Whole-exome sequencing of breast cancer, malignant peripheral nerve sheath tumor and neurofibroma from a patient with neurofibromatosis type 1

Abstract

Neurofibromatosis type 1 (NF1) is a genetic disorder characterized by the development of multiple neurofibromas, cafe-au-lait spots, and Lisch nodules. Individuals with NF1 are at increased risk of developing various tumors, such as malignant peripheral nerve sheath tumor (MPNST), pheochromocytoma, leukemia, glioma, rhabdomyosarcoma, and breast cancer. Here, we describe the exome sequencing of breast cancer, MPNST, and neurofibroma from a patient with NF1. We identified a germline mutation in the NF1 gene which resulted in conversion of leucine to proline at amino acid position 847. In addition, we showed independent somatic NF1 mutations in all the three tumors (frameshift insertion in breast cancer (p.A985fs), missense mutation in MPNST (p.G23R), and inframe deletion in dermal neurofibroma (p.L1876del-Inf)), indicating that a second hit in NF1 resulting in the loss of function could be important for tumor formation. Each tumor had a distinct genomic profile with mutually exclusive mutations in different genes. Copy number analysis revealed multiple copy number alterations in the breast cancer and the MPNST, but not the benign neurofibroma. Germline loss of chromosome 6q22.33, which harbors two potential tumor suppressor genes, PTPRK and LAMA2, was also identified; this may increase tumor predisposition further. In the background of NF1 syndrome, although second-hit NF1 mutation is critical in tumorigenesis, different additional mutations are required to drive the formation of different tumors.

Keywords: Breast cancer; neurofibromatosis type 1.

Figure 1

Somatic mutations in the three sequenced tumors.

Figure 2

Analysis of copy number alterations in breast cancer (A), malignant peripheral nerve sheath tumor (MPNST) (B) and dermal neurofibroma (C), based on paired tumor and nontumor DNA analysis of exome sequencing data. Each red dot represents a genomic coordinate that was heterozygous in the germline sample. The breast cancer shows the most chromosomal rearrangements while the dermal neurofibroma shows none. Regions of allelic imbalance that also show a decrease in Log R typically represent Loss‐of‐heterozygosity (LOH); regions of allelic imbalance with no change in Log R show Copy‐Number Neutral LOH, and regions of allelic imbalance that correspond with increased Log R correspond to either focal amplifications (for example, several loci in chromosome 2 of the breast cancer) or large‐scale amplifications. The changes in Log R and allele frequency observed across multiple chromosomes in breast cancer and MPNST indicate allelic imbalance or copy number alterations in these samples, but not in the dermal neurofibroma.

Figure 3

Cytoscan HD SNP Array analysis reveals a germline Loss‐of‐heterozygosity event of around 3.3 Mbases at chr6q22.33 (indicated by dotted line) which harbor PTPRK and LAMA2, in blood, breast cancer, and dermal neurofibroma.