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WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing.

Holt C, Losic B, Pai D, Zhao Z, Trinh Q, Syam S, Arshadi N, Jang GH, Ali J, Beck T, McPherson J, Muthuswamy LB.

Bioinformatics. 2014 Mar 15;30(6):768-74. doi: 10.1093/bioinformatics/btt611. Epub 2013 Nov 4.


Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.

Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, Szallasi Z, Eklund AC.

Ann Oncol. 2015 Jan;26(1):64-70. doi: 10.1093/annonc/mdu479. Epub 2014 Oct 15.


OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes.

Yau C.

Bioinformatics. 2013 Oct 1;29(19):2482-4. doi: 10.1093/bioinformatics/btt416. Epub 2013 Aug 7.


Quantitative analysis of differences in copy numbers using read depth obtained from PCR-enriched samples and controls.

Reinecke F, Satya RV, DiCarlo J.

BMC Bioinformatics. 2015 Jan 28;16:17. doi: 10.1186/s12859-014-0428-5.


Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity.

Li Y, Xie X.

Bioinformatics. 2014 Aug 1;30(15):2121-9. doi: 10.1093/bioinformatics/btu174. Epub 2014 Apr 2. Erratum in: Bioinformatics. 2015 Feb 15;31(4):618.


Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data.

Gusnanto A, Wood HM, Pawitan Y, Rabbitts P, Berri S.

Bioinformatics. 2012 Jan 1;28(1):40-7. doi: 10.1093/bioinformatics/btr593. Epub 2011 Oct 28.


The algorithm of equal acceptance region for detecting copy number alterations: applications to next-generation sequencing data.

Lin YX.

Int J Bioinform Res Appl. 2012;8(3-4):245-62. doi: 10.1504/IJBRA.2012.048969.


MixClone: a mixture model for inferring tumor subclonal populations.

Li Y, Xie X.

BMC Genomics. 2015;16 Suppl 2:S1. doi: 10.1186/1471-2164-16-S2-S1. Epub 2015 Jan 21.


Copy number variation detection using next generation sequencing read counts.

Wang H, Nettleton D, Ying K.

BMC Bioinformatics. 2014 Apr 14;15:109. doi: 10.1186/1471-2105-15-109.


FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data.

Shi Y, Majewski J.

Bioinformatics. 2013 Jun 1;29(11):1461-2. doi: 10.1093/bioinformatics/btt151. Epub 2013 Mar 28.


Mutation discovery in regions of segmental cancer genome amplifications with CoNAn-SNV: a mixture model for next generation sequencing of tumors.

Crisan A, Goya R, Ha G, Ding J, Prentice LM, Oloumi A, Senz J, Zeng T, Tse K, Delaney A, Marra MA, Huntsman DG, Hirst M, Aparicio S, Shah S.

PLoS One. 2012;7(8):e41551. doi: 10.1371/journal.pone.0041551. Epub 2012 Aug 16.


Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data.

Boeva V, Popova T, Bleakley K, Chiche P, Cappo J, Schleiermacher G, Janoueix-Lerosey I, Delattre O, Barillot E.

Bioinformatics. 2012 Feb 1;28(3):423-5. doi: 10.1093/bioinformatics/btr670. Epub 2011 Dec 6.


Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives.

Zhao M, Wang Q, Wang Q, Jia P, Zhao Z.

BMC Bioinformatics. 2013;14 Suppl 11:S1. doi: 10.1186/1471-2105-14-S11-S1. Epub 2013 Sep 13.


Next-generation sequence analysis of cancer xenograft models.

Rossello FJ, Tothill RW, Britt K, Marini KD, Falzon J, Thomas DM, Peacock CD, Marchionni L, Li J, Bennett S, Tantoso E, Brown T, Chan P, Martelotto LG, Watkins DN.

PLoS One. 2013 Sep 26;8(9):e74432. doi: 10.1371/journal.pone.0074432. eCollection 2013.


cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate.

Klambauer G, Schwarzbauer K, Mayr A, Clevert DA, Mitterecker A, Bodenhofer U, Hochreiter S.

Nucleic Acids Res. 2012 May;40(9):e69. doi: 10.1093/nar/gks003. Epub 2012 Feb 1.


Detection of recurrent rearrangement breakpoints from copy number data.

Ritz A, Paris PL, Ittmann MM, Collins C, Raphael BJ.

BMC Bioinformatics. 2011 Apr 21;12:114. doi: 10.1186/1471-2105-12-114.


Allele-specific copy number profiling by next-generation DNA sequencing.

Chen H, Bell JM, Zavala NA, Ji HP, Zhang NR.

Nucleic Acids Res. 2015 Feb 27;43(4):e23. doi: 10.1093/nar/gku1252. Epub 2014 Dec 3.


CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data.

Packer JS, Maxwell EK, O'Dushlaine C, Lopez AE, Dewey FE, Chernomorsky R, Baras A, Overton JD, Habegger L, Reid JG.

Bioinformatics. 2016 Jan 1;32(1):133-5. doi: 10.1093/bioinformatics/btv547. Epub 2015 Sep 17.


The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome.

Przybytkowski E, Ferrario C, Basik M.

BMC Med Genomics. 2011 Jan 27;4:16. doi: 10.1186/1755-8794-4-16.

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