Many of our most common diseases run in families, but they lack the simple inheritance patterns characteristic of single gene disorders . These complex diseases include asthma, diabetes, epilepsy, hypertension, manic depression and schizophrenia. Certain developmental abnormalities are also included in this category, such as cleft lip/palate, congenital heart defects and neural tube defects.

Complex diseases have a low heritability (tendency to be inherited) compared to single gene disorders. For example, only 2-5 per cent of the close relatives of diabetics also suffer from diabetes, much lower than would be the case for a single gene disorder like cystic fibrosis. This indicates that no single genetic factor is responsible for the disease. Several to many genes may contribute, and there may be additional environmental causes such as poor diet and exposure to hazardous chemicals.

It is thought that the incidence of any complex disease is dependent on a balance of risks. There is a balance between gene variants (alleles) with positive and negative effects, and between environmental factors with positive and negative effects. Too many negative factors, both genetic and environmental, can tip the balance towards disease.

Large-scale studies can help to isolate genes that contribute to complex diseases since individuals with alleles that predispose them towards a disease will statistically be more likely to be affected. Similarly, those with alleles that protect them from a disease will statistically be less likely to be affected. Many disease genes have been identified by looking for correlations between single nucleotide polymorphisms (SNPs) and complex diseases in large populations.