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  1. Method: Identification of complex genomic rearrangements in cancers using CouGaR
    • Misko Dzamba,
    • Arun K. Ramani,
    • Pawel Buczkowicz,
    • Yue Jiang,
    • Man Yu,
    • Cynthia Hawkins,
    • and Michael Brudno
    Genome Res. January 2017 27: 107-117; Published in Advance November 14, 2016, doi:10.1101/gr.211201.116
    ...), use discordant insert sizes in paired-end whole- sequencing (WGS) and precise mapping of split reads to infer the breakpoints of novel structural variants. However, because they predict structural variants without utilizing coverage information, the overall genomic structure is inconsistent...
  2. Method: TIGRA: A targeted iterative graph routing assembler for breakpoint assembly
    • Ken Chen,
    • Lei Chen,
    • Xian Fan,
    • John Wallis,
    • Li Ding,
    • and George Weinstock
    Genome Res. February 2014 24: 310-317; Published in Advance December 4, 2013, doi:10.1101/gr.162883.113
    ...-generation sequencing has greatly facilitated our study of genomic structural variation. Unlike single nucleotide variants and small indels, many structural variants have not been completely characterized at nucleotide resolution. Deriving the complete sequences underlying such breakpoints is crucial for not only...
  3. Method: Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer
    • Eva K.F. Chan,
    • Daniel L. Cameron,
    • Desiree C. Petersen,
    • Ruth J. Lyons,
    • Benedetta F. Baldi,
    • Anthony T. Papenfuss,
    • David M. Thomas,
    • and Vanessa M. Hayes
    Genome Res. May 2018 28: 726-738; Published in Advance April 4, 2018, doi:10.1101/gr.227975.117
    ...of GRIDSS-derived rearrangement breakpoints to reconstruct chains of local rearrangement events within the unmapped fusion junctions (Fig. 8). Together, these results suggest the unaligned regions represent highly fragmented genomic loci revealing the complex nature of the neochromosomes. Given the results...
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  4. Research: Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicase
    • Ayako Yamanishi,
    • Kosuke Yusa,
    • Kyoji Horie,
    • Masahiro Tokunaga,
    • Kohji Kusano,
    • Chikara Kokubu,
    • and Junji Takeda
    Genome Res. September 2013 23: 1462-1473; Published in Advance August 1, 2013, doi:10.1101/gr.152744.112
    ...hybridization and high-density single nucleotide polymorphism genotyping, revealing that the combination of BLM suppression and DSB induction enhanced genomic rearrangements, including deletions and insertions, whose breakpoints were clustered in genomic inverted repeats and associated with junctional...
  5. Research: Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability
    • Keiko Akagi,
    • Jingfeng Li,
    • Tatevik R. Broutian,
    • Hesed Padilla-Nash,
    • Weihong Xiao,
    • Bo Jiang,
    • James W. Rocco,
    • Theodoros N. Teknos,
    • Bhavna Kumar,
    • Danny Wangsa,
    • Dandan He,
    • Thomas Ried,
    • David E. Symer,
    • and Maura L. Gillison
    Genome Res. February 2014 24: 185-199; Published in Advance November 7, 2013, doi:10.1101/gr.164806.113
    ...(CNVs) HPV insertional breakpoints detected byWGS were observed to be less numerous than viral copy numbers in some cases (Table 1).We hypothesized that this discrepancy was due to amplification of viral integrants and flanking genomic sequences, leading to Figure 1. The HPV virome in human cancers. WGS...
  6. Method: Discovery of recurrent structural variants in nasopharyngeal carcinoma
    • Anton Valouev,
    • Ziming Weng,
    • Robert T. Sweeney,
    • Sushama Varma,
    • Quynh-Thu Le,
    • Christina Kong,
    • Arend Sidow,
    • and Robert B. West
    Genome Res. February 2014 24: 300-309; Published in Advance November 8, 2013, doi:10.1101/gr.156224.113
    ...generated by circularization of two (rather than a single) genomic fragments into a single construct. Such discordant mate pairs are randomly distributed throughout the andnot expected to cluster. In contrast, the discordant reads that result from rearrangements will form large clusters near the breakpoint...
  7. Perspective: From human genome to cancer genome: The first decade
    • David A. Wheeler and
    • Linghua Wang
    Genome Res. July 2013 23: 1054-1062; doi:10.1101/gr.157602.113
    .... 2012. Mutations in the spliceosome machinery, a novel and ubiquitous pathway in leukemogenesis. Blood 119: 3203–3210. Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM. 2013. Breakpoint profiling of 64 cancer s reveals numerous complex rearrangements spawned...
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