Genetic genealogy uncovers a founder deletion mutation in the cerebral cavernous malformations 2 gene

Abstract

Cerebral cavernous malformations (CCM) are vascular malformations consisting of collections of enlarged capillaries occurring in the brain or spinal cord. These vascular malformations can occur sporadically or susceptibility to develop these can be inherited as an autosomal dominant trait due to mutation in one of three genes. Over a decade ago, we described a 77.6 Kb germline deletion spanning exons 2-10 in the CCM2 gene found in multiple affected individuals from seemingly unrelated families. Segregation analysis using linked, microsatellite markers indicated that this deletion may have arisen at least twice independently. In the ensuing decades, many more CCM patients have been identified with this deletion. In this present study we examined 27 reportedly unrelated affected individuals with this deletion. To investigate the origin of the deletion at base pair level resolution, we sequenced approximately 10 Kb upstream and downstream from the recombination junction on the deleted allele. All patients showed the identical SNP haplotype across this combined 20 Kb interval. In parallel, genealogical records have traced 11 of these individuals to five separate pedigrees dating as far back as the 1600-1700s. These haplotype and genealogical data suggest that these families and the remaining "unrelated" samples converge on a common ancestor due to a founder mutation occurring centuries ago on the North American continent. We also note that another gene, NACAD, is included in this deletion. Although patient self-reporting does not indicate an apparent phenotypic consequence for heterozygous deletion of NACAD, further investigation is warranted for these patients.

Fig. 1

Schematic diagram of the CCM2 exons 2-10 deletion. The 77.6 Kb deletion begins in an AluSx site in intron 1 of CCM2 (orange bar) and extends to an AluSg site in the intergenic region between NACAD and TBRG4 (yellow bar). The red arrows represent the primers used to test for the deletion in the samples [16]. The green and purple arrows represent amplification primers for sequencing. Due to the size of the deletion, only the affected allele will amplify in these reactions

Fig. 2

SNPs evaluated approximately 10 Kb upstream and downstream of the AluSx/AluSg recombination junction. The disease haplotype is noted above the SNP names. The base pair location on Chromosome 7 is indicated under the line (Hg38) and the small marks indicate 1 Kb increments

Fig. 3

Family pedigrees. The trimmed pedigrees of the families represented in the sequencing cohort. The five larger families are noted with the founders’ birth centuries and locations. The individuals included in this study are indicated by numbers below the dark symbols. The dark blue represents a clinical diagnosis of CCM, the light blue represents inferred CCM, and the dot represents a positive deletion test. Individuals from the original cohort [16] are marked with an asterisk*. Note that two of these are now connected through genealogical records in Family R/H. The smaller families are trimmed to show first degree relatives with a positive MRI for CCM. The additional 11 patients sequenced were individuals not known to be connected to any of these families nor to each other

Fig. 4

Migration map of the five large CCM2 deletion families. The birth locations of members of the five large families beginning with the proposed founders and ending with the samples included in the sequencing cohort. The colors represent the half-centuries of the birth years of the family members shown in the trimmed pedigrees in Fig. 3