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Resource: An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- Chong Li,
- Marc Jan Bonder,
- Sabriya Syed,
- Matthew Jensen,
- Human Genome Structural Variation Consortium (HGSVC),
- HGSVC Functional Analysis Working Group,
- Mark B. Gerstein,
- Michael C. Zody,
- Mark J.P. Chaisson,
- Michael E. Talkowski,
- Tobias Marschall,
- Jan O. Korbel,
- Evan E. Eichler,
- Charles Lee,
- and Xinghua Shi
Genome Res. December 2024 34: 2304-2318; Published in Advance December 5, 2024, doi:10.1101/gr.279419.124
....65% of the PanGenie SV set, 1674 deletions [DELs], and 2391 insertions [INSs]) appear at TAD boundaries do not significantly affect the 3D chromatin structure, we indeed identified 185 SVs (66 deletions and 119 insertions) that significantly disrupted TAD boundaries (referred to as TAD–SVs; False discovery rate...
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Method: CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
- Marzia Rossato,
- Luca Marcolungo,
- Luca De Antoni,
- Giulia Lopatriello,
- Elisa Bellucci,
- Gaia Cortinovis,
- Giulia Frascarelli,
- Laura Nanni,
- Elena Bitocchi,
- Valerio Di Vittori,
- Leonardo Vincenzi,
- Filippo Lucchini,
- Kirstin E. Bett,
- Larissa Ramsay,
- David James Konkin,
- Massimo Delledonne,
- and Roberto Papa
Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
...CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant s Marzia Rossato1,2,6, Luca Marcolungo1,6, Luca De Antoni1, Giulia Lopatriello1, Elisa Bellucci3, Gaia Cortinovis3, Giulia Frascarelli3, Laura Nanni3, Elena Bitocchi3, Valerio Di Vittori3, Leonardo Vincenzi1, Filippo...
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Mini-Review: The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
- Giulia F. Del Gobbo and
- Kym M. Boycott
Genome Res. April 2025 35: 559-571; Published in Advance February 3, 2025, doi:10.1101/gr.279970.124
...that the generation of a graph pan of 574 assemblies from a pediatric RD cohort and 94 control assemblies improved the reproducibility of SVs compared to standard reference-based approaches (Groza et al. 2024). It also improved the prioritization of rare, potentially disease-associated SVs, leading to the discovery...
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Resource: Discordant calls across genotype discovery approaches elucidate variants with systematic errors
- Elizabeth G. Atkinson,
- Mykyta Artomov,
- Alexander A. Loboda,
- Heidi L. Rehm,
- Daniel G. MacArthur,
- Konrad J. Karczewski,
- Benjamin M. Neale,
- and Mark J. Daly
Genome Res. May 30, 2023 ; Published in Advance May 30, 2023, doi:10.1101/gr.277908.123
...). Although novel discordant variants were discovered in each population, most variants observed in other populations were shared with C D Figure 1. Discordance in genotype calls across high-throughput genotype discovery approaches. (A) Fisher’s exact test concordance test P-value for shared, PASS sites...
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Method: A complete pedigree-based graph workflow for rare candidate variant analysis
- Charles Markello,
- Charles Huang,
- Alex Rodriguez,
- Andrew Carroll,
- Pi-Chuan Chang,
- Jordan Eizenga,
- Thomas Markello,
- David Haussler,
- and Benedict Paten
Genome Res. May 2022 32: 893-903; Published in Advance April 28, 2022, doi:10.1101/gr.276387.121
...tasks of gene discovery is the detection of variants in highly polymorphic, repetitive, and incompletely represented regions of the , exactly where pan graphs can potentially extend accuracy and precision.We first describe VG-Pedigree, a software workflow for mapping and variant calling high-throughput...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...; LaCroix et al. 2019; Yeetong et al. 2019; Katsumata et al. 2020; Ruggieri et al. 2020).View larger version: In this window In a new window Figure 1. Overview of disease-associated repeat discovery by year, with colored inserts specifying the major technological breakthroughs that were used to make...
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Method: High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome
- Sam Alsford,
- Daniel J. Turner,
- Samson O. Obado,
- Alejandro Sanchez-Flores,
- Lucy Glover,
- Matthew Berriman,
- Christiane Hertz-Fowler,
- and David Horn
Genome Res. June 2011 21: 915-924; Published in Advance March 1, 2011, doi:10.1101/gr.115089.110
...High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Sam Alsford 1 , 6 , Daniel J. Turner 2 , 3 , 6 , Samson O. Obado 1 , 4 , Alejandro Sanchez-Flores 2 , Lucy Glover 1...
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Resource: Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis
- Leslie O. Goodwin,
- Erik Splinter,
- Tiffany L. Davis,
- Rachel Urban,
- Hao He,
- Robert E. Braun,
- Elissa J. Chesler,
- Vivek Kumar,
- Max van Min,
- Juliet Ndukum,
- Vivek M. Philip,
- Laura G. Reinholdt,
- Karen Svenson,
- Jacqueline K. White,
- Michael Sasner,
- Cathleen Lutz,
- and Stephen A. Murray
Genome Res. March 2019 29: 494-505; Published in Advance January 18, 2019, doi:10.1101/gr.233866.117
...mutagenesis at the integration site. Inverse PCR can be used to clone the actual fusion sequence but has a high failure rate owing to the multicopy nature of most transgenes. More recently, high-throughput sequencing (HTS) has been employed to identify transgene insertion sites (Dubose et al. 2013...
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Method: The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology
- Eugene J. Gardner,
- Vincent K. Lam,
- Daniel N. Harris,
- Nelson T. Chuang,
- Emma C. Scott,
- W. Stephen Pittard,
- Ryan E. Mills,
- The 1000 Genomes Project Consortium,
- and Scott E. Devine
Genome Res. November 2017 27: 1916-1929; Published in Advance August 30, 2017, doi:10.1101/gr.218032.116
...a series of simulation studies (Fig. 1D–K; Supplemental Figs. S4, S5; Supplemental Tables S5, S6). Briefly, a test set ofAlu, L1, and SVA MEIs was inserted randomly into the reference human multiple times to generate a series of simulated s Figure 1. Comparisons of MEI discovery algorithms. (A–C) Runtime...
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Research: Rare allelic forms of PRDM9 associated with childhood leukemogenesis
- Julie Hussin,
- Daniel Sinnett,
- Ferran Casals,
- Youssef Idaghdour,
- Vanessa Bruat,
- Virginie Saillour,
- Jasmine Healy,
- Jean-Christophe Grenier,
- Thibault de Malliard,
- Stephan Busche,
- Jean-François Spinella,
- Mathieu Larivière,
- Greg Gibson,
- Anna Andersson,
- Linda Holmfeldt,
- Jing Ma,
- Lei Wei,
- Jinghui Zhang,
- Gregor Andelfinger,
- James R. Downing,
- Charles G. Mullighan,
- and Philip Awadalla
Genome Res. March 2013 23: 419-430; Published in Advance December 5, 2012, doi:10.1101/gr.144188.112
...of rare allelic forms of PRDM9 . The rare PRDM9 alleles are transmitted to the affected children in half the cases; nonetheless there remains a significant excess of rare alleles among patients relative to controls. We successfully replicated this latter observation in an independent cohort of 50...
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