Genetic contribution to the aggregation of schizophrenia and bipolar disorder in multiplex consanguineous Pakistani pedigrees

Schizophrenia (SCZ) and bipolar disorder (BP) are two major psychiatric disorders. SCZ is a primary psychotic disorder that typically involves symptoms of delusions and hallucinations, by comparison BP is a mood disorder engaging mania and depression but it can also involve psychosis. A 2010 estimation of these disorders highlighted that they respectively contributed to ~7.4% and ~7.0% of the global burden of disease. The high prevalence (~0.4% for SCZ and ~2.4% for BP) and estimated heritability (~80%) suggest a strong genetic influence. Evidence shows that there are some genetic overlaps between the two conditions but also disorder-independent genetic components. Over the past decade, genome-wide association studies (GWAS) identified hundreds of SCZ and BP loci, and other approaches identified various forms of potential genetic risk factors, for instance rare copy number variants (CNVs), rare single nucleotide variants (SNVs) and de novo mutations (DNMs). While our knowledge of the genetic architecture of these conditions grow, a large of portion of the genetic heritability of each disorder still remains unexplained.  The combination of a long history of genetic admixture, and the tradition of consanguineous marriages (50% of unions are consanguineous), makes Pakistani families promising for population based medical genetics studies. Consanguinity has previously been associated with an increased risk of numerous traits in epidemiological studies. Family-based designs have been widely applied in the genetic mapping of Mendelian and complex traits. However, few studies have used large multiplex consanguineous families to thoroughly investigate the role of consanguinity in neuropsychiatric disorders such as SCZ and BP. CNVs have been implicated in SCZ and BP since the discovery of 22q11.2 deletions, however, most of them are rare in the population but contribute significantly to the risk. Association studies of CNVs found enrichment of rare deletions and duplications, and a higher rate of de novo CNVs in cases relative to controls. Whole-genome sequencing of multiplex SCZ families reported increased burden of rare, exonic CNV in SCZ probands and genetic heterogeneity. Using large multiplex families could be statistically powerful to investigate the role of segregating, and possibly pathogenic, CNVs.  In order to better understand the genetic heterogeneity and look for missing heritability of these two common disorders in Pakistani families, we used SNP genotyping and whole-exome sequencing to examine the genetic profile of ten large multiplex consanguineous pedigrees; each of these families involved more than ten members affected by SCZ or BP. In this thesis, we characterized the population background which includes admixture and recent inbreeding of our cohort. We tested if the inbreeding level was associated with the binary phenotype and its subphenotype dimensions. We also included large external dataset of matched population control individuals to compute and compare the inbreeding coefficient. Our approach, which included linkage analysis, autozygosity mapping, runs of homozygosity (ROH) and rare deleterious homozygous variants segregation analysis, led us to reject the hypothesis of a recessive inheritance model across these families (despite of their high inbreeding). We subsequently looked if any CNV segregated across some of the families. This examination involved multiple steps: 1 - a systematic comparison of a range of CNV detection algorithms currently available through different platforms, 2 - a cross validation of true and false positive CNV calls through the use of in silico or experimental approaches, 3 - the development of our own segregation and annotation software. This effort both emphasized the methodological advances and limitations of CNV studies. In the end, none of the potentially pathogenic CNV identified appeared to account for the genetic variance of SCZ and BP observed in the families examined here. The results presented in this thesis provide support for an alternate hypothesis that would involve a polygenic pattern where both rare variants and common variants would be at play.

Keyphrases: Pakistani, Multiplex families, consanguinity, SNP chip genotyping, Whole-exome sequencing, Schizophrenia, Bipolar disorder, Copy number variants