Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome amplified DNA

Nucleic Acids Research
Lovisa LovmarAnn-Christine Syvänen

Abstract

Whole genome amplification (WGA) procedures such as primer extension preamplification (PEP) or multiple displacement amplification (MDA) have the potential to provide an unlimited source of DNA for large-scale genetic studies. We have performed a quantitative evaluation of PEP and MDA for genotyping single nucleotide polymorphisms (SNPs) using multiplex, four-color fluorescent minisequencing in a microarray format. Forty-five SNPs were genotyped and the WGA methods were evaluated with respect to genotyping success, signal-to-noise ratios, power of genotype discrimination, yield and imbalanced amplification of alleles in the MDA product. Both PEP and MDA products provided genotyping results with a high concordance to genomic DNA. For PEP products the power of genotype discrimination was lower than for MDA due to a 2-fold lower signal-to-noise ratio. MDA products were indistinguishable from genomic DNA in all aspects studied. To obtain faithful representation of the SNP alleles at least 0.3 ng DNA should be used per MDA reaction. We conclude that the use of WGA, and MDA in particular, is a highly promising procedure for producing DNA in sufficient amounts even for genome wide SNP mapping studies.

References

Nov 25, 2004·Progress in Biophysics and Molecular Biology·Simon HughesJeremy Squire
Mar 11, 2008·Nature Methods·Doris ChenBarry J Dickson
Oct 25, 2008·Nature Protocols·Frank SchnorrerAnn-Christine Syvänen
Mar 31, 2007·Genetic Testing·Karina Meden SørensenPaal Skytt Andersen
Apr 18, 2009·Genetic Testing and Molecular Biomarkers·Mads V HollegaardDavid M Hougaard
Oct 23, 2010·Human Reproduction·G L HartonEuropean Society for Human Reproduction and Embryology (ESHRE) PGD Consortium
Aug 2, 2005·Nucleic Acids Research·Peter A DicksonMichael R James
Nov 3, 2004·Genome Research·Gang WangG Mike Makrigiorgos
Dec 2, 2008·Annals of Human Genetics·Tuuli LappalainenP Lahermo
Aug 7, 2004·Journal of Clinical Microbiology·Verena GrimmTill T Bachmann
Jul 17, 2008·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Julie M CunninghamEllen L Goode
Dec 10, 2008·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Farzana JasmineMuhammad G Kibriya
Jul 6, 2011·BMC Genetics·Mads V HollegaardDavid M Hougaard
Apr 16, 2009·BMC Genomics·Emiliano GiardinaGiuseppe Novelli
Jul 7, 2009·BMC Genomics·Mads V HollegaardDavid M Hougaard
Mar 12, 2005·BMC Genomics·Lovisa LovmarAnn-Christine Syvänen
Oct 27, 2004·BMC Biotechnology·Ulrika LiljedahlAnn-Christine Syvänen
Aug 20, 2008·BMC Research Notes·Bente A Talseth-PalmerRodney J Scott
Aug 22, 2007·Twin Research and Human Genetics : the Official Journal of the International Society for Twin Studies·Ulf HanneliusCecilia M Lindgren
Feb 11, 2010·Future Microbiology·Tomasz A LeskiBaochuan Lin
May 6, 2014·Molecular Phylogenetics and Evolution·Natalie M Jameson KieslingDerek E Wildman
Jun 14, 2008·Reproductive Biomedicine Online·Belén LledóRafael Bernabeu
Apr 12, 2008·The Journal of Molecular Diagnostics : JMD·Daniel T CroftDarrell L Ellsworth
Aug 11, 2007·The Journal of Molecular Diagnostics : JMD·Fengfei WangG Mike Makrigiorgos
Dec 13, 2006·European Journal of Obstetrics, Gynecology, and Reproductive Biology·Wen PengKazumi Ikawa
Jul 29, 2006·Pediatric Clinics of North America·David P Bick, Eduardo C Lau

Citations

Jul 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·L ZhangN Arnheim
Sep 13, 1996·Science·N Risch, K Merikangas
Dec 10, 1996·Proceedings of the National Academy of Sciences of the United States of America·V G Cheung, S F Nelson
Jan 23, 1999·The American Journal of Pathology·W DietmaierJ Rüschoff
Mar 10, 2001·Nature·R SachidanandamInternational SNP Map Working Group
Dec 6, 2001·Nature Reviews. Genetics·A C Syvänen
Apr 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·Frank B DeanRoger S Lasken
Jul 24, 2002·Nucleic Acids Research·Katarina LindroosAnn-Christine Syvänen
Nov 16, 2002·Nucleic Acids Research·Struan F A GrantRalf Tolle
Mar 26, 2003·Human Molecular Genetics·Sagiv ShifmanAriel Darvasi
Apr 16, 2003·Genome Research·Seiyu HosonoRoger S Lasken

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Fluorescent Dyes
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