Evaluation of DNA Whole
Genome Amplification
Technologies for Genotyping
Genomic Variation Research
Group (GVRG)
WGA Kits Tested
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GE Healthcare illustraTM GenomiPhiTM V2 DNA
Amplification Kit
NuGen® Ovation® WGA System
NuGEN® Ovation® WGA FFPE System
Qiagen® REPLI-g® Mini
Sigma-Aldrich® GenomePlex® Complete Whole
Genome Amplification Kit (WGA2)
Sigma-Aldrich® GenomePlex® Single Cell Whole
Genome Amplification Kit (WGA4)
GE Healthcare illustra GenomiPhi
&
Qiagen REPLI-g
NuGEN Ovation WGA System
*The Ovation WGA FFPE System
differs slightly. The first step is an
enzymatic fragmentation of the
dsDNA, followed by end-repair and
a-tailing. Adaptors containing
target hybridization sequences are
then ligated to the end-repaired,
A-tailed dsDNA to create SPIA
templates.
Sigma-Aldrich GenomePlex
Technology
Samples Tested
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CEPH/Utah Pedigree 1463 Trio from
HapMap Project
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FFPE Derived Sample
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NA12891 (Father)
NA12892 (Mother)
NA12878 (Daughter)
Newly extracted
Extracted 2 years ago
Fragmented Sample
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NA12891 (average fragment length: 477 bp)
Kit Information
Kit
Req.
Input
Input Types
Exp.
Yield
Exp. Product
Length (in Kb)
Process
Time
Hands
on Time
GenomiPhi
10 ng
Purified gDNA, whole
blood, mouth wash,
buccal, dried blood cards
4-7 ug
Average: 10
Range: 2-100
2 hours
20 min
Ovation
10 ng
Purified gDNA
3-6 ug
Average: 0.2
Range: 0.05-1.5
?
?
Sigma
Complete
(WGA2)
10 ng
Purified gDNA
10 ug
Average: 0.4
Range: 0.1-1
3.5 hours
1 hour
REPLI-g
10 ng
Purified gDNA, whole
blood, mouth wash,
buccal, dried blood cards
10 ug
Average: 10
Range: 2-100
17 hours
40 min
Sigma
Single Cell
(WGA4)
1 cell
or
< 100
pg
Single cell
or
Purified gDNA
Millionfold
Average: 0.4
Range: 0.1-1
3.5 hours
1 hour
100
ng
Purified gDNA
3.5-5 ug
Average: 0.2
Range: 0.05-1.5
8.5 hours
4 hours
Ovation
FFPE
Quality Analysis of
wgaDNA Product
 Yield

Quantitation via PicoGreen assay and
NanoDrop UV-Vis
 Fragment
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Agilent BioAnalyzer DNA 12000 Chip
 Allelic

Size
Representation
Applied Biosystems Identifiler Assay
Product Yield
Size of Product
Quality of Allelic Representation
Genotyping Platforms Assessed
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TaqMan SNP Assays
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18 assays duplicated with Infinium
TaqMan Copy Number Assays
Infinium Human Omni1Quad
TaqMan Call Rates by Sample
TaqMan Call Rates by Kit
TaqMan Concordance
Copy Number Call Rate By Sample
Copy Number Call Rate By Kit
Copy Number Call Rate By
Assay and Kit
Copy Number Concordance
Infinium Call Rates
Across All Kits
Infinium Call Rates
Genomic Control
Infinium Call Rates
GenomiPhi V2
Infinium Call Rates
Ovation
Infinium Call Rates
Ovation FFPE
Infinium Call Rates
Repli-G
Infinium Call Rates
WGA2
Infinium Call Rates
WGA4
Infinium Concordance
 Every
sample with a completion
rate above 90% had
concordance rate greater than
99.8% with genomic results
 Mendelian Check
 100% Concordant
18 Duplicated Assays Between
TaqMan and Infinium:
A Closer Look
Infinium Call Rates Across
Duplicated Assays By Sample
Infinium Call Rates Across
Duplicated Assays By Kit
Infinium Call Rates Across
Duplicated Assays
Infinium Concordance
Comparing TaqMan Results To
Infinium Results Across
Duplicated Assays
TaqMan to Infinium Comparison
Across 18 Duplicated Assays
Breakdown of Differences Between
TaqMan and Infinium Results
Breakdown of Differences Between
TaqMan and Infinium Results
Breakdown of Differences Between
TaqMan and Infinium Results
Breakdown of Differences Between
TaqMan and Infinium Results
Breakdown of Differences Between
TaqMan and Infinium Results
Final Thoughts…
What else could have been done…
 aCGH
Platform for CNVs
 NGS Platforms
Acknowledgements
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Corporate Sponsors
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Additional Thanks
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GE Healthcare Life Sciences
NuGen Technologies
Qiagen
Sigma-Aldrich
All generously donated the WGA kits for this study.
Alex McCary from SAIC-Frederick
Supriya Singh from Eurofins
Bruce Kingham for supplying the FFPE samples
used in this study.
Current GVRG Members
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Amy Hutchinson
Casey Dagnall
Charles Nicolet
Helaman Escobar
Sean Blake
Brian Sanderson
Bruce Kingham
Karen Jonscher
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Looking to join? We’re always looking for new
members…
Questions?