http://www.dspace.cam.ac.uk:80/handle/1810/224161 Sat, 25 May 2013 23:53:42 GMT 2013-05-25T23:53:42Z http://www.dspace.cam.ac.uk:80/handle/1810/242182 Title: The functional impact of copy number variation in the human genome Authors: Huang, Ni Abstract: Copy number variation (CNV) is a class of genetic variation where large segments of the genome vary in copy number among different individuals. It has become clear in the past decade that CNV affects a significant proportion of the human genome and can play an important role in human disease. With array-based copy number detection and the current generation of sequencing technologies, our ability to discover genetic variants is running far ahead of our ability to interpret their functional impact. One approach to close this gap is to explore statistical association between genetic variants and phenotypes. In contrast to the successes of genome-wide association studies for common disease using common single nucleotide polymorphism (SNP) as markers, the majority of disease CNVs discovered so far have low population frequencies and are mainly involved in rare developmental disorders. Another strategy to improve interpretation of genomic variants is to establish a predictive understanding of their functional impact. Large heterozygous deletions are of particular interest, since (i) loss-of-function (LOF) of coding sequences encompassed by large deletions can be relatively unambiguously ascribed and (ii) haploinsufficiency (HI), wherein only one functional copy of a gene is not sufficient to maintain normal phenotype, is a major cause of dominant diseases. This thesis explored both approaches. Initially, I developed an informatics pipeline for robust discovery of CNVs from large numbers of samples genotyped using the Affymetrix whole-genome SNP array 6.0, to support both the association-based and prediction-based study. For the disease association strategy, I studied the role of both common and rare CNVs in severe early-onset obesity using a case-control design, from which a rare 220kb heterozygous deletion at 16p11.2 that encompasses SH2B1 was found causal for the phenotype and an 8kb common deletion upstream of NEGR1 was found to be significantly associated with the disease, particularly in females. Using the prediction-based approach, I characterized the properties of HI genes by comparing with genes observed to be deleted in apparently healthy individuals and I developed a prediction model to distinguish HI and haplosufficient (HS) genes using the most informative properties identified from these comparisons. An HI-based pathogenicity score was devised to distinguish pathogenic genic CNVs from benign genic CNVs. Finally, I proposed a probabilistic diagnostic framework to incorporate population variation, and integrate other sources of evidence, to enable an improved, and quantitative, identification of causal variants. Tue, 06 Mar 2012 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/242182 2012-03-06T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/230115 Title: Mechanisms 
of
 change 
in 
protein 
architecture Authors: Buljan, Marija Abstract: Proteins are the basic building blocks and functional units in all living organisms. Moreover, differences between species can frequently be explained with differences in their protein complements. Importantly, proteins are often composed of segments, i.e. domains that have a certain level of evolutionary, structural and/or functional independence. The majority of proteins in nature contain two or more domains, and an individual domain can often occur in combinations with different domain partners. In the first part of my thesis, I traced the history of animal gene families and the proteins these genes encode. By this means, I was able to infer events where changes in protein domain architectures took place. This showed that both insertions and deletions of single copy domains preferentially occur at protein termini, but also that changes are more likely to occur after gene duplication than organism speciation. Finally, domains that were most frequently gained were the ones that are related to an increase in organismal complexity, thus underlining the important role of domain shuffling in animal evolution. In the second part of my thesis, I focused on a set of high confidence domain gain events and investigated the evidence for molecular mechanisms that caused these domain gains. In agreement with observations from the first part - that changes preferentially occur at the termini - I have found that the strongest contribution to gains of novel domains in proteins comes from gene fusion through the joining of exons from adjacent genes into a novel gene unit. Two other mechanisms that have been suggested to play a major role in the evolution of animal proteins, retroposition and middle insertions through intronic recombination, have a smaller role in comparison to gene fusions. Since the majority of these domain gains are again observed after gene duplication, this suggests a powerful mechanism for neofunctionalization after gene duplication. iii Finally, in the last part of my thesis, I address a mechanism that increases the number and variety of proteins in an organism – alternative splicing. In particular, I investigate the functional consequences of tissue-specific alternative splicing events. I found that tissue-specific splicing tends to affect exons that encode protein regions without defined secondary or tertiary structure. Importantly, it is known that these disordered regions frequently play a role in protein interactions. In agreement with this, I observed significant enrichment of tissue-specifically encoded protein segments in disordered binding peptides and posttranslationally modified sites. A possible result of the finely regulated alternative splicing of these segments is a tissue-specific rewiring of protein network. In conclusion, both alternative splicing and domain shuffling can increase proteome diversity. However, a protein with a new function can often directly or indirectly shape the functions of other proteins in its environment. Tue, 11 Jan 2011 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/230115 2011-01-11T00:00:00Z