Methods and References

Methods and References

Methods:

R-3.0.1 (http://www.r-project.org/)

Bioconductor (http://www.bioconductor.org/)

Primer3-2.3.5 (http://sourceforge.net/projects/primer3/files/)

in-silico PCR 3.3 (http://genome.ucsc.edu/cgi-bin/hgPcr)

ANNOVAR (http://www.openbioinformatics.org/annovar/annovar_download.html)

Other bioinformatics tools (http://bioinformaticssoftwareandtools.co.in/bio_tools.php)

References (methods):

Untergrasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3 – new capabilities and interfaces. Nucleic Acids Research 40(15):e115
Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3 Bioinformatics 23(10):1289-91

Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data, Nucleic Acids Research, 38:e164, 2010

References (Application):

Clonal genotype and population structure inference from single-cell tumor sequencing. Roth A, McPherson A, Laks E, Biele J, Yap D, Wan A, Smith MA, Nielsen CB, McAlpine JN, Aparicio S, Bouchard-Côté A, Shah SP. Nat Methods. 2016 Jul;13(7):573-6. doi: 10.1038/nmeth.3867. Epub 2016 May 16.

Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer. McPherson A, Roth A, Laks E, Masud T, Bashashati A, Zhang AW, Ha G, Biele J, Yap D, Wan A, Prentice LM, Khattra J, Smith MA, Nielsen CB, Mullaly SC, Kalloger S, Karnezis A, Shumansky K, Siu C, Rosner J, Chan HL, Ho J, Melnyk N, Senz J, Yang W, Moore R, Mungall AJ, Marra MA, Bouchard-Côté A, Gilks CB, Huntsman DG, McAlpine JN, Aparicio S, Shah SP. Nat Genet. 2016 Jul;48(7):758-67. doi: 10.1038/ng.3573. Epub 2016 May 16.

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. Eirew P, Steif A, Khattra J, Ha G, Yap D, Farahani H, Gelmon K, Chia S, Mar C, Wan A, Laks E, Biele J, Shumansky K, Rosner J, McPherson A, Nielsen C, Roth AJ, Lefebvre C, Bashashati A, de Souza C, Siu C, Aniba R, Brimhall J, Oloumi A, Osako T, Bruna A, Sandoval JL, Algara T, Greenwood W, Leung K, Cheng H, Xue H, Wang Y, Lin D, Mungall AJ, Moore R, Zhao Y, Lorette J, Nguyen L, Huntsman D, Eaves CJ, Hansen C, Marra MA, Caldas C, Shah SP, Aparicio S. Nature. 2015 Feb 19;518(7539):422-6. doi: 10.1038/nature13952. Epub 2014 Nov 26.

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data. Ha G, Roth A, Khattra J, Ho J, Yap D, Prentice LM, Melnyk N, McPherson A, Bashashati A, Laks E, Biele J, Ding J, Le A, Rosner J, Shumansky K, Marra MA, Gilks CB, Huntsman DG, McAlpine JN, Aparicio S, Shah SP. Genome Res. 2014 Nov;24(11):1881-93. doi: 10.1101/gr.180281.114. Epub 2014 Jul 24.

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