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

Annals of Oncology

Volumn 26, Issue 1, 2015, Pages 64-70

  Favero, F ^a   Joshi, T ^a   Marquard, A M ^a   Birkbak, N J ^a   Krzystanek, M ^a   Li, Q ^a,b   Szallasi, Z ^a,c   Eklund, Aron C ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b XIAMEN UNIVERSITY   (China)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Cancer genomics; Copy number alterations; Mutations; Next generation sequencing; Software

Indexed keywords

ABSCN SEQ ALGORITHM; ABSOLUTE ALGORITHM; ALGORITHM; ALLELE SPECIFIC COPY NUMBER ANALYSIS OF TUMOR ALGORITHM; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; COPY NUMBER VARIATION; CORRELATION ANALYSIS; DNA SEQUENCE; GENE SEQUENCE; HUMAN; INTERMETHOD COMPARISON; KARYOTYPE; KIDNEY CANCER; MUTATIONAL ANALYSIS; OVARY CANCER; PLOIDY; SEQUENCE ANALYSIS; SEQUENZA; SINGLE NUCLEOTIDE POLYMORPHISM; ALLELE; EXOME; GENE DOSAGE; GENETICS; HIGH THROUGHPUT SEQUENCING; MUTATION; NEOPLASM; NUCLEOTIDE SEQUENCE; PROCEDURES; SOFTWARE;

ALGORITHMS; ALLELES; BASE SEQUENCE; DNA COPY NUMBER VARIATIONS; EXOME; GENE DOSAGE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION; NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84922572688     PISSN: 09237534     EISSN: 15698041     Source Type: Journal    
DOI: 10.1093/annonc/mdu479     Document Type: Article

References (25)

1. Hudson TJ, Anderson W, Artez A et al. International network of cancer genome projects. Nature 2010; 464(7291): 993-998.
2. Popova T, Manié E, Stoppa-Lyonnet D et al. Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Genome Biol 2009; 10(11): R128.
3. Van Loo P, Nordgard SH, Lingjærde OC et al. Allele-specific copy number analysis of tumors. Proc Natl Acad Sci USA 2010 107(39): 16910-5.
4. Carter SL, Cibulskis K, Helman E et al. Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol 2012; 30(5): 413-421.
5. Lamy P, Andersen CL, Dyrskjot L et al. A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays. BMC Bioinformatics 2007; 8: 434.
6. Cibulskis K, Lawrence MS, Carter SL et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 2013; 31 (3): 213-219.
7. Koboldt DC, Zhang Q, Larson DE et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 2012; 22(3): 568-576.
8. Ha G, Roth A, Lai D et al. Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer. Genome Res 2012; 22(10): 1995-2007.
9. Su X, Zhang L, Zhang J et al. PurityEst: estimating purity of human tumor samples using next-generation sequencing data. Bioinformatics 2012; 28(17): 2265-2266.
10. Larson NB, Fridley BL. PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data. Bioinformatics 2013; 29(15): 1888-1889.
11. Bao L, Pu M, Messer K. AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data. Bioinformatics 2014; 30(8): 1056-1063.
12. Li H, Handsaker B, Wysoker A et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25(16): 2078-2079.
13. Rigo A, Pedroni S. PyPy's approach to virtual machine construction. Companion to 21st ACM SIGPLAN symposium on Object-oriented programming systems, languages, and applications. In OOPSLA '06. New York: ACM Press 2006; 944-953.
14. Nilsen G, Liestøl K, Van Loo P et al. Copynumber: efficient algorithms for singleand multi-track copy number segmentation. BMC Genomics 2012; 13: 591.
15. Bengtsson H, Wirapati P, Speed TP. A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. Bioinformatics 2009; 25(17): 2149-2156.
16. Martinez P, Birkbak NJ, Gerlinger M et al. Parallel evolution of tumour subclones mimics diversity between tumours. J Pathol 2013; 230(4): 356-364.
17. Abaan OD, Polley EC, Davis SR et al. The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology. Cancer Res 2013; 73(14): 4372-4382.
18. The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 2011; 474(7353): 609-615.
19. The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 2013; 499(7456): 43-49.
20. Roschke AV, Tonon G, Gehlhaus KS et al. Karyotypic complexity of the NCI-60 drug-screening panel. Cancer Res 2003; 63(24): 8634-8647.
21. TCGA Mutation Calling Benchmark 4 Datasets. https://cghub.ucsc.edu/datasets/benchmark_download.html (29 October 2014, date last accessed).
22. Gerlinger M, Rowan AJ, Horswell S et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 2012; 366(10): 883-892.
23. Ding L, Raphael BJ, Chen F, Wendl MC. Advances for studying clonal evolution in cancer. Cancer Lett 2013; 340(2): 212-219.
24. Horswell S, Matthews N, Swanton C. Cancer heterogeneity and "The Struggle for Existence": diagnostic and analytical challenges. Cancer Lett 2012; 340(2): 220-226.
25. Shah SP, Roth A, Goya R et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 2012; 486(7403): 395-399.