Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay.
Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color, single array detection, applied to large-scale genotyping of up to 12,000 SNPs per reaction. While generating 38,429 SNP assays using this technology in a population of 30 trios from the Centre d'Etude Polymorphisme Humain family panel as part of the International HapMap project, we established SNP conversion rates of approximately 90% with concordance rates >99.6% and completeness levels >98% for assays multiplexed up to 12,000plex levels. Furthermore, these individual metrics can be "traded off" and, by sacrificing a small fraction of the conversion rate, the accuracy can be increased to very high levels. No loss of performance is seen when scaling from 6,000plex to 12,000plex assays, strongly validating the ability of the technology to suppress cross-reactivity at high multiplex levels. The results of this study demonstrate the suitability of this technology for comprehensive association studies that use targeted SNPs in indirect linkage disequilibrium studies or that directly screen for causative mutations.
Hardenbol
Paul
P
ParAllele BioScience, Inc., South San Francisco, California 94080, USA.
Yu
Fuli
F
Belmont
John
J
Mackenzie
Jennifer
J
Bruckner
Carsten
C
Brundage
Tiffany
T
Boudreau
Andrew
A
Chow
Steve
S
Eberle
Jim
J
Erbilgin
Ayca
A
Falkowski
Mat
M
Fitzgerald
Ron
R
Ghose
Sy
S
Iartchouk
Oleg
O
Jain
Maneesh
M
Karlin-Neumann
George
G
Lu
Xiuhua
X
Miao
Xin
X
Moore
Bridget
B
Moorhead
Martin
M
Namsaraev
Eugeni
E
Pasternak
Shiran
S
Prakash
Eunice
E
Tran
Karen
K
Wang
Zhiyong
Z
Jones
Hywel B
HB
Davis
Ronald W
RW
Willis
Thomas D
TD
Gibbs
Richard A
RA
D007446:Chromosome Inversion / Q000235:genetics* / Q000706:statistics & numerical data; D016000:Cluster Analysis; D015342:DNA Probes / Q000235:genetics; D020869:Gene Expression Profiling; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D015336:Molecular Probe Techniques / Q000592:standards / Q000706:statistics & numerical data / Q000639:trends*; D015335:Molecular Probes / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012107:Research Design
D015342:DNA Probes; D015335:Molecular Probes