Genotype analyses using SNP (using MALDI-TOF Mass spectrometry) and STR (microsatellite) markers in the determination of zygosity status of Chinese Twins

Abstract

It has been argued that single nucleotide polymorphisms (SNPs) is a very useful tool complementary to microsatellite analyses in the near future due to its relative ease of automation and interpretation. However, because allele frequencies can vary greatly among populations, it is important to validate and identify the informative SNPs that are useful for sample identification in biomedical and epidemiological studies. We have genotyped 768 individuals (384 pairs of twins) with a panel of SNPs based mostly on the SNPs chosen by an earlier work conducted by Lee et al., 2005 for Koreans, which we hypothesized to be useful for our Chinese subjects. The MALDI-TOF mass spectrometry based iPLEX Gold assay on the MassARRAY® Platform method using Sequenom was used for determination of the zygosity status of the twins. The ABI microsatellite kit (AmpFISTR identifiler PCR amplifcation kit) for measuring 16 loci was used to confirm the zygosity status. We found that some of the SNPs (2/22) used in Lee’s paper were not suitable for our Hong Kong Chinese samples. The zygosity status as determined by the mass spectrometry method can be validated with microsatellite method using 76 samples. In summary, we have studied a panel of 25 SNPs on their effectiveness in distinguishing identical and non-identical twins (768 individuals) for the Hong Kong Chinese population using the iPLEX method of Sequenom. It is important to optimize SNP panels for genotyping depending on the population and the platform used for the studies.