic approaches. Here, we leverage ultra-long whole- and Cas9-targeted sequencing to develop a fast and accurate workflow, D4Z4End2End, for comprehensive genetic and methylation analysis of D4Z4 alleles. We apply it to samples...
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  10. Research: Deletions of recessive disease genes: CNV contribution to carrier states and disease-causing alleles
    • Philip M. Boone,
    • Ian M. Campbell,
    • Brett C. Baggett,
    • Zachry T. Soens,
    • Mitchell M. Rao,
    • Patricia M. Hixson,
    • Ankita Patel,
    • Weimin Bi,
    • Sau Wai Cheung,
    • Seema R. Lalani,
    • Arthur L. Beaudet,
    • Pawel Stankiewicz,
    • Chad A. Shaw,
    • and James R. Lupski
    Genome Res. September 2013 23: 1383-1394; Published in Advance May 16, 2013, doi:10.1101/gr.156075.113
    ...or diagnostic test should detect CNV alleles. [Supplemental material is available for this article.] Over 1000 recessive genetic disorders have been described, and many of their corresponding disease genes identified (http:// www.omim.org). While most of these conditions are individually rare (Srinivasan et al...
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