Mitotic recombination of chromosome arm 17q as a cause of loss of heterozygosity of NF1 in neurofibromatosis type 1-associated glomus tumors

Abstract

Neurofibromatosis type 1 (NF1) is a common, autosomal dominant, tumor-predisposition syndrome that arises secondary to mutations in NF1. Glomus tumors are painful benign tumors that originate from the glomus body in the fingers and toes due to biallelic inactivation of NF1. We karyotyped cultures from four previously reported and one new glomus tumor and hybridized tumor (and matching germline) DNA on Illumina HumanOmni1-Quad SNP arrays (≈ 1 × 10(6) SNPs). Two tumors displayed evidence of copy-neutral loss of heterozygosity of chromosome arm 17q not observed in the germline sample, consistent with a mitotic recombination event. One of these two tumors, NF1-G12, featured extreme polyploidy (near-tetraploidy, near-hexaploidy, or near-septaploidy) across all chromosomes. In the remaining four tumors, there were few cytogenetic abnormalities observed, and copy-number analysis was consistent with diploidy in all chromosomes. This is the first study of glomus tumors cytogenetics, to our knowledge, and the first to report biallelic inactivation of NF1 secondary to mitotic recombination of chromosome arm 17q in multiple NF1-associated glomus tumors. We have observed mitotic recombination in 22% of molecularly characterized NF1-associated glomus tumors, suggesting that it is a not uncommon mechanism in the reduction to homozygosity of the NF1 germline mutation in these tumors. In tumor NF1-G12, we hypothesize that mitotic recombination also "unmasked" (reduced to homozygosity) a hypomorphic germline allele in a gene on chromosome arm 17q associated with chromosomal instability, resulting in the extreme polyploidy.

Figure 1

Evidence of mitotic recombination in glomus tumors NF1-G12 and NF1-G13. A. B-allele frequency and Log R ratio plots of SNP array data of chromosome 17 (only) showing copy-neutral loss of heterozygosity of chromosome arm 17q likely secondary to mitotic recombination (NF1-G12 shown; NF1-G13 similar). B. ASCAT profile of copy-number across all chromosomes in tumor NF1-G12. X-axis = chromosome number; Y-axis = copy-number. Purple = total copy-number; Blue = copy-number of the minor allele. Note the copy-number of the minor allele for chromosome arm 17q is zero, consistent with mitotic recombination.

Figure 2

Karyotype (124, XX) of cell 612-11 from tumor NF1-G12 (see Supplementary Table 1).

Figure 3

Clustering analysis of karyotyped metaphases in culture of glomus tumor G12. Names of individual metaphases are shown on the bottom; total number of chromosomes is shown in parenthesis. Correlation distance is shown on the left.