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PMID: 15123587 Published · ppublish English Comparative Study Journal Article

Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel.

Genome research ·Vol. 14 ·No. 5 ·2004-05-00 ·Pages 901-7

Barker DL, Hansen MS, Faruqi AF, Giannola D, Irsula OR, Lasken RS, Latterich M, Makarov V, Oliphant A, Pinter JH, Shen R, Sleptsova I, Ziehler W, Lai E

Abstract

Comprehensive genome scans involving many thousands of SNP assays will require significant amounts of genomic DNA from each sample. We report two successful methods for amplifying whole-genomic DNA prior to SNP analysis, multiple displacement amplification, and OmniPlex technology. We determined the coverage of amplification by analyzing a SNP linkage marker set that contained 2320 SNP markers spread across the genome at an average distance of 2.5 cM. We observed a concordance of >99.8% in genotyping results from genomic DNA and amplified DNA, strongly indicating the ability of both methods used to amplify genomic DNA in a highly representative manner. Furthermore, we were able to achieve a SNP call rate of >98% in both genomic and amplified DNA. The combination of whole-genome amplification and comprehensive SNP linkage analysis offers new opportunities for genetic analysis in clinical trials, disease association studies, and archiving of DNA samples.

MeSH Terms
DNA/genetics Genetic Linkage/genetics Genome, Human Genotype Humans Nucleic Acid Amplification Techniques/methods,standards Polymorphism, Single Nucleotide/genetics Reproducibility of Results
Chemicals
DNA
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
Barker David L
Illumina, Inc., San Diego, California 92121, USA.
Hansen Mark S T
Faruqi A Fawad
Giannola Diane
Irsula Orlando R
Lasken Roger S
Latterich Martin
Makarov Vladimir
Oliphant Arnold
Pinter Jonathon H
Shen Richard
Sleptsova Irina
Ziehler William
Lai Eric
References (24)
24 references, click to expand
  1. Whole genome amplification and high-throughput allelotyping identified five distinct deletion regions on chromosomes 5 and 6 in microdissected early-stage ovarian tumors.
    Cancer Res. 2001 May 15;61(10):4169-74 PMID: 11358841
  2. Mutation detection and single-molecule counting using isothermal rolling-circle amplification.
    Nat Genet. 1998 Jul;19(3):225-32 PMID: 9662393
  3. Genetic polymorphism of the MxA gene promoter and interferon responsiveness of hepatitis C patients: revisited by analyzing two SNP sites (-123 and -88) in vivo and in vitro.
    Intervirology. 2001;44(6):379-82 PMID: 11805446
  4. Comprehensive human genome amplification using multiple displacement amplification.
    Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5261-6 PMID: 11959976
  5. BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping.
    Biotechniques. 2002 Jun;Suppl:56-8, 60-1 PMID: 12083399
  6. Genome-based pharmacogenetics and the pharmaceutical industry.
    Nat Rev Drug Discov. 2002 Jul;1(7):541-9 PMID: 12120260
  7. Rubicon Genomics, Inc.
    Pharmacogenomics. 2002 Jul;3(4):557-60 PMID: 12164778
  8. Association of novel polymorphisms with the expression of SPARC in normal fibroblasts and with susceptibility to scleroderma.
    Arthritis Rheum. 2002 Nov;46(11):2990-9 PMID: 12428242
  9. A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications.
    Hum Mol Genet. 2002 Dec 1;11(25):3221-9 PMID: 12444106
  10. Diversity of mutations and distribution of single nucleotide polymorphic alleles in the human alpha-L-iduronidase (IDUA) gene.
    Genet Med. 2002 Nov-Dec;4(6):420-6 PMID: 12509712
  11. In silico quantitative trait locus map for atherosclerosis susceptibility in apolipoprotein E-deficient mice.
    Arterioscler Thromb Vasc Biol. 2003 Jan 1;23(1):117-22 PMID: 12524234
  12. Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH.
    Genome Res. 2003 Feb;13(2):294-307 PMID: 12566408
  13. Genomic basis of cystathioninuria (MIM 219500) revealed by multiple mutations in cystathionine gamma-lyase (CTH).
    Hum Genet. 2003 Apr;112(4):404-8 PMID: 12574942
  14. Unbiased whole-genome amplification directly from clinical samples.
    Genome Res. 2003 May;13(5):954-64 PMID: 12695328
  15. Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome amplified DNA.
    Nucleic Acids Res. 2003 Nov 1;31(21):e129 PMID: 14576329
  16. Chromosome paints from single copies of chromosomes.
    Chromosome Res. 2004;12(2):143-51 PMID: 15053484
  17. Decoding randomly ordered DNA arrays.
    Genome Res. 2004 May;14(5):870-7 PMID: 15078854
  18. Highly parallel SNP genotyping.
    Cold Spring Harb Symp Quant Biol. 2003;68:69-78 PMID: 15338605
  19. Whole genome amplification from a single cell: implications for genetic analysis.
    Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):5847-51 PMID: 1631067
  20. Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer.
    Genomics. 1992 Jul;13(3):718-25 PMID: 1639399
  21. PicoGreen quantitation of DNA: effective evaluation of samples pre- or post-PCR.
    Nucleic Acids Res. 1996 Jul 1;24(13):2623-5 PMID: 8692708
  22. Preimplantation diagnosis by whole-genome amplification, PCR amplification, and solid-phase minisequencing of blastomere DNA.
    Clin Chem. 1996 Sep;42(9):1382-90 PMID: 8787693
  23. 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. 1996 Dec 10;93(25):14676-9 PMID: 8962113
  24. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification.
    Genome Res. 2001 Jun;11(6):1095-9 PMID: 11381035
Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.1949704
Published
2004-05-00
Pages
901-7
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC479118
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.1949704 PMC Full Text View journal details
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