A highly sensitive and specific system for large-scale gene expression profiling

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Hu, Guohong ^a   Yang, Qifeng ^a   Cui, Xiangfeng ^a   Yue, Gang ^a   Azaro, Marco A ^a   Wang, Hui Yun ^a   Li, Honghua ^a  

^a RUTGERS CANCER INSTITUTE OF NEW JERSEY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; MESSENGER RNA; PRIMER DNA; RNA;

ARTICLE; BREAST CANCER; CANCER CELL CULTURE; CANCER GENETICS; CELL STRAIN MCF 7; CONTROLLED STUDY; DNA MICROARRAY; EXON; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; NUCLEOTIDE SEQUENCE; OVARY CANCER; PROCESS DEVELOPMENT; PSEUDOGENE; REPRODUCIBILITY; RNA ANALYSIS; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY; UNINDEXED SEQUENCE; BREAST TUMOR; FEMALE; GENETICS; METHODOLOGY; OVARY TUMOR; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STATISTICS; TUMOR CELL LINE;

BASE SEQUENCE; BREAST NEOPLASMS; CELL LINE, TUMOR; DNA PRIMERS; EXONS; FEMALE; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OVARIAN NEOPLASMS; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; RNA, NEOPLASM; SENSITIVITY AND SPECIFICITY;

EID: 40549084990     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-9     Document Type: Article

References (46)

1. Schena M Shalon D Davis RW Brown PO Quantitative monitoring of gene expression patterns with a cDNA microarray Science 1995, 270:467-470 10.1126/science.270.5235.467 7569999
2. Lockhart DJ Dong H Byrne MC Follettie MT Gallo MV Chee MS Mittmann M Wang C Kobayashi M Horton H Expression monitoring by hybridization to high-density oligonucleotide arrays Nat Biotechnol 1996, 14:13-1675 1680 10.1038/nbt1296-1675 9634850
3. Goncalves I Duret L Mouchiroud D Nature and structure of human genes that generate retropseudogenes Genome Res 2000, 10(5):672-678 310883 10810090 10.1101/gr.10.5.672
4. Harrison PM Hegyi H Balasubramanian S Luscombe NM Bertone P Echols N Johnson T Gerstein M Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22 Genome Res 2002, 12(2):272-280 155275 11827946 10.1101/gr.207102
5. Zhang J Finney RP Clifford RJ Derr LK Buetow KH Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach Genomics 2005, 85(3):297-308 10.1016/j.ygeno.2004.11.004 15718097
6. Stalteri MA Harrison AP Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips BMC Bioinformatics 2007, 8:13 1784106 17224057 10.1186/1471-2105-8-13
7. Elbez Y Farkash-Amar S Simon I An analysis of intra array repeats: The good, the bad and the non informative BMC genomics 2006, 7:136 1501018 16753054 10.1186/1471-2164-7-136
8. Singh R Maganti RJ Jabba SV Wang M Deng G Heath JD Kurn N Wangemann P Microarray-based comparison of three amplification methods for nanogram amounts of total RNA Am J Physiol Cell Physiol 2005, 288(5):C1179-1189 2020524 15613496 10.1152/ajpcell.00258.2004
9. Lander ES Array of hope Nat Genet 1999 21(1 Suppl):3-4 10.1038/4427 9915492
10. Symmans WF Ayers M Clark EA Stec J Hess KR Sneige N Buchholz TA Krishnamurthy S Ibrahim NK Buzdar AU Total RNA yield and microarray gene expression profiles from fine-needle aspiration biopsy and core-needle biopsy samples of breast carcinoma Cancer 2003, 97(12):2960-2971 10.1002/ cncr.11435 12784330
11. Gustincich S Contini M Gariboldi M Puopolo M Kadota K Bono H LeMieux J Walsh P Carninci P Hayashizaki Y Gene discovery in genetically labeled single dopaminergic neurons of the retina Proc Natl Acad Sci USA 2004, 101(14):5069-5074 387375 15047890 10.1073/pnas.0400913101
12. Wang HY Luo M Tereshchenko IV Frikker DM Cui X Li JY Hu G Chu Y Azaro MA Lin Y A genotyping system capable of simultaneously analyzing >1000 single nucleotide polymorphisms in a haploid genome Genome Res 2005, 15(2):276-283 546529 15687291 10.1101/gr.2885205
13. Shumaker JM Metspalu A Caskey CT Mutation detection by solid phase primer extension Hum Mutat 1996, 7(4):346-354 10.1002/ (SICI)1098-1004(1996)7:4<346::AID-HUMU9<3.0.CO;2-6 8723685
14. Pastinen T Raitio M Lindroos K Tainola P Peltonen L Syvanen AC A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays Genome Res 2000, 10(7):1031-1042 310927 10899152 10.1101/gr.10.7.1031
15. Paik S Shak S Tang G Kim C Baker J Cronin M Baehner FL Walker MG Watson D Park T A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer N Engl J Med 2004, 351(27):2817-2826 10.1056/ NEJMoa041588 15591335
16. Hu Y Hines LM Weng H Zuo D Rivera M Richardson A LaBaer J Analysis of genomic and proteomic data using advanced literature mining J Proteome Res 2003, 2(4):405-412 10.1021/pr0340227 12938930
17. Golub TR Slonim DK Tamayo P Huard C Gaasenbeek M Mesirov JP Coller H Loh ML Downing JR Caligiuri MA Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring Science 1999, 286(5439):531-537 10.1126/science.286.5439.531 10521349
18. Perou CM Jeffrey SS van de Rijn M Rees CA Eisen MB Ross DT Pergamenschikov A Williams CF Zhu SX Lee JC Distinctive gene expression patterns in human mammary epithelial cells and breast cancers Proc Natl Acad Sci USA 1999, 96(16):9212-9217 17759 10430922 10.1073/ pnas.96.16.9212
19. Perou CM Sorlie T Eisen MB van de Rijn M Jeffrey SS Rees CA Pollack JR Ross DT Johnsen H Akslen LA Molecular portraits of human breast tumours Nature 2000, 406(6797):747-752 10.1038/35021093 10963602
20. van de Vijver MJ He YD van't Veer LJ Dai H Hart AA Voskuil DW Schreiber GJ Peterse JL Roberts C Marton MJ A gene-expression signature as a predictor of survival in breast cancer N Engl J Med 2002, 347(25):1999-2009 10.1056/NEJMoa021967 12490681
21. Sotiriou C Powles TJ Dowsett M Jazaeri AA Feldman AL Assersohn L Gadisetti C Libutti SK Liu ET Gene expression profiles derived from fine needle aspiration correlate with response to systemic chemotherapy in breast cancer Breast Cancer Res 2002, 4(3):R3 111028 12052255 10.1186/ bcr433
22. Sotiriou C Neo SY McShane LM Korn EL Long PM Jazaeri A Martiat P Fox SB Harris AL Liu ET Breast cancer classification and prognosis based on gene expression profiles from a population-based study Proc Natl Acad Sci USA 2003, 100(18):10393-10398 193572 12917485 10.1073/pnas.1732912100
23. Hedenfalk I Ringner M Ben-Dor A Yakhini Z Chen Y Chebil G Ach R Loman N Olsson H Meltzer P Molecular classification of familial non-BRCA1/BRCA2 breast cancer Proc Natl Acad Sci USA 2003, 100(5):2532-2537 151375 12610208 10.1073/pnas.0533805100
24. Chang JC Wooten EC Tsimelzon A Hilsenbeck SG Gutierrez MC Elledge R Mohsin S Osborne CK Chamness GC Allred DC Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer Lancet 2003, 362(9381):362-369 10.1016/ S0140-6736(03)14023-8 12907009
25. Coradini D Daidone MG Biomolecular prognostic factors in breast cancer Curr Opin Obstet Gynecol 2004, 16(1):49-55 10.1097/ 00001703-200402000-00010 15128008
26. Wajapeyee N Somasundaram K Pharmacogenomics in breast cancer: Current trends and future directions Curr Opin Mol Ther 2004, 6(3):296-301 15264432
27. Dowsett M Designing the future shape of breast cancer diagnosis, prognosis and treatment Breast Cancer Res Treat 2004, 87(Suppl 1):S27-29 10.1007/s10549-004-1580-9 15597218
28. Piccart MJ Sotiriou C Cardoso F New data on chemotherapy in the adjuvant setting Breast 2003, 12(6):373-378 10.1016/S0960-9776(03)00139-5 14659108
29. Greenawalt DM Cui X Wu Y Lin Y Wang HY Luo M Tereshchenko IV Hu G Li JY Chu Y Strong correlation between meiotic crossovers and haplotype structure in a 2.5-Mb region on the long arm of chromosome 21 Genome Res 2006, 16(2):208-214 1361716 16385099 10.1101/gr.4641706
30. Hu G Wang HY Greenawalt DM Azaro MA Luo M Tereshchenko IV Cui X Yang Q Gao R Shen L AccuTyping: New algorithms for automated analysis of data from high-throughput genotyping with oligonucleotide microarrays Nucleic Acids Res 2006, 34(17):e116 1635267 16982644 10.1093/nar/gkl601
31. Gene Expression Omnibus (GEO) Main page http://www.ncbi.nlm.nih.gov/geo/
32. Liscovitch M Ravid D A case study in misidentification of cancer cell lines: MCF-7/AdrR cells (re-designated NCI/ADR-RES) are derived from OVCAR-8 human ovarian carcinoma cells Cancer Lett 2007, 245(1-2):350-352 10.1016/j.canlet.2006.01.013 16504380
33. Aguilar JC Perez-Brena MP Garcia ML Cruz N Erdman DD Echevarria JE Detection and identification of human parainfluenza viruses 1, 2, 3, and 4 in clinical samples of pediatric patients by multiplex reverse transcription-PCR J Clin Microbiol 2000, 38(3):1191-1195 86373 10699020
34. Cerveira N Ferreira S Doria S Veiga I Ferreira F Mariz JM Marques M Castedo S Detection of prognostic significant translocations in childhood acute lymphoblastic leukaemia by one-step multiplex reverse transcription polymerase chain reaction Br J Haematol 2000, 109(3):638-640 10.1046/j.1365-2141.2000.02051.x 10886216
35. Pallisgaard N Hokland P Riishoj DC Pedersen B Jorgensen P Multiplex reverse transcription-polymerase chain reaction for simultaneous screening of 29 translocations and chromosomal aberrations in acute leukemia Blood 1998, 92(2):574-588 9657758
36. Malhotra K Foltz L Mahoney WC Schueler PA Interaction and effect of annealing temperature on primers used in differential display RT-PCR Nucleic Acids Res 1998, 26(3):854-856 147309 9443980 10.1093/nar/26.3.854
37. Tietjen I Rihel JM Cao Y Koentges G Zakhary L Dulac C Single-cell transcriptional analysis of neuronal progenitors Neuron 2003, 38(2):161-175 10.1016/S0896-6273(03)00229-0 12718852
38. Clipsham RC McCabe ER Single-tube gene-specific expression analysis by high primer density multiplex reverse transcription Mol Genet Metab 2001, 74(4):435-448 10.1006/mgme.2001.3261 11749049
39. Pantel K Cote RJ Fodstad O Detection and clinical importance of micrometastatic disease J Natl Cancer Inst 1999, 91(13):1113-1124 10.1093/jnci/91.13.1113 10393719
40. Menard S Pupa SM Campiglio M Tagliabue E Biologic and therapeutic role of HER2 in cancer Oncogene 2003, 22(42):6570-6578 10.1038/sj.onc.1206779 14528282
41. To MD Done SJ Redston M Andrulis IL Analysis of mRNA from microdissected frozen tissue sections without RNA isolation Am J Pathol 1998, 153(1):47-51 1852932 9665464
42. Wu H Hait WN Yang JM Small interfering RNA-induced suppression of MDR1 (P-glycoprotein) restores sensitivity to multidrug-resistant cancer cells Cancer Res 2003, 63(7):1515-1519 12670898
43. Human BLAT Search http://www.genome.ucsc.edu/cgi-bin/hgBlat?db=hg8
44. blast Basic Local Alignment and Search Tool http://www.ncbi.nlm.nih.gov/ BLAST/
45. Yang YH Dudoit S Luu P Lin DM Peng V Ngai J Speed TP Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res 2002, 30(4):e15 100354 11842121 10.1093/nar/30.4.e15
46. Quackenbush J Microarray data normalization and transformation Nat Genet 2002 32(Suppl):496-501 10.1038/ng1032 12454644