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ARTICLES: Regional assignment of 68 new human gene transcripts on chromosome 11.
- M F Rosier,
- I Reguigne-Arnould,
- P Couillin,
- M D Devignes,
- and C Auffray
Genome Res. August 1995 5: 60-70; doi:10.1101/gr.5.1.60
..., for the Jacobsen Syndrome localized to 11q24.1, on ly six gene transcripts hould be considered as possible can- didates. D11S2278E and DS11S2279E have been mapped close to the BDNF gene. This region be- tween FSHB and HBVS1 (Fig. 1) has been pro- posed previously to conta in a locus specific for the WAGR menta l...
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Research: Genetic and phenotypic intra-species variation in Candida albicans
- Matthew P. Hirakawa,
- Diego A. Martinez,
- Sharadha Sakthikumar,
- Matthew Z. Anderson,
- Aaron Berlin,
- Sharvari Gujja,
- Qiandong Zeng,
- Ethan Zisson,
- Joshua M. Wang,
- Joshua M. Greenberg,
- Judith Berman,
- Richard J. Bennett,
- and Christina A. Cuomo
Genome Res. March 2015 25: 413-425; Published in Advance December 11, 2014, doi:10.1101/gr.174623.114
...) for the final 200 kb on the right arm of Chr 3; interestingly, a larger hemizygous region encompassing 433 kb of this chromosome was previously noted in strainWO-1 (Butler et al. 2009). Because P76067 is a clade II strain, whereas WO-1 maps to a different clade (Odds et al. 2007), this loss is best explained...
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Research: Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis
- Brooke Weckselblatt,
- Karen E. Hermetz,
- and M. Katharine Rudd
Genome Res. July 2015 25: 937-947; Published in Advance June 12, 2015, doi:10.1101/gr.191247.115
...has one simple balanced translocation between Chromosomes 1 and 3 and a complex unbalanced translocation between Chromosomes 10 and 17. To fine-map breakpoints, we designed custom oligonucleotide microarrays with dense probe coverage in 1-megabase (Mb) windows centered around the breakpoints...
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Research: Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response
- Ariadna Picart-Picolo,
- Stefan Grob,
- Nathalie Picault,
- Michal Franek,
- Christel Llauro,
- Thierry Halter,
- Tom R. Maier,
- Edouard Jobet,
- Julie Descombin,
- Panpan Zhang,
- Vijayapalani Paramasivan,
- Thomas J. Baum,
- Lionel Navarro,
- Martina Dvořáčková,
- Marie Mirouze,
- and Frédéric Pontvianne
Genome Res. November 2020 30: 1583-1592; Published in Advance October 8, 2020, doi:10.1101/gr.261586.120
...in soybean. Science 338: 1206–1209. doi:10.1126/science.1228746 ↵Copenhaver GP, Pikaard CS. 1996. RFLP and physical mapping with an rDNA-specific endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4. Plant J 9: 259–272. doi:10.1046/j.1365...
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Method: SvABA: genome-wide detection of structural variants and indels by local assembly
- Jeremiah A. Wala,
- Pratiti Bandopadhayay,
- Noah F. Greenwald,
- Ryan O'Rourke,
- Ted Sharpe,
- Chip Stewart,
- Steve Schumacher,
- Yilong Li,
- Joachim Weischenfeldt,
- Xiaotong Yao,
- Chad Nusbaum,
- Peter Campbell,
- Gad Getz,
- Matthew Meyerson,
- Cheng-Zhong Zhang,
- Marcin Imielinski,
- and Rameen Beroukhim
Genome Res. April 2018 28: 581-591; Published in Advance March 13, 2018, doi:10.1101/gr.221028.117
...no significant difference in the mean number of breakpoint-supporting reads between simple and complex events (52.4 reads in complex, 50.4 reads in simple, P = 0.69, t-test). There was no significant difference in the mean mapping quality of the alignments between simple and complex rearrangements (55.1 reads...
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Research: Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics
- Coralie Zangarelli,
- Olivier Arnaiz,
- Mickaël Bourge,
- Kevin Gorrichon,
- Yan Jaszczyszyn,
- Nathalie Mathy,
- Loïc Escoriza,
- Mireille Bétermier,
- and Vinciane Régnier
Genome Res. November/December 2022 32: 2028-2042; Published in Advance November 23, 2022, doi:10.1101/gr.277027.122
...is indicated above each pair of boxplots. (C) Abundance of telomere addition sites during autogamy. The schema above the bars illustrates the method for detection of telomere addition sites using the sequencing data. For each data set, the bar shows the normalized number (per million mapped reads [RPM...
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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
...Chr 13 view of TLA reads mapped to the mouse . (E) Schematic of the insertion locus in the Tek-cre [Tg(Tek-cre)12Flv] line. Blue bars indicate the 5′ and 3′ limits of the deleted region, with the relative orientation of transgene copies adjacent to the breakpoint as determined from sequence...
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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
.... 1991) and soon after revealed as a CGG expansion (Fu et al. 1991; Kremer et al. 1991; Pieretti et al. 1991; Verkerk et al. 1991). This was possible through using cytogenetics/FISH, coupled with somatic cell hybrids for FRAXA breakpoint mapping, Alu-PCR, and positional cloning, which together permitted...
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Research: Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability
- Yotam Drier,
- Michael S. Lawrence,
- Scott L. Carter,
- Chip Stewart,
- Stacey B. Gabriel,
- Eric S. Lander,
- Matthew Meyerson,
- Rameen Beroukhim,
- and Gad Getz
Genome Res. February 2013 23: 228-235; Published in Advance November 2, 2012, doi:10.1101/gr.141382.112
..., Butler A, Stevens C, et al. 2007. Patterns of somaticmutation in human cancer s. Nature 446: 153–158. Guelen L, Pagie L, Brasset E, MeulemanW, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, et al. 2008. Domain organization of human chromosomes revealed by mapping of nuclear lamina...
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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
...breakpoints to cluster at specific chromosomal regions in different cell lines (Fig. 2; Supplemental Fig. 5). Genomic distances between viral integrants in a ‘‘cluster,’’ defined by three or more unique insertional breakpoints, spanned up to 3 Mb (Tumor A). As examples, HPV integrant clusters mapped...

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