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  1. Research: Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome
    • Lisanne Vervoort,
    • Nicolas Dierckxsens,
    • Marta Sousa Santos,
    • Senne Meynants,
    • Erika Souche,
    • Ruben Cools,
    • Tracy Heung,
    • Koen Devriendt,
    • Hilde Peeters,
    • Donna M. McDonald-McGinn,
    • Ann Swillen,
    • Jeroen Breckpot,
    • Beverly S. Emanuel,
    • Hilde Van Esch,
    • Anne S. Bassett,
    • and Joris R. Vermeesch
    Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124
    ...-read sequencing cannot resolve the complex segmental duplications (SDs) to provide direct confirmation of the hypothesis that the rearrangements are caused by nonallelic homologous recombination between the low copy repeats on Chromosome 22 (LCR22s). To enable haplotype-specific assembly and rearrangement mapping...
  2. Method: Transcriptional fates of human-specific segmental duplications in brain
    • Max L. Dougherty,
    • Jason G. Underwood,
    • Bradley J. Nelson,
    • Elizabeth Tseng,
    • Katherine M. Munson,
    • Osnat Penn,
    • Tomasz J. Nowakowski,
    • Alex A. Pollen,
    • and Evan E. Eichler
    Genome Res. October 2018 28: 1566-1576; Published in Advance September 18, 2018, doi:10.1101/gr.237610.118
    ...identity (>90%; also known as segmental duplications [SDs]) pose particular challenges for gene annotation because (1) they are enriched in assembly gaps (Alkan et al. 2011), (2) they are more prone to copy number polymorphism among individuals of the same species (Sudmant et al. 2015), and (3) different...
  3. Resource: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
    • Jonas A. Gustafson,
    • Sophia B. Gibson,
    • Nikhita Damaraju,
    • Miranda P.G. Zalusky,
    • Kendra Hoekzema,
    • David Twesigomwe,
    • Lei Yang,
    • Anthony A. Snead,
    • Phillip A. Richmond,
    • Wouter De Coster,
    • Nathan D. Olson,
    • Andrea Guarracino,
    • Qiuhui Li,
    • Angela L. Miller,
    • Joy Goffena,
    • Zachary B. Anderson,
    • Sophie H.R. Storz,
    • Sydney A. Ward,
    • Maisha Sinha,
    • Claudia Gonzaga-Jauregui,
    • Wayne E. Clarke,
    • Anna O. Basile,
    • André Corvelo,
    • Catherine Reeves,
    • Adrienne Helland,
    • Rajeeva Lochan Musunuri,
    • Mahler Revsine,
    • Karynne E. Patterson,
    • Cate R. Paschal,
    • Christina Zakarian,
    • Sara Goodwin,
    • Tanner D. Jensen,
    • Esther Robb,
    • The 1000 Genomes ONT Sequencing Consortium,
    • University of Washington Center for Rare Disease Research (UW-CRDR),
    • Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium,
    • William Richard McCombie,
    • Fritz J. Sedlazeck,
    • Justin M. Zook,
    • Stephen B. Montgomery,
    • Erik Garrison,
    • Mikhail Kolmogorov,
    • Michael C. Schatz,
    • Richard N. McLaughlin, Jr.,
    • Harriet Dashnow,
    • Michael C. Zody,
    • Matt Loose,
    • Miten Jain,
    • Evan E. Eichler,
    • and Danny E. Miller
    Genome Res. November 2024 34: 2061-2073; Published in Advance October 2, 2024, doi:10.1101/gr.279273.124
    ...; Ebert et al. 2021; Liao et al. 2023).SVs—defined as insertions, deletions, duplications, inversions, repeat expansions, and translocations at least 50 bp in size—are major contributors to genetic diversity and disease susceptibility and are more likely to have a larger effect size than single nucleotide...
    OPEN ACCESS ARTICLE
  4. Research: Copy number variation modifies expression time courses
    • Evelyne Chaignat,
    • Emilie Aït Yahya-Graison,
    • Charlotte N. Henrichsen,
    • Jacqueline Chrast,
    • Frédéric Schütz,
    • Sylvain Pradervand,
    • and Alexandre Reymond
    Genome Res. January 2011 21: 106-113; Published in Advance November 17, 2010, doi:10.1101/gr.112748.110
    .... 2004. Large-scale copy number polymorphism in the human . Science 305: 525–528. She X, Cheng Z, Zollner S, Church DM, Eichler EE. 2008. Mouse segmental duplication and copy number variation. Nat Genet 40: 909–914. Smyth GK. 2004. Linear models and empirical Bayes methods for assessing differential...
  5. LETTER: Segmental Duplications Flank the Multiple Sclerosis Locus on Chromosome 17q
    • Daniel C. Chen,
    • Janna Saarela,
    • Royden A. Clark,
    • Timo Miettinen,
    • Anthony Chi,
    • Evan E. Eichler,
    • Leena Peltonen,
    • and Aarno Palotie
    Genome Res. August 2004 14: 1483-1492; Published in Advance July 15, 2004, doi:10.1101/gr.2340804
    ...of interchromosomal and intrachromosomal segmental duplications, also known as duplicons or low-copy repeat sequences ( Saarela et al. 2002 ). Such regions often demarcate regions of genomic instability associated within recurrent chromosomal structural rearrangements and disease ( Stankiewicz and Lupski 2002...
  6. ARTICLE: Analysis of Segmental Duplications and Genome Assembly in the Mouse
    • Jeffrey A. Bailey,
    • Deanna M. Church,
    • Mario Ventura,
    • Mariano Rocchi,
    • and Evan E. Eichler
    Genome Res. May 2004 14: 789-801; doi:10.1101/gr.2238404
    ...variation of the C57BL/6J strain. We conservatively estimate that ∼57% of all highly identical segmental duplications (≥90%) were misassembled or collapsed within the working draft WGS assembly. The WGS approach often leaves duplications fragmented and unassigned to a chromosome when compared with the clone...
  7. ARTICLE: Traffic of genetic information between segmental duplications flanking the typical 22q11.2 deletion in velo-cardio-facial syndrome/DiGeorge syndrome
    • Adam Pavlicek,
    • Reniqua House,
    • Andrew J. Gentles,
    • Jerzy Jurka,
    • and Bernice E. Morrow
    Genome Res. November 2005 15: 1487-1495; doi:10.1101/gr.4281205
    ..., b ). Both deletions and duplications can occur during meiosis, resulting in altered gene dosage associated with mental retardation and congenital malformation syndromes. The most well-recognized include Williams-Beuren syndrome on Chromosome 7q11.2, Prader-Willi/Angelman syndromes on Chromsome 15q11...
  8. LETTER: Copy number variation at the breakpoint region of isochromosome 17q
    • Claudia M.B. Carvalho and
    • James R. Lupski
    Genome Res. November 2008 18: 1724-1732; Published in Advance August 19, 2008, doi:10.1101/gr.080697.108
    ...(PFGE), and public array comparative genomic hybridization (array CGH) data, we show that the REPA/B structure is also susceptible to frequent meiotic rearrangements. It is a highly dynamic genomic region undergoing deletions, inversions, and duplications likely produced by non-allelic homologous...
  9. REVIEW: Copy number variation: New insights in genome diversity
    • Jennifer L. Freeman,
    • George H. Perry,
    • Lars Feuk,
    • Richard Redon,
    • Steven A. McCarroll,
    • David M. Altshuler,
    • Hiroyuki Aburatani,
    • Keith W. Jones,
    • Chris Tyler-Smith,
    • Matthew E. Hurles,
    • Nigel P. Carter,
    • Stephen W. Scherer,
    • and Charles Lee
    Genome Res. August 2006 16: 949-961; Published in Advance June 29, 2006, doi:10.1101/gr.3677206
    ...the overall size distribution of human CNVs. Furthermore, the possibility that larger CNVs tend to represent multi-copy duplications is consistent with earlier observations that large segmental duplications are more likely to be tolerated by a than are deletions of similar sizes (i.e., >100 kb) ( Lindsley...
  10. Research: NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits
    • Piotr Dittwald,
    • Tomasz Gambin,
    • Przemyslaw Szafranski,
    • Jian Li,
    • Stephen Amato,
    • Michael Y. Divon,
    • Lisa Ximena Rodríguez Rojas,
    • Lindsay E. Elton,
    • Daryl A. Scott,
    • Christian P. Schaaf,
    • Wilfredo Torres-Martinez,
    • Abby K. Stevens,
    • Jill A. Rosenfeld,
    • Satish Agadi,
    • David Francis,
    • Sung-Hae L. Kang,
    • Amy Breman,
    • Seema R. Lalani,
    • Carlos A. Bacino,
    • Weimin Bi,
    • Aleksandar Milosavljevic,
    • Arthur L. Beaudet,
    • Ankita Patel,
    • Chad A. Shaw,
    • James R. Lupski,
    • Anna Gambin,
    • Sau Wai Cheung,
    • and Pawel Stankiewicz
    Genome Res. September 2013 23: 1395-1409; Published in Advance May 8, 2013, doi:10.1101/gr.152454.112
    ...(NAHR)-mediated copy-number variants (CNVs). The most commonly observed recurrent CNVs were NPHP1 duplications (233), CHRNA7 duplications (175), and 22q11.21 deletions (DiGeorge/velocardiofacial syndrome, 166). In the ∼25% of CMA cases for which parental studies were available, we identified 190 de...
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