Searching journal content for articles similar to Mefford et al. 19 (9): 1579.

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  1. Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
    • Tanner D. Jensen,
    • Bohan Ni,
    • Chloe M. Reuter,
    • John E. Gorzynski,
    • Sarah Fazal,
    • Devon Bonner,
    • Rachel A. Ungar,
    • Pagé C. Goddard,
    • Archana Raja,
    • Euan A. Ashley,
    • Jonathan A. Bernstein,
    • Stephan Zuchner,
    • Undiagnosed Diseases Network,
    • Michael D. Greicius,
    • Stephen B. Montgomery,
    • Michael C. Schatz,
    • Matthew T. Wheeler,
    • and Alexis Battle
    Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
    ...are concordant with previous analysis in GTEx, where CNVs were enriched for proximity to genes with outlying expression (Chiang et al. 2017; Ferraro et al. 2020).View larger version: In this window In a new window Figure 3. Rare long-read-discovered SVs are strongly enriched proximal to gene expression outliers...
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  2. 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
    ...CNVs and aneuploidies. For data analysis, variants were filtered using the following criteria: (1) The manufacturer's recommended confidence scores were applied: insertion: 0, deletion: 0, inversion: 0.01, duplication: − 1, translocation: 0, and copy number: 0.99 (low stringency, filter set to 0); (2...
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  3. Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
    • David R. Lougheed,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
    ...disease and complex traits but can be difficult to resolve with short-read sequencing. We present STRkit, a software package for genotyping STRs using long-read sequencing (LRS) that uses proximate single-nucleotide variants to improve genotyping accuracy without a priori haplotype information. We show...
  4. Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
    • Jung-Wan Mok,
    • Shelley B. Gibson,
    • Haley A. Dostalik,
    • and Shinya Yamamoto
    Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
    ...human variants can often be studied by investigating the effect of LOF of the orthologous fly gene (Fig. 3A). If similarities between phenotypes of Drosophila mutants and rare disease patients can be identified, such data can be utilized to provide supporting data on pathogenicity (Fig. 2). In addition...
  5. 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
    ...only be fixed by resolving the contig assembly, a task that is beyond the scope of our work. As a result, we look primarily at allele presence and exclude CNVs when comparing our results to the assembly-derived genotype (for a reference, see CNV-sensitive results in Supplemental Table 3). Accuracy...
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  6. 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
    ...Corresponding author: francescopaolo.casale@helmholtz-munich.deAbstractGene-level rare variant association tests (RVATs) are essential for uncovering disease mechanisms and identifying therapeutic targets. Advances in sequence-based machine learning have generated diverse variant pathogenicity scores, creating...
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  7. Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
    • Nora Zidane,
    • Carla Rodrigues,
    • Valérie Bouchez,
    • Martin Rethoret-Pasty,
    • Virginie Passet,
    • Sylvain Brisse,
    • and Chiara Crestani
    Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
    ...and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol 16: 114. doi:10.1186/s13059-015-0677-2 ↵Revez J, Espinosa L, Albiger B, Leitmeyer KC, Struelens MJ. 2017. Survey on the use of whole- sequencing for infectious diseases surveillance: rapid expansion of European national...
  8. 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
    ...in insufficient read coverage, thereby limiting our ability to perform mutation calling for specific genes. Here, we developed a single-cell Rapid Capture Hybridization sequencing (scRaCH-seq) method that demonstrates high specificity and efficiency in capturing targeted transcripts using long-read sequencing...
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  9. 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
    ...to use measures of functional and evolutionary constraint to identify new variants with a high probability of impacting gene function.This study focuses, specifically, on identifying genotypes that are rare overall, but common within a single breed or groups of related breeds that share a particular...
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  10. Research: Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing
    • Wouter Steyaert,
    • Lydia Sagath,
    • German Demidov,
    • Vicente A. Yépez,
    • Anna Esteve-Codina,
    • Julien Gagneur,
    • Kornelia Ellwanger,
    • Ronny Derks,
    • Marjan Weiss,
    • Amber den Ouden,
    • Simone van den Heuvel,
    • Hilde Swinkels,
    • Nick Zomer,
    • Marloes Steehouwer,
    • Luke O'Gorman,
    • Galuh Astuti,
    • Kornelia Neveling,
    • Rebecca Schüle,
    • Jishu Xu,
    • Matthis Synofzik,
    • Danique Beijer,
    • Holger Hengel,
    • Ludger Schöls,
    • Kristl G. Claeys,
    • Jonathan Baets,
    • Liedewei Van de Vondel,
    • Alessandra Ferlini,
    • Rita Selvatici,
    • Heba Morsy,
    • Marwa Saeed Abd Elmaksoud,
    • Volker Straub,
    • Juliane Müller,
    • Veronica Pini,
    • Luke Perry,
    • Anna Sarkozy,
    • Irina Zaharieva,
    • Francesco Muntoni,
    • Enrico Bugiardini,
    • Kiran Polavarapu,
    • Rita Horvath,
    • Evan Reid,
    • Hanns Lochmüller,
    • Marco Spinazzi,
    • Marco Savarese,
    • Solve-RD DITF-ITHACA, Solve-RD DITF-Euro-NMD, Solve-RD DITF-RND, Solve-RD DITF-EpiCARE,
    • Leslie Matalonga,
    • Steven Laurie,
    • Han G. Brunner,
    • Holm Graessner,
    • Sergi Beltran,
    • Stephan Ossowski,
    • Lisenka E.L.M. Vissers,
    • Christian Gilissen,
    • Alexander Hoischen,
    • and on behalf of the Solve-RD consortium
    Genome Res. April 2025 35: 755-768; Published in Advance March 26, 2025, doi:10.1101/gr.279414.124
    ...and orthogonal validation of variants in known disease genes yielded 12 novel genetic diagnoses due to de novo and rare inherited SNVs, indels, SVs, and STR expansions. In an additional five families, we identified a candidate disease-causing variant, including an MCF2/FGF13 fusion and a PSMA3 deletion. However...
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