Searching journal content for articles similar to Ji et al. 4 (2): 109.

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  1. Research: Alu insertion variants alter gene transcript levels
    • Lindsay M. Payer,
    • Jared P. Steranka,
    • Maria S. Kryatova,
    • Giacomo Grillo,
    • Mathieu Lupien,
    • Pedro P. Rocha,
    • and Kathleen H. Burns
    Genome Res. December 2021 31: 2236-2248; Published in Advance November 19, 2021, doi:10.1101/gr.261305.120
    ...that the Alu reduces expression of a nearby gene, potentially PTHLH, which in turn leads to cancer risk. We measured expression of the genes near the Alu insertion site in the CRISPR-edited 293T cell lines by qRT-PCR. The presence of the Alu results in a 0.49-fold change in PTHLH expression relative to when...
  2. Method: Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II
    • Paul J. Norman,
    • Steven J. Norberg,
    • Lisbeth A. Guethlein,
    • Neda Nemat-Gorgani,
    • Thomas Royce,
    • Emily E. Wroblewski,
    • Tamsen Dunn,
    • Tobias Mann,
    • Claudia Alicata,
    • Jill A. Hollenbach,
    • Weihua Chang,
    • Melissa Shults Won,
    • Kevin L. Gunderson,
    • Laurent Abi-Rached,
    • Mostafa Ronaghi,
    • and Peter Parham
    Genome Res. May 2017 27: 813-823; Published in Advance March 30, 2017, doi:10.1101/gr.213538.116
    ...been mapped to the reference sequence (also derived from Clint) and PCR duplicates removed. Stringent alignment criteria were used to map the sequence reads back to the chimpanzee genomic segment that is equivalent to the human MHC region (the panTro4 MHC, Chr 6: 28774516-33956232). Characterizing 95...
  3. ARTICLE: Degenerate oligonucleotide sequence-directed cross-species PCR cloning of the BCP 54/ALDH 3 cDNA: priming from inverted repeats and formation of tandem primer arrays.
    • D L Cooper and
    • E W Baptist
    Genome Res. August 1991 1: 57-62; doi:10.1101/gr.1.1.57
    ....L. and C.T. Caskey. 1989. Alu PCR: The use of repeat sequence primers for amplification of human DNA from complex sources. In PCR technology (ed. H.A. Erlich), pp. 113–116. Stockton Press, New York. Genome Res Genome Research Genome Res. 1088-9051 Cold Spring Harbor Laboratory Press 10.1101/gr.1...
  4. 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
    ...in LCR22 clusters, we combined fiber-FISH optical mapping with whole- (ultra-)long-read sequencing or rearrangement-specific long-range PCR on 25 families comprising several different LCR22-mediated rearrangements. We demonstrate that not only different paralogous SDs but also palindromic AT-rich repeats...
  5. RESEARCH: Complex β-Satellite Repeat Structures and the Expansion of the Zinc Finger Gene Cluster in 19p12
    • Evan E. Eichler,
    • Susan M. Hoffman,
    • Aaron A. Adamson,
    • Laurie A. Gordon,
    • Paula McCready,
    • Jane E. Lamerdin,
    • and Harvey W. Mohrenweiser
    Genome Res. August 1, 1998 8: 791-808; doi:10.1101/gr.8.8.791
    ...within the center of the β-satellite repeat element. In two of the three blocks examined, the Alu repeat element is conspicuously oriented in an inverted orientation with respect to other repeat elements within the superstructure. View larger version: In this window In a new window Figure 5. Higher order...
  6. 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
    ...). Additionally, examples of insertions involving transposable elements, highly repetitive DNA sequences that can insert themselves into new places in the and potentially disrupt coding sequences, splicing, or gene regulation, have been reported. These include SINE-VNTR-Alu (SVA) element insertions in introns...
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  7. ARTICLE: Genome walking with 2- to 4-kb steps using panhandle PCR.
    • D H Jones and
    • S C Winistorfer
    Genome Res. February 1993 2: 197-203; doi:10.1101/gr.2.3.197
    ...and is shown in Figure 4B. The first 226 nucleotides (bases -4394 to -4169) are part of an Alu se- quence. (31) PCR was applied to unmodi- fied genomic DNA to confirm the se- quence located from -4375 bp to -3765 bp relative to the DNA sequence and also to confirm the presence of two alleles, one...
  8. Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
    • Susan M. Hiatt,
    • James M.J. Lawlor,
    • Lori H. Handley,
    • Donald R. Latner,
    • Zachary T. Bonnstetter,
    • Candice R. Finnila,
    • Michelle L. Thompson,
    • Lori Beth Boston,
    • Melissa Williams,
    • Ivan Rodriguez Nunez,
    • Jerry Jenkins,
    • Whitley V. Kelley,
    • E. Martina Bebin,
    • Michael A. Lopez,
    • Anna C.E. Hurst,
    • Bruce R. Korf,
    • Jeremy Schmutz,
    • Jane Grimwood,
    • and Gregory M. Cooper
    Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
    ...shown here overlap Alu sequence in the RepeatMasker track. Alignment of the proband's assembled maternal (B) or paternal contig (C) versus the reference supports the two deletions (red dashed lines).Proband 3 is a male, enrolled in our research study at age ∼50 years, and has a strong X-linked family...
  9. Research: The shared genomic architecture of human nucleolar organizer regions
    • Ioanna Floutsakou,
    • Saumya Agrawal,
    • Thong T. Nguyen,
    • Cathal Seoighe,
    • Austen R.D. Ganley,
    • and Brian McStay
    Genome Res. December 2013 23: 2003-2012; Published in Advance August 29, 2013, doi:10.1101/gr.157941.113
    ...a panel of mouse somatic cell hybrids, each containing a single human acrocentric chromosome for flanking region sequence. PCR at five intervals across the DJ each gave the expected product for all five acrocentric chromosomes (Fig. 2A). We could not screen across the PJ because only one unique region...
    OPEN ACCESS ARTICLE
  10. LETTER: Independent intrachromosomal recombination events underlie the pericentric inversions of chimpanzee and gorilla chromosomes homologous to human chromosome 16
    • Violaine Goidts,
    • Justyna M. Szamalek,
    • Pieter J. de Jong,
    • David N. Cooper,
    • Nadia Chuzhanova,
    • Horst Hameister,
    • and Hildegard Kehrer-Sawatzki
    Genome Res. September 2005 15: 1232-1242; doi:10.1101/gr.3732505
    ...then have been determined by local DNA sequence homologies between the inversion breakpoints, including a 22-base pair direct repeat. The similarly located pericentric inversion of gorilla ( GGO ) chromosome XVI, was studied by FISH and PCR analysis. The p- and q-arm breakpoints of the inversions in PTR...
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