Genotyping of multiple single nucleotide polymorphisms with hyperbranched rolling circle amplification and microarray.
BACKGROUND
The emerging role of single nucleotide polymorphisms (SNPs) in clinical diagnostics and studies has created a need for simple and high-throughput genotyping methods. Previously, we developed a 3-dimensional polyacrylamide gel-based microarray (3-D microarray) of PCR-product. This method can detect single SNP locus from multiple DNA samples on one chip.


METHODS
Hyperbranched rolling circle amplification (HRCA) was used to recognize different SNP loci and amplify the fragments from genomic samples. Different HRCA products were used to fabricate the 3-D microarray, and dual-color fluorescent probes were used to detect signals.


RESULTS
This assay was applied to genotype 2 SNP loci from a set of 6 genomic DNA samples on one chip. Universal acryl-modified primer and one pair of dual-color fluorescent probes were used for all sample detection to reduce the cost. We demonstrate that this assay can detect 10 ng genomic DNA.


CONCLUSIONS
Combination of HRCA and 3-D microarray allows parallel discrimination of different alleles from different samples on a single chip. It is a feasible method for high-throughput mutation analysis and disease diagnosis.
Li
Xiujie
X
State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, Jiangsu Province, China.
Luo
Junfeng
J
Xiao
Pengfeng
P
Shi
Xiaolong
X
Tang
Chao
C
Lu
Zuhong
Z
D001483:Base Sequence; D004247:DNA / Q000235:genetics; D011088:DNA Ligases / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D005838:Genotype; D006801:Humans; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
D004247:DNA; D011088:DNA Ligases