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Resolving genomic disorder-associated breakpoints within segmental DNA duplications using massively parallel sequencing.

Nuttle X, Itsara A, Shendure J, Eichler EE.

Nat Protoc. 2014;9(6):1496-513. doi: 10.1038/nprot.2014.096. Epub 2014 May 29.


Resolving the breakpoints of the 17q21.31 microdeletion syndrome with next-generation sequencing.

Itsara A, Vissers LE, Steinberg KM, Meyer KJ, Zody MC, Koolen DA, de Ligt J, Cuppen E, Baker C, Lee C, Graves TA, Wilson RK, Jenkins RB, Veltman JA, Eichler EE.

Am J Hum Genet. 2012 Apr 6;90(4):599-613. doi: 10.1016/j.ajhg.2012.02.013.


A common copy-number breakpoint of ERBB2 amplification in breast cancer colocalizes with a complex block of segmental duplications.

Marotta M, Chen X, Inoshita A, Stephens R, Budd GT, Crowe JP, Lyons J, Kondratova A, Tubbs R, Tanaka H.

Breast Cancer Res. 2012 Nov 26;14(6):R150. doi: 10.1186/bcr3362.


Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome.

Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM.

Genome Res. 2010 May;20(5):623-35. doi: 10.1101/gr.102970.109. Epub 2010 Mar 22.


Large inverted duplications in the human genome form via a fold-back mechanism.

Hermetz KE, Newman S, Conneely KN, Martin CL, Ballif BC, Shaffer LG, Cody JD, Rudd MK.

PLoS Genet. 2014 Jan 30;10(1):e1004139. doi: 10.1371/journal.pgen.1004139. eCollection 2014 Jan.


Analysis of segmental duplications, mouse genome synteny and recurrent cancer-associated amplicons in human chromosome 6p21-p12.

Martin JW, Yoshimoto M, Ludkovski O, Thorner PS, Zielenska M, Squire JA, Nuin PA.

Cytogenet Genome Res. 2010 Jun;128(4):199-213. doi: 10.1159/000308353. Epub 2010 May 6.


Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints.

Newman S, Hermetz KE, Weckselblatt B, Rudd MK.

Am J Hum Genet. 2015 Feb 5;96(2):208-20. doi: 10.1016/j.ajhg.2014.12.017. Epub 2015 Jan 29.


Molecular characterization of ring chromosome 18 by low-coverage next generation sequencing.

Ji X, Liang D, Sun R, Liu C, Ma D, Wang Y, Hu P, Xu Z.

BMC Med Genet. 2015 Jul 30;16:57. doi: 10.1186/s12881-015-0206-x.


Detection of variations and identifying genomic breakpoints for large deletions in the LDLR by Ion Torrent semiconductor sequencing.

Faiz F, Allcock RJ, Hooper AJ, van Bockxmeer FM.

Atherosclerosis. 2013 Oct;230(2):249-55. doi: 10.1016/j.atherosclerosis.2013.07.050. Epub 2013 Aug 4.


Observation and prediction of recurrent human translocations mediated by NAHR between nonhomologous chromosomes.

Ou Z, Stankiewicz P, Xia Z, Breman AM, Dawson B, Wiszniewska J, Szafranski P, Cooper ML, Rao M, Shao L, South ST, Coleman K, Fernhoff PM, Deray MJ, Rosengren S, Roeder ER, Enciso VB, Chinault AC, Patel A, Kang SH, Shaw CA, Lupski JR, Cheung SW.

Genome Res. 2011 Jan;21(1):33-46. doi: 10.1101/gr.111609.110.


Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation.

Brand H, Collins RL, Hanscom C, Rosenfeld JA, Pillalamarri V, Stone MR, Kelley F, Mason T, Margolin L, Eggert S, Mitchell E, Hodge JC, Gusella JF, Sanders SJ, Talkowski ME.

Am J Hum Genet. 2015 Jul 2;97(1):170-6. doi: 10.1016/j.ajhg.2015.05.012. Epub 2015 Jun 18.


Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements.

Armengol L, Pujana MA, Cheung J, Scherer SW, Estivill X.

Hum Mol Genet. 2003 Sep 1;12(17):2201-8. Epub 2003 Jul 8.


Genome rearrangements detected by SNP microarrays in individuals with intellectual disability referred with possible Williams syndrome.

Pani AM, Hobart HH, Morris CA, Mervis CB, Bray-Ward P, Kimberley KW, Rios CM, Clark RC, Gulbronson MD, Gowans GC, Gregg RG.

PLoS One. 2010 Aug 31;5(8):e12349. doi: 10.1371/journal.pone.0012349.


Signals of historical interlocus gene conversion in human segmental duplications.

Dumont BL, Eichler EE.

PLoS One. 2013 Oct 4;8(10):e75949. doi: 10.1371/journal.pone.0075949. eCollection 2013.


Genome-wide signatures of 'rearrangement hotspots' within segmental duplications in humans.

Uddin M, Sturge M, Peddle L, O'Rielly DD, Rahman P.

PLoS One. 2011;6(12):e28853. doi: 10.1371/journal.pone.0028853. Epub 2011 Dec 14.


Mis-assembled "segmental duplications" in two versions of the Bos taurus genome.

Zimin AV, Kelley DR, Roberts M, Marçais G, Salzberg SL, Yorke JA.

PLoS One. 2012;7(8):e42680. doi: 10.1371/journal.pone.0042680. Epub 2012 Aug 3.


A programmable method for massively parallel targeted sequencing.

Hopmans ES, Natsoulis G, Bell JM, Grimes SM, Sieh W, Ji HP.

Nucleic Acids Res. 2014 Jun;42(10):e88. doi: 10.1093/nar/gku282. Epub 2014 Apr 29.


Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome.

Korbel JO, Urban AE, Grubert F, Du J, Royce TE, Starr P, Zhong G, Emanuel BS, Weissman SM, Snyder M, Gerstein MB.

Proc Natl Acad Sci U S A. 2007 Jun 12;104(24):10110-5. Epub 2007 Jun 5.


Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations.

Patel A, Schwab R, Liu YT, Bafna V.

Genome Res. 2014 Feb;24(2):318-28. doi: 10.1101/gr.161497.113. Epub 2013 Dec 4.

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