Comparison of whole genome amplification methods for further quantitative analysis with microarray-based comparative genomic hybridization

Taiwanese Journal of Obstetrics and Gynecology

Volumn 47, Issue 1, 2008, Pages 32-41

  Lee, Yun Shien ^a,b   Tsai, Chi Neu ^c   Tsai, Chia Lung ^d   Chang, Shuenn Dyh ^d   Hsueh, Ding Wei ^a   Liu, Chun Ting ^a   Ma, Chung Chun ^a   Lin, Seng Hsuan ^a   Wang, Tzu Hao ^a,d   Wang, Hsin Shih ^c,d  

^a CHANG GUNG MEMORIAL HOSPITAL   (Taiwan)

^b MING CHUAN UNIVERSITY   (Taiwan)

^c Institute of Molecular and Cellular Biology   (Taiwan)

^d CHANG GUNG UNIVERSITY   (Taiwan)

Author keywords

A; Array CGH; D; DOP PCR; LM PCR; S; Whole genome amplification

Indexed keywords

ACCURACY; AMNION CELL; ARTICLE; CANCER CELL CULTURE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DEGENERATE OLIGONUCLEOTIDE PRIMED POLYMERASE CHAIN REACTION; GENE AMPLIFICATION; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; KARYOTYPE; LIGATION MEDIATED POLYMERASE CHAIN REACTION; MICROARRAY ANALYSIS; MICROSATELLITE MARKER; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STRAND DISPLACEMENT AMPLIFICATION;

EID: 42949161728     PISSN: 10284559     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1028-4559(08)60052-2     Document Type: Article

References (33)

1. KK Mantripragada PG Buckley TD de Stahl JP Dumanski Genomic microarrays in the spotlight Trends Genet 20 2004 87 94
2. JR Pollack CM Perou AA Alizadeh Genome-wide analysis of DNA copy-number changes using cDNA microarrays Nat Genet 23 1999 41 46
3. JR Pollack T SorYlie CM Perou Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors Proc Natl Acad Sci USA 99 2002 12963 12968
4. MA Heiskanen ML Bittner Y Chen J Khan KE Adler JM Trent PS Meltzer Detection of gene amplification by genomic hybridization to cDNA microarrays Cancer Res 60 2000 799 802
5. S Coskun O Alsmadi Whole genome amplification from a single cell: a new era for preimplantation genetic diagnosis Prenat Diagn 27 2007 297 302
6. TL Hawkins JC Detter PM Richardson Whole genome amplification: applications and advances Curr Opin Biotechnol 13 2002 65 67
7. G Sun R Kaushal P Pal Whole-genome amplification: relative efficiencies of the current methods Leg Med (Tokyo) 7 2005 279 286
8. AW Bergen Y Qi KA Haque RA Welch SJ Chanock Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance BMC Biotechnol 5 2005 24
9. H O'Geen CM Nicolet K Blahnik R Green PJ Farnham Comparison of sample preparation methods for ChIP-chip assays Biotechniques 41 2006 577 580
10. G Ng I Roberts N Coleman Evaluation of 3 methods of whole-genome amplification for subsequent metaphase comparative genomic hybridization Diagn Mol Pathol 14 2005 203 212
11. CK Chen SD Chang YJ Chen DW Hsueh YK Soong Comparative genomic hybridization-assisted prenatal diagnosis of a de novo inverted duplication of chromosome 10q. A case report J Reprod Med 48 2003 391 394
12. Q Huang SP Schantz PH Rao J Mo SA McCormick RS Chaganti Improving degenerate oligonucleotide primed PCR-comparative genomic hybridization for analysis of DNA copy number changes in tumors Genes Chromosomes Cancer 28 2000 395 403
13. CA Klein O Schmidt-Kittler JA Schardt K Pantel MR Speicher G Riethmuller Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells Proc Natl Acad Sci USA 96 1999 4494 4499
14. JM Lage JH Leamon T Pejovic Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH Genome Res 13 2003 294 307
15. KP Chang SP Hao CT Liu Promoter polymorphisms of DNMT3B and the risk of head and neck squamous cell carcinoma in Taiwan: a case-control study Oral Oncol 43 2007 345 351
16. M Salman SC Jhanwar H Ostrer Will the new cytogenetics replace the old cytogenetics? Clin Genet 66 2004 265 275
17. C Tanabe K Aoyagi T Sakiyama Evaluation of a whole-genome amplification method based on adaptorligation PCR of randomly sheared genomic DNA Genes Chromosomes Cancer 38 2003 168 176
18. S Solinas-Toldo S Lampel S Stilgenbauer Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances Genes Chromosomes Cancer 20 1997 399 407
19. AB Hui KW Lo XL Yin WS Poon HK Ng Detection of multiple gene amplifications in glioblastoma multiforme using array-based comparative genomic hybridization Lab Invest 81 2001 717 723
20. WW Cai JH Mao CW Chow S Damani A Balmain A Bradley Genome-wide detection of chromosomal imbalances in tumors using BAC microarrays Nat Biotechnol 20 2002 393 396
21. AS Ishkanian CA Malloff SK Watson A tiling resolution DNA microarray with complete coverage of the human genome Nat Genet 36 2004 299 303
22. B Beheshti I Braude P Marrano P Thorner M Zielenska JA Squire Chromosomal localization of DNA amplifications in neuroblastoma tumors using cDNA microarray comparative genomic hybridization Neoplasia 5 2003 53 62
23. R Lucito J Healy J Alexander Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation Genome Res 13 2003 2291 2305
24. GR Bignell J Huang J Greshock High-resolution analysis of DNA copy number using oligonucleotide microarrays Genome Res 14 2004 287 295
25. TH Wang YS Lee ES Chen Establishment of cDNA microarray analysis at the Genomic Medicine Research Core Laboratory (GMRCL) of Chang Gung Memorial Hospital Chang Gung Med J 27 2004 243 260
26. P Kauraniemi M Barlund O Monni A Kallioniemi New amplified and highly expressed genes discovered in the ERBB2 amplicon in breast cancer by cDNA microarrays Cancer Res 61 2001 8235 8240
27. O Monni M Barlund S Mousses Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer Proc Natl Acad Sci USA 98 2001 5711 5716
28. K Porkka O Saramaki M Tanner T Visakorpi Amplification and overexpression of Elongin C gene discovered in prostate cancer by cDNA microarrays Lab Invest 82 2002 629 637
29. J Clark S Edwards M John Identification of amplified and expressed genes in breast cancer by comparative hybridization onto microarrays of randomly selected cDNA clones Genes Chromosomes Cancer 34 2002 104 114
30. S Hosono AF Faruqi FB Dean Unbiased wholegenome amplification directly from clinical samples Genome Res 13 2003 954 964
31. FB Dean S Hosono L Fang Comprehensive human genome amplification using multiple displacement amplification Proc Natl Acad Sci USA 99 2002 5261 5266
32. JA Esteban M Salas L Blanco Fidelity of phi 29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization J Biol Chem 268 1993 2719 2726
33. KA Eckert TA Kunkel DNA polymerase fidelity and the polymerase chain reaction PCR Methods Appl 1 1991 17 24