Optimizing PCR assays for DNA-based cancer diagnostics

Journal of Computational Biology

Volumn 17, Issue 3, 2010, Pages 369-381

  Bashir, Ali ^a   Lu, Qing ^a,c   Carson, Dennis ^a,c   Raphael, Benjamin J ^b,d   Liu, Yu Tsueng ^a,c   Bafna, Vineet ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Brown University   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d BROWN UNIVERSITY   (United States)

Author keywords

Biology; Cancer genomics; DNA arrays; Genomic rearrangements; Genomics; Sequence analysis; Viruses

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 2A; DNA;

ALGORITHM; CHROMOSOME ABERRATION; CHROMOSOME BREAKAGE; COMPUTER SIMULATION; CONFERENCE PAPER; DIAGNOSTIC PROCEDURE; GENE REARRANGEMENT; GENETICS; HUMAN; METHODOLOGY; NEOPLASM; POLYMERASE CHAIN REACTION; REPRODUCIBILITY; TIME; TUMOR CELL LINE;

ALGORITHMS; CELL LINE, TUMOR; CHROMOSOME ABERRATIONS; CHROMOSOME BREAKAGE; COMPUTER SIMULATION; CYCLIN-DEPENDENT KINASE INHIBITOR P16; DIAGNOSTIC TECHNIQUES AND PROCEDURES; DNA, NEOPLASM; GENE REARRANGEMENT; HUMANS; NEOPLASMS; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; TIME FACTORS;

EID: 77950851118     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2009.0203     Document Type: Conference Paper

References (21)

1. Bashir, A., Liu, Y., Raphael, B., et al. 2007. Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinformatics 23, 2807. (Pubitemid 350162884)
2. Bashir, A., Volik, S., Collins, C., et al. 2008. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput. Biol. 4, 4. (Pubitemid 351656709)
3. Beigel, R., Alon, N., Apaydin, S., et al. 2001. An optimal multiplex PCR protocol for closing gaps in whole genomes. Proc. RECOMB 2001.
4. Brooks, R. 1941. On colouring the nodes of a network. Proc. Cambridge Phil. Soc. 37, 194-197.
5. Campbell, P., Stephens, P., Pleasance, E., et al. 2008. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat. Genet. 40, 722. (Pubitemid 351748860)
6. Dasgupta, B., Jun, J., and Mandoiu, I. 2008. Primer selection methods for detection of genomic inversions and deletions via PAMP. Proc. 6th Asia-Pacif. Bioinform. Conf.
7. Fan, J., Chee, M., Gunderson, K., et al. 2006. Highly parallel genomic assays. Nat. Rev. Genet. 7, 632. (Pubitemid 44100520)
8. Kirkpatrick, S., Gelatt, C.D., and Vecchi, M.P. 1983. Optimization by simulated annealing. Science 220, 671-680.
9. Kitagawa, Y., Inoue, K., Sasaki, S., et al. 2002. Prevalent involvement of illegitimate V (D) J recombination in chromosome 9p21 deletions in lymphoid leukemia. J. Biol. Chem. 277, 46289-46297. (Pubitemid 35417622)
10. Lipson, D. 2002. Optimization problems in design of oligonucleotides for hybridization-based methods [Master's thesis]. Technion-Israel Institute of Technology.
11. Liu, Y., and Carson, D. 2007. A novel approach for determining cancer genomic breakpoints in the presence of normal DNA. PLoS ONE 2, e380.
12. Lu, Q., Nunez, E., Lin, C., et al. 2008. A sensitive array-based assay for identifying multiple TMPRSS2: ERG fusion gene variants. Nucleic Acids Res.
13. Mitelman, F., Johansson, B., and Mertens, F. 2007. The impact of translocations and gene fusions on cancer causation. Nat. Rev. Cancer, 7, 233-245. (Pubitemid 46480968)
14. Raphael, B., Volik, S., Yu, P., et al. 2008. A sequence-based survey of the complex structural organization of tumor genomes. Genome Biol. 9, 3. (Pubitemid 351959556)
15. Rocco, J., and Sidransky, D. 2001. p16 (MTS-1=CDKN2=INK4a) in cancer progression. Exp. Cell Res. 264, 42-55.
16. Ruan, Y., Ooi, H., Choo, S., et al. 2007. Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res. 17, 828-838. (Pubitemid 46919718)
17. Sasaki, S., Kitagawa, Y., Sekido, Y., et al. 2003. Molecular processes of chromosome 9p21 deletions in human cancers. Oncogene 22, 3792-3798. (Pubitemid 36760741)
18. Tomlins, S., Rhodes, D., Perner, S., et al. 2005. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310, 644-648. (Pubitemid 41528150)
19. Wang, D., Urisman, A., Liu, Y., et al. 2003. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 1, E2. (Pubitemid 39112167)
20. Wang, J., Cai, Y., Ren, C., et al. 2006. Expression of variant TMPRSS2=ERG fusion messenger RNAs is associated with aggressive prostate cancer. Cancer Res. 66, 8347-8351. (Pubitemid 44449142)
21. Welsh, D., and Powell, M. 1967. An upper bound for the chromatic number of a graph and its application to timetabling problems. Comput. J. 10, 85-86.