Clinical application value of targeted amplicon sequencing technology in fetuses with uniparental disomy-related...

To evaluate the application of targeted amplicon sequencing (TA-seq)-a method based on multiplex PCR and high-throughput sequencing-for the prenatal detection of uniparental disomy (UPD)-related imprinting disorders (ImpDis).

This retrospective study included 370 samples suspected of UPD from 42 hospitals across China. Of these, 294 samples were successfully tested by TA-seq, and methylation multiplex ligation-dependent probe amplification (MS-MLPA) being regarded as the reference method for methylation-based detection of imprinting disorders.

TA-seq identified 36 positives and 258 negatives, of which 30 positives and 255 negatives were consistent with the findings from MS-MLPA. The sensitivity, specificity, positive predictive value, and negative predictive value of TA-seq were 90.9% (30/33), 97.7% (255/261), 83.3% (30/36), and 98.8% (255/258), respectively. The concordance between the two methods was 96.9% (285/294). Additionally, we observed that the positive rates vary widely among different testing indication groups. The group of ≥ 5 Mb region of homozygosity (ROH) detected by SNP-array on chromosomes 6, 7, 11, 14, 15, or 20 exhibited positive rates of 13.4% (17/127) and 11.0% (14/127) for TA-seq and MS-MLPA, respectively. In contrast, the group of familial or de novo balanced Robertsonian translocation or isochromosome involving chromosome 14 or 15 based on CVS or amniocentesis and the group of de novo small supernumerary marker chromosomes with no apparent euchromatic material in the fetus both demonstrated positive rates of 0% (0/23 and 0/6 for TA-seq and MS-MLPA, respectively).

This retrospective study demonstrates TA-seq as a potentially effective method for prenatal screening of UPD-related ImpDis. Its cost-effectiveness, adaptability, and reliability make it promising for future clinical use. However, limitations inherent in this study-including its retrospective design, lack of trio validation, and chromosomal bias among true positives-warrant further investigation before broader application of TA-seq.