Searching journal content for articles similar to Price et al. 14 (11): 2245.

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  1. Resource: Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
    • Bo Zhou,
    • Steve S. Ho,
    • Stephanie U. Greer,
    • Xiaowei Zhu,
    • John M. Bell,
    • Joseph G. Arthur,
    • Noah Spies,
    • Xianglong Zhang,
    • Seunggyu Byeon,
    • Reenal Pattni,
    • Noa Ben-Efraim,
    • Michael S. Haney,
    • Rajini R. Haraksingh,
    • Giltae Song,
    • Hanlee P. Ji,
    • Dimitri Perrin,
    • Wing H. Wong,
    • Alexej Abyzov,
    • and Alexander E. Urban
    Genome Res. March 2019 29: 472-484; Published in Advance February 8, 2019, doi:10.1101/gr.234948.118
    ...; histogram (log-scale) of allele-specifically methylated CpGs in 50-kb windows; nonreference Alu and LINE-1 insertions; allele-specific CRISPR target sites; large-scale rearrangements detected by Long Ranger (Zheng et al. 2016; Marks et al. 2018) (light blue: intrachromosomal; dark blue: interchromosomal...
  2. Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
    • Tianfu Zeng,
    • Haotian Liao,
    • Lin Xia,
    • Siyao You,
    • Yanqun Huang,
    • Jiaxun Zhang,
    • Yahui Liu,
    • Xuyan Liu,
    • and Dan Xie
    Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
    ...samples, with breakpoint variations confined within 10 bp. Short-read sequencing in the samples failed to detect this DEL, primarily due to the tandem-repeated Alu sequences present within the corresponding region of the reference (Supplemental Fig. S10A,B).To assess the functional impact...
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  3. Research: Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance
    • Tim Downing,
    • Hideo Imamura,
    • Saskia Decuypere,
    • Taane G. Clark,
    • Graham H. Coombs,
    • James A. Cotton,
    • James D. Hilley,
    • Simonne de Doncker,
    • Ilse Maes,
    • Jeremy C. Mottram,
    • Mike A. Quail,
    • Suman Rijal,
    • Mandy Sanders,
    • Gabriele Schönian,
    • Olivia Stark,
    • Shyam Sundar,
    • Manu Vanaerschot,
    • Christiane Hertz-Fowler,
    • Jean-Claude Dujardin,
    • and Matthew Berriman
    Genome Res. December 2011 21: 2143-2156; Published in Advance October 28, 2011, doi:10.1101/gr.123430.111
    ..., isolated from visceral leishmaniasis patients from the same region, which also differ in their response to in vitro drug susceptibility. We show that whole-genome sequence data reveals genetic structure within these lines not shown by multilocus typing, and suggests that drug resistance has emerged...
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  4. Resource: Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans
    • Adam D. Ewing and
    • Haig H. Kazazian, Jr.
    Genome Res. June 2011 21: 985-990; Published in Advance October 27, 2010, doi:10.1101/gr.114777.110
    ...). A recent study reporting a highly efficient approach for identifyingmobile element insertions by sequence capture identified 487 nonreferenceAluYb8/ Table 1. Population-specific L1 polymorphisms A. Population-specific insertions among 10 populationsa Populationb Individuals Total insertions Population...
  5. Methods: Identification of transposable elements using multiple alignments of related genomes
    • Anat Caspi and
    • Lior Pachter
    Genome Res. February 2006 16: 260-270; Published in Advance December 14, 2005, doi:10.1101/gr.4361206
    ...on the host genome, and improve the quality of assembled genomes. Using the availability of several nearly complete Drosophila genomes and developments in whole genome alignment methods, we introduce a large-scale comparative method for identifying repetitive mobile DNA regions. These regions are highly...
  6. Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
    • Xuyan Liu,
    • Lin Xia,
    • Yixin Qiao,
    • Yang Li,
    • Yan Huang,
    • Bingyan Yue,
    • Xi Liang,
    • Xin Yang,
    • Honghui Zhang,
    • Jiaxun Zhang,
    • Xiao Chen,
    • Dan Xie,
    • and Jifeng Liu
    Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
    ...co-occurring SV patterns 575 within individual reads, which may represent complex structural rearrangements. For instance, 576 in sample LSCC1, a single read simultaneously contained an insertion of a simple repeat (AT), 577 a deletion within a LINE/L1 element, and an insertion of a SINE/Alu...
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  7. LETTER: Retroelement Distributions in the Human Genome: Variations Associated With Age and Proximity to Genes
    • Patrik Medstrand,
    • Louie N. van de Lagemaat,
    • and Dixie L. Mager
    Genome Res. October 1, 2002 12: 1483-1495; doi:10.1101/gr.388902
    ...in Methods. View this table: In this window In a new window Table 3. Significance ( P -Values) of Distributional Difference Between Alus on the Y Chromosome vs. the Whole Genome Potential Explanations for Alu Distribution Patterns The density patterns of Alu elements do not conform to trends observed...
  8. ARTICLE: Evolutionary mechanisms shaping the genomic structure of the Williams-Beuren syndrome chromosomal region at human 7q11.23
    • Anna Antonell,
    • Oscar de Luis,
    • Xavier Domingo-Roura,
    • and Luis Alberto Pérez-Jurado
    Genome Res. September 2005 15: 1179-1188; doi:10.1101/gr.3944605
    ...elements have been found to accumulate at the junction sites of segmental duplications -wide ( Batzer and Deininger 2002 ; Bailey et al. 2003 ). In fact, Alu s have been directly implicated in the generation of the segmental duplications in 22q11 ( Babcock et al. 2003 ). The presence of Alu repeats...
  9. Methods: Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes
    • Fereydoun Hormozdiari,
    • Can Alkan,
    • Evan E. Eichler,
    • and S. Cenk Sahinalp
    Genome Res. July 2009 19: 1270-1278; Published in Advance May 15, 2009, doi:10.1101/gr.088633.108
    ...) to Figure 1. Deletion length histogram of detected SVs from NA18507 in human build 36 with the weighted VariationHunter-SC algorithm (weighted_support $ 3). Increased numbers of predicted deletions of size 300 bp and 6 Kbp (due to AluY and L1Hs repeat units, respectively) are clearly seen in the histogram...
  10. Letter: Evolutionary descent of a human chromosome 6 neocentromere: A jump back to 17 million years ago
    • Oronzo Capozzi,
    • Stefania Purgato,
    • Pietro D'Addabbo,
    • Nicoletta Archidiacono,
    • Paola Battaglia,
    • Anna Baroncini,
    • Antonella Capucci,
    • Roscoe Stanyon,
    • Giuliano Della Valle,
    • and Mariano Rocchi
    Genome Res. May 2009 19: 778-784; doi:10.1101/gr.085688.108
    ...:57.2%). Repeat element distribution within the CENP-A/C domain, in the 300 kb flanking the domain on both sides, as well as in the entire chromosome 6 and in the human , are reported in Table 3. AluY and AluSx are separately reported because they appear to be themore activeAlu elements (Bennett et al...
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