dcDegenerate oligonucleotide primed-PCR for multilocus, genome-wide analysis from limited quantities of DNA

Diagnostic Molecular Pathology

Volumn 18, Issue 3, 2009, Pages 165-175

  Bonnette, Michelle D ^a   Pavlova, Victoria R ^b   Rodier, Denise N ^f   Thompson, Lindsay P ^g   Boone, Edward L ^b   Brown, Kelly L ^h   Meyer, Kristin M ⁱ   Trevino, Michelle B ^d   Champagne, Jarrod R ^e   Cruz, Tracey Dawson ^b,c  

^a Texas Department of Public Safety   (United States)

^b Department of Biology ^*

^c VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^d Forensic Biology   (United States)

^e Fairfax Identity Laboratory   (United States)

^f Washington State Patrol   (United States)

^g South Carolina Law Enforcement Division   (United States)

^h Forensic Sciences Division   (United States)

ⁱ North Carolina State Bureau of Investigation   (United States)

Author keywords

Degenerate oligonucleotide primed PCR; Low copy number DNA; Short tandem repeat; Whole genome amplification

Indexed keywords

DNA; DNA POLYMERASE; PRIMER DNA;

ALLELE; ARTICLE; CAPILLARY ELECTROPHORESIS; CHEEK MUCOSA; CHROMOSOMAL LOCALIZATION; CONTROLLED STUDY; DEGENERATE OLIGONUCLEOTIDE PRIMED POLYMERASE CHAIN REACTION; DNA DETERMINATION; GENE AMPLIFICATION; GENETIC ANALYSIS; HUMAN; HUMAN CELL; MICROSATELLITE MARKER; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SHORT TANDEM REPEAT;

CHROMOSOMES; DNA; DNA PRIMERS; ELECTROPHORESIS, CAPILLARY; GENOME; HUMANS; POLYMERASE CHAIN REACTION;

EID: 69749117264     PISSN: 10529551     EISSN: None     Source Type: Journal    
DOI: 10.1097/PDM.0b013e31818d34d1     Document Type: Article

References (51)

1. Dickson PA, Montgomery GW, Henders A, et al. Evaluation of multiple displacement amplification in a 5cM STR genome-wide scan. Nucleic Acids Res. 2005;33:e119. (Pubitemid 41487305)
2. Ludecke H, Senger G, Claussen U, et al. Cloning defined regions of the human genome by microdissection of banded chromosomes and enzymatic amplification. Nature. 1989;348:348-350. (Pubitemid 19082977)
3. Telenius H, Carter M, Bebb C, et al. Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics. 1992;13:718-725.
4. Sun F, Arnheim N, Waterman MS. Whole genome amplification of single cells: mathematical analysis of PEP and tagged PCR. Nucleic Acids Res. 1995;23:3034-3040.
5. Jasper M, Liebelt J, Hussey N. Preimplantation genetic diagnosis for BRCA1 exon 13 duplication mutation using linked polymorphic markers resulting in a live birth. Prenat Diagn. 2008;28:292-298.
6. Peng W, Takabayashi H, Ikawa K. Whole genome amplification from single cells in preimplantation genetic diagnosis and prenatal diagnosis. Eur J Obstet Gynecol Reprod Biol. 2007;131:13-20. (Pubitemid 46283202)
7. Buchanan AV, Risch GM, Robichaux M, et al. Long DOP-PCR of rare archival anthropological samples. Hum Biol. 2000;72:911-925. (Pubitemid 32152218)
8. Butler JM. Forensic DNA Typing: Biology, Technology, and Genetics of STR Markers. 2nd ed. Burlington, MA: Elsevier Academic Press; 2005.
9. Lovmar L, Fredriksson M, Liljedahl U, et al. Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome amplified DNA. Nucleic Acids Res. 2003;31:e129.
10. Kittler R, Stoneking M, Kayser M. A whole genome amplification method to generate long fragments from low quantities of genomic DNA. Anal Biochem. 2002;300:237-244. (Pubitemid 34093699)
11. Lasken RS, Egholm M. Whole genome amplification: abundant supplies of DNA from precious samples or clinical specimens. Trends Biotechnol. 2003;21:531-535. (Pubitemid 37415004)
12. Cheung VG, Nelson SF. 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 USA. 1996;93:14676-14679.
13. Bergen AW, Qi Y, Haque KA, et al. Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance. BMC Biotechnol. 2005;16:1-11. (Pubitemid 41461008)
14. Paez JG, Lin M, Beroukhim R, et al. Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification. Nucleic Acids Res. 2004;32:e71.
15. Hanson EK, Ballantyne J. Whole genome amplification strategy for forensic genetic analysis using single or a few cell equivalents of genomic DNA. Anal Biochem. 2005;346:246-257. (Pubitemid 41550255)
16. Sanchez-Cespedes M, Cairns P, Jen J, et al. Degenerate oligonucleotide primed-PCR (DOP-PCR): evaluation of its reliability for screening of genetic alteration in neoplasia. BioTechniques. 1998;25:1036-1038. (Pubitemid 29005817)
17. Cheng J, Waters LC, Fortina P, et al. Degenerate oligonucleotide-primed- polymerase chain reaction and capillary electrophoretic analysis of human DNA on microchip based devices. Anal Biochem. 1998;257:101-106. (Pubitemid 28128970)
18. Sorensen KJ, Turteltaub K, Vrankovich G, et al. Whole-genome amplification of DNA from residual cells left by incidental contact. Anal Biochem. 2004;324:312-314. (Pubitemid 38019026)
19. Tie J, Serizawa Y, Oshida S, et al. Individual identification by DNA polymorphism using formalin-fixed placenta with whole genome amplification. Pathol Int. 2005;55:343-347. (Pubitemid 40910667)
20. Barrett MT, Reid BJ, Joslyn G. Genotypic analysis of multiple loci in somatic cells by whole genome amplification. Nucleic Acids Res. 1995;23:3488-3492.
21. Barber AL, Foran DR. The utility of whole genome amplification for typing compromised forensic samples. J Forensic Sci. 2006;51:1344-1349.
22. Grubic Z, Stingl K, Cecuk JE, et al. Repetitive DNA polymorphisms in following chimerism after allogeneic bone marrow transplantation. Clin Transplant. 2005;19:586-590. (Pubitemid 41341688)
23. Butler JM. Short tandem repeat analysis for human identification. Curr Protoc Hum Genet. 2004;14:14.8.
24. Pu CE, Linacre A. Systematic evaluation of sensitivity and specificity of sibship determination by using 15 STR loci. J Forensic Leg Med. 2008;15:329-1324
25. Short Tandem Repeat DNA Internet DataBase. 2007 NIST Biochemical Science Division. May 11, 2007. Available at: http://www.cstl.nist.gov/biotech/strbase/.
26. Collins PJ, Hennessy LK, Leibelt CS, et al. Developmental validation of a single-tube amplification of the 13 CODIS STR loci, D2S1338, D19S433, and amelogenin: the AmpFlSTR® Identifiler® PCR Amplification Kit. J Forensic Sci. 2004;49:1265-1277.
27. Frank WE, Llewellyn BE, Fish PA, et al. Validation of the AmpFlSTR Profiler Plus PCR amplification kit for use in forensic casework. J Forensic Sci. 2001;46:642-646. (Pubitemid 32520590)
28. AmpFlSTR® Profiler Plus™ PCR Amplification Kit User's manual. Applied Biosystems. Foster City, CA; 2000.
29. DOP PCR Master. Roche Molecular Biochemicals. Mannheim, Germany; 1999.
30. Thompson LP. Degenerate oligonucleotide primed-polymerase chain reaction evaluation and optimization to improve downstream forensic STR analysis of low quality/low quantity DNA [MS thesis]: Virginia Commonwealth University; 2006.
31. Rodier DN. Degenerate oligonucleotide primed-PCR: thermalcycling modifications and comparison studies [MS thesis]: Virginia Commonwealth University; 2006.
32. Beaulieu M, Larson G, Geller L, et al. PCR candidate region mismatch scanning: adaptation to quantitative, high-throughput genotyping. Nucleic Acids Res. 2001;29:1114-1124. (Pubitemid 32186197)
33. High fidelity PCR enzymes: properties and error rate determination technical notes. Stratagene Corporation. La Jolla, CA; 2006.
34. Hogrefe H, Brons M. High Fidelity PCR Enzymes. Stratagene Corporation Laboratory Manual. La Jolla, CA: Cold Springs Harbor Laboratory Press; 2003.
35. Greenspoon SA, Scarpetta MA, Drayton ML, et al. QIAamp spin columns as a method of DNA isolation for forensic casework. J Forensic Sci. 1998;43:1024-1030.
36. Green RL, Roinestad IC, Boland C, et al. Developmental validation of the Quantifilert real-time PCR kits for the quantification of human nuclear DNA Samples. J Forensic Sci. 2005;50:809-825. (Pubitemid 40917796)
37. Microcon® Centrifuge Filter Devices Users Guide. Millipore Corporation. Billerica, MA; 2005.
38. Walsh PS, Varlaro J, Reynolds R. A rapid chemiluminescent method for quantitation of human DNA. Nucleic Acids Res. 1992;20:;5061-5065.
39. Moretti TR, Baumstark AL, Defenbaugh DA, et al. Validation of short tandem repeats (STRs) for forensic usage: performance testing of fluorescent multiplex STR systems and analysis of authentic and simulated forensic samples. J Forensic Sci. 2001;46:647-660.
40. Platinum® Pfx DNA polymerase product insert. Invitrogen Corporation. Carlsbad, CA; 2003.
41. Platinum® Taq DNA polymerase high fidelity product insert. Invitrogen Corporation. Carlsbad, CA; 2006.
42. PicoMaxx® High Fidelity PCR System. Stratagene Corporation. La Jolla, CA; 2006.
43. FastStart High Fidelity PCR System product insert. Roche Applied Science. Roche Diagnostics Corporation. Indianapolis, IN; 2006.
44. GeneAmp® High Fidelity PCR System protocol. Applied Biosystems. Foster City, CA; 2001.
45. MinElute® Handbook. Qiagen Inc. Valencia, CA; 2006.
46. Smith P, Ballentyne J. Simplified low-copy-number DNA analysis by post-PCR purification. J Forensic Sci. 2007;52:820-829. (Pubitemid 46918581)
47. Baylor College of Medicine, inventors. PE Applied Biosystems Corporation, assignee. AmpFlSTR Profiler Plus PCR Amplification Kit. US Patent 5,364,759.
48. Kiss C, Kost-Alimova M, Klein G, et al. Optimisation of the degenerate oligonucleotide primed PCR (DOP-PCR) for capillary thermocycler. Biomol Eng. 2002;19:31-34. (Pubitemid 34717860)
49. Deep Vent® DNA Polymerase. New England Biolabs Inc. Ipswich, MA; 2006.
50. Tsurumi T, Daikoku T, Nishiyama Y. Further characterization of the interaction between the Epstein-Barr Virus DNA polymerase catalytic subunit and its accessory subunit with regard to the 3′-to-5′ exonuclease activity and stability of initiation complex at primer terminus. J Virol. 1994;68:3354-3363. (Pubitemid 24129785)
51. Gill P. Application of low copy number DNA profiles. Croat Med J. 2001;42:229-232. (Pubitemid 32606981)