Noninvasive genotyping of 9 Y-chromosome specific STR loci using circulatory fetal DNA in maternal plasma by multiplex PCR.

Background: Human Y-Chromosome specific STR (Y-STR) has now become a useful loci in casework. However, noninvasive genotyping of multiple Y-STR loci and its application in prenatal genetic diagnosis haven't been reported. The purpose of this study is to develop a Y-STR multiplex PCR amplification system that is suitable for the amplification of short-sized templates of circulatory male fetal DNA and use the established multiplex in noninvasive prenatal genetic diagnosis and its further applications in forensic casework.

Methods: On the basis of the characteristic of circulatory fetal DNA in maternal plasma, we selected 9 Y-STR loci in which the allele size was less than 180 bp in length and developed two multiplexes that allowed fluorescent genotyping of 9 Y-STR loci simultaneously. These Y-STR loci include two trinucleotide repeats (DYS426 and DYS388) and seven tetranucleotide repeats (DYS393, DYS460, H4; DYS391, DYS389 I, DYS456 and DYS458). Sixty-four pairs of plasma DNA samples from pregnant women and genomic DNA samples from their husbands were detected by our method.

Results: As a result, an average of 7.3 Y-STR specific alleles was detected in each of the 30 plasma DNA samples from pregnancies with male fetuses. However, none of these 9 Y-STR specific alleles was detected in 34 plasma samples from pregnant women carrying female babies. The chances of detecting Y-STR alleles ranged from 66.7 to 93.3%. Fifty-eight haplotypes were detected in 64 unrelated Chinese male individuals; haplotype diversity was 0.9966. This highly polymorphic Y-STR multiplex has greatly improved the chances of detecting the Y-STR allele.

Conclusions: This assay provides a sensitive, accurate and efficient method for noninvasive prenatal genetic diagnosis and forensic casework.