Germline mutations in candidate predisposition genes in individuals with cutaneous melanoma and at least two independent additional primary cancers

<div><p>Background</p><p>While a number of autosomal dominant and autosomal recessive cancer syndromes have an associated spectrum of cancers, the prevalence and variety of cancer predisposition mutations in patients with multiple primary cancers have not been extensively investigated. An understanding of the variants predisposing to more than one cancer type could improve patient care, including screening and genetic counselling, as well as advancing the understanding of tumour development.</p><p>Methods</p><p>A cohort of 57 patients ascertained due to their cutaneous melanoma (CM) diagnosis and with a history of two or more additional non-cutaneous independent primary cancer types were recruited for this study. Patient blood samples were assessed by whole exome or whole genome sequencing. We focussed on variants in 525 pre-selected genes, including 65 autosomal dominant and 31 autosomal recessive cancer predisposition genes, 116 genes involved in the DNA repair pathway, and 313 commonly somatically mutated in cancer. The same genes were analysed in exome sequence data from 1358 control individuals collected as part of non-cancer studies (UK10K). The identified variants were classified for pathogenicity using online databases, literature and <i>in silico</i> prediction tools.</p><p>Results</p><p>No known pathogenic autosomal dominant or previously described compound heterozygous mutations in autosomal recessive genes were observed in the multiple cancer cohort. Variants typically found somatically in haematological malignancies (in <i>JAK1</i>, <i>JAK2</i>, <i>SF3B1</i>, <i>SRSF2</i>, <i>TET2</i> and <i>TYK2</i>) were present in lymphocyte DNA of patients with multiple primary cancers, all of whom had a history of haematological malignancy and cutaneous melanoma, as well as colorectal cancer and/or prostate cancer. Other potentially pathogenic variants were discovered in <i>BUB1B</i>, <i>POLE2</i>, <i>ROS1</i> and <i>DNMT3A</i>. Compared to controls, multiple cancer cases had significantly more likely damaging mutations (nonsense, frameshift ins/del) in tumour suppressor and tyrosine kinase genes and higher overall burden of mutations in all cancer genes.</p><p>Conclusions</p><p>We identified several pathogenic variants that likely predispose to at least one of the tumours in patients with multiple cancers. We additionally present evidence that there may be a higher burden of variants of unknown significance in ‘cancer genes’ in patients with multiple cancer types. Further screens of this nature need to be carried out to build evidence to show if the cancers observed in these patients form part of a cancer spectrum associated with single germline variants in these genes, whether multiple layers of susceptibility exist (oligogenic or polygenic), or if the occurrence of multiple different cancers is due to random chance.</p></div

The cancer types and age at onset in the individuals with multiple independent primary cancers.

<p>A) Pie chart showing the frequency of cancer types in the total series of individuals with multiple independent primary cancer. All individuals were ascertained in Australia and were selected from those collected as part of the Q-MEGA project, a Queensland population-based study investigating the genetics of melanoma development; all individuals therefore presented with a history of cutaneous melanoma (CM) and are not represented in this figure. B) Age of onset for each of the cancers present in the multiple cancer patients. The dotted line at 60 years of age shows that the majority of cancers developed later in life. CRC: Colorectal cancer; UM: Uveal melanoma; SCC: Head and Neck Squamous Cell Carcinoma.</p

Cumulative percentage plots of variant burdens.

<p>The numbers of variants present at a frequency of <1:2000 in Kaviar in each of the gene classification lists (‘cancer’ genes and DNA repair genes) were calculated for each individual in the multiple cancer patients and the UK10K controls. The cumulative percentage of individuals with a given ‘burden’ of variants was then calculated and plotted for each cohort. A) The cumulative percentage plots of variant burden for all ‘cancer’ genes in the multiple cancer cases (blue) compared to the UK10K controls (red). B) The cumulative percentage plots of variant burden for DNA repair genes in the multiple cancer cases (blue) compared to the UK10K controls (red).</p

Case-control analysis on non-synonymous <i>PALB2</i> variants.

<p>Case-control analysis on non-synonymous <i>PALB2</i> variants.</p

Co-segregation analysis of <i>PALB2</i> variants in two high-risk CMM families.

<p>Individuals that have melanoma (MM) are represented by black circles (female) and black boxes (male). The age of diagnosis of each cancer is indicated in brackets. A line through a symbol indicates that the person is deceased. Individuals carrying a <i>PALB2</i> mutation are indicated by an ‘M’, while those wild-type for the variant are indicated by ‘WT’. Other cancer types are also indicated on the pedigree. Unaffected siblings are represented by a diamond with the number indicating the number of siblings. The arrow indicates the proband in each family.</p

<i>PALB2</i> variants detected through Sanger sequencing and exome sequencing.

<p>*European American population.</p><p>na is not available.</p