[Genotyping and parental related methylation of SNRPN gene rs220030].
OBJECTIVE
To establish two methods by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing for genotyping rs220030 (a SNP in the promoter region of small nuclear ribonucleoprotein polypeptide N, SNRPN). To establish an analytical technique for detecting CpG methylation status by pyrosequencing and to further investigate the feasibility of applying rs220030 to the determination of parental origin allele.


METHODS
The rs220030 of 97 blood samples from individuals of Shanghai Han population were genotyped by DGGE, meanwhile the rs220030 of 25 blood samples of them were genotyped by pyrosequencing to compare the two methods in genotyping SNP. Pyrosequencing united bisulfite conversion method was applied to detect CpG methylation status of region upstream rs220030 of two random blood genealogical samples and investigate whether the methylation status was parental related.


RESULTS
The rs220030 genotyping results of 97 blood samples detected by DGGE were 20 C homozygote, 29 T homozygote, and 48 C/T heterozygote. Twenty-five blood samples genotyped by pyrosequencing showed the same result with DGGE. The CpG methylation status of region upstream rs220030 of the child was similar to the mother.


CONCLUSIONS
Compared with DGGE, pyrosequencing is more accurate, convenient, and suitable for large samples and high throughput SNP genotyping. Pyrosequencing united bisulfite conversion can be used to detect CpG methylation status precisely. It is feasible to apply rs220030 to parental origin allele determination.
Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China. 10211010055@fudan.edu.cn
Hui
H
Li
Hong-Mei
HM
Xu
Yun
Y
Zhao
Bei-Xu
BX
Li
Huai-Gu
HG
Zhou
Zi-Qin
ZQ
Zhao
D044466:Asian People / Q000235:genetics; D018899:CpG Islands; D004247:DNA / Q000097:blood / Q000235:genetics; D019175:DNA Methylation; D017931:DNA Primers; D018392:Genomic Imprinting; D005838:Genotype; D006579:Heterozygote; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013447:Sulfites / Q000378:metabolism; D055517:snRNP Core Proteins / Q000235:genetics*
D017931:DNA Primers; D013447:Sulfites; D055517:snRNP Core Proteins; D004247:DNA