Searching journal content for articles similar to Ji et al. 34 (4): 633.

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  1. Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
    • Kohei Hagiwara,
    • Andrew Thrasher,
    • Nadezhda V. Terekhanova,
    • and Jinghui Zhang
    Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
    ...of this model to intratumor heterogeneity. As a byproduct of this confounding effect, we evaluate whether the inverse relationship between mutant allele enrichment in RNA and tumor purity could be leveraged to complement DNA-based somatic mutation detection in low purity samples. Indeed, our de novo somatic...
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  2. Method: Detection of structural mosaicism from targeted and whole-genome sequencing data
    • Daniel A. King,
    • Alejandro Sifrim,
    • Tomas W. Fitzgerald,
    • Raheleh Rahbari,
    • Emma Hobson,
    • Tessa Homfray,
    • Sahar Mansour,
    • Sarju G. Mehta,
    • Mohammed Shehla,
    • Susan E. Tomkins,
    • Pradeep C. Vasudevan,
    • Matthew E. Hurles,
    • and The Deciphering Developmental Disorders Study
    Genome Res. October 2017 27: 1704-1714; Published in Advance August 30, 2017, doi:10.1101/gr.212373.116
    ...Research 27:1704–1714 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/17; www..org www..org protein-coding regions (“exons”) of the , an approach called whole-exome sequencing (WES) (Koboldt et al. 2013). Indeed, sequencing of the whole (WGS) offers several advantages compared to WES...
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  3. Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
    • Li-Ting Chen,
    • Myrthe Jager,
    • Dàmi Rebergen,
    • Geertruid J. Brink,
    • Tom van den Ende,
    • Willem Vanderlinden,
    • Pauline Kolbeck,
    • Marc Pagès-Gallego,
    • Ymke van der Pol,
    • Nicolle Besselink,
    • Norbert Moldovan,
    • Nizar Hami,
    • Wigard P. Kloosterman,
    • Hanneke van Laarhoven,
    • Florent Mouliere,
    • Ronald Zweemer,
    • Jan Lipfert,
    • Sarah Derks,
    • Alessio Marcozzi,
    • and Jeroen de Ridder
    Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
    ...number alterations (CNAs), which occur in more than 90% of solid tumors (Hieronymus et al. 2018; Hoadley et al. 2018; Steele et al. 2022; Martínez-Jiménez et al. 2023). In addition to traditional genomic mutation features, -wide cfDNA sequencing also enables the detection of so-called fragmentomics...
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  4. Research: Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing
    • Elena Helman,
    • Michael S. Lawrence,
    • Chip Stewart,
    • Carrie Sougnez,
    • Gad Getz,
    • and Matthew Meyerson
    Genome Res. July 2014 24: 1053-1063; Published in Advance May 13, 2014, doi:10.1101/gr.163659.113
    ...Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing Elena Helman 1 , 2 , Michael S. Lawrence 2 , Chip Stewart 2 , Carrie Sougnez 2 , Gad Getz 2 , 3 and Matthew Meyerson 1 , 2 , 4 , 5 , 6...
  5. Method: Detection of long repeat expansions from PCR-free whole-genome sequence data
    • Egor Dolzhenko,
    • Joke J.F.A. van Vugt,
    • Richard J. Shaw,
    • Mitchell A. Bekritsky,
    • Marka van Blitterswijk,
    • Giuseppe Narzisi,
    • Subramanian S. Ajay,
    • Vani Rajan,
    • Bryan R. Lajoie,
    • Nathan H. Johnson,
    • Zoya Kingsbury,
    • Sean J. Humphray,
    • Raymond D. Schellevis,
    • William J. Brands,
    • Matt Baker,
    • Rosa Rademakers,
    • Maarten Kooyman,
    • Gijs H.P. Tazelaar,
    • Michael A. van Es,
    • Russell McLaughlin,
    • William Sproviero,
    • Aleksey Shatunov,
    • Ashley Jones,
    • Ahmad Al Khleifat,
    • Alan Pittman,
    • Sarah Morgan,
    • Orla Hardiman,
    • Ammar Al-Chalabi,
    • Chris Shaw,
    • Bradley Smith,
    • Edmund J. Neo,
    • Karen Morrison,
    • Pamela J. Shaw,
    • Catherine Reeves,
    • Lara Winterkorn,
    • Nancy S. Wexler,
    • The US–Venezuela Collaborative Research Group,
    • David E. Housman,
    • Christopher W. Ng,
    • Alina L. Li,
    • Ryan J. Taft,
    • Leonard H. van den Berg,
    • David R. Bentley,
    • Jan H. Veldink,
    • and Michael A. Eberle
    Genome Res. November 2017 27: 1895-1903; Published in Advance September 8, 2017, doi:10.1101/gr.225672.117
    ...pathogenic repeats is unlikely to work with whole-exome sequence data because (1) many repeats of interest are not exonic; and (2) size estimates for large repeats require assumptions about the average number of reads per base. Additionally, some important repeats, like the repeat in FMR1 gene that causes...
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  6. Research: Frequent somatic gene conversion as a mechanism for loss of heterozygosity in tumor suppressor genes
    • Kazuki K. Takahashi and
    • Hideki Innan
    Genome Res. June 2022 32: 1017-1025; Published in Advance May 26, 2022, doi:10.1101/gr.276617.122
    ...(SNVs) and small indels (i.e., SNVs exclusively mean base substitutions). We used the whole-exome sequences (WXSs) data of 3,349,768 somatic mutations in 32 cancer types in 9482 patient samples in The Cancer Genome Atlas (TCGA; see Methods) (for details, see Supplemental Table S1). The coverage exceeded...
  7. Research: Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution
    • Hoon Kim,
    • Siyuan Zheng,
    • Seyed S. Amini,
    • Selene M. Virk,
    • Tom Mikkelsen,
    • Daniel J. Brat,
    • Jonna Grimsby,
    • Carrie Sougnez,
    • Florian Muller,
    • Jian Hu,
    • Andrew E. Sloan,
    • Mark L. Cohen,
    • Erwin G. Van Meir,
    • Lisa Scarpace,
    • Peter W. Laird,
    • John N. Weinstein,
    • Eric S. Lander,
    • Stacey Gabriel,
    • Gad Getz,
    • Matthew Meyerson,
    • Lynda Chin,
    • Jill S. Barnholtz-Sloan,
    • and Roel G.W. Verhaak
    Genome Res. March 2015 25: 316-327; Published in Advance February 3, 2015, doi:10.1101/gr.180612.114
    ...architecture of this residual population is critical for the development of successful therapies. We used whole-genome sequencing and whole-exome sequencing of multiple sectors from primary and paired recurrent GBM tumors to reconstruct the genomic profile of residual, therapy resistant tumor initiating cells...
  8. Research: Whole genome sequencing of matched primary and metastatic acral melanomas
    • Samra Turajlic,
    • Simon J. Furney,
    • Maryou B. Lambros,
    • Costas Mitsopoulos,
    • Iwanka Kozarewa,
    • Felipe C. Geyer,
    • Alan MacKay,
    • Jarle Hakas,
    • Marketa Zvelebil,
    • Christopher J. Lord,
    • Alan Ashworth,
    • Meirion Thomas,
    • Gordon Stamp,
    • James Larkin,
    • Jorge S. Reis-Filho,
    • and Richard Marais
    Genome Res. February 2012 22: 196-207; Published in Advance December 19, 2011, doi:10.1101/gr.125591.111
    ...Next generation sequencing has enabled systematic discovery of mutational spectra in cancer samples. Here, we used whole genome sequencing to characterize somatic mutations and structural variation in a primary acral melanoma and its lymph node metastasis. Our data show that the somatic mutational...
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  9. Method: TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data
    • Gavin Ha,
    • Andrew Roth,
    • Jaswinder Khattra,
    • Julie Ho,
    • Damian Yap,
    • Leah M. Prentice,
    • Nataliya Melnyk,
    • Andrew McPherson,
    • Ali Bashashati,
    • Emma Laks,
    • Justina Biele,
    • Jiarui Ding,
    • Alan Le,
    • Jamie Rosner,
    • Karey Shumansky,
    • Marco A. Marra,
    • C. Blake Gilks,
    • David G. Huntsman,
    • Jessica N. McAlpine,
    • Samuel Aparicio,
    • and Sohrab P. Shah
    Genome Res. November 2014 24: 1881-1893; Published in Advance July 24, 2014, doi:10.1101/gr.180281.114
    ..., simulating clonal populations from whole-genome sequences taken from genomically heterogeneous ovarian tumor sites collected from the same patient. In addition, we show in 23 whole genomes of breast tumors that the inference of CNA and LOH using TITAN critically informs population structure and the nature...
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  10. Research: Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia
    • Pedro G. Ferreira,
    • Pedro Jares,
    • Daniel Rico,
    • Gonzalo Gómez-López,
    • Alejandra Martínez-Trillos,
    • Neus Villamor,
    • Simone Ecker,
    • Abel González-Pérez,
    • David G. Knowles,
    • Jean Monlong,
    • Rory Johnson,
    • Victor Quesada,
    • Sarah Djebali,
    • Panagiotis Papasaikas,
    • Mónica López-Guerra,
    • Dolors Colomer,
    • Cristina Royo,
    • Maite Cazorla,
    • Magda Pinyol,
    • Guillem Clot,
    • Marta Aymerich,
    • Maria Rozman,
    • Marta Kulis,
    • David Tamborero,
    • Anaïs Gouin,
    • Julie Blanc,
    • Marta Gut,
    • Ivo Gut,
    • Xose S. Puente,
    • David G. Pisano,
    • José Ignacio Martin-Subero,
    • Nuria López-Bigas,
    • Armando López-Guillermo,
    • Alfonso Valencia,
    • Carlos López-Otín,
    • Elías Campo,
    • and Roderic Guigó
    Genome Res. February 2014 24: 212-226; Published in Advance November 21, 2013, doi:10.1101/gr.152132.112
    ...behavior. Whole-genome and -exome sequencing has contributed to the characterization of the mutational spectrum of the disease, but the underlying transcriptional profile is still poorly understood. We have performed deep RNA sequencing in different subpopulations of normal B-lymphocytes and CLL cells from...
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