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Items: 1 to 20 of 101

1.

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line.

Nattestad M, Goodwin S, Ng K, Baslan T, Sedlazeck FJ, Rescheneder P, Garvin T, Fang H, Gurtowski J, Hutton E, Tseng E, Chin CS, Beck T, Sundaravadanam Y, Kramer M, Antoniou E, McPherson JD, Hicks J, McCombie WR, Schatz MC.

Genome Res. 2018 Aug;28(8):1126-1135. doi: 10.1101/gr.231100.117. Epub 2018 Jun 28.

2.

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.

3.

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.

4.

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.

Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo AS, Woo XY, Zhang Z, Zhao H, Ukil L, Chen JP, Zhu F, So JB, Salto-Tellez M, Poh WT, Zawack KF, Nagarajan N, Gao S, Li G, Kumar V, Lim HP, Sia YY, Chan CS, Leong ST, Neo SC, Choi PS, Thoreau H, Tan PB, Shahab A, Ruan X, Bergh J, Hall P, Cacheux-Rataboul V, Wei CL, Yeoh KG, Sung WK, Bourque G, Liu ET, Ruan Y.

Genome Res. 2011 May;21(5):665-75. doi: 10.1101/gr.113555.110. Epub 2011 Apr 5.

5.

Characterization of structural variants with single molecule and hybrid sequencing approaches.

Ritz A, Bashir A, Sindi S, Hsu D, Hajirasouliha I, Raphael BJ.

Bioinformatics. 2014 Dec 15;30(24):3458-66. doi: 10.1093/bioinformatics/btu714. Epub 2014 Oct 28.

6.

MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome.

Tyson JR, O'Neil NJ, Jain M, Olsen HE, Hieter P, Snutch TP.

Genome Res. 2018 Feb;28(2):266-274. doi: 10.1101/gr.221184.117. Epub 2017 Dec 22.

7.

Palindromic amplification of the ERBB2 oncogene in primary HER2-positive breast tumors.

Marotta M, Onodera T, Johnson J, Budd GT, Watanabe T, Cui X, Giuliano AE, Niida A, Tanaka H.

Sci Rep. 2017 Feb 17;7:41921. doi: 10.1038/srep41921.

8.

Novel anti-HER2 monoclonal antibodies: synergy and antagonism with tumor necrosis factor-α.

Ceran C, Cokol M, Cingoz S, Tasan I, Ozturk M, Yagci T.

BMC Cancer. 2012 Oct 4;12:450. doi: 10.1186/1471-2407-12-450.

9.

Chromoanasynthesis is a common mechanism that leads to ERBB2 amplifications in a cohort of early stage HER2+ breast cancer samples.

Vasmatzis G, Wang X, Smadbeck JB, Murphy SJ, Geiersbach KB, Johnson SH, Gaitatzes AG, Asmann YW, Kosari F, Borad MJ, Serie DJ, McLaughlin SA, Kachergus JM, Necela BM, Aubrey Thompson E.

BMC Cancer. 2018 Jul 13;18(1):738. doi: 10.1186/s12885-018-4594-0.

10.

A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers.

Ferrari A, Vincent-Salomon A, Pivot X, Sertier AS, Thomas E, Tonon L, Boyault S, Mulugeta E, Treilleux I, MacGrogan G, Arnould L, Kielbassa J, Le Texier V, Blanché H, Deleuze JF, Jacquemier J, Mathieu MC, Penault-Llorca F, Bibeau F, Mariani O, Mannina C, Pierga JY, Trédan O, Bachelot T, Bonnefoi H, Romieu G, Fumoleau P, Delaloge S, Rios M, Ferrero JM, Tarpin C, Bouteille C, Calvo F, Gut IG, Gut M, Martin S, Nik-Zainal S, Stratton MR, Pauporté I, Saintigny P, Birnbaum D, Viari A, Thomas G.

Nat Commun. 2016 Jul 13;7:12222. doi: 10.1038/ncomms12222.

11.

High-resolution genomic and expression analyses of copy number alterations in HER2-amplified breast cancer.

Staaf J, Jönsson G, Ringnér M, Vallon-Christersson J, Grabau D, Arason A, Gunnarsson H, Agnarsson BA, Malmström PO, Johannsson OT, Loman N, Barkardottir RB, Borg A.

Breast Cancer Res. 2010;12(3):R25. doi: 10.1186/bcr2568. Epub 2010 May 6.

12.

Detection and visualization of complex structural variants from long reads.

Stephens Z, Wang C, Iyer RK, Kocher JP.

BMC Bioinformatics. 2018 Dec 21;19(Suppl 20):508. doi: 10.1186/s12859-018-2539-x.

13.

Next generation mapping reveals novel large genomic rearrangements in prostate cancer.

Jaratlerdsiri W, Chan EKF, Petersen DC, Yang C, Croucher PI, Bornman MSR, Sheth P, Hayes VM.

Oncotarget. 2017 Apr 4;8(14):23588-23602. doi: 10.18632/oncotarget.15802.

14.

Systems consequences of amplicon formation in human breast cancer.

Inaki K, Menghi F, Woo XY, Wagner JP, Jacques PÉ, Lee YF, Shreckengast PT, Soon WW, Malhotra A, Teo AS, Hillmer AM, Khng AJ, Ruan X, Ong SH, Bertrand D, Nagarajan N, Karuturi RK, Miranda AH, Liu ET.

Genome Res. 2014 Oct;24(10):1559-71. doi: 10.1101/gr.164871.113. Epub 2014 Sep 3.

15.

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.

Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, Teague JW, Menzies A, Goodhead I, Turner DJ, Clee CM, Quail MA, Cox A, Brown C, Durbin R, Hurles ME, Edwards PA, Bignell GR, Stratton MR, Futreal PA.

Nat Genet. 2008 Jun;40(6):722-9. doi: 10.1038/ng.128. Epub 2008 Apr 27.

16.

Integrative molecular and functional profiling of ERBB2-amplified breast cancers identifies new genetic dependencies.

Shiu KK, Wetterskog D, Mackay A, Natrajan R, Lambros M, Sims D, Bajrami I, Brough R, Frankum J, Sharpe R, Marchio C, Horlings H, Reyal F, van der Vijver M, Turner N, Reis-Filho JS, Lord CJ, Ashworth A.

Oncogene. 2014 Jan 30;33(5):619-31. doi: 10.1038/onc.2012.625. Epub 2013 Jan 21.

17.

Genome-wide reconstruction of complex structural variants using read clouds.

Spies N, Weng Z, Bishara A, McDaniel J, Catoe D, Zook JM, Salit M, West RB, Batzoglou S, Sidow A.

Nat Methods. 2017 Sep;14(9):915-920. doi: 10.1038/nmeth.4366. Epub 2017 Jul 17.

18.

Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines.

Ha KC, Lalonde E, Li L, Cavallone L, Natrajan R, Lambros MB, Mitsopoulos C, Hakas J, Kozarewa I, Fenwick K, Lord CJ, Ashworth A, Vincent-Salomon A, Basik M, Reis-Filho JS, Majewski J, Foulkes WD.

BMC Med Genomics. 2011 Oct 27;4:75. doi: 10.1186/1755-8794-4-75.

19.

Nonamplification ERBB2 genomic alterations in 5605 cases of recurrent and metastatic breast cancer: An emerging opportunity for anti-HER2 targeted therapies.

Ross JS, Gay LM, Wang K, Ali SM, Chumsri S, Elvin JA, Bose R, Vergilio JA, Suh J, Yelensky R, Lipson D, Chmielecki J, Waintraub S, Leyland-Jones B, Miller VA, Stephens PJ.

Cancer. 2016 Sep 1;122(17):2654-62. doi: 10.1002/cncr.30102. Epub 2016 Jun 10.

20.

Detection of HER-2 oncogene amplification in breast cancer by differential polymerase chain reaction from single cryosections.

Friedrichs K, Lohmann D, Höfler H.

Virchows Arch B Cell Pathol Incl Mol Pathol. 1993;64(4):209-12.

PMID:
7904515

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