Reinvestigation of a paternity case with three CODIS core STR inconsistencies using MPS-based multi-marker analysis

A routine paternity test with 23 autosomal STRs (A-STRs) showed three Mendelian inconsistencies (D21S11, D13S317, D7S820) between the alleged father and child, resulting in a combined paternity index (CPI) below the Chinese confirmation threshold (>104), initially excluding paternity. Extended testing with 48 A-STRs and 17 Y-STRs raised the CPI above the threshold. Definitive resolution came from massively parallel sequencing (MPS) of 54 A-STRs, 27 X-STRs, 48 Y-STRs, 132 iiSNPs, and mtDNA, yielding CPIs of 2.78×10²¹ (A-STRs) and 6.28×10¹7 (iiSNPs), strongly supporting paternity. All other markers were consistent. The inconsistencies were attributed to single-step paternal mutations. This case highlights the risk of misinterpreting multi-locus STR exclusions and the value of MPS in complex paternity testing