Exome sequencing and mutation identification in familial coeliac disease
Lead Research Organisation:
Queen Mary University of London
Department Name: Blizard Institute of Cell and Molecular
Abstract
Coeliac disease (a common immune condition of the gut caused by reaction to dietary wheat and cereals) runs strongly in families, however at most half of this heritability can be explained by our current knowledge of inherited genetic risk factors.
We think that mutations in DNA sequence that alters the protein coding sequence of genes may contribute to coeliac disease heritability. There is evidence for this in other diseases. These risk mutations are likely to be relatively rare in the population.
We propose to use new technology to sequence all protein coding genes (the exome) in 50 selected very large multiply affected families with coeliac disease. Each family has at least 5 people with coeliac disease, one has 13 affected individuals. We will study three distantly related individuals per family and look for mutations shared between the people with coeliac disease. This will enable us to narrow down the possibilities from the many thousands of variants the sequencing uncovers.
We will also use relatively cheap BeadChips to analyse hundreds of thousands of known variants in every affected individuals in each family. This will give us complementary information, showing which large regions of the genome are shared between the affected individuals.
We will subsequently test all individuals (affected and unaffected) in a family for promising candidates for disease causing risk mutations.
Once we have found new disease risk mutations in several genes, we will then look for different, possibly rare mutations in thousands of more samples. Finding multiple mutations in a gene gives further evidence that we are on the right track, and also provides information to develop diagnostic and risk-predicting tests.
Finally, we will also test several thousand mutations in over ten thousand coeliac and healthy individuals. This will give further evidence to implicate disease mutations, and tell us precise details about each mutation.
Identifying rare high effect size mutations in coeliac disease will give us direct leads into how disease develops and possibly identify new targets for treatments. We have previously shown that insights in coeliac disease are likely to give insights relevant to other chronic immune diseases.These rare mutations often have readily predictable consequences, and are of high value for disease understanding. Follow on studies will investigate the effects of these mutations on biological function. The study will likely also generate methodological advances relevant to other conditions.
We think that mutations in DNA sequence that alters the protein coding sequence of genes may contribute to coeliac disease heritability. There is evidence for this in other diseases. These risk mutations are likely to be relatively rare in the population.
We propose to use new technology to sequence all protein coding genes (the exome) in 50 selected very large multiply affected families with coeliac disease. Each family has at least 5 people with coeliac disease, one has 13 affected individuals. We will study three distantly related individuals per family and look for mutations shared between the people with coeliac disease. This will enable us to narrow down the possibilities from the many thousands of variants the sequencing uncovers.
We will also use relatively cheap BeadChips to analyse hundreds of thousands of known variants in every affected individuals in each family. This will give us complementary information, showing which large regions of the genome are shared between the affected individuals.
We will subsequently test all individuals (affected and unaffected) in a family for promising candidates for disease causing risk mutations.
Once we have found new disease risk mutations in several genes, we will then look for different, possibly rare mutations in thousands of more samples. Finding multiple mutations in a gene gives further evidence that we are on the right track, and also provides information to develop diagnostic and risk-predicting tests.
Finally, we will also test several thousand mutations in over ten thousand coeliac and healthy individuals. This will give further evidence to implicate disease mutations, and tell us precise details about each mutation.
Identifying rare high effect size mutations in coeliac disease will give us direct leads into how disease develops and possibly identify new targets for treatments. We have previously shown that insights in coeliac disease are likely to give insights relevant to other chronic immune diseases.These rare mutations often have readily predictable consequences, and are of high value for disease understanding. Follow on studies will investigate the effects of these mutations on biological function. The study will likely also generate methodological advances relevant to other conditions.
Technical Summary
Coeliac disease is highly heritable, however at most 50% of this heritability is explained by HLA-DQ and new risk variants from genome wide association studies.
We hypothesise that rare heritable genetic mutations (protein coding changes) of relatively large effect size (allelic odds ratios ~ 2 - 5) account for a substantial proportion of the remaining heritability in coeliac disease.
We propose to use whole exome resequencing to identify mutations in 50 selected very large multiply affected families. We will resequence exons of all protein coding genes in, where possible, three distantly related individuals per family (each pair at least 1st cousin or more distant). We have already identified and collected DNA and phenotypes on over 100 families with at least 5 affected coeliac individuals and will select 50 of the most informative families to exome resequence 3 distantly related affecteds per family..
Importantly, the use of relatively inexpensive genome wide SNP chips in large pedigrees allows us to accurately identify extended genomic segments shared between distantly related affecteds that are likely to be the regions containing mutations. We will subsequently genotype a set of candidate mutations per family in all affected and unaffected individuals to confirm segregation with affection status.
We will then perform deep resequencing of the 4 most interesting genes containing mutations segregating with disease in ~1000 samples, to obtain the full mutation spectrum in coeliac disease. We will proceed to genotype these mutations; promising mutations from exome resequencing in sporadic extreme-phenotype coeliac disease (a separate Coeliac UK funded project); and other promising mutations from familial resequencing in our entire collection of over 8000 cases and 8000 controls.
Identifying rare high effect size mutations in coeliac disease will give us direct leads into the causation of disease, and identify novel therapeutic targets. Rare mutations often have readily predicatable pathological consequences, e.g. stop mutations or deleted exons. Follow on studies will investigate the effects of these mutations on biological function. The study will likely also generate methodological advances relevant to other diseases with complex inheritance.
We hypothesise that rare heritable genetic mutations (protein coding changes) of relatively large effect size (allelic odds ratios ~ 2 - 5) account for a substantial proportion of the remaining heritability in coeliac disease.
We propose to use whole exome resequencing to identify mutations in 50 selected very large multiply affected families. We will resequence exons of all protein coding genes in, where possible, three distantly related individuals per family (each pair at least 1st cousin or more distant). We have already identified and collected DNA and phenotypes on over 100 families with at least 5 affected coeliac individuals and will select 50 of the most informative families to exome resequence 3 distantly related affecteds per family..
Importantly, the use of relatively inexpensive genome wide SNP chips in large pedigrees allows us to accurately identify extended genomic segments shared between distantly related affecteds that are likely to be the regions containing mutations. We will subsequently genotype a set of candidate mutations per family in all affected and unaffected individuals to confirm segregation with affection status.
We will then perform deep resequencing of the 4 most interesting genes containing mutations segregating with disease in ~1000 samples, to obtain the full mutation spectrum in coeliac disease. We will proceed to genotype these mutations; promising mutations from exome resequencing in sporadic extreme-phenotype coeliac disease (a separate Coeliac UK funded project); and other promising mutations from familial resequencing in our entire collection of over 8000 cases and 8000 controls.
Identifying rare high effect size mutations in coeliac disease will give us direct leads into the causation of disease, and identify novel therapeutic targets. Rare mutations often have readily predicatable pathological consequences, e.g. stop mutations or deleted exons. Follow on studies will investigate the effects of these mutations on biological function. The study will likely also generate methodological advances relevant to other diseases with complex inheritance.
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| David Van Heel (Principal Investigator) |