Multiplexed variation scanning for 1,000 amplicons in hundreds of patients using mismatch repair detection (MRD) on tag arrays.
Identification of the genetic basis of common disease may require comprehensive sequence analysis of coding regions and regulatory elements in patients and controls to find genetic effects caused by rare or heterogeneous mutations. In this study, we demonstrate how mismatch repair detection on tag arrays can be applied in a case-control study. Mismatch repair detection allows >1,000 amplicons to be screened for variations in a single laboratory reaction. Variation scanning in 939 amplicons, mostly in coding regions within a linkage peak, was done for 372 patients and 404 controls. In total, >180 Mb of DNA was scanned. Several variants more prevalent in patients than in controls were identified. This study demonstrates an approach to the discovery of susceptibility genes for common disease: large-scale direct sequence comparison between patients and controls. We believe this approach can be scaled up to allow sequence comparison in the whole-genome coding regions among large sets of cases and controls at a reasonable cost in the near future.
Faham
Malek
M
ParAllele BioScience, 7300 Shoreline Court, South San Francisco, CA 94080, USA.
Zheng
Jianbiao
J
Moorhead
Martin
M
Fakhrai-Rad
Hossein
H
Namsaraev
Eugeni
E
Wong
Kee
K
Wang
Zhiyong
Z
Chow
Shu G
SG
Lee
Liana
L
Suyenaga
Kent
K
Reichert
Jennifer
J
Boudreau
Andrew
A
Eberle
James
J
Bruckner
Carsten
C
Jain
Maneesh
M
Karlin-Neumann
George
G
Jones
Hywel B
HB
Willis
Thomas D
TD
Buxbaum
Joseph D
JD
Davis
Ronald W
RW
D001321:Autistic Disorder / Q000235:genetics*; D020137:Base Pair Mismatch / Q000235:genetics*; D002889:Chromosomes, Human, Pair 2 / Q000235:genetics*; D016000:Cluster Analysis; D005091:Exons / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D005820:Genetic Testing / Q000379:methods*; D006801:Humans; D009154:Mutation / Q000235:genetics