The general focus of the work to be carried out is to understand the importance of the TP53 gene and its product (p53 protein) to several aspects of human health and disease (comprehensively available in the ALSPAC cohort database), including cancer, reproductive traits (such as pregnancy loss and success of assited reproduction) and viral infections. The p53 protein is essentially a transcription factor that is well-understood to play crucial roles in cancer. This protein mediates the response to DNA damage signals by activating cellular pathways that result in senescence or apoptosis. Mutations in the coding region of TP53 have been found in approximately 50% of all human cancers (although this can vary considerably depending on the cancer type), thus being a hallmark of tumourigenesis. More recently, p53 has been evidenced to participate of other biological contexts, including skin colour, embryo implantation to the uterus, metabolic disorders, ageing and viral infections.

Germline genomic variations (mainly Single Nucleotide polymorphism - SNPs) in TP53 have thus been extensively studied as an attempt to identify genetic markers of cancer predisposition, which would represent a contribution to the clinical field. SNPs are, in general, low-penetrance genetic variations that depend on complex interactions with other genetic profiles and environmental factors to be associated with a certain phenotype or disease. Considering that SNPs that change protein primary amino acid sequence (non-synonymous SNPs - nsSNPs) tend to have more prominent effects on protein function than synonymous or non-coding SNPs (although the relevance of these two last have been evidenced in the context of mRNA expression, splicing or translation), the majority of the currently available association studies has given attention to TP53 nsSNPs. Although there is a considerable amount of nsSNPs reported for TP53, the current work focus is on four of them, which may be considered the best validated: P47S, R72P, V217M and G360A. The two first nsSNPs have been substantially evidenced to functionally impact p53 function (p53 transactivation activity and apoptosis efficiency, respectively) and have been associated with cancer risk, while the remaining two currently lack such association findings. Interestingly, both these nsSNPs have functional experiments suggesting they might be important in cancer (V217M is located in the DNA binding domain of p53 and G360A has been evidenced to impact the transactivation of some p53-interacting proteins).

The notion that the association between a SNP and a phenotype is complex and the experimental evidences for assuming V217M and G360 SNPs might have significant impacts on p53 function, the current project proposes the investigation of TP53 haplotypes (set of SNPs on a single chromosome that are statistically associated) regarding the four nsSNPs described, as well as linkage disequilibrium (LD) blocks (which are composed of genetic loci that do not - in a statistical sense - do not segregate randomly) with SNPs in other genes. For instance, the association of TP53 R72P SNP and response to UV exposure (and, consequently, associations with tanning and skin cancer) are dependent on SNPs in the MC1R gene (a typical epistatic effect).

Studies of this nature are particularly suitable for large population cohorts such as ALSPAC, since the tendency of reducing the number of individuals per genetic subgroup when analyzing haplotypes would not result in insufficient statistical power. Moreover, there are comprehensive data available regarding ALSPAC mothers health, which is invaluable for the present study. Since TP53 R72P SNP is well-established to be associated with skin color, ALSPAC data is also of interest because it has little ethnic admixture, reducing bias. In this topic, the large and high-quality characterization of the sample (including massive data at the genetic level) allows the construction and assessment of LD blocks with high accuracy, converging information of different pathways at the genetic level.

The aims of the project can be divided in: 1) Identify haplotype and LD blocks involving the nsSNPs of interest. 2) Investigate possible associations of these blocks with different disease traits available for ALSPAC cohort. 3) Investigate possible interactions of TP53 nsSNPs with SNPs in LD with them regarding the associations of the latter with traits currently not described as affected by TP53. 4) Understand how TP53-associated SNPs interact with each other in order to provide substantial insights related to the genetics of complex traits. ((5) With a possibel amendment, extend analyses to other variants collected in ALSPAC (from GWAS/sequence data) across the TP53 locus).