Mutascope: Sensitive detection of somatic mutations from deep amplicon sequencing

Bioinformatics

Volumn 29, Issue 15, 2013, Pages 1908-1909

  Yost, Shawn E ^a   Alakus, Hakan ^a,b   Matsui, Hiroko ^a,b   Schwab, Richard B ^c,d   Jepsen, Kristen ^a,b   Frazer, Kelly A ^a,b,c   Harismendy, Olivier ^a,b,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INTERNET; METHODOLOGY; MUTATION; NEOPLASM; NUCLEOTIDE SEQUENCE; PROCEDURES;

DNA MUTATIONAL ANALYSIS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTERNET; MUTATION; NEOPLASMS; SOFTWARE;

EID: 84880542660     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt305     Document Type: Article

References (10)

1. Boyd, S.D. (2013) Diagnostic applications of high-throughput DNA sequencing. Annu. Rev. Pathol., 8, 381-410.
2. Cibulskis, K. et al. (2013) Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol., 31, 213-219.
3. Harismendy, O. et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol., 10, R32.
4. Harismendy, O. et al. (2011) Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing. Genome Biol., 12, R124.
5. Hiatt, J.B. et al. (2013) Single molecule molecular inversion probes for targeted, high accuracy detection of low frequency variation. Genome Res., 23, 843-854.
6. Koboldt, D.C. et al. (2012) VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res., 22, 568-576.
7. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
8. McKenna, A. et al. (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res., 20, 1297-1303.
9. Sing, T. et al. (2005) ROCR: visualizing classifier performance in R. Bioinformatics, 21, 3940-3941. (Pubitemid 41535515)
10. Wilm, A. et al. (2012) LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res., 40, 11189-11201.