Microdeletion at 8q24.13 rather than multistep microsatellite mutation resulting in the genetic inconsistency at the D8S1179 locus in a true trio

Abstract

When using microsatellite loci for DNA paternity testing, genetic inconsistencies sometimes occur in true trios and duos and may be erroneously attributed to germline mutations of microsatellite alleles. Here, we reported a typical case and discussed the issue of how to find out the cause of a genetic inconsistency. In our case, a genetic inconsistency in a true trio was observed at the D8S1179 locus, where the father has only allele 10 as compared to only allele 16 of his son. A set of tests were then performed. The results showed that the inconsistency was not result from the germline mutation of allele 10 to allele 16, or from the presence of null alleles due to primer binding site mutations, but from the microdeletion at 8q24.13, about 2.99 to 49.76 kb, detected in both the father and his son, which revealed by deletion mapping using short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). In conclusion, genetic inconsistencies observed in true trios or duos cannot be rashly attributed to germline STR mutations, especially multistep mutations, in the absence of verification or specification; otherwise, the reliability of the genetic proofs established will be challenged.

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Acknowledgements

The authors would like to thank Professor Hong Tian for her support in the karyotype analysis.

Funding

This research was supported by the National Natural Science Foundation of China (No. 81373250) and the Fundamental Research Funds for the Central Universities (HUST No. 2016YXZD025).

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Corresponding author

Correspondence to Daixin Huang.

Electronic supplementary material

Fig. S1
figure4

The genotypes of 7 STRs across 8q24.11 – 8q24.2 shown by silver staining. 1: the father, 2: the mother, 3: the child, M: DNA molecular weight marker. (PNG 3448 kb)

Fig. S3
figure5

The sequences of the repeat and flanking regions for the alleles of the D8S1179 locus by bidirectional Sanger sequencing. The chromatograms from allele 10 of the alleged father (A and B), from allele 13 (C and D) and allele 16 (E and F) of the mother, and from allele 16 (G and H) of the child were shown. (PNG 2599 kb)

Fig. S4
figure6

The karyotype of the child (46, XY). (PNG 1026 kb)

Fig. S6
figure7

The approximate chromosomal position of the microdeletion shown on the UCSC genome browser. Based on data generated from deletion mapping, we can determine that the microdeletion is within the region chr8:124,861,050 – 124,910,806 (hg38), with the smallest range being chr8: 124,893,438 – 124,896,415 (hg38). CHLC.GATA7G07: D8S1179; LINC00964: long intergenic non-protein coding RNA 964 (position: hg38 chr8:124,848,766 – 124,944,612). (PNG 254 kb)

High resolution image (TIF 9148 kb)

Fig. S2

The recovery of possible null alleles at the D8S1179 locus. The annealing temperature (Ta) of PCRs for the AGCU EX22 kit and the AmpFℓSTR® Identifiler kit were reduced to 55 °C and 50 °C for the amplification of genomic DNA from the alleged father (A and C) and his child (B and D). The allele 11 at the D8S1179 locus (D) may be due to exaggerated stochastic effects during the PCR. (BMP 2078 kb)

High resolution image (TIF 4756 kb)

High resolution image (TIF 4473 kb)

Fig. S5

The identification of genotypes of SNP rs6470322 used as an example to interpret how to obtain the genotypes of the target SNPs based on the bidirectional sequencing chromatograms. ChromasPro can identify possible point mutations (highlighted in yellow) between sequencing reads of different clones, and heterogeneous point mutations (highlighted in light purple) where both alleles are sequenced in the one reaction, leading to a double-peak in the chromatogram. Therefore, the genotypes of the father, the child and the mother at SNP rs6470322 can be determined as C, T and C/T respectively based on the sequencing chromatograms by the forward primer (A). These results are also verified with reverse primers (B). (BMP 6042 kb)

High resolution image (TIF 384 kb)

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Xiao, C., Wang, Y., Liao, F. et al. Microdeletion at 8q24.13 rather than multistep microsatellite mutation resulting in the genetic inconsistency at the D8S1179 locus in a true trio. Int J Legal Med 133, 999–1006 (2019). https://doi.org/10.1007/s00414-018-1900-y

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Keywords

  • Genetic inconsistency
  • D8S1179
  • Germline mutation
  • Allelic dropout
  • Microdeletion
  • STR
  • SNP