Final Report Summary - GENOMEL (Genetic and environmental determinants of melanoma: translation into behavioural change)
The ultimate aim of the GENOMEL project was to investigate the genetic and environmental risk factors for melanoma. For this purpose it sought to develop and support collaborations between member groups to:
- identify melanoma susceptibility genes;
- assess the risk of melanoma and other cancers related to variations in these genes;
- assess the risk of melanoma and other cancers related to variations in these genes
GENOMEL activities are grouped into four platforms:
Platform 1: Developing shared resources and activities to increase efficiency and improve the quality of control data
Review bodies: GENOMEL created an appropriate management structure incorporating external review bodies and a successful website. Originally three bodies were planned, namely a patient advocacy board, a project ethics committee and a Scientific advisory board (SAB). It was quickly decided that the ethics committee and patient advocacy board had overlapping functions and were merged into the Joint advisory group (JAG).
The website: a website for the project was developed in which there is a members' section that acts as a secure depository for minutes and presentations. It has over 200 presentations and other files for members to refer to. The public section of the website provides information and resources for research participants, melanoma patients, clinicians, researchers and the public.
Annual meetings: a series of annual meetings were held to discuss progress and develop future projects. All of these meetings provided GENOMELs younger researchers with the opportunity to present their work. This worked in combination with the project's exchange opportunities, namely the annual meeting providing an opportunity to network with potential research hosts, as well as a forum for the dissemination of their results.
Shared biological resources - somatic samples: shared resources in terms of pooled biological samples were developed. Somatic samples from 135 familial primary melanomas and 52 matched primary sporadic melanomas from the GENOMEL centres were gathered.
Shared biological resources - germline samples: in addition to somatic samples, GENOMEL gathered germline DNA samples from thousands of research participants and sent them to Leiden. These samples were used in the Genome wide association studies (GWAS) and in a project examining the effect of additional inherited genes (modifier genes) on melanoma risk in families genetically predisposed to melanoma. There were considerable quantities of residual samples and the GENOMEL analysis team (GAT) was considering their use in future collaborative projects.
Joint training and new questionnaires: specific training meetings in Genoa in 2005 and in Slovenia in 2006 were held in order to familiarise the project's group with its database, as well as engage them with GENOMELs study protocols and questionnaires.
The GENOMEL exchange activities
Project management
Platform 2: Identifying new susceptibility genes and understanding their role in tumours
The GENOMEL GWAS: The genome-wide screen identified five regions with genotyped or imputed Single nucleotide polymorphisms (SNPs) reaching p < 5x10-7. Three regions were replicated in this study: 16q24 encompassing MC1R, 11q14-q21 encompassing TYR, and 9p21 adjacent to MTAP and flanking CDKN2A and CDKN2B. MC1R and Tyrosine (TYR) were associated with pigmentation and cutaneous sun sensitivity, well-recognised melanoma risk factors, while the 9p21 locus is novel for common variation underlying susceptibility to melanoma. Subsequently, additional analyses showing that the chromosome 16 finding is due entirely to genetic variants in MC1R were conducted. It was also shown that the chromosome 11 effect is entirely due to variants in the pigment gene, TYR. Thus, this work confirmed the role of common inherited pigmented genes in melanoma susceptibility and the possibility of a new gene on chromosome 9.
The second stage of the GENOMEL GWAS study involved a further case-control analysis of 1200 cases and 1200 controls, with the results being merged to produce a combined genome-wide study. Additional GENOMEL funds also supported genotyping on a further sample set. This genotyping focused on regions identified in the course of this study as containing susceptibility loci. 800 cases and 800 controls were genotyped with the customised 220k Illumina SNP array to identify with more precision the critical SNP variants in the CDKN2A/MTAP region and around TERT. Phase two of this work identified entirely new melanoma susceptibility genes such as CASP8 whose role in melanoma carcinogenesis were explored.
Studying somatic mutations: GENOMELs extensive GWAS projects examined susceptibility and inherited genes. They involved DNA samples extracted from blood or cheek cells. However, GENOMEL conducted a research into the changes in the tissue that cause particular melanomas to develop, and to inherited genetic variation. These studies involved samples of genetic material taken from actual tumours. Primary melanoma tumours are very small and working with such small quantities is technically challenging. GENOMEL was a pioneer in this area and produced reliable results using techniques, such as coring of paraffin embedded tumours, microdissection and DASL arrays.
Somatic mutations in CDKN2A gene carriers: It is well known that particular alterations of the CDKN2A gene can increase susceptibility to melanoma. GENOMELs online database was used to identify samples for a collaborative study on tumours from carriers and non-carriers of these mutations. The groups gathered almost 200 tumour samples together and examined if there were different, additional mutations in the actual tumours between carriers and non-carriers, and between familial melanoma and sporadic melanoma. The researchers looked for mutations in genes that code for particular proteins, the BRAF and NRAS genes. There was no significant difference in the frequency of BRAF mutations between familial melanomas with CDKN2A mutations and those without CDKN2A mutations. Similarly, the frequency of NRAS mutations did not differ when tumours from patients with and without CDKN2A mutations were compared. In no case were BRAF and NRAS mutations found to co-exist in the same tumour. In conclusion, a comprehensive investigation of somatic genomic events in CDKN2A mutated melanomas was performed.
Platform 3: Investigation of genotype / phenotype interaction, gene / gene interaction and gene / environment interaction for known susceptibility genes
The GENOMEL Pennsylvania (PENN) database: A new, online database at the University of Pennsylvania was created. This resource builds on an existing consortium database, but grants groups online access to their own data and enables the database manager to generate reports and resolve queries. The database held at that time information on 16 251 individuals with over 5000 melanoma patients. Information is available from 3828 questionnaire modules on family history and 2830 questionnaires on sun exposure. The database also contains information about cancers other than melanoma, CDKN2A / CDK4 mutation status and nevus phenotype information.
Screening for modifier genes: Mutations in the CDK4 and CDKN2A genes are known to increase susceptibility. GENOMEL used SNP arrays to screen other genes that could modify the effect of these mutations. Study was performed into the effect on the penetrance of these mutations, the risk of other cancers and the influence on a person's nevus phenotype. The research suggested a role for genes involved in pigmentation and nevus susceptibility and a set of 30 SNPs covering the known pigmentation variation and the nevus count variation was identified.
Platform 4: Attitudes to risk of melanoma and behavioural modification
The consortium's genetic and epidemiological research was extended and was combined with information technology and health psychology expertise. This enabled the project to undertake an ambitious programme of online research and dissemination. It was GENOMELs hypothesis that health education was designed to prevent melanoma will be more effective if directed towards those at increased risk. This hypothesis was tested by questionnaire studies in families and in general European populations by correlating estimation of self-risk with reported behaviour. The literature would then be surveyed in order to design a computer-based tool to be used by family members and the general population to estimate risk and this tool will be evaluated. Finally, this risk estimation tool would be linked to a multi-media package mounted on the GENOMEL website in which appropriate sun protection strategies and early detection strategies are linked to the estimation of risk.
A major output of the project was a series of Content management systems (CMSs). Two of these were placed on the patient information page and were specifically aimed at melanoma patients with a diagnosis of melanoma. A major component of these packages was the interviews held with actual patients who talked about their experiences and how they managed to deal with melanoma.
- identify melanoma susceptibility genes;
- assess the risk of melanoma and other cancers related to variations in these genes;
- assess the risk of melanoma and other cancers related to variations in these genes
GENOMEL activities are grouped into four platforms:
Platform 1: Developing shared resources and activities to increase efficiency and improve the quality of control data
Review bodies: GENOMEL created an appropriate management structure incorporating external review bodies and a successful website. Originally three bodies were planned, namely a patient advocacy board, a project ethics committee and a Scientific advisory board (SAB). It was quickly decided that the ethics committee and patient advocacy board had overlapping functions and were merged into the Joint advisory group (JAG).
The website: a website for the project was developed in which there is a members' section that acts as a secure depository for minutes and presentations. It has over 200 presentations and other files for members to refer to. The public section of the website provides information and resources for research participants, melanoma patients, clinicians, researchers and the public.
Annual meetings: a series of annual meetings were held to discuss progress and develop future projects. All of these meetings provided GENOMELs younger researchers with the opportunity to present their work. This worked in combination with the project's exchange opportunities, namely the annual meeting providing an opportunity to network with potential research hosts, as well as a forum for the dissemination of their results.
Shared biological resources - somatic samples: shared resources in terms of pooled biological samples were developed. Somatic samples from 135 familial primary melanomas and 52 matched primary sporadic melanomas from the GENOMEL centres were gathered.
Shared biological resources - germline samples: in addition to somatic samples, GENOMEL gathered germline DNA samples from thousands of research participants and sent them to Leiden. These samples were used in the Genome wide association studies (GWAS) and in a project examining the effect of additional inherited genes (modifier genes) on melanoma risk in families genetically predisposed to melanoma. There were considerable quantities of residual samples and the GENOMEL analysis team (GAT) was considering their use in future collaborative projects.
Joint training and new questionnaires: specific training meetings in Genoa in 2005 and in Slovenia in 2006 were held in order to familiarise the project's group with its database, as well as engage them with GENOMELs study protocols and questionnaires.
The GENOMEL exchange activities
Project management
Platform 2: Identifying new susceptibility genes and understanding their role in tumours
The GENOMEL GWAS: The genome-wide screen identified five regions with genotyped or imputed Single nucleotide polymorphisms (SNPs) reaching p < 5x10-7. Three regions were replicated in this study: 16q24 encompassing MC1R, 11q14-q21 encompassing TYR, and 9p21 adjacent to MTAP and flanking CDKN2A and CDKN2B. MC1R and Tyrosine (TYR) were associated with pigmentation and cutaneous sun sensitivity, well-recognised melanoma risk factors, while the 9p21 locus is novel for common variation underlying susceptibility to melanoma. Subsequently, additional analyses showing that the chromosome 16 finding is due entirely to genetic variants in MC1R were conducted. It was also shown that the chromosome 11 effect is entirely due to variants in the pigment gene, TYR. Thus, this work confirmed the role of common inherited pigmented genes in melanoma susceptibility and the possibility of a new gene on chromosome 9.
The second stage of the GENOMEL GWAS study involved a further case-control analysis of 1200 cases and 1200 controls, with the results being merged to produce a combined genome-wide study. Additional GENOMEL funds also supported genotyping on a further sample set. This genotyping focused on regions identified in the course of this study as containing susceptibility loci. 800 cases and 800 controls were genotyped with the customised 220k Illumina SNP array to identify with more precision the critical SNP variants in the CDKN2A/MTAP region and around TERT. Phase two of this work identified entirely new melanoma susceptibility genes such as CASP8 whose role in melanoma carcinogenesis were explored.
Studying somatic mutations: GENOMELs extensive GWAS projects examined susceptibility and inherited genes. They involved DNA samples extracted from blood or cheek cells. However, GENOMEL conducted a research into the changes in the tissue that cause particular melanomas to develop, and to inherited genetic variation. These studies involved samples of genetic material taken from actual tumours. Primary melanoma tumours are very small and working with such small quantities is technically challenging. GENOMEL was a pioneer in this area and produced reliable results using techniques, such as coring of paraffin embedded tumours, microdissection and DASL arrays.
Somatic mutations in CDKN2A gene carriers: It is well known that particular alterations of the CDKN2A gene can increase susceptibility to melanoma. GENOMELs online database was used to identify samples for a collaborative study on tumours from carriers and non-carriers of these mutations. The groups gathered almost 200 tumour samples together and examined if there were different, additional mutations in the actual tumours between carriers and non-carriers, and between familial melanoma and sporadic melanoma. The researchers looked for mutations in genes that code for particular proteins, the BRAF and NRAS genes. There was no significant difference in the frequency of BRAF mutations between familial melanomas with CDKN2A mutations and those without CDKN2A mutations. Similarly, the frequency of NRAS mutations did not differ when tumours from patients with and without CDKN2A mutations were compared. In no case were BRAF and NRAS mutations found to co-exist in the same tumour. In conclusion, a comprehensive investigation of somatic genomic events in CDKN2A mutated melanomas was performed.
Platform 3: Investigation of genotype / phenotype interaction, gene / gene interaction and gene / environment interaction for known susceptibility genes
The GENOMEL Pennsylvania (PENN) database: A new, online database at the University of Pennsylvania was created. This resource builds on an existing consortium database, but grants groups online access to their own data and enables the database manager to generate reports and resolve queries. The database held at that time information on 16 251 individuals with over 5000 melanoma patients. Information is available from 3828 questionnaire modules on family history and 2830 questionnaires on sun exposure. The database also contains information about cancers other than melanoma, CDKN2A / CDK4 mutation status and nevus phenotype information.
Screening for modifier genes: Mutations in the CDK4 and CDKN2A genes are known to increase susceptibility. GENOMEL used SNP arrays to screen other genes that could modify the effect of these mutations. Study was performed into the effect on the penetrance of these mutations, the risk of other cancers and the influence on a person's nevus phenotype. The research suggested a role for genes involved in pigmentation and nevus susceptibility and a set of 30 SNPs covering the known pigmentation variation and the nevus count variation was identified.
Platform 4: Attitudes to risk of melanoma and behavioural modification
The consortium's genetic and epidemiological research was extended and was combined with information technology and health psychology expertise. This enabled the project to undertake an ambitious programme of online research and dissemination. It was GENOMELs hypothesis that health education was designed to prevent melanoma will be more effective if directed towards those at increased risk. This hypothesis was tested by questionnaire studies in families and in general European populations by correlating estimation of self-risk with reported behaviour. The literature would then be surveyed in order to design a computer-based tool to be used by family members and the general population to estimate risk and this tool will be evaluated. Finally, this risk estimation tool would be linked to a multi-media package mounted on the GENOMEL website in which appropriate sun protection strategies and early detection strategies are linked to the estimation of risk.
A major output of the project was a series of Content management systems (CMSs). Two of these were placed on the patient information page and were specifically aimed at melanoma patients with a diagnosis of melanoma. A major component of these packages was the interviews held with actual patients who talked about their experiences and how they managed to deal with melanoma.
