Natural and orthogonal model for estimating gene-gene interactions applied to cutaneous melanoma

Familial Melanoma and Susceptibility Genes: A Review of the Most Common Clinical and Dermoscopic Phenotypic Aspect, Associated Malignancies and Practical Tips for Management

A family history of melanoma greatly increases the risk of developing cutaneous melanoma, a highly aggressive skin cancer whose incidence has been steadily increasing worldwide. Familial melanomas account for about 10% of all malignant melanomas and display an inheritance pattern consistent with the presence of pathogenic germline mutations, among which those involving CDKN2A are the best characterized. In recent years, a growing number of genes, such as MC1R, MITF, CDK4, POT1, TERT, ACD, TERF2IP, and BAP1, have been implicated in familial melanoma. The fact that individuals harboring these germline mutations along with their close blood relatives have a higher risk of developing multiple primary melanomas as well as other internal organ malignancies, especially pancreatic cancer, makes cascade genetic testing and surveillance of these families of the utmost importance. Unfortunately, due to a polygenic inheritance mechanism involving multiple low-risk alleles, genetic modifiers, and environmental factors, it is still very difficult to predict the presence of these mutations. It is, however, known that germline mutation carriers can sometimes develop specific clinical traits, such as high atypical nevus counts and specific dermoscopic features, which could theoretically help clinicians predict the presence of these mutations in prone families. In this review, we provide a comprehensive overview of the high- and intermediate-penetrance genes primarily linked to familial melanoma, highlighting their most frequently associated non-cutaneous malignancies and clinical/dermoscopic phenotypes.

HERC Ubiquitin Ligases in Cancer

HERC proteins are ubiquitin E3 ligases of the HECT family. The HERC subfamily is composed of six members classified by size into large (HERC1 and HERC2) and small (HERC3-HERC6). HERC family ubiquitin ligases regulate important cellular processes, such as neurodevelopment, DNA damage response, cell proliferation, cell migration, and immune responses. Accumulating evidence also shows that this family plays critical roles in cancer. In this review, we provide an integrated view of the role of these ligases in cancer, highlighting their bivalent functions as either oncogenes or tumor suppressors, depending on the tumor type. We include a discussion of both the molecular mechanisms involved and the potential therapeutic strategies.

Joint modeling of eQTLs and parent-of-origin effects using an orthogonal framework with RNA-seq data

Extensive studies have been conducted on the analysis of genome function, especially on the expression quantitative trait loci (eQTL). These studies offered promising results for characterization of the functional sequencing variation and understanding of the basic processes of gene regulation. Parent of origin effect (POE) is an important epigenetic phenomenon describing that the expression of certain genes depends on their allelic parent-of-origin and it is known to play important roles in human complex diseases. However, traditional eQTL mapping approaches do not allow for the detection of imprinting, or they focus on modeling the additive genetic effect thereby ignoring the estimation of the dominance genetic effect. In this study, we proposed a statistical framework to test the additive and dominance genetic effects of the candidate eQTLs along with detection of the POE with a functional model and an orthogonal model for RNA-seq data. We demonstrated the desirable power and preserved Type I errors of the methods in most scenarios, especially the orthogonal model with un-biased estimation of the genetic effects and over-dispersion of the RNA-seq data. The application to a HapMap project trio dataset validated existing imprinting genes and discovered two novel imprinting genes with potential dominance genetic effect and RB1 and IGF1R genes. This study provides new insights into the next generation statistical modeling of eQTL mapping for better understanding of the genetic architecture underlying the mechanisms of gene expression regulation.

Orthogonal Decomposition of the Genetic Variance for Epistatic Traits Under Linkage Disequilibrium-Applications to the Analysis of Bateson-Dobzhansky-Müller Incompatibilities and Sign Epistasis

The one-century-old theory of orthogonal genetic variance decomposition originated the field of quantitative genetics and has kept on being improved ever since. Recently, serious concerns about the possibility of attaining a satisfactory implementation of genetic variance decomposition with linkage disequilibrium (LD) and epistasis have been raised. In this paper we dissipate such doubts by completing the classical theory of variance decomposition into additive, dominance and epistasis components with LD. We apply that theory to the analysis of the genotype-to-phenotype maps of two cases of particular evolutionary interest-Bateson-Dobzhansky-Müller incompatibilities and sign epistasis. For the first case we show how negative LD and reduction of heterozygotes may contribute to maintain genetic variability after secondary contact. For the second case we show that LD transforms the set of frequencies leading to an evolutionary plateau into a ridge. Our theoretical developments reassuringly reflect the complexity LD conveys to genetic systems throughout novel properties-as compared with systems under linkage equilibrium. We argue that such particularities might have actually contributed to cause confusion about the feasibility of developing this methodology. In any case, the theory we provide in this paper enables new perspectives in both evolutionary and quantitative genetics studies.

Melanoma genetics

Approximately 10% of melanoma cases report a relative affected with melanoma, and a positive family history is associated with an increased risk of developing melanoma. Although the majority of genetic alterations associated with melanoma development are somatic, the underlying presence of heritable melanoma risk genes is an important component of disease occurrence. Susceptibility for some families is due to mutation in one of the known high penetrance melanoma predisposition genes: CDKN2A, CDK4, BAP1, POT1, ACD, TERF2IP and TERT. However, despite such mutations being implicated in a combined total of approximately 50% of familial melanoma cases, the underlying genetic basis is unexplained for the remainder of high-density melanoma families. Aside from the possibility of extremely rare mutations in a few additional high penetrance genes yet to be discovered, this suggests a likely polygenic component to susceptibility, and a unique level of personal melanoma risk influenced by multiple low-risk alleles and genetic modifiers. In addition to conferring a risk of cutaneous melanoma, some 'melanoma' predisposition genes have been linked to other cancers, with cancer clustering observed in melanoma families at rates greater than expected by chance. The most extensively documented association is between CDKN2A germ line mutations and pancreatic cancer, and a cancer syndrome including cutaneous melanoma, uveal melanoma and mesothelioma has been proposed for BAP1 germ line mutations. Other medium to high penetrance melanoma predisposition genes have been associated with renal cell carcinoma (MITF, BAP1) and glioma (POT1). These associations between melanoma and other cancers hint at the possibility of common pathways for oncogenesis, and better knowledge of these pathways may improve understanding of the genetic basis underpinning familial melanoma. It is likely that 'melanoma' risk genes will impact on mutation screening and genetic counselling not only for melanoma but also a range of other cancers.