The BRCA1 c.4096+1G>A Is a Founder Variant Which Originated in Ancient Times

Abstract

Approximately 30-50% of hereditary breast and ovarian cancer (HBOC) is due to the presence of germline pathogenic variants in the BRCA1 (OMIM 113705) and BRCA2 (OMIM 600185) onco-suppressor genes, which are involved in DNA damage response. Women who carry pathogenic BRCA1 variants are particularly likely to develop breast cancer (BC) and ovarian cancer (OC), with a 45-79 percent and 39-48 percent chance, respectively. The BRCA1 c.4096+1G>A variant has been frequently ascertained in Tuscany, Italy, and it has also been detected in other Italian regions and other countries. Its pathogenetic status has been repeatedly changed from a variant of uncertain significance, to pathogenic, to likely pathogenic. In our study, 48 subjects (38 of whom are carriers) from 27 families were genotyped with the Illumina OncoArray Infinium platform (533,531 SNPs); a 20 Mb region (24.6 cM) around BRCA1, including 4130 SNPs (21 inside BRCA1) was selected for haplotype analysis. We used a phylogenetic method to estimate the time to the most recent common ancestor (MRCA) of BRCA1 c.4096+1G>A founder pathogenic variant. This analysis suggests that the MRCA lived about 155 generations ago-around 3000 years ago.

Keywords: BRCA1; Italy; founder variant; hereditary breast and ovarian cancer; pathogenic variant.

Figure 1

Small snippet of the spreadsheet used to determine the length of the carrier haplotype shared by pairs of individuals. The analyzed segment is delimited by markers chr17_39890876_C_T (position 39,890,876, left) and rs12948043 (position 41,615,830, right), thus encompassing 1.7 Mb or 1.2 cM. The implemented algorithm requires four lines for each subject to decode the two strings of 0 and 1 provided by the phasing software into the original DNA bases. Here, the reference subject is P019 (bottom), whose two inferred haplotypes are highlighted in yellow (carrier) and green (non-carrier). The yellow lines of the tested subjects (here P0111, P0112, P0113, and P114) highlight their carrier haplotype shared with P019. The blue positions, left blank by the algorithm, indicate markers where test and reference subjects are homozygous for alternative alleles; these represent “hard stops”; i.e., markers where any shared haplotype is necessarily broken off. Red dots mark suspicious typings (which are practically irrelevant here). In subject P012, the phasing software proposes what is to be interpreted as a spurious double recombinant. Eliminating these unreliable “soft” breaks leads to a more conservative estimate of the time to the MRCA.

Figure 2

Symmetric square matrix of the estimated number of generations separating each pair of individuals from their MRCA carrying the c.4096+1G>A variant. Blue: minimum value (the common ancestor of P0126 and P0112b lived 6/7 generations ago). Green: maximum value (about 300 generations from the common ancestor of 019 and P015). The randomness of the recombination process that shortens the haplotype shared by multiple individuals descending from the same MRCA in different ways is taken into account by the tree-building algorithm.

Figure 3

Extended genealogical tree for 27 independently families carrying the BRCA1 c.4096+1G>A variant. It has been obtained using the UPGMA clustering method through DendroUPGMA online software. The numbers on each branches indicate the number of generations.

Figure 4

The timeline shows the temporal distance separating today’s variant carriers of c.4096+1G>A from their ancestor, who lived approximately 3000 years ago, around 155 generations back.