Dr Ioannis Ragoussis
| Research Area: | Cell and Molecular Biology |
|---|---|
| Technology Exchange: | Bioinformatics, Chromosome mapping, Mass spectrometry, SNP typing and Transcript profiling |
| Keywords: | SNP Genotyping, mutation detection, microarray and transcription factors |
| Web Links: |
The Genomics Group undertakes research and development and also provides a number of services for the Centre, as well as for other University of Oxford groups upon request. The current areas of interest include Microarray (collaborative expression profiling projects and own microarray production), High-Throughput Quantitative Gene Expression, Developing and implementing high-throughput genotyping technologies (Sequenom and Illumina), Characterisation of patients with deletion of chromosome 6p and identification of candidate genes involved in the resulting phenotypes through a mouse chromosomal region specific screen and Functional Genomics (Profiling of TF DNA Binding specificities using microarrays and SPR and Establishing Yeast-two-hybrid Screening Methodology).
| Name | Department | Institution | Country |
|---|---|---|---|
| Douglas Higgs | WIMM, Oxford | UK | |
| Adrian Harris | University of Oxford | UK |
2005. Genetically indistinguishable SNPs and their influence on inferring the location of disease-associated variants. Genome Res, 15 (11), pp. 1503-1510. Read abstract | Read more
As part of a recent high-density linkage disequilibrium (LD) study of chromosome 20, we obtained genotypes for approximately 30,000 SNPs at a density of 1 SNP/2 kb on four different population samples (47 CEPH founders; 91 UK unrelateds [unrelated white individuals of western European ancestry]; 97 African Americans; 42 East Asians). We observed that approximately 50% of SNPs had at least one genetically indistinguishable partner; i.e., for every individual considered, their genotype at the first locus was identical to their genotype at the second locus, or in LD terms, the SNPs were in "perfect" LD (r2 = 1.0). These "genetically indistinguishable SNPs" (giSNPs) formed into clusters of varying size. The larger the cluster, the greater the tendency to be located within genes and to overlap with giSNP clusters in other population samples. As might be expected for this map density, many giSNPs were located close to one another, thus reflecting local regions of undetected recombination or haplotype blocks. However, approximately 1/3 of giSNP clusters had intermingled, non-indistinguishable SNPs with incomplete LD (D' and r2 <1), sometimes spanning hundreds of kilobases, comprising up to 70 indistinguishable markers and overlapping multiple haplotype blocks. These long-range, nonconsecutive giSNPs have implications for disease gene localization by allelic association as evidence for association at one locus will be indistinguishable from that at another locus, even though both loci may be situated far apart. We describe the distribution of giSNPs on this map of chromosome 20 and illustrate the potential impact they can have on association mapping. Hide abstract
2005. Dissecting the genetic complexity of human 6p deletion syndromes by using a region-specific, phenotype-driven mouse screen. Proc Natl Acad Sci U S A, 102 (35), pp. 12477-12482. Read abstract | Read more
Monosomy of the human chromosome 6p terminal region results in a variety of congenital malformations that include brain, craniofacial, and organogenesis abnormalities. To examine the genetic basis of these phenotypes, we have carried out an unbiased functional analysis of the syntenic region of the mouse genome (proximal Mmu13). A genetic screen for recessive mutations in this region recovered thirteen lines with phenotypes relevant to a variety of clinical conditions. These include two loci that cause holoprosencephaly, two that underlie anophthalmia, one of which also contributes to other craniofacial abnormalities such as microcephaly, agnathia, and palatogenesis defects, and one locus responsible for developmental heart and kidney defects. Analysis of heterozygous carriers of these mutations shows that a high proportion of these loci manifest with behavioral activity and sensorimotor deficits in the heterozygous state. This finding argues for the systematic, reciprocal phenotypic assessment of dominant and recessive mouse mutants. In addition to providing a resource of single gene mutants that model 6p-associated disorders, the work reveals unsuspected genetic complexity at this region. In particular, many of the phenotypes associated with 6p deletions can be elicited by mutation in one of a number of genes. This finding implies that phenotypes associated with contiguous gene deletion syndromes can result not only from dosage sensitivity of one gene in the region but also from the combined effect of monosomy for multiple genes that function within the same biological process. Hide abstract
2005. SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data. Nucleic Acids Res, 33 (11), pp. 3455-3464. Read abstract | Read more
Comparative genome hybridization (CGH) to DNA microarrays (array CGH) is a technique capable of detecting deletions and duplications in genomes at high resolution. However, array CGH studies of the human genome noting false negative and false positive results using large insert clones as probes have raised important concerns regarding the suitability of this approach for clinical diagnostic applications. Here, we adapt the Smith-Waterman dynamic-programming algorithm to provide a sensitive and robust analytic approach (SW-ARRAY) for detecting copy-number changes in array CGH data. In a blind series of hybridizations to arrays consisting of the entire tiling path for the terminal 2 Mb of human chromosome 16p, the method identified all monosomies between 267 and 1567 kb with a high degree of statistical significance and accurately located the boundaries of deletions in the range 267-1052 kb. The approach is unique in offering both a nonparametric segmentation procedure and a nonparametric test of significance. It is scalable and well-suited to high resolution whole genome array CGH studies that use array probes derived from large insert clones as well as PCR products and oligonucleotides. Hide abstract
2004. Refined genotype-phenotype correlations in cases of chromosome 6p deletion syndromes. Eur J Hum Genet, 12 (9), pp. 718-728. Read abstract | Read more
Clinical reports of cases with deletions in chromosome 6p are relatively rare. We present a detailed study by fluorescent in situ hybridisation (FISH) of six new cases with distinct but overlapping 6p deletions involving the 6p24-pter chromosomal segment. Chromosomal breakpoints in individual cases were investigated using a large panel of probes previously mapped and characterised in our laboratory to cover the distal region of 6p. These cases have allowed refinement of genotype-phenotype correlations and strongly suggest a gene involved in regulating the development of hearing is localised within 6p25. There is also evidence for one or more loci involved in heart, skeletal and craniofacial development in the 6p24-p25 region. Furthermore, the Dandy-Walker malformation is associated with deletion of 6p24-pter. Hide abstract
2004. Mapping of three translocation breakpoints associated with orofacial clefting within 6p24 and identification of new transcripts within the region. Cytogenet Genome Res, 105 (1), pp. 47-53. Read abstract | Read more
Orofacial clefting (OFC) is a common congenital malformation. Here we report the refinement of three translocation breakpoints of patients exhibiting OFC within the 6p24 region, and the isolation and characterisation of novel genes, one of which is directly disrupted by the translocation breakpoint of a patient. The gene has been characterized and orthologues identified in bovine, murine and pufferfish. Hide abstract
2004. Quantitative high-throughput analysis of transcription factor binding specificities. Nucleic Acids Res, 32 (4), pp. e44. Read abstract | Read more
We present a general high-throughput approach to accurately quantify DNA-protein interactions, which can facilitate the identification of functional genetic polymorphisms. The method tested here on two structurally distinct transcription factors (TFs), NF-kappaB and OCT-1, comprises three steps: (i) optimized selection of DNA variants to be tested experimentally, which we show is superior to selecting variants at random; (ii) a quantitative protein-DNA binding assay using microarray and surface plasmon resonance technologies; (iii) prediction of binding affinity for all DNA variants in the consensus space using a statistical model based on principal coordinates analysis. For the protein-DNA binding assay, we identified a polyacrylamide/ester glass activation chemistry which formed exclusive covalent bonds with 5'-amino-modified DNA duplexes and hindered non-specific electrostatic attachment of DNA. Full accessibility of the DNA duplexes attached to polyacrylamide-modified slides was confirmed by the high degree of data correlation with the electromobility shift assay (correlation coefficient 93%). This approach offers the potential for high-throughput determination of TF binding profiles and predicting the effects of single nucleotide polymorphisms on TF binding affinity. New DNA binding data for OCT-1 are presented. Hide abstract
2004. The androgen receptor CAG repeat and serum testosterone in the risk of Alzheimer's disease in men. J Neurol Neurosurg Psychiatry, 75 (1), pp. 163-164.
2003. Association of the androgen receptor CAG repeat polymorphism with Alzheimer's disease in men. Neurosci Lett, 340 (2), pp. 87-90. Read abstract | Read more
We examined the CAG repeat polymorphism in exon 1 of the androgen receptor (AR) in an Oxford cohort of 150 cases (101 men) of definite or probable Alzheimer's disease (AD) and 190 elderly controls (140 men). We found that short alleles (< or = 20 CAG repeats) were associated with AD (adjusted odds ratio = 2.5, 95% confidence intervals: 1.2-5.0) in men, but not in women. This association appeared stronger in early-onset AD (< 65 years). We conclude that this AR polymorphism is of potential relevance to the risk of AD in men. Hide abstract
