Genomic strategies towards the dissection of human complex disease

Abstract: Complex diseases are caused by the activities of many genes acting in concert with environmental factors. A major challenge facing human genetic research is to unravel the genetic factors behind complex disorders.Oxidative damage by free oxygen radicals is believed to contribute to many complex disorders, particularly degenerative disorders such as Alzheimer's disease. A principle source of oxygen free radicals in a human cell is the mitochondrial Oxidative Phosphorylation pathway. This consists of five protein complexes whose subunits are encoded both by the mitochondrial and the nuclear genomes. The least genetically defined complex is Complex I, which comprises 41 genes, of which 34 are encoded by the nuclear genome and the remaining seven by the mitochondrial genome. By exploiting publicly available EST sequences and by radiation hybrid mapping, I successfully characterized and mapped 20 nuclear complex I genes to precise chromosomal locations. These genes can now be tested in positional candidate scenarios.Turning my attention to encephalomyopathies, I analyzed eight patients from Italy suffering severe myopathic disease. All eight individuals had confirmed Oxidative Phosphorylation Complex I biochemical deficiency but did not carry known mitochondrial DNA mutations. We mutation scanned over 20 Complex I cDNAs and found one rare alteration causing the substitution of an evolutionary conserved glycine to arginine at amino acid position 32 in the NDUFA1 gene. The pathogenic role of this mutation is unclear.Polymorphism is an important investigation tool in genetic research, without which disease genes could not be identified. Single nucleotide polymorphisms (SNPs) are one base differences within a population. They have high prevalence in the human genome, are easy to score, and are suitable for automated genotyping techniques. I therefore worked to identify 167 SNPs in 88 candidate genes for neurodegenerative disorders. These SNPs would provide a valuable resource for subsequent association analysis.Alzheimer's disease (AD) is a complex disease where many risk genes have been reported to be associated with the disease, but only one (APOE) has been independently replicated. I performed large scale (60 SNPs) association analysis to test for association with early onset form of AD. Despite observing 12 positive association signals in a set of 121 patients and matched controls, the signals were not robust enough to survive an independent confirmation study in a set of 117 patients and 176 controls.