A whole-genome amplification protocol for a wide variety of DNAs, including those from formalin-fixed and paraffin-embedded tissue

Methods in Molecular Biology

Volumn 556, Issue , 2009, Pages 89-98

  Paris, Pamela L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

array comparative genomic hybridization (aCGH); clinical specimens; DNA extraction; formalin fixed paraffin embedded; Whole genome amplification

Indexed keywords

DNA; FORMALDEHYDE; PARAFFIN;

ANALYTICAL EQUIPMENT; ARTICLE; CHEMISTRY; COMPARATIVE GENOMIC HYBRIDIZATION; GENETICS; GENOME; HUMAN; INSTRUMENTATION; METHODOLOGY; NUCLEIC ACID AMPLIFICATION; TISSUE FIXATION;

COMPARATIVE GENOMIC HYBRIDIZATION; DNA; FORMALDEHYDE; GENOME; HUMANS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PARAFFIN EMBEDDING; REAGENT KITS, DIAGNOSTIC; TISSUE FIXATION;

EID: 70349575436     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-192-9_7     Document Type: Article

References (21)

1. Pinkel, D., Segraves, R., Sudar, D., Clark, S., Poole, I., Kowbel, D., Collins, C., Kuo, W.L., Chen, C., Zhai, Y. et al. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet, 20, 207-211.
2. Paris, P.L., Albertson, D.G., Alers, J.C., Andaya, A., Carroll, P., Fridlyand, J., Jain, A.N., Kamkar, S., Kowbel, D., Krijtenburg, P.J. et al. (2003) High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays. Am J Pathol, 162, 763-770.
3. Paris, P.L., Sridharan, S., Scheffer, A., Tsalenko, A., Bruhn, L. and Collins, C. (2007) High resolution oligonucleotide CGH using DNA from archived prostate tissue. Prostate, 67, 1447-1455.
4. Monzon, F.A., Hagenkord, J.M., Lyons- Weiler, M.A., Balani, J.P., Parwani, A.V., Sciulli, C.M., Li, J., Chandran, U.R., Bastacky, S.I. and Dhir, R. (2008) Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors. Mod Pathol, 21, 599-608.
5. Thompson, E.R., Herbert, S.C., Forrest, S.M. and Campbell, I.G. (2005) Whole genome SNP arrays using DNA derived from formalin-fixed, paraffin-embedded ovarian tumor tissue. Hum Mutat, 26, 384-389.
6. Mardis, E.R. (2008) The impact of nextgeneration sequencing technology on genetics. Trends Genet, 24, 133-141.
7. Schuster, S.C. (2008) Next-generation sequencing transforms today's biology. Nat Methods, 5, 16-18.
8. Zhang, L., Cui, X., Schmitt, K., Hubert, R., Navidi, W. and Arnheim, N. (1992) Whole genome amplification from a single cell: Implications for genetic analysis. Proc Natl Acad Sci U S A, 89, 5847-5851.
9. Cheung, V.G. and Nelson, S.F. (1996) Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA. Proc Natl Acad Sci U S A, 93, 14676-14679.
10. Klein, C.A., Schmidt-Kittler,O., Schardt, J.A., Pantel,K., Speicher,M.R. andRiethmuller, G. (1999) Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells. Proc Natl Acad Sci U S A, 96, 4494-4499.
11. Dean, F.B., Hosono, S., Fang, L., Wu, X., Faruqi, A.F., Bray-Ward, P., Sun, Z., Zong, Q., Du, Y., Du, J. et al. (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A, 99, 5261-5266.
12. Lage, J.M., Leamon, J.H., Pejovic, T., Hamann, S., Lacey, M., Dillon, D., Segraves, R., Vossbrinck, B., Gonzalez, A., Pinkel, D. et al. (2003) Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res, 13, 294-307.
13. Little, S.E., Vuononvirta, R., Reis-Filho, J.S., Natrajan, R., Iravani, M., Fenwick, K., Mackay, A., Ashworth, A., Pritchard-Jones, K. and Jones, C. (2006) Array CGH using whole genome amplification of fresh-frozen and formalin-fixed, paraffin-embedded tumor DNA. Genomics, 87, 298-306.
14. Lizardi, P.M., Huang, X., Zhu, Z., Bray- Ward, P., Thomas, D.C. and Ward, D.C. (1998) Mutation detection and singlemolecule counting using isothermal rolling- circle amplification. Nat Genet, 19, 225-232.
15. Pirker, C., Raidl, M., Steiner, E., Elbling, L., Holzmann, K., Spiegl-Kreinecker, S., Aubele, M., Grasl-Kraupp, B., Marosi, C., Micksche, M. et al. (2004) Whole genome amplification for CGH analysis: Linkeradapter PCR as the method of choice for difficult and limited samples. Cytometry A, 61, 26-34.
16. Wang, G., Maher, E., Brennan, C., Chin, L., Leo, C., Kaur, M., Zhu, P., Rook, M., Wolfe, J.L. and Makrigiorgos, G.M. (2004) DNA amplification method tolerant to sample degradation. Genome Res, 14, 2357-2366.
17. Bagheri-Yarmand, R., Mazumdar, A., Sahin, A.A. and Kumar, R. (2006) LIM kinase 1 increases tumor metastasis of human breast cancer cells via regulation of the urokinase-type plasminogen activator system. Int J Cancer, 118, 2703-2710.
18. Hittelman, A., Sridharan, S., Roy, R., Fridlyand, J., Loda, M., Collins, C. and Paris, P.L. (2007) Evaluation of whole genome amplification protocols for array and oligonucleotide CGH. Diagnostic Molecular Pathology, 16, 198-206.
19. Paris, P.L., Andaya, A., Fridlyand, J., Jain, A.N., Weinberg, V., Kowbel, D., Brebner, J.H., Simko, J., Watson, J.E., Volik, S. et al. (2004) Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Hum Mol Genet, 13, 1303-1313.
20. van Dekken, H., Paris, P.L., Albertson, D.G., Alers, J.C., Andaya, A., Kowbel, D., van der Kwast, T.H., Pinkel, D., Schroder, F.H., Vissers, K.J. et al. (2004) Evaluation of genetic patterns in different tumor areas of intermediate-grade prostatic adenocarcinomas by high-resolution genomic array analysis. Genes Chromosomes Cancer, 39, 249-256.
21. Huang, Q., Schantz, S.P., Rao, P.H., Mo, J., McCormick, S.A. and Chaganti, R.S. (2000) Improving degenerate oligonucleotide primed PCR-comparative genomic hybridization for analysis of DNA copy number changes in tumors. Genes Chromosomes Cancer, 28, 395-403.