A Study Of STR And SNP On Chromosome Y

Objective In order to improve the discrimination power and exclusion chance of polymorphic markers on chromosome Y, it is necessary to cast about for novel Y-STR loci and to develop a new method to genotype Y-SNP for forensic science. In order to providing a gist for forensic application, allelic sequences of 8 novel Y-STR loci were analyzed, and frequencies of haplotypes for these loci were surveyed. To quantify the products of single nucleotide primer extension (SNuPE), the single strain oligonucleotides were separated by High Performance Liquid Chromatography (HPLC). The reactions of SNuPE were established for two Y-SNP loci. The rule of SNuPE was revealed for analyzing Y-SNP of forensic science. Methods A total of 8 novel Y-STR loci were retrieved from database of internet. Primers of DYS443 and DYS444 were redesigned by us. These 8 Y-STR loci were amplified with PCR and the products of PCR were analyzed using gel electrophoresis. Each allele of these 8 Y-STR loci was sequenced and the allele ladders were constructed in house. Alleles of these Y-STR lociwere nominated according to recommends of the International Society of Forensic Genetics. The synthesized single strain oligonucleotides were separated by High Performance Liquid Chromatography. The thermostable DNA polymerase was used to catalyze SNuPE and the reactions of SNuPE for two Y-SNP loci were developed. Results Allelic sequences of 8 Y-STR revealed that DYS443, DYS453, DYS455 and DYS456 were simple STR systems, while DYS444, DYS448, DYS457 and DYS458 were complex STR systems. The gene diversity of DYS443, DYS444, DYS448, DYS453, DYS455, DYS456, DYS457 and DYS458 was 0.7742, 0.7671, 0.7453, 0.3545, 0.0549, 0.6988, 0.5058 and 0.8213 in our population studied, respectively. The diversity of haplotype for these Y-STR loci was 0.9991. The value of discrimination power and the exclusion chance of paternity for these Y-STR loci are same as the value of haplotype diversity. Utilizing ion-pair reversed-phase HPLC, four kinds of oligonucleotides with size 18, 19, 20 and 21nt, respectively, were separated successfully. Furthermore, two kinds of oligonucleotides with same size and difference sequence were successfully separated. Linear regression equations of two standard samples have been set up. Reactions of SNuPE for 2 Y-SNP loci were established and rules of SNuPE were revealed. The products of SNuPE for 2 Y-SNP loci were qualified and quantified with the ion-pair reversed-phase HPLC. Conclusion While primers of DYS443 and DYS444 were redesigned, amplicons of these two loci were shortened to be exactly genotyped. The results revealed that design of primers was successful. The nomenclatures of alleles at 8 new Y-STR loci were successfully established based on allelic sequences according to recommends of ISFG. The haplotype diversity for 8 Y-STR locidemonstrated that these loci showed good discrimination power and high exclusion chance. They were suitable for improving identification power of polymorphic markers on chromosome Y. Our approach of HPLC can separate the oligonucleotides with different size and same size with different sequences, and provide a method to quantity products of SNuPE. Establishing SNuPE for 2 Y-SNP loci, we understand that the suitable thermostable DN A polymerase and proportion of template and primer are the keys to reaction of SNuPE. The SNuPE provides novel genotyping method of Y-SNP for forensic application.