Indiana University-Purdue University Indianapolis (IUPUI) / Population genetics has been revolutionized by the advent of high-throughput sequencing (HTS) methods in the 21st century. Modern day sequencers are now capable of sequencing entire exomes and genomes at unprecedented speed and accuracy. An explosion of bioinformatics software and data analysis tools now makes sequencing accessible for gene discovery in both rare Mendelian and complex disease. Family-based sequencing studies in particular have great potential for elucidating the genetic basis for many more diseases. We apply both whole exome and genome sequencing to three different cases of familial disease: intracranial aneurysm (IA), Parkinson disease (PD), and X-linked ataxia dementia (XLAD). IA and PD are both common, complex traits that inflict a devastating disease burden worldwide, mostly due to few effective therapeutic interventions. Little of the heritability of both IA and PD has been explained to date, especially as it relates to the impact of rare variation on disease. XLAD is an extremely rare neurological disease described thus far in one kindred. Although promising results have been achieved through previous genetic study designs, the causative gene has not yet been identified. For all three diseases, HTS offers an opportunity to explore the role of rare variation in disease pathogenesis. In each study, we explore the opportunities and challenges of family-based HTS for different disease models. The work presented herein contributes effective practices for study design, analysis, and interpretation in a rapidly growing field still replete with questions about how best to implement HTS in studying familial disease.

Pheochromocytomas and paragangliomas are neuroendocrine tumors that arise from neural crest-derived cells of the adrenal medulla and the extra-adrenal paraganglia. They cause hypertension due to an abnormally high production of catecholamines (mainly adrenaline and noradrenaline), with symptoms including recurrent episodes of headache, palpitations and sweating, and an increased risk of cardiovascular disease. Malignancy in the form of distant metastases occurs in 10-15% of the patients. The malignant cases are difficult to predict and cure, and have a poor prognosis. About a third of pheochromocytomas and paragangliomas are caused by hereditary mutations in a growing list of known susceptibility genes. However, the cause of the remaining, sporadic, tumors is still largely unknown. The aim of this thesis project has been to further characterize the genetic background of pheochromocytomas and paragangliomas, with a focus on the sporadic tumors. First, we investigated the role of the genes known from the familial tumors in the sporadic form of the disease. By studying mutations, copy number variations, DNA methylation and gene expression, we found that many of the known susceptibility genes harbor somatic alterations in sporadic pheochromocytomas. Particularly, we found that the NF1 gene, which plays an important role in suppressing cell growth and proliferation by regulating the RASMAPK pathway, was inactivated by mutations in more than 20% of the cases. The mutations occurred together with deletions of the normal allele and were associated with a reduced NF1 gene expression and a specific hormone profile. We also detected activating mutations in the gene EPAS1, which encodes HIF-2α, in a subset of sporadic cases. Microarray analysis of gene expression showed that several genes involved in angiogenesis and cell metabolism were upregulated in EPAS1-mutated tumors, which is in agreement with the role of HIF-2α in the cellular response to hypoxia. In order to comprehensively investigate all the known susceptibility genes in a larger patient cohort, we designed a targeted next-generation sequencing approach and could conclude that it was fast and cost-efficient for genetic testing of pheochromocytomas and paragangliomas. The results showed that about 40% of the sporadic cases had mutations in the tested genes. The majority of the mutations were somatic, but some apparently sporadic cases in fact carried germline mutations. Such knowledge of the genetic background can be of importance to facilitate early detection and correct treatment of pheochromocytomas, paragangliomas and potential co-occurring cancers, and also to identify relatives that might be at risk. By sequencing all the coding regions of the genome, the exome, we then identified recurrent activating mutations in a novel gene, in which mutations have previously only been reported in subgroups of brain tumors. The identified mutations are proposed to cause constitutive activation of the encoded receptor tyrosine kinase, resulting in the activation of downstream kinase signaling pathways that promote cell growth and proliferation. In summary, the studies increase our biological understanding of pheochromocytoma and paraganglioma, and possibly also co-occurring cancers in which the same genes and pathways are involved. Together with the findings of other scientific studies, our results may contribute to the development of future treatment options.

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