Inter and intra-regional variations are mostly due to environment factors. The environment plays an important role in carcinogenesis and it is postulated that it contributes about 70% to lifetime risks of most cancers (Wu et al. 2016). In SSA, 32.7% of cancers are attributable to infection compared to 7.4% in more developed countries (De Martel et al. 2012; Okuku et al. 2013). Hepatitis B and C viruses (HBV, HCV), Human papilloma virus (HPV), Helicobacter pylori, Epstein-Barr virus (EPV) and Human herpes virus (HHV) type B accounted for over 97% of all infected related cancer in 2008 (De Martel et al. 2012). There are however other environmental factors involved in carcinogenesis with differing relative contributions (Table 2.1). These environmental factors may lead to extrinsic mutational signatures (Wu et al. 2016).

With many cancers, there is an accumulation of an average of 90 mutant genes but only a subset contribute to neoplastic process, with each cancer having its own distinct mutational signature (Sjöblom et al. 2006). Analysis of these mutational signatures, the fingerprints left on cancer genomes by different mutagenic processes, showed that intrinsic cancer mutations (random errors in DNA replication) showed strong positive correlations with age suggesting acquisition at a relative constant rate over lifetime. However, it is postulated that all other mutational signatures that lack consistent correlations with age, suggests acquisition at different rates in life and are thus likely a consequence of extrinsic carcinogen exposure (Wu et al. 2016). Cancers that have substantial environmental risk proportions (Table 2.1) harbour large percentages of extrinsic mutational signatures (environmental factors that affect mutagenesis rate), for example approximately, 100% for myeloma, lung, and thyroid cancers, and approximately 80–90% for bladder, colorectal and uterine cancers (Wu et al. 2016).

These extrinsic mutational signatures are most likely to partly explain the geographical variation in cancer epidemiology in terms of incidence and biology. Amongst migrants moving from low-risk to high-risk countries, the incidence of colorectal cancer tend to increase towards that of the local population (Haggar and Boushey 2009). Apart from migration, other geographical factors come into play and that includes urban residency. Current urban residency is a stronger predictor of risk than is an urban location of birth (Haggar and Boushey 2009).

Global molecular pathways for most cancers are well established. Geographical and/or racial differences tend to be in the prevalence of mutations in candidate genes and the effect and types of polymorphisms and epigenetic phenomena have on these genes. All these may enhance understanding of differences in tumour biology, identify tumours with poor prognosis, serve as biomarkers, and importantly, help direct appropriate therapy.

Cancer genomic research output from SSA is low apart from South Africa who has taken strides in developing biotechnology industry. However, there were only 31 published research papers in cancer genomics in SSA between 2004 and 2013 (Adedokun et al. 2016). Encouragingly, with increasing collaboration between institutions in SSA countries and those in United States and Europe, cancer genomic research output is increasing. The rest of the chapter will give a selective, brief overview. It is not meant to be exhaustive but to highlight the theme as it relates to SSA.

Global genomic pathways for most cancers are well established. The importance of assessing differences in different geographic regions and races is to help in prognostication and/or planning treatment. Another important aspect is finding out different mutations that may affect the function of the affected gene. Two common cancers are used to illustrate this.

Another important aspect in cancer pathway are genetic variants, and these include single nucleotide polymorphism (SNP) and copy number variation (CNV). They help in determining susceptibility to certain type of cancers (Chung et al. 2010; Redon et al. 2006). SNPs are single nucleotide base substitution that affects at least 1% of the population. The important ones alter coding sequence and result in a non-synonymous change, a shift in the amino acid sequence of protein that may change its function (Chung et al. 2010).

Genome wide association studies (GWAS) with SNPs investigate mainly susceptibility to cancer and outcome. Outcome studies help to determine prognostic information for survival, complications or response to pharmacological interventions (Erichsen and Chanock 2004). While there is plethora of GWAS, there is growing evidence that these may be different within racial groups and between geographical regions (Cook et al. 2014; Murphy et al. 2012).