Parental somatic mosaicism is underrecognized and influences recurrence risk of genomic disorders

Abstract

New human mutations are thought to originate in germ cells, thus making a recurrence of the same mutation in a sibling exceedingly rare. However, increasing sensitivity of genomic technologies has anecdotally revealed mosaicism for mutations in somatic tissues of apparently healthy parents. Such somatically mosaic parents might also have germline mosaicism that can potentially cause unexpected intergenerational recurrences. Here, we show that somatic mosaicism for transmitted mutations among parents of children with simplex genetic disease is more common than currently appreciated. Using the sensitivity of individual-specific breakpoint PCR, we prospectively screened 100 families with children affected by genomic disorders due to rare deletion copy-number variants (CNVs) determined to be de novo by clinical analysis of parental DNA. Surprisingly, we identified four cases of low-level somatic mosaicism for the transmitted CNV in DNA isolated from parental blood. Integrated probabilistic modeling of gametogenesis developed in response to our observations predicts that mutations in parental blood increase recurrence risk substantially more than parental mutations confined to the germline. Moreover, despite the fact that maternally transmitted mutations are the minority of alleles, our model suggests that sexual dimorphisms in gametogenesis result in a greater proportion of somatically mosaic transmitting mothers who are thus at increased risk of recurrence. Therefore, somatic mosaicism together with sexual differences in gametogenesis might explain a considerable fraction of unexpected recurrences of X-linked recessive disease. Overall, our results underscore an important role for somatic mosaicism and mitotic replicative mutational mechanisms in transmission genetics.

Figure 1

Low-Level Combined Germline and Somatic Mosaicism Inferred from Familial Recurrence of SMS Family 1 was identified with three individuals suspected to have SMS and born to one mother but two different fathers. (A) aCGH analysis of genomic DNA from the mother, two affected half siblings, and one unaffected half sibling. No detectable copy-number change was seen in the mother. (B) LR-PCR analysis of genomic DNA from available family members. The familial deletion-specific amplicon segregated with the SMS phenotype in the children and was clearly visible from maternal peripheral-blood DNA. (C) Digital PCR analysis of affected, maternal, and unaffected blood samples revealed mutations in 25.1% of maternal nucleated blood cells.

Figure 2

Low-Level Somatic Mosaicism Prospectively Identified in Four Families (A) Microarray analysis of family 3 revealed an apparently de novo 250 kb deletion in chromosomal region 12p12.1. (B) Deletion-specific LR-PCR in family 3 identified the amplicon detected in the affected son’s peripheral-blood DNA also in the mother’s DNA. (C) Microarray analysis of family 4 revealed an apparently de novo 350 kb deletion in chromosomal region 6q13. (D) Deletion-specific LR-PCR in family 4 identified the amplicon detected in the affected son’s peripheral-blood DNA also in the mother’s DNA. (E) Microarray analysis of family 5 revealed an apparently de novo 100 kb deletion in chromosomal region 9q33.1. (F) Deletion-specific LR-PCR in family 5 identified the amplicon detected in the affected daughter’s peripheral-blood DNA also in the father’s DNA. (G) Microarray analysis of family 6 revealed an apparently de novo 608 kb deletion in chromosomal region 2q24.3. (H) Deletion-specific LR-PCR in family 6 identified the amplicon detected in the affected daughter’s peripheral-blood DNA also in the father’s DNA.

Figure 3

Human Germ Cell Development (A) Epiblast cells invaginate during the third week of embryogenesis to form the future endoderm and mesoderm. Some dorsal endoderm cells near the allantois become situated in the wall of the yolk sac and later differentiate into primordial germ cells (PGCs). During the fourth and fifth weeks of gestation, these PGCs migrate to the primitive gonads to become gametes. If a CNV were to occur in an epiblast cell before the third week, later divisions could contribute to both PGC and mesoderm lineages, including hematopoietic stem cells (HSCs). (B) Distribution of cell divisions during gametogenesis. (C) Probabilistic model of development. Both males and females experience a stochastic exponential cell-expansion phase modeling embryogenesis and germ cell proliferation. In males, expansion is followed by a stochastic but nonexpanding process of self-renewal modeling spermatogenesis. A single sperm and egg are then randomly sampled after meiosis to fertilize an offspring. Mutations can arise in any cell division, contributing to the gamete pool, and are ultimately available to be transmitted to the next generation. Mutations that occur during the exponential-expansion phase can divide to comprise a larger proportion of the germ cell pool. In contrast, mutations that occur during the self-renewal phase expand into fewer mutant sperm because of asymmetric cell division.