A fast modified protocol for random-access ultra-high density whole-genome scan: a tool for personalized genomic medicine, positional mapping, and cytogenetic analysis.
BACKGROUND
High density single nucleotide polymorphism (SNP) genotyping array is widely applied on genome-wide association study of common diseases. In these studies, a fixed batch-size of 48 or 96 samples allows high-throughput analysis. To enhance the clinical application of microarray analysis on personalized medicine, we describe a modified PCR purification protocol without batch-size limitation for whole-genome scan using ultra-high density SNP microarray.


METHODS
Enzyme-digested PCR products were purified with the use of magnetic beads. Separation of the magnetic particles applies magnetic stand devices instead of vacuum pumps. With no batch-size limitation, we genotyped 17 genomic samples and 3 whole genome amplified samples in order to examine the performance of the modified protocol.


RESULTS
Our method is simple and fast, provides sufficient amount and high quality PCR products for subsequent fragmentation and labeling procedures prior to GeneChip hybridization. We show that the purified DNA can be genotyped with good QC call rate of >93% in average similar to standard protocol. With the use of the short protocol, we successfully identified the breakpoint localization of a ring chromosome in a female and located the disease gene in a consanguineous family affected by limb-girdle muscular dystrophy.


CONCLUSIONS
By modifying a single step in the original protocol, we are able to speed up the overall genotyping analysis and change the batch-wise analysis to random-access analysis for ultra-high density whole-genome scan for personalized medicine, positional mapping, and cytogenetic analysis.
Lau
Kin-Chong
KC
Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China.
Mak
Chloe M
CM
Leung
Kwok-Yin
KY
Tsoi
Tak-Hong
TH
Tang
Hoi-Yin
HY
Lee
Patrizia
P
Lam
Ching-Wan
CW
D002280:Basal Cell Carcinoma / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D020732:Cytogenetic Analysis / Q000379:methods*; D005260:Female; D005826:Genetics, Medical / Q000379:methods*; D015894:Genome, Human; D055106:Genome-Wide Association Study / Q000379:methods*; D023281:Genomics / Q000379:methods*; D006720:Homozygote; D006801:Humans; D015203:Reproducibility of Results; D012878:Skin Neoplasms / Q000235:genetics; D013997:Time Factors