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Methods: Intra- and interpopulation genotype reconstruction from tagging SNPs
- Peristera Paschou,
- Michael W. Mahoney,
- Asif Javed,
- Judith R. Kidd,
- Andrew J. Pakstis,
- Sheng Gu,
- Kenneth K. Kidd,
- and Petros Drineas
Genome Res. January 2007 17: 96-107; Published in Advance December 6, 2006, doi:10.1101/gr.5741407
..., Troy, New York 12180, USA Abstract The optimal method to be used for tSNP selection, the applicability of a reference LD map to unassayed populations, and the scalability of these methods to genome-wide analysis, all remain subjects of debate. We propose novel, scalable matrix algorithms...
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Method: Calling amplified haplotypes in next generation tumor sequence data
- Ninad Dewal,
- Yang Hu,
- Matthew L. Freedman,
- Thomas LaFramboise,
- and Itsik Pe'er
Genome Res. February 2012 22: 362-374; Published in Advance November 16, 2011, doi:10.1101/gr.122564.111
...—are a hallmark of tumor genomics. Recurrent amplicons have been observed over two decades (Kallioniemi et al. 1992; Joos et al. 1995; Cher et al. 1996; Korn et al. 1999; Paris et al. 2004; Zhao et al. 2005; Sun et al. 2007a) and are believed to be advantageous to the tumor during tumor development.Genome-wide...

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