Human Genome Project (HGP) revealed the existence of some 25,000 genes in the human genome; however the function of most of these genes, especially their role in human health and disease, remains uncovered. Elucidating the basis of inherited human disease essentially involves linking genomic variation to clinical phenotype. In this context rare monogenic diseases, often referred to as Mendelian disorders, are of substantial interest because identification of their genetic bases provides insights into the physiological role of the underlying protein, disease pathways and potential therapeutic targets. The recent introduction of next generation sequencing (NGS) technologies has enhanced the disease gene discovery process by replacing the laborious positional cloning studies. Of particular importance is exome sequencing whereby a single streamlined laboratory workflow identifies most of the coding genomic variations. This thesis is an effort to explore the genetic basis of alopecia and skeletal dysplasia in Pakistani populace. Alopecia is a rare heterogeneous common form of hereditary hair loss characterised by a sudden patchy hair loss most commonly occurring on the scalp but occasionally extended to the entire surface of the body. Hypotrichosis refers to diffuse thinning of the scalp hair without any gross defect of the hair shaft morphology while woolly hair is the anomalous variant of strongly curled hair. Evidence for the genetic basis of these disorders has been well established, however a phenotype to genotype relationship is still lacking. Skeletal dysplasias encompass a genetically heterogeneous group of more than 250 disorders of bone and cartilage. They are characterized by abnormal pattering, linear growth, differentiation and maintenance of the human skeleton with the resultant uneven short stature, or dwarfism. Progressive pseudorheumatoid dysplasia (PPD) is a rare autosomal recessive disease characterised by axial and peripheral skeletal dysplasia. Patients with PPD present with stiffness and swelling of joints, motor weakness and joint contractures. Just like alopecia, a phenotype to genotype relation is lacking for skeletal dysplasia, mainly due to variation in clinical phenotype. In this study, 10 unrelated consanguineous families (A to J) were ascertained from different areas of Pakistan. Eight of these families (A to H) were segregating alopecia xiv and two families (I and J) were inheriting skeletal dysplasia. Of the 8 alopecia families, seven families (A to G) showed autosomal recessive mode of inheritance while family H inherited alopecia in autosomal dominant fashion. Both family I and J were segregating skeletal dysplasia in autosomal recessive fashion. Following candidate gene approach all the families were investigated for the involvement of reported genes. Families excluded to known loci/genes were subjected to genome wide scan through microsatellite markers. In the absence of a candidate gene families were subjected to exome sequencing. Families A, B and C were linked to P2RY5 gene locus on chromosome 13q14.11– q21.32. Direct sequencing of the gene revealed a novel mutation (c.insT583) in family A, and a previously known mutation (c. 436 G>A) in the rest of the two families (B and C). Families D, E, F and G were linked to LIPH gene locus on chromosome 3q27-q28. Direct sequencing revealed two known mutations; c.659_660delTA in family D and c.280_369dup in family E. Family F revealed a novel nonsense mutation c.778A>T. Family G was linked to LIPH gene locus but no functional variation could be found when the gene was sequenced. Family H was linked to a novel locus on chromosome 16p13.3. Exome sequencing did not show any functional variant in the entire coding portion of the genome. In both families G and H, the possibility of a mutation in the regulatory region cannot be ruled out. Family I was linked to a large region on chromosome 16 through genome wide scan with microsatellite markers. Exome sequencing identified a missense mutation (c.1415C>G) in the conserved part of a novel gene IRX5 which encodes a transcription factor. This gene will be subjected to further functional assays to get an insight into the mechanism underlying skeletal dysplasia. Family J was subjected to exome sequencing exclusion to a candidate gene. A nonsense mutation (c.156 C>A) associated with a missense mutation (c.248 G>A) in WISP3 gene on chromosome 6q21. Exon 3 of WISP3 gene which carries these mutations is suspected to harbour a mutation hotspot. These findings will provide the basis for genetic counselling and carrier screening in families inheriting alopecia and skeletal dysplasia. These results will also help to establish prenatal diagnosis for the disorders under study. The novel findings of this study will serve as a starting point for future investigations towards understanding the pathogenesis of skeletal dysplasia. Publications 1. Tariq, M., Azhar, A., Baig, S., M., Dahl, N. and Klar, J. 2012. A novel mutation in the Lipase H gene in autosomal recessive hypotrichosis and woolly hair. Sci Rep. Epub ahead of print. DOI: 10.1038/srep00730 2. Tariq, M., Azhar, A., Baig, S. M., Dahl, N., Klar, J. 2012. A novel mutation in Lysophosphatidic Acid Receptor 6 gene in autosomal recessive hypotrichosis and evidence for a founder effect. Eur J. Dermatol. 22(4): 464-6. 3. Khan, T. N., Tariq, M., Malik, N. A., Klar, J., Baig, S., M and Dahl, N. 2014. Evidence for autosomal recessive inheritance in SPG3A caused by homozygosity for a novel ATL1 missense mutation. (Accepted: European journal of Human Genetics). 4. Hussain, M. S., Baig, S. M., Neumann, S., Peche, V. S., Nurnberg, G., Tariq, M., Jameel, M., Khan, T. N., Fatima, A., Malik, N. A., Ahmad, I., Altmuller, J., Frommolt, P., Thiele, H., Hohne, W., Yigit, G., Wollnik, B., Neubauer, B. A., Nurnberg, P. Jand Noegel, A. A. 2013. A gene associated with the centrosome during mitosis and is mutated in a large Pakistani family with autosomal recessive primary microcephaly. Hum mol genet. 20;22(25):5199-214 5. Khan, T. N., Klar, J., Nawaz, S., Jameel, M., Tariq, M., Malik, N, A., Baig, S. M. and Dahl, N. 2013. Novel missense mutation in the RSPO4 gene in congenital hyponychia and evidence for a polymorphic initiation codon (p.M1I). BMC Med Genet. Epub ahead of print. DOI: 10.1186/1471-2350-13-120 6. Baig, S.M., Sabih, D., Rahim, K., Azhar, A., Tariq, M., Hussain, M. S., Naqvi, S. M. S., Raja, G. K., Khan, T. N., Jameel, M., Iram, Z., Noor, S., Baig, U.R., Qureshi, J. A., Baig, S. A., Bakhtiar, S. M. 2012. β-Thalsssemia in Pakistan: a pilot program on prenatal diagnosis in Multan. J of Pediatr Hematol Oncol. 34(2):90-2. 7. Nawaz, S., Tariq, M., Ahmad, I., Baig, S. M., Dahl, N., Klar, J. 2012. Non-bullous congenital ichthyosiform erythroderma associated with homozygosity for a novel missense mutation in an ATP binding domain of ABCA12. Eur J. Dermatol. 22(2):178-81. 8. Nawaz, S., Tariq, M., Azhar, A., Rasool, M., Bakhtiar, S. M., Ahmad, I., Rehman, S. U., Jameel, M., Khan, T. N., Baig, S. A., Klar, J., Dahl, N., Baig, S. M. 2011. Report of a recurrent mutation in ARS (component B) gene with severe Mal de Meleda in a large consanguineous Pakistani family. Pak J Med Sci. 27(3):686-9. 9. Nawaz, S., Klar, J., Wajid, M., Aslam, M., Tariq, M., Schuster, J., Baig, S.M. and Dahl N. 2009. WNT10A missense mutation associated with a complete Odonto-Onycho-Dermal Dysplasia syndrome. Eur J Hum Genet. 17:1600-5. 10. Rasool, M., Schuster, J., Aslam, M., Tariq, M., Ahmad, I., Ali, A., Entesarian, M., Dahl, N., Baig, S. M. 2008. A novel missense mutation in the EDA gene associated with X-linked recessive isolated hypodontia. J Hum Genet. 53:894-8.