Background: Although many technologies can identify chromosomal abnormalities, they can’t completely replace the advantages of short tandem repeat (STR) genotyping technology. The miniSTR typing based on next generation sequencing (NGS-miniSTR) with high throughput, accuracy and sensitivity has the potential to determine the trisomy and overcome the limitations of conventional STR techniques, which never be tried. The study aimed to explore the value of the NGS-miniSTR in trisomy testing, which is an extension and improvement of the methodology of chromosomal detection technology.
Methods: A total of 140 fetal materials in miscarriages (70 trisomy 16 and 70 normal karyotypes) screened by copy-number variation sequencing (CNV-seq) were genotyped using the customed panel containing 11 miniSTRs based on NGS. Direct counting method, chi-square (χ2) test, k-means clustering analysis and Mahalanobis distance were operated to compare the difference of miniSTR between trisomy 16 and normal group, and then analyze whether trisomy 16 could be identified.
Results: All miniSTR results based on NGS were successfully obtained, except for D16S771 in 21 samples. There were significant differences in the average depth of coverage at each locus in each sample. Direct counting method and chi-square (χ2) test showed significant differences in allelic pattern and read ratio between trisomy and normal group, respectively. Almost all samples correctly divided into 2 clusters based on diallelic STR reads ratios according to k-means clustering analysis. In addition, the Mahalanobis distance showed that D16S771 had multiple outliers.
Conclusion: A new strategy of miniSTR-NGS was firstly introduced to successfully detect all samples of trisomy 16 in the fetal material in miscarriages, which revealed that the allelic pattern and allelic read ratio could be effective indexes to identify the number of chromosomes.