Searching journal content for articles similar to Mitchell et al. 15 (7): 960.

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  1. Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
    • Susan M. Hiatt,
    • James M.J. Lawlor,
    • Lori H. Handley,
    • Donald R. Latner,
    • Zachary T. Bonnstetter,
    • Candice R. Finnila,
    • Michelle L. Thompson,
    • Lori Beth Boston,
    • Melissa Williams,
    • Ivan Rodriguez Nunez,
    • Jerry Jenkins,
    • Whitley V. Kelley,
    • E. Martina Bebin,
    • Michael A. Lopez,
    • Anna C.E. Hurst,
    • Bruce R. Korf,
    • Jeremy Schmutz,
    • Jane Grimwood,
    • and Gregory M. Cooper
    Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
    ...(i.e., would be P/LP regardless of P/LP variation in the other gene), and it is possible if not probable that at least some conditions result from combinations of variants in different genes that are not pathogenic in isolation (Papadimitriou et al. 2019). At the further end of this spectrum...
  2. Method: Polishing copy number variant calls on exome sequencing data via deep learning
    • Furkan Özden,
    • Can Alkan,
    • and A. Ercüment Çiçek
    Genome Res. June 2022 32: 1170-1182; Published in Advance June 13, 2022, doi:10.1101/gr.274845.120
    ...; Pankratz et al. 2011; Zarrei et al. 2019) and various cancers such as breast, ovary, and pancreas cancers (Kumaran et al. 2017; Hieronymus et al. 2018; Macintyre et al. 2018; Reid et al. 2019). Karyotyping and microarray analyses have been the standard clinical testing for disease-causing CNVs for many...
  3. 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
    ...-person load of variants was not enumerated. The 1000GP pilot phase data were furthermined by Xue et al. (2012) to more accurately identify likely damaging mutations; however, the predicted consequence of each variant (i.e., disease-causing vs. carrier) was not systematically addressed in light...
  4. Method: Identification of pathogenic variant enriched regions across genes and gene families
    • Eduardo Pérez-Palma,
    • Patrick May,
    • Sumaiya Iqbal,
    • Lisa-Marie Niestroj,
    • Juanjiangmeng Du,
    • Henrike O. Heyne,
    • Jessica A. Castrillon,
    • Anne O'Donnell-Luria,
    • Peter Nürnberg,
    • Aarno Palotie,
    • Mark Daly,
    • and Dennis Lal
    Genome Res. January 2020 30: 62-71; Published in Advance December 23, 2019, doi:10.1101/gr.252601.119
    ...to identify protein regions constrained for variants in the general population and likely disease causing when mutated. Protein regions that can confer risk to disease through low penetrance variants or late onset of disease after typical reproductive age are unlikely to be identified in PERs owing to little...
  5. 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
    ...be explored, from small gene sets with very rare co-occurring variants of high impact to larger gene sets that include small-effect, possibly damaging variants that could modify the effects of other primary disease-causing variant(s) or otherwise contribute to a polygenic signal.Here we use the terms...
    OPEN ACCESS ARTICLE
  6. LETTER: Features of 5′-splice-site efficiency derived from disease-causing mutations and comparative genomics
    • Xavier Roca,
    • Andrew J. Olson,
    • Atmakuri R. Rao,
    • Espen Enerly,
    • Vessela N. Kristensen,
    • Anne-Lise Børresen-Dale,
    • Brage S. Andresen,
    • Adrian R. Krainer,
    • and Ravi Sachidanandam
    Genome Res. January 2008 18: 77-87; Published in Advance November 21, 2007, doi:10.1101/gr.6859308
    ...Features of 5′-splice-site efficiency derived from disease-causing mutations and comparative genomics Xavier Roca 1 , Andrew J. Olson 1 , Atmakuri R. Rao 1 , 6 , Espen Enerly 2 , 3 , Vessela N. Kristensen 2 , 3 , Anne-Lise Børresen...
    OPEN ACCESS ARTICLE
  7. Method: Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation
    • Joshua Traynelis,
    • Michael Silk,
    • Quanli Wang,
    • Samuel F. Berkovic,
    • Liping Liu,
    • David B. Ascher,
    • David J. Balding,
    • and Slavé Petrovski
    Genome Res. October 2017 27: 1715-1729; Published in Advance September 1, 2017, doi:10.1101/gr.226589.117
    ...disease-causing from benign variants. Large samples of human standing variation data highlight regional variation in the tolerance to missense variation within the protein-coding sequence of genes. This information is not well captured by existing bioinformatic tools, but is effective in improving variant...
    OPEN ACCESS ARTICLE
  8. 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
    ...motif composition can also affect phenotype: insertion of a stretch of a noncanonical motif into a noncoding STR in the DAB1 gene is responsible for a form of spinocerebellar ataxia (Seixas et al. 2017). Beyond expansion detection, precisely determining copy number and motif composition in disease-causing...
  9. Research: Actionable exomic incidental findings in 6503 participants: challenges of variant classification
    • Laura M. Amendola,
    • Michael O. Dorschner,
    • Peggy D. Robertson,
    • Joseph S. Salama,
    • Ragan Hart,
    • Brian H. Shirts,
    • Mitzi L. Murray,
    • Mari J. Tokita,
    • Carlos J. Gallego,
    • Daniel Seung Kim,
    • James T. Bennett,
    • David R. Crosslin,
    • Jane Ranchalis,
    • Kelly L. Jones,
    • Elisabeth A. Rosenthal,
    • Ella R. Jarvik,
    • Andy Itsara,
    • Emily H. Turner,
    • Daniel S. Herman,
    • Jennifer Schleit,
    • Amber Burt,
    • Seema M. Jamal,
    • Jenica L. Abrudan,
    • Andrew D. Johnson,
    • Laura K. Conlin,
    • Matthew C. Dulik,
    • Avni Santani,
    • Danielle R. Metterville,
    • Melissa Kelly,
    • Ann Katherine M. Foreman,
    • Kristy Lee,
    • Kent D. Taylor,
    • Xiuqing Guo,
    • Kristy Crooks,
    • Lesli A. Kiedrowski,
    • Leslie J. Raffel,
    • Ora Gordon,
    • Kalotina Machini,
    • Robert J. Desnick,
    • Leslie G. Biesecker,
    • Steven A. Lubitz,
    • Surabhi Mulchandani,
    • Greg M. Cooper,
    • Steven Joffe,
    • C. Sue Richards,
    • Yaoping Yang,
    • Jerome I. Rotter,
    • Stephen S. Rich,
    • Christopher J. O’Donnell,
    • Jonathan S. Berg,
    • Nancy B. Spinner,
    • James P. Evans,
    • Stephanie M. Fullerton,
    • Kathleen A. Leppig,
    • Robin L. Bennett,
    • Thomas Bird,
    • Virginia P. Sybert,
    • William M. Grady,
    • Holly K. Tabor,
    • Jerry H. Kim,
    • Michael J. Bamshad,
    • Benjamin Wilfond,
    • Arno G. Motulsky,
    • C. Ronald Scott,
    • Colin C. Pritchard,
    • Tom D. Walsh,
    • Wylie Burke,
    • Wendy H. Raskind,
    • Peter Byers,
    • Fuki M. Hisama,
    • Heidi Rehm,
    • Debbie A. Nickerson,
    • and Gail P. Jarvik
    Genome Res. March 2015 25: 305-315; Published in Advance January 30, 2015, doi:10.1101/gr.183483.114
    ...criteria and categories are presented in Table 1A and Table 1B, respectively. There were 615 distinct variants annotated in the Human Gene Mutation Database (HGMD) as disease causing in these 6503 participants’ exomes: 224were identified in the original 1000 participants (500 European ancestry and 500...
    OPEN ACCESS ARTICLE
  10. Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
    • Hao Zhu,
    • Jiao Zhang,
    • Soumya Rao,
    • Matthew D. Durbin,
    • Ying Li,
    • Ruirui Lang,
    • Jiqiang Liu,
    • Baichuan Xiao,
    • Hailin Shan,
    • Ziqiu Meng,
    • Jinmo Wang,
    • Xiaokai Tang,
    • Zhenni Shi,
    • Liza L. Cox,
    • Shouqin Zhao,
    • Stephanie M. Ware,
    • Tiong Y. Tan,
    • Michelle de Silva,
    • Lyndon Gallacher,
    • Ting Liu,
    • Jie Mi,
    • Changqing Zeng,
    • Hou-Feng Zheng,
    • Qingguo Zhang,
    • Stylianos E. Antonarakis,
    • Timothy C. Cox,
    • and Yong-Biao Zhang
    Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
    ...posterior probabilities as potential causal factors (Uffelmann et al. 2021). We included the top 10 variants of each algorithm and found that half of them were eQTLs (Supplemental Table 6). Combining the results from these fine-mapping methods, we identified two unlinked eQTLs, rs10017322 and rs344131 (r2...
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