Exploring Novel STR Loci On Human Chromosome 21 For Forensic And Medical Genetics

Objective We focus on exploring novel STR loci on human chromosome 21 in order to develope a set of new markers for forensic genetics and to provide a molecular genetic method for diagnosing Down syndrome. Methods the DNA sequence of human chromosome 21 was browsed to find out novel STR loci. Primers for PCR were designed using Primer3 software. The novel STR loci were analyzed with PCR amplification and gel electrophoresis. All alleles of novel STR loci were sequenced and nominated according to recommendation of the International Society of Forensic Genetics. The allele ladders were constructed in house. Allele frequencies and genotype distributions of novel STR loci were investigated in Han population in Chengdu. The independence test was carried out for novel STR loci with x~2 test.Moreover, a diagnostic system for Down syndrome was constructed with novel STR markers on chromosome 21. The system was evaluated with different approaches. Results We found out 18 novel STR locion chromosome 21,seven loci of which had more than five alleles and were also easy to be genotyped accurately. They were named as LFG20,LFG21,LFG24,LFG26,LFG29,LFG33 and LFG34,respectively.The independence test of five loci revealed that there were no correlations between LFG26 and LFG21, LFG20 and LFG24, LFG21 and LFG24,LFG24 and LFG26 as well as LFG24 and LFG29 . The discrimination power of each STR exceeded 0.79, and the exclusion probability was 0.28 and above. Based on three different diagnostic standards, the sensitivities of the diagnostic system for Down syndrome were 100 % , 83.3 % and 77.8 %,respectively, while the specificities were 60.8%, 100% and 100%, respectively. There was no significant difference of diagnostic results between our new assay and cytogenetic analysis if that Down syndrome was determined depended upon that three bands at a STR locus were observed . New formulas were proposed by us in order to calculate probability.Using the formulas, the probability P I that three bands were observed in more than one STR locus was 0.995 while the probability PII that three bands were observed in more than two STR loci was 0.959.Conclusion Using the DNA sequence information of chromosome 21,we identified seven STR loci that were highly polymorphic and easy to be genotyped accurately. Our results revealed the five pairs of STR loci on chromosome 21 were independent, and they can be used simultaneously for forensic genetics. A diagnostic system for Down syndrome was successfully established with the novel STR loci on chromosome 21.This system showed a high efficiency as a confirmatory test because no false positive result was observed. However,the negative cases in the method need to confirm by other methods.The formulasproposed by us laid the foundation of evaluation for STR markers,when they were employed to diagnose Down syndrome.