Combined Genetic and Genealogic Studies Uncover a Large BAP1 Cancer Syndrome Kindred Tracing Back Nine Generations to a Common Ancestor from the 1700s

<div><p>We recently discovered an inherited cancer syndrome caused by BRCA1-Associated Protein 1 (<i>BAP1</i>) germline mutations, with high incidence of mesothelioma, uveal melanoma and other cancers and very high penetrance by age 55. To identify families with the BAP1 cancer syndrome, we screened patients with family histories of multiple mesotheliomas and melanomas and/or multiple cancers. We identified four families that shared an identical <i>BAP1</i> mutation: they lived across the US and did not appear to be related. By combining family histories, molecular genetics, and genealogical approaches, we uncovered a BAP1 cancer syndrome kindred of ~80,000 descendants with a core of 106 individuals, whose members descend from a couple born in Germany in the early 1700s who immigrated to North America. Their descendants spread throughout the country with mutation carriers affected by multiple malignancies. Our data show that, once a proband is identified, extended analyses of these kindreds, using genomic and genealogical studies to identify the most recent common ancestor, allow investigators to uncover additional branches of the family that may carry <i>BAP1</i> mutations. Using this knowledge, we have identified new branches of this family carrying BAP1 mutations. We have also implemented early-detection strategies that help identify cancers at early-stage, when they can be cured (melanomas) or are more susceptible to therapy (MM and other malignancies).</p></div

BAP1 cytoplasmic staining and LOH in MM biopsies.

<p><b>(A)</b> Representative histology (Hematoxylin and Eosin staining) and BAP1 IHC. Controls: Panel a, normal strip of pleural mesothelial cells; d, MM biopsy containing wild-type BAP1. Note BAP1 nuclear staining and faint cytoplasmic staining; black arrows identify representative normal mesothelial cells in a and MM cells in d. Panels b, c, e and f, BAP1-mutant MM biopsies from MARF11-III-1 (b,e) and MARF18-III-1 (c,f). Note cytoplasmic BAP1 staining and absence of nuclear staining in MM cells; black arrows identify representative tumor cells indicating LOH for BAP1. Note that nearby infiltrating “normal” lymphocytes and endothelial cells show nuclear BAP1 staining (red arrows) as they retain one normal BAP1 allele. Original magnification, 400X. <b>(B)</b><i>BAP1</i> sequencing of germline and tumor DNAs from MARF11-III-1 and MARF18-III-1 reveals heterozygosity in germline DNA and LOH in tumor cell DNA. Top panels, germline DNA from both patients shows a ‘C’ deletion (grey shadowed area): the wild-type allele and the mutant allele show the same peak intensity indicating a heterozygous mutation. Bottom Panels, tumor cell DNA, from both patients, shows a homozygous C deletion. The electropherogram of tumor cell DNA shows that the allele with the C deletion has a higher peak, indicating that only the mutant allele is present in the tumor cells. The lower peak is likely generated by the wild type allele of some contaminating normal cells. DNA sequence of wild-type—AGTCCCCTGGC; DNA sequence of mutant—AGTCCCTGGCG.</p

Electropherogram of BAP1 c.1717_1717delC mutation and chromosome 3 IBD shared haplotypes in the 4 founder MARF patients studied.

<p><b>(A)</b> Representative electropherogram of germline <i>BAP1</i> MARF2-IV-2 founder mutation. The heterozygous C deletion at nucleotide position c.1717 of the <i>BAP1</i> gene is predicted to be a frame-shift mutation leading to a truncated protein of 573 amino acids in length. Nucleotide sequence is shown above the electropherogram and predicted amino acid changes are below. <b>(B)</b> Idiogram showing Identity By Descent (IBD) shared haplotypes of the DNA regions surrounding <i>BAP1</i> in the germline DNA of the 4 founder MARF patients studied. The p-arm of chromosome 3 depicts the position and extent of shared IBD haplotype segments (LOD>3) that overlap the <i>BAP1</i> gene. Red line: MARF11-III-1 + MARF40-III-1 (chr3:21.8–55.9, 34.2 Mbp, LOD = 176.6); green line: MARF2-IV-2 + MARF40-III-1 (chr3:25.55–55.12, 29.6 Mbp, LOD = 145.2); blue line: MARF2-IV-2 + MARF11-III-1 (chr3:25.55–55.12, 29.6 Mbp, LOD = 142.1); gray line: MARF2-IV-2 + MARF18-III-1 (chr3:45.40–54.5, 9.1 Mbp, LOD = 38.8); orange line: MARF18-III-1 + MARF40-III-1 (chr3:45.40–54.5, 9.1 Mbp, LOD = 38.1); purple line: MARF11-III-1 + MARF18-III-1 (chr3:45.40–54.5, 9.1 Mbp, LOD = 37.1). Gray oval represents the centromere.</p

Core of the 106-member nine-generation pedigree, K4.

<p>Numbers above symbols represent year of birth; dates of death are not shown to maintain confidentiality. The founding couple was born in Germany in 1710 and 1712, respectively. We were able to trace the origin of the founder male to a Swiss couple, born in 1588 and in 1591, respectively. De-identified patient IDs are shown below the symbols (e.g.11-III-4). Slashed symbols represent deceased individuals. Obligate carriers are indicated with red symbols. All individuals who were tested for presence of germline <i>BAP1</i> mutations are indicated with a star: green stars indicate <i>BAP1</i> wild type status; red stars indicate <i>BAP1</i> mutant carriers. When available, types of malignancies are listed below symbols and ages of diagnoses are indicated in parentheses. Red arrows indicate the probands; blue symbols indicate individuals that we identified through our genealogy search and found to be affected with MM and/or other BAP1 associated malignancies; orange symbols indicate newly identified family branches, that we are actively recruiting into our study, with currently unknown medical history or <i>BAP1</i> status. MM, mesothelioma; UM, uveal melanoma; BCC, basal cell carcinoma; RCC, renal cell carcinoma; CM, cutaneous melanoma; SCC, squamous cell carcinoma; all other cancer types are indicated by their full name or anatomical location; “unknown”, the cause of death was cancer, but the histological type was not identified. “other cancers”, malignancies possibly associated with <i>BAP1</i> mutations.</p