Targeted germline sequencing of patients with three or more primary melanomas reveals high rate of pathogenic variants

Prior information-assisted integrative analysis of multiple datasets

MOTIVATION

Analyzing genetic data to identify markers and construct predictive models is of great interest in biomedical research. However, limited by cost and sample availability, genetic studies often suffer from the "small sample size, high dimensionality" problem. To tackle this problem, an integrative analysis that collectively analyzes multiple datasets with compatible designs is often conducted. For regularizing estimation and selecting relevant variables, penalization and other regularization techniques are routinely adopted. "Blindly" searching over a vast number of variables may not be efficient.

RESULTS

We propose incorporating prior information to assist integrative analysis of multiple genetic datasets. To obtain accurate prior information, we adopt a convolutional neural network with an active learning strategy to label textual information from previous studies. Then the extracted prior information is incorporated using a group LASSO-based technique. We conducted a series of simulation studies that demonstrated the satisfactory performance of the proposed method. Finally, data on skin cutaneous melanoma are analyzed to establish practical utility.

AVAILABILITY AND IMPLEMENTATION

Code is available at https://github.com/ldz7/PAIA. The data that support the findings in this article are openly available in TCGA (The Cancer Genome Atlas) at https://portal.gdc.cancer.gov/.

CDKN2A genetic testing in melanoma-prone families in Sweden in the years 2015-2020: implications for novel national recommendations

Background: Inherited pathogenic variants (PVs) in the CDKN2A gene are among the strongest known risk factors for cutaneous melanoma. Carriers are at high risks to develop multiple primary melanomas and other cancers, in particular pancreatic cancer. In this study, the CDKN2A testing, carried out in Sweden in the years 2015-2020, was evaluated.Materials and methods: Included families had (1) three or more cases of melanoma and/or pancreatic cancer, (2) two melanomas in first-degree relatives, the youngest case <55 years or (3) individuals with three or more multiple primary melanomas, the first before the age of 55 years, and no other affected family members. The included families had at least one affected member that had been tested for CDKN2A PVs.Results: In total, 403 families were included, whereof 913 family members had been diagnosed with cutaneous melanoma and 129 with pancreatic cancer, 33 (8.2%) were found to have PVs in CDKN2A. Frequencies ranged from 0.9% in families with only two melanomas to 43.2% in families with three or more melanoma cases and pancreatic cancer (p < 0.001). The frequency of PVs ranged from 2.1% to 16.5% in families where the youngest case was ≥55 years or <35 years (p = 0.040). In families with or without CDKN2A PVs, 37.6% and 10.0% had melanoma cases that had died from melanoma, respectively (p < 0.001).Discussion: Significant differences were seen in the frequencies of CDKN2A PVs, dependent on numbers or age at diagnosis of melanomas and diagnoses of pancreatic cancers in the family. Further, melanoma cases belonging to families that tested positive for CDKN2A PVs had a significantly higher mortality. To summarize, the current evaluation shows that, with adequately selected criteria to guide genetic testing, CDKN2A PVs are identified at significant frequencies. Identification of carrier families is of importance to ensure that members are enrolled in a preventive surveillance program.

3'UTR-CDKN2A and CDK4 Germline Variants Are Associated With Susceptibility to Cutaneous Melanoma

BACKGROUND/AIM

Genetic variations of the CDKN2A and CDK4 gene have been associated to melanoma development. In the present study we investigated the potential associations of CDKN2A and CDK4 gene variants in a colombian population diagnosed with melanoma.

MATERIALS AND METHODS

DNA was extracted from whole blood samples from 85 patients diagnosed with cutaneous melanoma and 166 healthy controls. CDKN2A and CDK4 genes were genotyped using a high-resolution melting assay.

RESULTS

A similar distribution of CDKN2A variants 500C>G and 540C>T was found among cases (12% and 31% respectively) and controls (15% and 31% respectively). The CDKN2A variants were present in 36% of acral lentiginous melanoma and 39.47% of lentigo maligna. The haplotype analysis showed an association with susceptibility in the development of melanoma.

CONCLUSION

The presence of haplotype 500G/540C in males is associated with an increased risk of melanoma in a colombian population, especially in subjects with a family history of cancer.

Multiple Primary Melanoma Incidence Trends Over Five Decades: A Nationwide Population-Based Study

BACKGROUND

Over the past decades, many regions have experienced a steady increase in the incidence of cutaneous melanoma. Here, we report on incidence trends for subsequent primary melanoma.

METHODS

In this nationwide population-based study, patients diagnosed with a first primary cutaneous melanoma reported to the Swedish Cancer Registry were followed for up to 10 years for a diagnosis of subsequent primary melanoma. Patients were grouped with patients diagnosed with first melanoma in the same decade (1960s, 1970s, 1980s, 1990s, and 2000s, respectively). Frequencies, incidence rates (IRs), standardized incidence ratios (SIRs), and 95% confidence intervals (CIs) for second melanomas were calculated. All tests of statistical significance were 2-sided.

RESULTS

Of patients with melanoma, 54 884 were included and 2469 were diagnosed, within 10 years, with subsequent melanomas. Over the 5 decades, there was a statistically significant steady increase in the frequency, IR, and SIR for second primary melanoma. For example, in the 1960s cohort, less than 1% (IR = 1.0, 95% CI = 0.5 to 1.7, and IR = 1.1, 95% CI = 0.5 to 1.9 per 1000 person-years in women and men, respectively) had second primary melanoma, and this rose to 6.4% (IR = 7.5, 95% CI = 6.8 to 8.3, per 1000 person-years) in the women and 7.9% (IR = 10.3, 95% CI = 9.3 to 11.2, per 1000 person-years) in the men in the 2000s cohort. This rise was seen independent of age, sex, invasiveness, or site of the melanoma. Further, in patients diagnosed with a second melanoma, the frequency of those having more than 2 melanomas increased statistically significantly and was 0.0% in the 1960s and rose to 18.0% in the 2000s (P < .001).

CONCLUSIONS

This is the first study to evaluate and report on a rising trend for subsequent primary melanoma. Additional primary melanomas worsen the patients' survival, and precautions are needed to turn this steep upgoing trend.

Skin cancer risk in CHEK2 mutation carriers

CHEK2 mutations have been linked with an increased risk of breast cancer. A unique challenge for oncodermatologists and oncologists is in the monitoring and counselling of patients regarding skin cancer risk due to CHEK2 mutation carrier status. In this review, we highlight current information in the literature on the risk of melanoma and non-melanoma skin cancers in CHEK2 mutation carriers. On the molecular level, CHEK2 is a cell cycle regulator that has been linked to cancer pathogenesis, though evidence from clinical studies regarding skin cancer risk has been inconsistent and conflicting. For melanoma, one study has demonstrated a statistically significant twofold risk of melanoma in individuals with CHEK2 mutations, particularly the CHEK2*1100delC variant. Five other studies did not show an association. For non-melanoma skin cancer, fewer data exist, with one prevalence study of CHEK2 mutations in a cohort of patients with basal cell carcinomas. Although there are currently no known studies of CHEK2 and cutaneous squamous cell carcinoma (SCC), data from other disciplines associating CHEK2 with head and neck SCCs are emerging. Overall, while there is currently not enough evidence to make conclusive statements regarding increased risk of melanoma and non-melanoma skin cancers in CHEK2 carriers, a molecular mechanism associating the mutation with cutaneous malignancy pathogenesis is evident, and further work is needed. Patient with CHEK2 mutations may benefit from screening dermatologic examinations with particular attention to skin cancers.