Samantha Knight Group
Research Overview
Our previous work within the Oxford Genetics Knowledge Park showed that array based comparative genomic hybridization (aCGH) is a powerful technique for detecting clinically relevant genome imbalance, offering 40-1000 times the resolution of karyotyping and making at least 10-15% more diagnoses in patients with idiopathic learning disability (ILD). In collaboration, this work has also led to the identification of novel syndromes, most notably a recurrent 17q21.31 microdeletion syndrome and more recently, 15q24 and 15q13 microdeletion syndromes. In addition, our evaluation of aCGH platforms for clinical diagnostic use has resulted in recommendation and implementation within the ORH Trust's Clinical Cytogenetics Laboratory at the Churchill Hospital, Oxford.
Building upon the achievements and expertise gained within the Oxford GKP, our current goal is to maximise the potential of microarray technology within the NHS. This is being undertaken as part of the Oxford Partnership Comprehensive Biomedical Research Centre (BRC), a newly funded Government initiative established to drive the development, evaluation, optimization and transfer of clinically useful research tools into the clinical diagnostic environment so that ill-health may be prevented, diagnosed and treated much sooner than previously possible. Genetics is a key cross-cutting theme of the Oxford BRC, with application in variety of disease themes including Immunology, Diabetes, Cardiology, Cancer and Neurology. Currently, our laboratory is situated within the Wellcome Trust Centre for Human Genetics, housing state of the art technologies including microarray, genotyping and high-throughput sequencing facilities. Initial aims include evaluating multi-sample array formats and investigating the use of high-resolution oligonucleotide arrays for the diagnosis of clinically important conditions such as idiopathic learning disability and disorders of speech and language impairment (working with Dr Simon Fisher and Professor Anthony Monaco). We are also embarking on collaborative studies with Professor Shoumo Bhattacharya investigating genome imbalance in congenital heart disease and with Dr Anna Schuh investigating chronic lymphocytic leukaemia. Soon, the work will expand to include other approaches such as gene expression, genotyping, biomarker and sequencing studies with clinical application in other diseases. Ultimately, we hope to achieve significant advances in diagnosis, genetic counselling, education, therapeutics and preventative strategies thereby resulting in the improved welfare of patients and their families.
Publications
Knight SJ, Regan R, Nicod A, Horsley SW, Kearney L, Homfray T, Winter RM, Bolton P, Flint J. 1999. Subtle chromosomal rearrangements in children with unexplained mental retardation. Lancet, 354 (9191), pp. 1676-81. Read abstract | View on PubMed
BACKGROUND: No explanation for moderate to severe mental retardation is apparent in about 40% of cases. Although small chromosomal rearrangements may account for some undiagnosed cases, a lack of genome-wide screening methods has made it impossible to ascertain the frequency of such abnormalities. METHODS: A fluorescence in-situ hybridisation (FISH) test was used to examine the integrity of chromosome ends in 284 children with unexplained moderate to severe retardation, and in 182 children with unexplained mild retardation. 75 normal men were also tested. When a chromosomal rearrangement was found, its size was estimated, and members of the child's family were investigated. FINDINGS: Subtle chromosomal abnormalities occurred with a frequency of 7.4% in the children with moderate to severe mental retardation, and of 0.5% in the children with mild retardation. The abnormalities had an estimated population prevalence of 2.1 per 10,000, and were familial in almost half of cases. INTERPRETATION: Once recognisable syndromes have been excluded, abnormalities that include the ends of chromosomes are the commonest cause of mental retardation in children with undiagnosed moderate to severe mental retardation. Owing to the high prevalence of familial cases, screening for subtle chromosomal rearrangements is warranted in children with unexplained moderate to severe mental retardation. Hide abstract
Knight SJ, Lese CM, Precht KS, Kuc J, Ning Y, Lucas S, Regan R, Brenan M, Nicod A, Lawrie NM, Cardy DL, Nguyen H, Hudson TJ, Riethman HC, Ledbetter DH, Flint J. 2000. An optimized set of human telomere clones for studying telomere integrity and architecture. American journal of human genetics, 67 (2), pp. 320-32. Read abstract | View on PubMed
Telomere-specific clones are a valuable resource for the characterization of chromosomal rearrangements. We previously reported a first-generation set of human telomere probes consisting of 34 genomic clones, which were a known distance from the end of the chromosome ( approximately 300 kb), and 7 clones corresponding to the most distal markers on the integrated genetic/physical map (1p, 5p, 6p, 9p, 12p, 15q, and 20q). Subsequently, this resource has been optimized and completed: the size of the genomic clones has been expanded to a target size of 100-200 kb, which is optimal for use in genome-scanning methodologies, and additional probes for the remaining seven telomeres have been identified. For each clone we give an associated mapped sequence-tagged site and provide distances from the telomere estimated using a combination of fiberFISH, interphase FISH, sequence analysis, and radiation-hybrid mapping. This updated set of telomeric clones is an invaluable resource for clinical diagnosis and represents an important contribution to genetic and physical mapping efforts aimed at telomeric regions. Hide abstract
Price TS, Regan R, Mott R, Hedman A, Honey B, Daniels RJ, Smith L, Greenfield A, Tiganescu A, Buckle V, Ventress N, Ayyub H, Salhan A, Pedraza-Diaz S, Broxholme J, Ragoussis J, Higgs DR, Flint J, Knight SJ. 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 research, 33 (11), pp. 3455-64. Read abstract | View on PubMed
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
Sharp AJ, Hansen S, Selzer RR, Cheng Z, Regan R, Hurst JA, Stewart H, Price SM, Blair E, Hennekam RC, Fitzpatrick CA, Segraves R, Richmond TA, Guiver C, Albertson DG, Pinkel D, Eis PS, Schwartz S, Knight SJ, Eichler EE. 2006. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nature genetics, 38 (9), pp. 1038-42. Read abstract | View on PubMed
Genomic disorders are characterized by the presence of flanking segmental duplications that predispose these regions to recurrent rearrangement. Based on the duplication architecture of the genome, we investigated 130 regions that we hypothesized as candidates for previously undescribed genomic disorders. We tested 290 individuals with mental retardation by BAC array comparative genomic hybridization and identified 16 pathogenic rearrangements, including de novo microdeletions of 17q21.31 found in four individuals. Using oligonucleotide arrays, we refined the breakpoints of this microdeletion, defining a 478-kb critical region containing six genes that were deleted in all four individuals. We mapped the breakpoints of this deletion and of four other pathogenic rearrangements in 1q21.1, 15q13, 15q24 and 17q12 to flanking segmental duplications, suggesting that these are also sites of recurrent rearrangement. In common with the 17q21.31 deletion, these breakpoint regions are sites of copy number polymorphism in controls, indicating that these may be inherently unstable genomic regions. Hide abstract
Sharp AJ, Mefford HC, Li K, Baker C, Skinner C, Stevenson RE, Schroer RJ, Novara F, De Gregori M, Ciccone R, Broomer A, Casuga I, Wang Y, Xiao C, Barbacioru C, Gimelli G, Bernardina BD, Torniero C, Giorda R, Regan R, Murday V, Mansour S, Fichera M, Castiglia L, Failla P, Ventura M, Jiang Z, Cooper GM, Knight SJ, Romano C, Zuffardi O, Chen C, Schwartz CE, Eichler EE. 2008. A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures. Nature genetics, 40 (3), pp. 322-8. Read abstract | View on PubMed
Funding Sources
NIHR Biomedical Research Centre, Oxford
Research Area
Translational Genetics, Neurogenetics, Cardiovascular Disease
Keywords
Learning disability, mental retardation, brain malformation, chronic lymphocytic leukaemia, congenital heart disease, speech and language impairment, autism, array comparative genomic hybridization (aCGH), copy number variant (CNV), genome imbalance, translational genetics, molecular diagnosis, clinical diagnostic laboratory
