Parental somatic mosaicism for CNV deletions - A need for more sensitive and precise detection methods in clinical diagnostics settings

Abstract

To further assess the scale and level of parental somatic mosaicism, we queried the CMA database at Baylor Genetics. We selected 50 unrelated families where clinically relevant apparent de novo CNV-deletions were found in the affected probands. Parental blood samples screening using deletion junction-specific PCR revealed four parents with somatic mosaicism. Droplet digital PCR (ddPCR), qPCR, and amplicon-based next-generation sequencing (NGS) were applied to validate these findings. Using ddPCR levels of mosaicism ranged from undetectable to 18.5%. Amplicon-based NGS and qPCR for the father with undetectable mosaicism was able to detect mosaicism at 0.39%. In one mother, ddPCR analysis revealed 15.6%, 10.6%, 8.2%, and undetectable levels of mosaicism in her blood, buccal cells, saliva, and urine samples, respectively. Our data suggest that more sensitive and precise methods, e.g. CNV junction-specific LR-PCR, ddPCR, or qPCR may allow for a more refined assessment of the potential disease recurrence risk for an identified variant.

Keywords: Clinical diagnostic testing; Copy-number variant (CNV); Mosaicism carrier; Parental somatic mosaicism; Recurrence risk.

Figure 1.

Mosaic CNV deletions detected by LR-PCR in four parental samples. The familial deletion-specific amplicon detected in the patient is clearly visible from the LR-PCR reaction performed on paternal or maternal DNA.

Figure 2.

Results of qPCR study in family 26. F: father 26; P: proband 26; C: unrelated control. A) Plots of qPCR amplifications. For deletion junction-specific amplification, the average Cq in the proband is 23.48, in the father is 30.38, and in the unrelated control is 33.81. The average Cq of GAPDH amplifications are similar among the three samples. B) Agarose gel electrophoresis image of the deletion junction-specific qPCR amplification.