Improving the performance of somatic mutation identification by recovering circulating tumor DNA mutations

Cancer Research

Volumn 76, Issue 20, 2016, Pages 5954-5961

  Fu, Yu ^a,b   Jovelet, Cécile ^c   Filleron, Thomas ^d   Pedrero, Marion ^a,c   Motté, Nelly ^c   Boursin, Yannick ^c   Luo, Yufei ^c   Massard, Christophe ^c   Campone, Mario ^e   Levy, Christelle ^f   Diéras, Véronique ^g   Bachelot, Thomas ^h   Garrabey, Julie ⁱ   Soria, Jean Charles ^a,b,c   Lacroix, Ludovic ^a,c   André, Fabrice ^a,b,c   Lefebvre, Celine ^a  

^a Universite Paris Sud   (France)

^b UNIVERSITÉ PARIS SACLAY   (France)

^c INSTITUT GUSTAVE ROUSSY   (France)

^d INSTITUT CLAUDIUS REGAUD   (France)

^e UMR INSERM U892 CNRS 6299   (France)

^f CENTRE FRANÇOIS BACLESSE   (France)

^g INSTITUT CURIE   (France)

^h CENTRE LÉON BÉRARD   (France)

ⁱ RandD Coal Chemistry   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULATING TUMOR DNA; DNA; EPIDERMAL GROWTH FACTOR RECEPTOR; GENOMIC DNA; PROTEIN P53; UNCLASSIFIED DRUG; PHOSPHATIDYLINOSITOL 3 KINASE; PIK3CA PROTEIN, HUMAN;

ARTICLE; BLOOD ANALYSIS; BLOOD SAMPLING; CANCER PATIENT; CLINICAL TRIAL (TOPIC); COHORT ANALYSIS; CONTROLLED STUDY; DNA MUTATIONAL ANALYSIS; EGFR GENE; GENETIC PROCEDURES; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; METASTATIC BREAST CANCER; MISSENSE MUTATION; MUTATION RATE; PIK3CA GENE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION; TP53 GENE; TUMOR GENE; WHOLE EXOME SEQUENCING; BENCHMARKING; BLOOD; BREAST TUMOR; EXOME; FEMALE; GENETICS; HIGH THROUGHPUT SEQUENCING; MUTATION; TUMOR SUPPRESSOR GENE;

BENCHMARKING; BREAST NEOPLASMS; DNA, NEOPLASM; EXOME; FEMALE; GENES, P53; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION; PHOSPHATIDYLINOSITOL 3-KINASES;

EID: 84991712890     PISSN: 00085472     EISSN: 15387445     Source Type: Journal    
DOI: 10.1158/0008-5472.CAN-15-3457     Document Type: Article

References (25)

1. Wang Q, Jia P, Li F, Chen H, Ji H, Hucks D, et al. Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers. Genome Med 2013;5:91.
2. Ignatiadis M, Dawson SJ. Circulating tumor cells and circulating tumor DNA for precision medicine: dream or reality? Ann Oncol 2014;25:2304-13.
3. Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N, et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med 2014;6:224ra24.
4. Diehl F, Schmidt K, Choti MA, Romans K, Goodman S, Li M, et al. Circulating mutant DNA to assess tumor dynamics. Nat Med 2008;14:985-90.
5. Spindler KL, Pallisgaard N, Andersen RF, Brandslund I, Jakobsen A. Circulating free DNA as biomarker and source for mutation detection in metastatic colorectal cancer. PLoS One 2015;10:e0108247.
6. Haber DA, Velculescu VE. Blood-based analyses of cancer: circulating tumor cells and circulating tumor DNA. Cancer Discov 2014;4:650-61.
7. Leary RJ, Kinde I, Diehl F, Schmidt K, Clouser C, Duncan C, et al. Development of personalized tumor biomarkers using massively parallel sequencing. Sci Transl Med 2010;2:20ra14.
8. McBride DJ, Orpana AK, Sotiriou C, Joensuu H, Stephens PJ, Mudie LJ, et al. Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors. Genes Chromosomes Cancer 2010;49:1062-9.
9. Jovelet C, Ileana E, Le Deley MC, Motté N, Rosellini S, Romero A, et al. Circulating cell-free tumorDNA analysis of 50 genes by next-generation sequencing in the prospective MOSCATO trial. Clin Cancer Res 2016;22:2960-8.
10. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, et al. Signatures of mutational processes in human cancer. Nature 2013;500:415-21.
11. Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, et al. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nat Methods 2015;12:623-30.
12. Clopper S, Pearson ES. The use of confidenceor fiducial limits illustrated in the case of the binomial. Biometrika 1934;26:404-13.
13. Andre F, Bachelot T, Commo F, Campone M, Arnedos M, Dieras V, et al. Comparative genomic hybridisation array and DNA sequencing to direct treatment of metastatic breast cancer: a multicentre, prospective trial (SAFIR01/UNICANCER). Lancet Oncol 2014;15:267-74.
14. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010;26:589-95.
15. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009;25:2078-9.
16. Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 2012;6:80-92.
17. Bansal V. A statistical method for the detection of variants from next-generation resequencing of DNA pools. Bioinformatics 2010;26:i318-24.
18. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, et al. An integrated map of genetic variation from 1,092 human genomes. Nature 2012;491:56-65.
19. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297-303.
20. Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res 2015;43:D805-11.
21. Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 2013;31:213-9.
22. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 2012;22:568-76.
23. Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 2012;490:61-70.
24. Dawson SJ, Tsui DW, Murtaza M, Biggs H, Rueda OM, Chin SF, et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med 2013;368:1199-209.
25. Bidard FC, Peeters DJ, Fehm T, Nolé F, Gisbert-Criado R, Mavroudis D, etal. Clinical validity of circulating tumour cells in patients with metastatic breast cancer: a pooled analysis of individual patient data. Lancet Oncol 2014;15:406-14.