Chromosomes are the organised structures within each cell consisting of single pieces of coiled DNA which contain a specified number of genes. In man there are normally 46 chromosomes, which contain many thousands of genes.
Having the correct number of genes and chromosomes in every cell in a body is obviously of great importance in terms of the normal development and functioning of a human being.
When there is a difference in the number of copies of a particular gene or chromosome - either too many or too few - this can result in genetic disorders.
Our aims
The Molecular cytogenetics team's aims are to develop ways of detecting changes in the numbers of genes and chromosomes both in the human and in other organisms that could shed light on the causes of certain inherited disorders in man.
We are examining variation in the number of copies of genes both in the normal situation and in relation to human disease.
Our research also enables us to make discoveries about mammalian chromosome evolution and chromosome organisation and structure.
Our approach
We use a variety of technologies to examine the number of genes and chromosomes in individual cells. Our main tools include fluorescence in situ hybridization (FISH) - a technique where certain segments of DNA are labelled with a dye that fluoresces under UV light rendering that segment visible under a high-power fluorescence microscope. This enables us to directly examine gene copy number in a cell. We have also developed a chromosome flow sorting technique, where we can separate out specific chromosomes from the rest of the chromosome complement.
We have used FISH since the Sanger Institute first opened, to generate so-called sequence-ready large insert clone maps for example segments of DNA that were used during the Human genome project for sequencing the human genome. Currently, we have developed multicolour technologies that enable us to unequivocally identify chromosomes in the zebrafish (an organism which has much smaller chromosomes than a mammal). This technique when applied to man allows us to see any changes in chromosome number and to be able to identify which chromosome is altered in number. All this information can be used for determining the causes of human genetic disorders.
In addition, we have been able to utilise the resources made available during the sequencing of the human genome to develop DNA microarrays - microscope slides that are spotted with tiny amounts of individual fragments of human DNA that can be used to capture similar DNA from other humans - in order to compare the number of DNA copies between unaffected individuals and those with a particular disorder. This is known as comparative genomic hybridisation (array-CGH). We have also recently constructed a DNA microarray covering the entire human genome which we have used for various studies including the identification of normal copy number variation in human populations and the detection of genetic gains and losses in single cells. Using ultra-high resolution microarrays and flow sorting we have developed a method called arraypainting that enables us to efficiently and rapidly map and sequence balanced translocation breakpoints for example segments of DNA that have swapped chromosomes.
A major use of the array-CGH technology has been to identify copy number changes that are associated with genetic disorders in patients with congenital abnormalities and/or learning disabilities. These changes are often so small and rare that international collaboration is needed to identify similar cases. We have developed a clinical database called DECIPHER which allows clinicians and researchers using array-CGH to submit their results and share findings over the internet. DECIPHER has already facilitated the identification of new disease syndromes and associated changes in DNA, and will become more useful and powerful as the database grows. Over 60 major clinical laboratories worldwide are now members of the DECIPHER consortium.
The DECIPHER database is a collection of reported chromosomal micro-deletions, duplications, insertions, translocations and inversions, together with their locations in the human genome, and information about how each relates to human developmental delay, learning difficulties and inherited disorders.
Selected publications
-
Ultra-high resolution array painting facilitates breakpoint sequencing.
Journal of medical genetics 2007;44;1;51-8
PUBMED: 16971479; PMC: 2597908; DOI: 10.1136/jmg.2006.044909
-
High resolution array-CGH analysis of single cells.
Nucleic acids research 2007;35;3;e15
PUBMED: 17178751; PMC: 1807964; DOI: 10.1093/nar/gkl1030
-
Global variation in copy number in the human genome.
Nature 2006;444;7118;444-54
PUBMED: 17122850; PMC: 2669898; DOI: 10.1038/nature05329
Team
Team members
Members
- Nigel Carter
- Consultant
- Tomas Fitzgerald
- Bioinformatician
- Solena Le Scouarnec
- sls2@sanger.ac.ukunknown
- Anna Middleton
- am33@sanger.ac.ukEthics Researcher
- Bee Ling Ng
- bln@sanger.ac.ukSenior Scientific Manager
- Caroline Wright
- Senior Scientific Manager
Nigel Carter
- Consultant
I received my BA in 1973 and DPhil in Biology in 1978 from the University of York. At York, my first post-doctoral fellowship was funded by the World Heath Organisation (WHO) and involved field studies of the transmission dynamics of the blood fluke, Schistosoma mansoni in Kenya. In 1981, I moved to the Nuffield Department of Surgery, University of Oxford where I developed the use of flow cytometry and image analysis in transplant immunology. In 1988, I joined the Department of Pathology, Cambridge University, to sort chromosomes on a commercial flow cytometer and develop fluorescence in situ hybridisation.
Research
In 1994, I moved to the Wellcome Trust Sanger Centre and I am now a Senior Group Leader and head of the Molecular Cytogenetics Group, which supports the mapping and sequencing efforts of the Institute by extensive use of chromosome sorting, FISH mapping onto metaphase chromosomes, interphase nuclei and DNA fibres. My dedicated team have research interests in chromosome rearrangement, chromosome organisation, karyotype evolution, DNA homology between species, the causes of developmental disorders and the ethical implications of clinical application of genomic technologies. Current major projects are the DECIPHER database and the Deciphering Developmental Disorders study.
References
-
Fetal-specific DNA methylation ratio permits noninvasive prenatal diagnosis of trisomy 21.
Cytogenetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.
The trials performed worldwide toward noninvasive prenatal diagnosis (NIPD) of Down's syndrome (or trisomy 21) have shown the commercial and medical potential of NIPD compared to the currently used invasive prenatal diagnostic procedures. Extensive investigation of methylation differences between the mother and the fetus has led to the identification of differentially methylated regions (DMRs). In this study, we present a strategy using the methylated DNA immunoprecipitation (MeDiP) methodology in combination with real-time quantitative PCR (qPCR) to achieve fetal chromosome dosage assessment, which can be performed noninvasively through the analysis of fetal-specific DMRs. We achieved noninvasive prenatal detection of trisomy 21 by determining the methylation ratio of normal and trisomy 21 cases for each tested fetal-specific DMR present in maternal peripheral blood, followed by further statistical analysis. The application of this fetal-specific methylation ratio approach provided correct diagnosis of 14 trisomy 21 and 26 normal cases.
Funded by: Wellcome Trust
Nature medicine 2011;17;4;510-3
PUBMED: 21378977; DOI: 10.1038/nm.2312
-
Laser excitation power and the flow cytometric resolution of complex karyotypes.
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom. bln@sanger.ac.uk
The analytical resolution of individual chromosome peaks in the flow karyotype of cell lines is dependent on sample preparation and the detection sensitivity of the flow cytometer. We have investigated the effect of laser power on the resolution of chromosome peaks in cell lines with complex karyotypes. Chromosomes were prepared from a human gastric cancer cell line and a cell line from a patient with an abnormal phenotype using a modified polyamine isolation buffer. The stained chromosome suspensions were analyzed on a MoFlo sorter (Beckman Coulter) equipped with two water-cooled lasers (Coherent). A bivariate flow karyotype was obtained from each of the cell lines at various laser power settings and compared to a karyotype generated using laser power settings of 300 mW. The best separation of chromosome peaks was obtained with laser powers of 300 mW. This study demonstrates the requirement for high-laser powers for the accurate detection and purification of chromosomes, particularly from complex karyotypes, using a conventional flow cytometer.
Funded by: Wellcome Trust: WT077008
Cytometry. Part A : the journal of the International Society for Analytical Cytology 2010;77;6;585-8
PUBMED: 20506467; DOI: 10.1002/cyto.a.20904
-
Origins and functional impact of copy number variation in the human genome.
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK.
Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs.
Funded by: Canadian Institutes of Health Research; NHGRI NIH HHS: HG004221; NIGMS NIH HHS: GM081533; Wellcome Trust: 077006/Z/05/Z, 077008, 077009, 077014
Nature 2010;464;7289;704-12
PUBMED: 19812545; PMC: 3330748; DOI: 10.1038/nature08516
-
DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.
Cambridge University Department of Medical Genetics, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK. hvf21@cam.ac.uk
Many patients suffering from developmental disorders harbor submicroscopic deletions or duplications that, by affecting the copy number of dosage-sensitive genes or disrupting normal gene expression, lead to disease. However, many aberrations are novel or extremely rare, making clinical interpretation problematic and genotype-phenotype correlations uncertain. Identification of patients sharing a genomic rearrangement and having phenotypic features in common leads to greater certainty in the pathogenic nature of the rearrangement and enables new syndromes to be defined. To facilitate the analysis of these rare events, we have developed an interactive web-based database called DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources) which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance, inversions, and translocations. DECIPHER catalogs common copy-number changes in normal populations and thus, by exclusion, enables changes that are novel and potentially pathogenic to be identified. DECIPHER enhances genetic counseling by retrieving relevant information from a variety of bioinformatics resources. Known and predicted genes within an aberration are listed in the DECIPHER patient report, and genes of recognized clinical importance are highlighted and prioritized. DECIPHER enables clinical scientists worldwide to maintain records of phenotype and chromosome rearrangement for their patients and, with informed consent, share this information with the wider clinical research community through display in the genome browser Ensembl. By sharing cases worldwide, clusters of rare cases having phenotype and structural rearrangement in common can be identified, leading to the delineation of new syndromes and furthering understanding of gene function.
Funded by: Wellcome Trust: WT077008
American journal of human genetics 2009;84;4;524-33
PUBMED: 19344873; PMC: 2667985; DOI: 10.1016/j.ajhg.2009.03.010
-
Array painting: a protocol for the rapid analysis of aberrant chromosomes using DNA microarrays.
Human Genetics, Sulston Laboratories, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK. smg@sanger.ac.uk
Array painting is a technique that uses microarray technology to rapidly map chromosome translocation breakpoints. Previous methods to map translocation breakpoints have used fluorescence in situ hybridization (FISH) and have consequently been labor-intensive, time-consuming and restricted to the low breakpoint resolution imposed by the use of metaphase chromosomes. Array painting combines the isolation of derivative chromosomes (chromosomes with translocations) and high-resolution microarray analysis to refine the genomic location of translocation breakpoints in a single experiment. In this protocol, we describe array painting by isolation of derivative chromosomes using a MoFlo flow sorter, amplification of these derivatives using whole-genome amplification and hybridization onto commercially available oligonucleotide microarrays. Although the sorting of derivative chromosomes is a specialized procedure requiring sophisticated equipment, the amplification, labeling and hybridization of DNA is straightforward, robust and can be completed within 1 week. The protocol described produces good quality data; however, array painting is equally achievable using any combination of the available alternative methodologies for chromosome isolation, amplification and hybridization.
Funded by: Wellcome Trust: 077008, WT077008
Nature protocols 2009;4;12;1722-36
PUBMED: 19893508; PMC: 3330750; DOI: 10.1038/nprot.2009.183
-
Copy number variation and evolution in humans and chimpanzees.
School of Human Evolution & Social Change, Arizona State University, Tempe, Arizona 85287, USA.
Copy number variants (CNVs) underlie many aspects of human phenotypic diversity and provide the raw material for gene duplication and gene family expansion. However, our understanding of their evolutionary significance remains limited. We performed comparative genomic hybridization on a single human microarray platform to identify CNVs among the genomes of 30 humans and 30 chimpanzees as well as fixed copy number differences between species. We found that human and chimpanzee CNVs occur in orthologous genomic regions far more often than expected by chance and are strongly associated with the presence of highly homologous intrachromosomal segmental duplications. By adapting population genetic analyses for use with copy number data, we identified functional categories of genes that have likely evolved under purifying or positive selection for copy number changes. In particular, duplications and deletions of genes with inflammatory response and cell proliferation functions may have been fixed by positive selection and involved in the adaptive phenotypic differentiation of humans and chimpanzees.
Funded by: Howard Hughes Medical Institute; NCRR NIH HHS: RR014491, RR015087, RR016483; NHGRI NIH HHS: HG004221; Wellcome Trust
Genome research 2008;18;11;1698-710
PUBMED: 18775914; PMC: 2577862; DOI: 10.1101/gr.082016.108
-
Global variation in copy number in the human genome.
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.
Funded by: Wellcome Trust: 077008, 077009, 077014
Nature 2006;444;7118;444-54
PUBMED: 17122850; PMC: 2669898; DOI: 10.1038/nature05329
Tomas Fitzgerald
- Bioinformatician
Having completed my undergraduate degree, in Molecular Biology from the University of Sheffield, I spent a number of years in scientific industry. I worked on the development of DNA finger printing techniques and specialised analytical methods for real-time DNA case work. I joined Nigel Carter's group in 2006 where i began work as part of the CNV project. In 2009 i completed a Master's degree in Bioinformatics from the University of Cranfield. Currently, i work as part of the Deciphering Developmental Disorders (DDD) project lead by Nigel Carter while undertaking a part-time PhD at the University of Cranfield.
Research
My research is mainly centered around the development of large-scale analytical techniques for the exploration and interpretation of genetic variation. I have developed a number of analytical techniques that can be applied to time-series like data, most notabaly, spline, wavelet and change point detection algorithms. I am currently interested in any technique that can aid in the determination of the scale to which genetic variation contributes to making any individual unique.
References
-
FoSTeS, MMBIR and NAHR at the human proximal Xp region and the mechanisms of human Xq isochromosome formation.
Department of Medical Genetics, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands.
The recently described DNA replication-based mechanisms of fork stalling and template switching (FoSTeS) and microhomology-mediated break-induced replication (MMBIR) were previously shown to catalyze complex exonic, genic and genomic rearrangements. By analyzing a large number of isochromosomes of the long arm of chromosome X (i(Xq)), using whole-genome tiling path array comparative genomic hybridization (aCGH), ultra-high resolution targeted aCGH and sequencing, we provide evidence that the FoSTeS and MMBIR mechanisms can generate large-scale gross chromosomal rearrangements leading to the deletion and duplication of entire chromosome arms, thus suggesting an important role for DNA replication-based mechanisms in both the development of genomic disorders and cancer. Furthermore, we elucidate the mechanisms of dicentric i(Xq) (idic(Xq)) formation and show that most idic(Xq) chromosomes result from non-allelic homologous recombination between palindromic low copy repeats and highly homologous palindromic LINE elements. We also show that non-recurrent-breakpoint idic(Xq) chromosomes have microhomology-associated breakpoint junctions and are likely catalyzed by microhomology-mediated replication-dependent recombination mechanisms such as FoSTeS and MMBIR. Finally, we stress the role of the proximal Xp region as a chromosomal rearrangement hotspot.
Funded by: Wellcome Trust: 077008
Human molecular genetics 2011;20;10;1925-36
PUBMED: 21349920; PMC: 3428953; DOI: 10.1093/hmg/ddr074
-
aCGH.Spline--an R package for aCGH dye bias normalization.
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK. tf2@sanger.ac.uk
MOTIVATION: The careful normalization of array-based comparative genomic hybridization (aCGH) data is of critical importance for the accurate detection of copy number changes. The difference in labelling affinity between the two fluorophores used in aCGH-usually Cy5 and Cy3-can be observed as a bias within the intensity distributions. If left unchecked, this bias is likely to skew data interpretation during downstream analysis and lead to an increased number of false discoveries. RESULTS: In this study, we have developed aCGH.Spline, a natural cubic spline interpolation method followed by linear interpolation of outlier values, which is able to remove a large portion of the dye bias from large aCGH datasets in a quick and efficient manner. Conclusions: We have shown that removing this bias and reducing the experimental noise has a strong positive impact on the ability to detect accurately both copy number variation (CNV) and copy number alterations (CNA).
Funded by: Wellcome Trust: WT077008
Bioinformatics (Oxford, England) 2011;27;9;1195-200
PUBMED: 21357574; PMC: 3077069; DOI: 10.1093/bioinformatics/btr107
-
High incidence of recurrent copy number variants in patients with isolated and syndromic Müllerian aplasia.
Department of Obstetrics and Gynecology, University-Clinic Erlangen, Erlangen, Germany.
Background: Congenital malformations involving the Müllerian ducts are observed in around 5% of infertile women. Complete aplasia of the uterus, cervix, and upper vagina, also termed Müllerian aplasia or Mayer-Rokitansky-Kuster-Hauser (MRKH) syndrome, occurs with an incidence of around 1 in 4500 female births, and occurs in both isolated and syndromic forms. Previous reports have suggested that a proportion of cases, especially syndromic cases, are caused by variation in copy number at different genomic loci.
Methods: In order to obtain an overview of the contribution of copy number variation to both isolated and syndromic forms of Müllerian aplasia, copy number assays were performed in a series of 63 cases, of which 25 were syndromic and 38 isolated.
Results: A high incidence (9/63, 14%) of recurrent copy number variants in this cohort is reported here. These comprised four cases of microdeletion at 16p11.2, an autism susceptibility locus not previously associated with Müllerian aplasia, four cases of microdeletion at 17q12, and one case of a distal 22q11.2 microdeletion. Microdeletions at 16p11.2 and 17q12 were found in 4/38 (10.5%) cases with isolated Müllerian aplasia, and at 16p11.2, 17q12 and 22q11.2 (distal) in 5/25 cases (20%) with syndromic Müllerian aplasia.
Conclusion: The finding of microdeletion at 16p11.2 in 2/38 (5%) of isolated and 2/25 (8%) of syndromic cases suggests a significant contribution of this copy number variant alone to the pathogenesis of Müllerian aplasia. Overall, the high incidence of recurrent copy number variants in all forms of Müllerian aplasia has implications for the understanding of the aetiopathogenesis of the condition, and for genetic counselling in families affected by it.
Funded by: Wellcome Trust: 077008, 077014, 079973
Journal of medical genetics 2011;48;3;197-204
PUBMED: 21278390; PMC: 3322361; DOI: 10.1136/jmg.2010.082412
-
Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls.
Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed approximately 19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated approximately 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
Funded by: Arthritis Research UK: 17552; Medical Research Council: G0701810(85517); Wellcome Trust: 061858, 083948, 089989
Nature 2010;464;7289;713-20
PUBMED: 20360734; PMC: 2892339; DOI: 10.1038/nature08979
-
Origins and functional impact of copy number variation in the human genome.
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK.
Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs.
Funded by: Canadian Institutes of Health Research; NHGRI NIH HHS: HG004221; NIGMS NIH HHS: GM081533; Wellcome Trust: 077006/Z/05/Z, 077008, 077009, 077014
Nature 2010;464;7289;704-12
PUBMED: 19812545; PMC: 3330748; DOI: 10.1038/nature08516
-
Reduced TFAP2A function causes variable optic fissure closure and retinal defects and sensitizes eye development to mutations in other morphogenetic regulators.
Department of Cell and Developmental Biology, UCL, London, UK.
Mutations in the transcription factor encoding TFAP2A gene underlie branchio-oculo-facial syndrome (BOFS), a rare dominant disorder characterized by distinctive craniofacial, ocular, ectodermal and renal anomalies. To elucidate the range of ocular phenotypes caused by mutations in TFAP2A, we took three approaches. First, we screened a cohort of 37 highly selected individuals with severe ocular anomalies plus variable defects associated with BOFS for mutations or deletions in TFAP2A. We identified one individual with a de novo TFAP2A four amino acid deletion, a second individual with two non-synonymous variations in an alternative splice isoform TFAP2A2, and a sibling-pair with a paternally inherited whole gene deletion with variable phenotypic expression. Second, we determined that TFAP2A is expressed in the lens, neural retina, nasal process, and epithelial lining of the oral cavity and palatal shelves of human and mouse embryos--sites consistent with the phenotype observed in patients with BOFS. Third, we used zebrafish to examine how partial abrogation of the fish ortholog of TFAP2A affects the penetrance and expressivity of ocular phenotypes due to mutations in genes encoding bmp4 or tcf7l1a. In both cases, we observed synthetic, enhanced ocular phenotypes including coloboma and anophthalmia when tfap2a is knocked down in embryos with bmp4 or tcf7l1a mutations. These results reveal that mutations in TFAP2A are associated with a wide range of eye phenotypes and that hypomorphic tfap2a mutations can increase the risk of developmental defects arising from mutations at other loci.
Funded by: Wellcome Trust: 074376, 078047, WT077008
Human genetics 2009;126;6;791-803
PUBMED: 19685247; PMC: 3083835; DOI: 10.1007/s00439-009-0730-x
-
Genomic and genic deletions of the FOX gene cluster on 16q24.1 and inactivating mutations of FOXF1 cause alveolar capillary dysplasia and other malformations.
Dept of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. pawels@bcm.edu
Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a rare, neonatally lethal developmental disorder of the lung with defining histologic abnormalities typically associated with multiple congenital anomalies (MCA). Using array CGH analysis, we have identified six overlapping microdeletions encompassing the FOX transcription factor gene cluster in chromosome 16q24.1q24.2 in patients with ACD/MPV and MCA. Subsequently, we have identified four different heterozygous mutations (frameshift, nonsense, and no-stop) in the candidate FOXF1 gene in unrelated patients with sporadic ACD/MPV and MCA. Custom-designed, high-resolution microarray analysis of additional ACD/MPV samples revealed one microdeletion harboring FOXF1 and two distinct microdeletions upstream of FOXF1, implicating a position effect. DNA sequence analysis revealed that in six of nine deletions, both breakpoints occurred in the portions of Alu elements showing eight to 43 base pairs of perfect microhomology, suggesting replication error Microhomology-Mediated Break-Induced Replication (MMBIR)/Fork Stalling and Template Switching (FoSTeS) as a mechanism of their formation. In contrast to the association of point mutations in FOXF1 with bowel malrotation, microdeletions of FOXF1 were associated with hypoplastic left heart syndrome and gastrointestinal atresias, probably due to haploinsufficiency for the neighboring FOXC2 and FOXL1 genes. These differences reveal the phenotypic consequences of gene alterations in cis.
Funded by: Wellcome Trust
American journal of human genetics 2009;84;6;780-91
PUBMED: 19500772; PMC: 2694971; DOI: 10.1016/j.ajhg.2009.05.005
-
Array painting: a protocol for the rapid analysis of aberrant chromosomes using DNA microarrays.
Human Genetics, Sulston Laboratories, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK. smg@sanger.ac.uk
Array painting is a technique that uses microarray technology to rapidly map chromosome translocation breakpoints. Previous methods to map translocation breakpoints have used fluorescence in situ hybridization (FISH) and have consequently been labor-intensive, time-consuming and restricted to the low breakpoint resolution imposed by the use of metaphase chromosomes. Array painting combines the isolation of derivative chromosomes (chromosomes with translocations) and high-resolution microarray analysis to refine the genomic location of translocation breakpoints in a single experiment. In this protocol, we describe array painting by isolation of derivative chromosomes using a MoFlo flow sorter, amplification of these derivatives using whole-genome amplification and hybridization onto commercially available oligonucleotide microarrays. Although the sorting of derivative chromosomes is a specialized procedure requiring sophisticated equipment, the amplification, labeling and hybridization of DNA is straightforward, robust and can be completed within 1 week. The protocol described produces good quality data; however, array painting is equally achievable using any combination of the available alternative methodologies for chromosome isolation, amplification and hybridization.
Funded by: Wellcome Trust: 077008, WT077008
Nature protocols 2009;4;12;1722-36
PUBMED: 19893508; PMC: 3330750; DOI: 10.1038/nprot.2009.183
-
A robust statistical method for case-control association testing with copy number variation.
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Copy number variation (CNV) is pervasive in the human genome and can play a causal role in genetic diseases. The functional impact of CNV cannot be fully captured through linkage disequilibrium with SNPs. These observations motivate the development of statistical methods for performing direct CNV association studies. We show through simulation that current tests for CNV association are prone to false-positive associations in the presence of differential errors between cases and controls, especially if quantitative CNV measurements are noisy. We present a statistical framework for performing case-control CNV association studies that applies likelihood ratio testing of quantitative CNV measurements in cases and controls. We show that our methods are robust to differential errors and noisy data and can achieve maximal theoretical power. We illustrate the power of these methods for testing for association with binary and quantitative traits, and have made this software available as the R package CNVtools.
Funded by: Wellcome Trust: 061860
Nature genetics 2008;40;10;1245-52
PUBMED: 18776912; PMC: 2784596; DOI: 10.1038/ng.206
-
Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.
Computational Biology Group, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, UK. J.Marioni@damtp.cam.ac.uk
Background: Large-scale high throughput studies using microarray technology have established that copy number variation (CNV) throughout the genome is more frequent than previously thought. Such variation is known to play an important role in the presence and development of phenotypes such as HIV-1 infection and Alzheimer's disease. However, methods for analyzing the complex data produced and identifying regions of CNV are still being refined.
Results: We describe the presence of a genome-wide technical artifact, spatial autocorrelation or 'wave', which occurs in a large dataset used to determine the location of CNV across the genome. By removing this artifact we are able to obtain both a more biologically meaningful clustering of the data and an increase in the number of CNVs identified by current calling methods without a major increase in the number of false positives detected. Moreover, removing this artifact is critical for the development of a novel model-based CNV calling algorithm - CNVmix - that uses cross-sample information to identify regions of the genome where CNVs occur. For regions of CNV that are identified by both CNVmix and current methods, we demonstrate that CNVmix is better able to categorize samples into groups that represent copy number gains or losses.
Conclusion: Removing artifactual 'waves' (which appear to be a general feature of array comparative genomic hybridization (aCGH) datasets) and using cross-sample information when identifying CNVs enables more biological information to be extracted from aCGH experiments designed to investigate copy number variation in normal individuals.
Funded by: Wellcome Trust
Genome biology 2007;8;10;R228
PUBMED: 17961237; PMC: 2246302; DOI: 10.1186/gb-2007-8-10-r228
Solena Le Scouarnec
sls2@sanger.ac.uk unknown
After an undergraduate education in 'Cellular Biology and Physiology' at the University of Rennes (France), I moved to the University of Nantes where I completed my Master's degree, and obtained a PhD in 'Molecular Genetics' in 2008. My PhD at the 'institut du thorax' (Inserm U533/U915) was funded by the Ministry of Higher Education and Research (MRT fellowship) and focussed on cardiovascular genetics. After a 1-year postdoctoral position funded by the 'Fondation pour la Recherche Medicale' to work as a visiting scientist at the Wellcome Trust Sanger Institute, I started my current position in July 2009.
Research
My aim is to gain a better understanding of the genetic component of cardiovascular diseases, in particular rare arrhythmia syndromes and late-onset valvular defects. I apply state-of-the-art techniques such as array-CGH, high-throughput genotyping and exome sequencing to familial cases, to characterize the underlying genetic defect. The identification of new disease genes will potentially improve molecular diagnosis and prevention of sudden cardiac death, and facilitate the emergence of new therapeutic targets.
References
-
aCGH.Spline--an R package for aCGH dye bias normalization.
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK. tf2@sanger.ac.uk
MOTIVATION: The careful normalization of array-based comparative genomic hybridization (aCGH) data is of critical importance for the accurate detection of copy number changes. The difference in labelling affinity between the two fluorophores used in aCGH-usually Cy5 and Cy3-can be observed as a bias within the intensity distributions. If left unchecked, this bias is likely to skew data interpretation during downstream analysis and lead to an increased number of false discoveries. RESULTS: In this study, we have developed aCGH.Spline, a natural cubic spline interpolation method followed by linear interpolation of outlier values, which is able to remove a large portion of the dye bias from large aCGH datasets in a quick and efficient manner. Conclusions: We have shown that removing this bias and reducing the experimental noise has a strong positive impact on the ability to detect accurately both copy number variation (CNV) and copy number alterations (CNA).
Funded by: Wellcome Trust: WT077008
Bioinformatics (Oxford, England) 2011;27;9;1195-200
PUBMED: 21357574; PMC: 3077069; DOI: 10.1093/bioinformatics/btr107
-
Variable Na(v)1.5 protein expression from the wild-type allele correlates with the penetrance of cardiac conduction disease in the Scn5a(+/-) mouse model.
INSERM, UMR915, l'Institut du Thorax, Nantes, France.
Background: Loss-of-function mutations in SCN5A, the gene encoding Na(v)1.5 Na+ channel, are associated with inherited cardiac conduction defects and Brugada syndrome, which both exhibit variable phenotypic penetrance of conduction defects. We investigated the mechanisms of this heterogeneity in a mouse model with heterozygous targeted disruption of Scn5a (Scn5a(+/-) mice) and compared our results to those obtained in patients with loss-of-function mutations in SCN5A.
Based on ECG, 10-week-old Scn5a(+/-) mice were divided into 2 subgroups, one displaying severe ventricular conduction defects (QRS interval>18 ms) and one a mild phenotype (QRS< or = 18 ms; QRS in wild-type littermates: 10-18 ms). Phenotypic difference persisted with aging. At 10 weeks, the Na+ channel blocker ajmaline prolonged QRS interval similarly in both groups of Scn5a(+/-) mice. In contrast, in old mice (>53 weeks), ajmaline effect was larger in the severely affected subgroup. These data matched the clinical observations on patients with SCN5A loss-of-function mutations with either severe or mild conduction defects. Ventricular tachycardia developed in 5/10 old severely affected Scn5a(+/-) mice but not in mildly affected ones. Correspondingly, symptomatic SCN5A-mutated Brugada patients had more severe conduction defects than asymptomatic patients. Old severely affected Scn5a(+/-) mice but not mildly affected ones showed extensive cardiac fibrosis. Mildly affected Scn5a(+/-) mice had similar Na(v)1.5 mRNA but higher Na(v)1.5 protein expression, and moderately larger I(Na) current than severely affected Scn5a(+/-) mice. As a consequence, action potential upstroke velocity was more decreased in severely affected Scn5a(+/-) mice than in mildly affected ones.
Conclusions: Scn5a(+/-) mice show similar phenotypic heterogeneity as SCN5A-mutated patients. In Scn5a(+/-) mice, phenotype severity correlates with wild-type Na(v)1.5 protein expression.
Funded by: NHLBI NIH HHS: R01 HL083422
PloS one 2010;5;2;e9298
PUBMED: 20174578; PMC: 2824822; DOI: 10.1371/journal.pone.0009298
-
SCN5A mutations and the role of genetic background in the pathophysiology of Brugada syndrome.
INSERM, UMR915, Nantes, France. vincent.probst@chu-nantes.fr
Background: Mutations in SCN5A are identified in approximately 20% to 30% of probands affected by Brugada syndrome (BrS). However, in familial studies, the relationship between SCN5A mutations and BrS remains poorly understood. The aim of this study was to investigate the association of SCN5A mutations and BrS in a group of large genotyped families.
Families were included if at least 5 family members were carriers of the SCN5A mutation, which was identified in the proband. Thirteen large families composed of 115 mutation carriers were studied. The signature type I ECG was present in 54 mutation carriers (BrS-ECG+; 47%). In 5 families, we found 8 individuals affected by BrS but with a negative genotype (mutation-negative BrS-ECG+). Among these 8 mutation-negative BrS-ECG+ individuals, 3, belonging to 3 different families, had a spontaneous type I ECG, whereas 5 had a type I ECG only after the administration of sodium channel blockers. One of these 8 individuals had also experienced syncope. Mutation carriers had, on average, longer PR and QRS intervals than noncarriers, demonstrating that these mutations exerted functional effects.
Conclusions: Our results suggest that SCN5A mutations are not directly causal to the occurrence of a BrS-ECG+ and that genetic background may play a powerful role in the pathophysiology of BrS. These findings add further complexity to concepts regarding the causes of BrS, and are consistent with the emerging notion that the pathophysiology of BrS includes various elements beyond mutant sodium channels.
Circulation. Cardiovascular genetics 2009;2;6;552-7
PUBMED: 20031634; DOI: 10.1161/CIRCGENETICS.109.853374
-
Exon organization and novel alternative splicing of the human ANK2 gene: implications for cardiac function and human cardiac disease.
Department of Internal Medicine, Division of Cardiovascular Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA. shane-cunha@uiowa.edu
Recent findings illustrate a critical role for ankyrin-B function in normal cardiovascular physiology. Specifically, decreased expression of ankyrin-B in mice or human mutations in the ankyrin-B gene (ANK2) results in potentially fatal cardiac arrhythmias. Despite the clear role of ankyrin-B in heart, the mechanisms underlying transcriptional regulation of ANK2 are unknown. In fact, to date there is no description of ANK2 genomic organization. The aims of this study were to provide a comprehensive description of the ANK2 gene and to evaluate the relative expression of alternative splicing events associated with ANK2 transcription in heart. Using reverse-transcriptase PCR on mRNA isolated from human hearts, we identify seven new exons associated with the ANK2 gene including an alternative first exon located approximately 145 kb upstream of the previously-identified first exon. In addition, we identify over thirty alternative splicing events associated with ANK2 mRNA transcripts. Using real-time PCR and exon boundary-spanning primers to selectively amplify these splice variants, we demonstrate that these variants are expressed at varying levels in human heart. Finally, ankyrin-B immunoblot analysis demonstrates the expression of a heterogeneous population of ankyrin-B polypeptides in heart. ANK2 consists of 53 exons that span approximately 560 kb on human chromosome 4. Additionally, our data demonstrates that ANK2 is subject to complex transcriptional regulation that likely results in differential ankyrin-B polypeptide function.
Funded by: NHLBI NIH HHS: HL083422, HL084583, R01 HL084583-01
Journal of molecular and cellular cardiology 2008;45;6;724-34
PUBMED: 18790697; PMC: 2630508; DOI: 10.1016/j.yjmcc.2008.08.005
-
Dysfunction in ankyrin-B-dependent ion channel and transporter targeting causes human sinus node disease.
Institut National de la Sante et de la Recherche Medicale, UMR 915, F-44000 Nantes, France.
The identification of nearly a dozen ion channel genes involved in the genesis of human atrial and ventricular arrhythmias has been critical for the diagnosis and treatment of fatal cardiovascular diseases. In contrast, very little is known about the genetic and molecular mechanisms underlying human sinus node dysfunction (SND). Here, we report a genetic and molecular mechanism for human SND. We mapped two families with highly penetrant and severe SND to the human ANK2 (ankyrin-B/AnkB) locus. Mice heterozygous for AnkB phenocopy human SND displayed severe bradycardia and rate variability. AnkB is essential for normal membrane organization of sinoatrial node cell channels and transporters, and AnkB is required for physiological cardiac pacing. Finally, dysfunction in AnkB-based trafficking pathways causes abnormal sinoatrial node (SAN) electrical activity and SND. Together, our findings associate abnormal channel targeting with human SND and highlight the critical role of local membrane organization for sinoatrial node excitability.
Funded by: NHLBI NIH HHS: HL079031, HL083422, HL084583, HL090905, HL62494, HL70250, R01 HL090905-05
Proceedings of the National Academy of Sciences of the United States of America 2008;105;40;15617-22
PUBMED: 18832177; PMC: 2563133; DOI: 10.1073/pnas.0805500105
-
Sodium channel β1 subunit mutations associated with Brugada syndrome and cardiac conduction disease in humans.
Department of Medicine and Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
Brugada syndrome is a genetic disease associated with sudden cardiac death that is characterized by ventricular fibrillation and right precordial ST segment elevation on ECG. Loss-of-function mutations in SCN5A, which encodes the predominant cardiac sodium channel alpha subunit NaV1.5, can cause Brugada syndrome and cardiac conduction disease. However, SCN5A mutations are not detected in the majority of patients with these syndromes, suggesting that other genes can cause or modify presentation of these disorders. Here, we investigated SCN1B, which encodes the function-modifying sodium channel beta1 subunit, in 282 probands with Brugada syndrome and in 44 patients with conduction disease, none of whom had SCN5A mutations. We identified 3 mutations segregating with arrhythmia in 3 kindreds. Two of these mutations were located in a newly described alternately processed transcript, beta1B. Both the canonical and alternately processed transcripts were expressed in the human heart and were expressed to a greater degree in Purkinje fibers than in heart muscle, consistent with the clinical presentation of conduction disease. Sodium current was lower when NaV1.5 was coexpressed with mutant beta1 or beta1B subunits than when it was coexpressed with WT subunits. These findings implicate SCN1B as a disease gene for human arrhythmia susceptibility.
Funded by: NHLBI NIH HHS: HL46681, HL65962
The Journal of clinical investigation 2008;118;6;2260-8
PUBMED: 18464934; PMC: 2373423; DOI: 10.1172/JCI33891
-
Sudden cardiac arrest associated with early repolarization.
Université Bordeaux, Hôpital Haut-Lévêque, Bordeaux-Pessac, France. michel.haissaguerre@chu-bordeaux.fr
Background: Early repolarization is a common electrocardiographic finding that is generally considered to be benign. Its potential to cause cardiac arrhythmias has been hypothesized from experimental studies, but it is not known whether there is a clinical association with sudden cardiac arrest.
Methods: We reviewed data from 206 case subjects at 22 centers who were resuscitated after cardiac arrest due to idiopathic ventricular fibrillation and assessed the prevalence of electrocardiographic early repolarization. The latter was defined as an elevation of the QRS-ST junction of at least 0.1 mV from baseline in the inferior or lateral lead, manifested as QRS slurring or notching. The control group comprised 412 subjects without heart disease who were matched for age, sex, race, and level of physical activity. Follow-up data that included the results of monitoring with an implantable defibrillator were obtained for all case subjects.
Results: Early repolarization was more frequent in case subjects with idiopathic ventricular fibrillation than in control subjects (31% vs. 5%, P<0.001). Among case subjects, those with early repolarization were more likely to be male and to have a history of syncope or sudden cardiac arrest during sleep than those without early repolarization. In eight subjects, the origin of ectopy that initiated ventricular arrhythmias was mapped to sites concordant with the localization of repolarization abnormalities. During a mean (+/-SD) follow-up of 61+/-50 months, defibrillator monitoring showed a higher incidence of recurrent ventricular fibrillation in case subjects with a repolarization abnormality than in those without such an abnormality (hazard ratio, 2.1; 95% confidence interval, 1.2 to 3.5; P=0.008).
Conclusions: Among patients with a history of idiopathic ventricular fibrillation, there is an increased prevalence of early repolarization.
The New England journal of medicine 2008;358;19;2016-23
PUBMED: 18463377; DOI: 10.1056/NEJMoa071968
-
[Genetic aspects of valvulopathies].
Institut du thorax, Institut de biologie, INSERM U533, Université de Nantes et CHU Nantes.
Valvular dystrophies due to myxoid degeneration are common and potentially serious cardiac pathologies. They constitute a heterogeneous group of which the most usual is idiopathic mitral valvular prolapse (Barlow's disease). The majority of mitral valvular prolapses are sporadic, but there are several familial forms. Transmission is usually autosomal dominant with incomplete penetrance and variable expression. The first chromosomal location to be identified was on the 16p11-13 chromosome. Since then, two other loci have been identified on the 11p15.4 and 13q31-32 chromosomes. Our team has recently identified the first gene responsible for myxoid valvulopathy linked to the X chromosome, from a large family of 318 members. This is the gene that codes for filamin A, which is a cytoskeleton protein. The frequency of mutations in this gene is still unknown, but out of 7 families in which transmission was compatible with X-linked transmission, mutations were discovered in 4 of the families. Thanks to a genetic epidemiological approach, we have also demonstrated that there are familial forms of aortic stenosis, which are probably common. Identification of the genes implicated in these common forms of valvular pathology is important, as it will allow a better understanding of the pathophysiology of these valvular disorders and could lead to better therapeutic management in the future.
Archives des maladies du coeur et des vaisseaux 2007;100;12;1013-20
PUBMED: 18223515
-
Defining the cellular phenotype of "ankyrin-B syndrome" variants: human ANK2 variants associated with clinical phenotypes display a spectrum of activities in cardiomyocytes.
Department of Internal Medicine, University of Iowa College of Medicine, Iowa City, USA. peter-mohler@uiowa.edu
Background: Mutations in the ankyrin-B gene (ANK2) cause type 4 long-QT syndrome and have been described in kindreds with other arrhythmias. The frequency of ANK2 variants in large populations and molecular mechanisms underlying the variability in the clinical phenotypes are not established. More importantly, there is no cellular explanation for the range of severity of cardiac phenotypes associated with specific ANK2 variants.
We performed a comprehensive screen of ANK2 in populations (control, congenital arrhythmia, drug-induced long-QT syndrome) of different ethnicities to discover unidentified ANK2 variants. We identified 7 novel nonsynonymous ANK2 variants; 4 displayed abnormal activity in cardiomyocytes. Including the 4 new variants, 9 human ANK2 loss-of-function variants have been identified. However, the clinical phenotypes associated with these variants vary strikingly, from no obvious phenotype to manifest long-QT syndrome and sudden death, suggesting that mutants confer a spectrum of cellular phenotypes. We then characterized the relative severity of loss-of-function properties of all 9 nonsynonymous ANK2 variants identified to date in primary cardiomyocytes and identified a range of in vitro phenotypes, including wild-type, simple loss-of-function, and severe loss-of-function activity, seen with the variants causing severe human phenotypes.
Conclusions: We present the first description of differences in cellular phenotypes conferred by specific ANK2 variants. We propose that the various degrees of ankyrin-B loss of function contribute to the range of severity of cardiac dysfunction. These data identify ANK2 variants as modulators of human arrhythmias, provide the first insight into the clinical spectrum of "ankyrin-B syndrome," and reinforce the role of ankyrin-B-dependent protein interactions in regulating cardiac electrogenesis.
Funded by: NHLBI NIH HHS: HL65962, R01HL083422, R01HL084583
Circulation 2007;115;4;432-41
PUBMED: 17242276; DOI: 10.1161/CIRCULATIONAHA.106.656512
-
Familial aggregation of calcific aortic valve stenosis in the western part of France.
l'Institut du thorax, Service de Cardiologie, Nantes, France. vincent.probst@chu-nantes.fr
Background: Calcific aortic valve stenosis (CAVS) is the most common valvular defect in developed countries. Unlike mitral valve prolapse, there is no demonstration that a familial factor could play a role in the occurrence of this disease. The aim of this study was to demonstrate a familial aggregation for CAVS.
We used the files of 2527 consecutive patients operated on for CAVS in our institution between 1992 and 2002 to map the distribution of operated CAVS in the western part of France. In a second step, we investigated clinically and genealogically the clusters with the highest rates of operated CAVS to detect familial forms of the disease. The geographic distribution of CAVS is highly heterogeneous, with an average frequency of operated CAVS of 1.13 per 1000 inhabitants but up to 9.38 per 1000 in specific parishes. A screening of the population from the parishes with the highest rate of operated CAVS allowed us to identify 5 families with > or =3 sibs affected by CAVS. A large genealogical analysis performed in one of these families allowed us to link 48 patients who derived from 34 nuclear families. Genealogical information could be traced to a common ancestor within 13 generations.
Conclusions: Identification of clusters and large families affected by a classic form of CAVS demonstrates a familial aggregation for this disease.
Circulation 2006;113;6;856-60
PUBMED: 16461814; DOI: 10.1161/CIRCULATIONAHA.105.569467
Anna Middleton
am33@sanger.ac.uk Ethics Researcher
Dr Anna Middleton is the only social scientist working full time at Sanger Institute on ethical issues surrounding genomic research studies.
Anna received her PhD in Genetics and Psychology in 2000 from the University of Leeds and completed her training as a genetic counsellor (MSc Genetic Counselling, University of Manchester) in 1995.
In her most recent academic position Anna was Chief and Principal Investigator on a 4 year, NIHR funded, research project at Cardiff University. She ran a mixed-method qualitative and quantitative research project that explored the attitudes of d/Deaf and hard of hearing people towards genetic counselling services.
Research
Together with Prof Mike Parker from Ethox at University of Oxford, Anna is designing and conducting an empirical quantitative and qualitative study to document the views of research participants, genetic health professionals, genomic researchers and members of the public. The online questionnaire (available for anyone to complete) can be found here: http://www.ddduk.org/ethicsresearch.html. Anna will also be conducting qualitative interviews, employing thematic analysis, to explore attitudes in more depth.
See: http://www.am3333.wix.com/annamiddleton
References
-
Communication about DTC testing: commentary on a 'family experience of personal genomics'.
This paper provides a commentary on 'Family Experience of Personal Genomics' (Corpas 2012). An overview is offered on the communication literature available to help support individuals and families to communicate about genetic information. Despite there being a wealth of evidence, built on years of genetic counseling practice, this does not appear to have been translated clearly to the Direct to Consumer (DTC) testing market. In many countries it is possible to order a DTC genetic test without the involvement of any health professional; there has been heated debate about whether this is appropriate or not. Much of the focus surrounding this has been on whether it is necessary to have a health professional available to offer their clinical knowledge and help with interpreting the DTC genetic test data. What has been missed from this debate is the importance of enabling customers of DTC testing services access to the abundance of information about how to communicate their genetic risks to others, including immediate family. Family communication about health and indeed genetics can be fraught with difficulty. Genetic health professionals, specifically genetic counselors, have particular expertise in family communication about genetics. Such information could be incredibly useful to kinships as they grapple with knowing how to communicate their genomic information with relatives.
Funded by: Wellcome Trust: WT077008
Journal of genetic counseling 2012;21;3;392-8
PUBMED: 22223062; DOI: 10.1007/s10897-011-9472-8
-
Preferences for communication in clinic from deaf people: a cross-sectional study.
Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK. Middletona1@cardiff.ac.uk
To explore the preferences of deaf people for communication in a hospital consultation.
Methods: Design--cross-sectional survey, using a structured, postal questionnaire. Setting--survey of readers of two journals for deaf and hard of hearing people. Participants--999 self-selected individuals with hearing loss in the UK, including those who use sign language and those who use speech. Main outcome measures--preferred mode of communication.
Results: A total of 11% of participants preferred to use sign language within everyday life, 70% used speech and 17% used a mixture of sign and speech. Within a clinic setting, 50% of the sign language users preferred to have a consultation via a sign language interpreter and 43% indicated they would prefer to only have a consultation directly with a signing health professional; 7% would accept a consultation in speech as long as there was good deaf awareness from the health professional, indicated by a knowledge of lip-reading/speech-reading. Of the deaf speech users, 98% preferred to have a consultation in speech and of this group 71% indicated that they would only accept this if the health professional had good deaf awareness. Among the participants who used a mixture of sign language and speech, only 5% said they could cope with a consultation in speech with no deaf awareness whereas 46% were accepting of a spoken consultation as long as it was provided with good deaf awareness; 30% preferred to use an interpreter and 14% preferred to have a consultation directly with a signing health professional.
Conclusions: The hospital communication preferences for most people with deafness could be met by increasing deaf awareness training for health professionals, a greater provision of specialized sign language interpreters and of health professionals who can use fluent sign language directly with clients in areas where contact with deaf people is frequent.
Funded by: Department of Health
Journal of evaluation in clinical practice 2010;16;4;811-7
PUBMED: 20557411; DOI: 10.1111/j.1365-2753.2009.01207.x
-
Communicating in a healthcare setting with people who have hearing loss.
Institute of Medical Genetics, Cardiff University, Cardiff CF14 4XN, UK.
BMJ (Clinical research ed.) 2010;341;c4672
PUBMED: 20880905
-
Reproductive liberty and deafness: Clause 14(4)(9) of embryo bill should be amended or deleted.
BMJ (Clinical research ed.) 2008;336;7651;976
PUBMED: 18456608; PMC: 2364821; DOI: 10.1136/bmj.39563.495741.80
-
Providing a transcultural genetic counseling service in the UK.
Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK. Middletona1@cardiff.ac.uk
This paper uses a broad definition of culture to explore the practice of transcultural genetic counseling through three case studies. The first case involves a White genetic counselor seeing an Asian family, the second, an Asian genetic counselor seeing an Asian family and the third, a hearing genetic counselor seeing a culturally Deaf client. Boundaries, transference and countertransference reactions are considered within each transcultural encounter and the author of each case reflects in detail on their role in the client interaction and their impact on the transcultural dynamic. The cases are used to illustrate some cultural beliefs or characteristics that may challenge the genetic counselor's expectations. The value of identifying and interpreting these differences to facilitate useful clinical work is considered. The paper debates, where possible, whether it is helpful to culturally match genetic counselor and client.
Journal of genetic counseling 2007;16;5;567-82
PUBMED: 17492497; DOI: 10.1007/s10897-007-9089-0
-
Editorial on supervision.
This Editorial provides background information to inform the report from the United Kingdom (UK) and Eire Association of Genetic Nurses and Counsellors (AGNC) Supervision Working Group on Genetic Counselling Supervision. We begin by introducing the context of practice as a genetic counselor in the UK and then follow with an overview of events that have happened in our profession that led to the need and creation of the report. Genetic counseling supervision has become instrumental to our practice, training and registration as genetic counselors in the UK.
Journal of genetic counseling 2007;16;2;123-5
PUBMED: 17333405; DOI: 10.1007/s10897-006-9063-2
-
Reflections on the experience of counseling supervision by a team of genetic counselors from the UK.
Institute of Medical Genetics, Heath Park, Cardiff, CF14 4XN, UK. middletonanna1@cardiff.ac.uk
Despite it being generally acknowledged that counseling supervision is a vital part of the work for experienced genetic counselors and not just students, not all practising genetic counselors in the United Kingdom and Eire have access to this yet. This case study documents the supervision experience of our team of genetic counselors from Cambridge in the U.K. We document our retrospective thoughts on working practice before supervision was available in our department. We also give an overview of the individual and collective views of having one-to-one supervision only and then one year later, the impact of adding group supervision. Our 'supervision journey' is recorded using a practitioner-centred approach with a mixed method of data collection. Two focus group discussions and two written questionnaires were used, at different time points to gather attitudes. This paper captures experiences as our practice of supervision has evolved. This work is relevant to practising genetic counselors around the world who either do not yet have access to supervision, are planning its implementation or else are adding different types of supervision to their practice.
Journal of genetic counseling 2007;16;2;143-55
PUBMED: 17333406; DOI: 10.1007/s10897-006-9074-z
-
Report from the UK and Eire Association of Genetic Nurses and Counsellors (AGNC) supervision working group on genetic counselling supervision.
Northwest Regional Genetics Service, St. Mary's Hospital, Manchester, UK.
The Association of Genetic Nurses and Counsellors (AGNC) is the professional organisation which represents genetic counsellors and genetic nurses in the United Kingdom (UK) and Eire. The AGNC recognises that genetic counselling supervision is instrumental to the practice, training and registration of genetic counsellors in the UK. The AGNC formed a Supervision Working Group, whose terms of reference were to collate information on supervision and create a list of 'best practice' recommendations for its genetic counsellor members. This report delivers the findings from the Supervision Working Group and has been peer reviewed by the AGNC membership in the UK and Eire and ratified by the AGNC Committee. It offers a working definition of genetic counselling supervision, gives an overview of some of the literature on supervision and concludes with practice recommendations.
Journal of genetic counseling 2007;16;2;127-42
PUBMED: 17308871; DOI: 10.1007/s10897-006-9065-0
-
Prenatal diagnosis for inherited deafness--what is the potential demand?
Department of Clinical Genetics, Ashley Wing, St. James's Hospital, Leeds, UK.
Genetic testing for inherited deafness is now available within some genetics centres. This study used a structured questionnaire to assess the potential uptake of prenatal diagnosis (PND) for inherited deafness, and document the opinions of deaf and hearing individuals toward PND and termination of pregnancy (TOP) for hearing status. Participants were self-selected from the whole of the UK, of whom 644 were deaf, 143 were hard of hearing or deafened, and 527 were hearing individuals who had either a deaf parent or child. The results showed that 21% of deaf, 39% of hard of hearing and deafened, and 49% of hearing participants said they would consider PND for deafness. Six percent of deaf, 11% of hard of hearing and deafened, and 16% of hearing participants said they would consider a TOP if the fetus was found to be deaf. Two percent of deaf participants said they would prefer to have deaf children and would consider a TOP if the fetus was found to be hearing.
Journal of genetic counseling 2001;10;2;121-31
PUBMED: 11767801
-
Attitudes of deaf adults toward genetic testing for hereditary deafness.
Department of Clinical Genetics, St. James's Hospital, University of Leeds, United Kingdom. am@psychology.leeds.ac.uk
Recent advances within molecular genetics to identify the genes for deafness mean that it is now possible for genetic-counseling services to offer genetic testing for deafness to certain families. The purpose of this study is to document the attitudes of deaf adults toward genetic testing for deafness. A structured, self-completion questionnaire was given to delegates at an international conference on the "Deaf Nation," held at the University of Central Lancashire in 1997. The conference was aimed at well-educated people, with an emphasis on Deaf culture issues. Eighty-seven deaf delegates from the United Kingdom returned completed questionnaires. The questionnaire had been designed to quantitatively assess attitudes toward genetics, interest in prenatal diagnosis (PND) for deafness, and preference for having deaf or hearing children. The results from this study provide evidence of a predominantly negative attitude toward genetics and its impact on deaf people, in a population for whom genetic-counseling services are relevant. Fifty-five percent of the sample thought that genetic testing would do more harm than good, 46% thought that its potential use devalued deaf people, and 49% were concerned about new discoveries in genetics. When asked about testing in pregnancy, 16% of participants said that they would consider having PND, and, of these, 29% said that they would prefer to have deaf children. Geneticists need to appreciate that some deaf persons may prefer to have deaf children and may consider the use of genetic technology to achieve this. Any genetic-counseling service set up for families with deafness can only be effective and appropriate if clinicians and counselors take into consideration the beliefs and values of the deaf community at large.
American journal of human genetics 1998;63;4;1175-80
PUBMED: 9758618; PMC: 1377492; DOI: 10.1086/302060
Bee Ling Ng
bln@sanger.ac.uk Senior Scientific Manager
I completed my first degree at the University of Wales (Cardiff). I then worked at National University Medical Institute (Confocal Microscopy and Cytometry Unit), in Singapore, providing flow cytometry service to researchers and postgraduates. During that time, I completed my postgraduate studies (part-time) and was awarded MSc in Environmental Engineering. I continued to pursue my interest in flow cytometry and joined Nigel Carter's group in 2003.
Research
I am the Senior Scientific Manager for the institute Cytometry Core Facility. We work closely with our institute researchers and actively participate in collaboration projects within and outside the institute. Currently, we work with MGP in providing the flow cytometry service and on collaborative with various genome project groups in the isolation of chromosomes from different species of animals.
My research interests include improving the data resolution of chromosome analysis in cell lines with complex karyotypes and sorting of chromosomes with high purity.
References
-
Reprogramming of T cells to natural killer-like cells upon Bcl11b deletion.
Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK.
T cells develop in the thymus and are critical for adaptive immunity. Natural killer (NK) lymphocytes constitute an essential component of the innate immune system in tumor surveillance, reproduction, and defense against microbes and viruses. Here, we show that the transcription factor Bcl11b was expressed in all T cell compartments and was indispensable for T lineage development. When Bcl11b was deleted, T cells from all developmental stages acquired NK cell properties and concomitantly lost or decreased T cell-associated gene expression. These induced T-to-natural killer (ITNK) cells, which were morphologically and genetically similar to conventional NK cells, killed tumor cells in vitro, and effectively prevented tumor metastasis in vivo. Therefore, ITNKs may represent a new cell source for cell-based therapies.
Funded by: Biotechnology and Biological Sciences Research Council; Medical Research Council; Wellcome Trust
Science (New York, N.Y.) 2010;329;5987;85-9
PUBMED: 20538915; PMC: 3628452; DOI: 10.1126/science.1188063
-
Laser excitation power and the flow cytometric resolution of complex karyotypes.
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom. bln@sanger.ac.uk
The analytical resolution of individual chromosome peaks in the flow karyotype of cell lines is dependent on sample preparation and the detection sensitivity of the flow cytometer. We have investigated the effect of laser power on the resolution of chromosome peaks in cell lines with complex karyotypes. Chromosomes were prepared from a human gastric cancer cell line and a cell line from a patient with an abnormal phenotype using a modified polyamine isolation buffer. The stained chromosome suspensions were analyzed on a MoFlo sorter (Beckman Coulter) equipped with two water-cooled lasers (Coherent). A bivariate flow karyotype was obtained from each of the cell lines at various laser power settings and compared to a karyotype generated using laser power settings of 300 mW. The best separation of chromosome peaks was obtained with laser powers of 300 mW. This study demonstrates the requirement for high-laser powers for the accurate detection and purification of chromosomes, particularly from complex karyotypes, using a conventional flow cytometer.
Funded by: Wellcome Trust: WT077008
Cytometry. Part A : the journal of the International Society for Analytical Cytology 2010;77;6;585-8
PUBMED: 20506467; DOI: 10.1002/cyto.a.20904
-
Array painting: a protocol for the rapid analysis of aberrant chromosomes using DNA microarrays.
Human Genetics, Sulston Laboratories, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK. smg@sanger.ac.uk
Array painting is a technique that uses microarray technology to rapidly map chromosome translocation breakpoints. Previous methods to map translocation breakpoints have used fluorescence in situ hybridization (FISH) and have consequently been labor-intensive, time-consuming and restricted to the low breakpoint resolution imposed by the use of metaphase chromosomes. Array painting combines the isolation of derivative chromosomes (chromosomes with translocations) and high-resolution microarray analysis to refine the genomic location of translocation breakpoints in a single experiment. In this protocol, we describe array painting by isolation of derivative chromosomes using a MoFlo flow sorter, amplification of these derivatives using whole-genome amplification and hybridization onto commercially available oligonucleotide microarrays. Although the sorting of derivative chromosomes is a specialized procedure requiring sophisticated equipment, the amplification, labeling and hybridization of DNA is straightforward, robust and can be completed within 1 week. The protocol described produces good quality data; however, array painting is equally achievable using any combination of the available alternative methodologies for chromosome isolation, amplification and hybridization.
Funded by: Wellcome Trust: 077008, WT077008
Nature protocols 2009;4;12;1722-36
PUBMED: 19893508; PMC: 3330750; DOI: 10.1038/nprot.2009.183
-
Array painting reveals a high frequency of balanced translocations in breast cancer cell lines that break in cancer-relevant genes.
Department of Pathology, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK.
Chromosome translocations in the common epithelial cancers are abundant, yet little is known about them. They have been thought to be almost all unbalanced and therefore dismissed as mostly mediating tumour suppressor loss. We present a comprehensive analysis by array painting of the chromosome translocations of breast cancer cell lines HCC1806, HCC1187 and ZR-75-30. In array painting, chromosomes are isolated by flow cytometry, amplified and hybridized to DNA microarrays. A total of 200 breakpoints were identified and all were mapped to 1 Mb resolution on bacterial artificial chromosome (BAC) arrays, then 40 selected breakpoints, including all balanced breakpoints, were further mapped on tiling-path BAC arrays or to around 2 kb resolution using oligonucleotide arrays. Many more of the translocations were balanced at 1 Mb resolution than expected, either reciprocal (eight in total) or balanced for at least one participating chromosome (19 paired breakpoints). Second, many of the breakpoints were at genes that are plausible targets of oncogenic translocation, including balanced breaks at CTCF, EP300/p300 and FOXP4. Two gene fusions were demonstrated, TAX1BP1-AHCY and RIF1-PKD1L1. Our results support the idea that chromosome rearrangements may play an important role in common epithelial cancers such as breast cancer.
Funded by: Cancer Research UK: A4392; Wellcome Trust: 077008
Oncogene 2008;27;23;3345-59
PUBMED: 18084325; PMC: 2423006; DOI: 10.1038/sj.onc.1210993
-
Flow analysis and sorting of microchromosomes (<3 Mb).
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom. bln@sanger.ac.uk
Background: The analysis and isolation of high numbers of chromosomes smaller than 3 Mb in size (microchromosomes) with good purity is dependent primarily on the detection sensitivity of the flow cytometer and the precision of the sort unit. The aim of this study was to investigate the capability of using a conventional flow cytometer for the detection and sorting at high purity microchromosomes with an estimated size of 2.7 Mb.
Methods: Chromosomes were isolated from a human cell line containing a pair of X-derived microchromosomes, using a modified polyamine isolation buffer. The chromosome preparation was labeled with Hoechst and Chromomycin and analyzed and purified using a MoFlo sorter (DAKO) configured for high-speed sorting. The purity of the flow-sorted microchromosomes was assessed by reverse chromosome painting.
Results: Improved resolution of the peak of microchromosomes in a bivariate plot of Hoechst versus Chromomycin fluorescence was obtainable after discriminating clumps and debris based on gating data within a FSC versus pulse width plot.
Conclusions: Chromosomes of smaller size, less than 3 Mb, can be detected with high resolution and flow-sorted with high purity using a conventional flow sorter.
Funded by: Wellcome Trust: 077008
Cytometry. Part A : the journal of the International Society for Analytical Cytology 2007;71;6;410-3
PUBMED: 17342775; PMC: 2672157; DOI: 10.1002/cyto.a.20394
-
Definition of the zebrafish genome using flow cytometry and cytogenetic mapping.
Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA. jfreeman7@partners.org <jfreeman7@partners.org>
Background: The zebrafish (Danio rerio) is an important vertebrate model organism system for biomedical research. The syntenic conservation between the zebrafish and human genome allows one to investigate the function of human genes using the zebrafish model. To facilitate analysis of the zebrafish genome, genetic maps have been constructed and sequence annotation of a reference zebrafish genome is ongoing. However, the duplicative nature of teleost genomes, including the zebrafish, complicates accurate assembly and annotation of a representative genome sequence. Cytogenetic approaches provide "anchors" that can be integrated with accumulating genomic data.
Results: Here, we cytogenetically define the zebrafish genome by first estimating the size of each linkage group (LG) chromosome using flow cytometry, followed by the cytogenetic mapping of 575 bacterial artificial chromosome (BAC) clones onto metaphase chromosomes. Of the 575 BAC clones, 544 clones localized to apparently unique chromosomal locations. 93.8% of these clones were assigned to a specific LG chromosome location using fluorescence in situ hybridization (FISH) and compared to the LG chromosome assignment reported in the zebrafish genome databases. Thirty-one BAC clones localized to multiple chromosomal locations in several different hybridization patterns. From these data, a refined second generation probe panel for each LG chromosome was also constructed.
Conclusion: The chromosomal mapping of the 575 large-insert DNA clones allows for these clones to be integrated into existing zebrafish mapping data. An accurately annotated zebrafish reference genome serves as a valuable resource for investigating the molecular basis of human diseases using zebrafish mutant models.
Funded by: NCI NIH HHS: R01-CA111560; Wellcome Trust
BMC genomics 2007;8;195
PUBMED: 17597531; PMC: 1925092; DOI: 10.1186/1471-2164-8-195
-
Factors affecting flow karyotype resolution.
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. bln@sanger.ac.uk
Background: One of the major factors which influences the chromosome purity achievable particularly during high speed sorting is the analytical resolution of individual chromosome peaks in the flow karyotype, as well as the amount of debris and fragmented chromosomes. We have investigated the factors involved in the preparation of chromosome suspensions that influence karyotype resolution.
Methods: Chromosomes were isolated from various human and animal cell types using a series of polyamine buffer isolation protocols modified with respect to pH, salt concentration, and chromosome staining time. Each preparation was analyzed on a MoFlo sorter (DAKO) configured for high speed sorting and the resolution of the flow karyotypes compared.
Results: High resolution flow cytometric data was obtained with chromosomes optimally isolated using hypotonic solution buffered at pH 8.0 and polyamine isolation buffer (with NaCl excluded) between pH 7.50 and 8.0. Extending staining time to more than 8 h with chromosome suspensions isolated from cell lines subjected to sufficient metaphase arrest times gave the best result with the lowest percentage of debris generated, tighter chromosome peaks with overall lower coefficients of variation, and a 1- to 5-fold increase in the yield of isolated chromosomes.
Conclusions: Optimization of buffer pH and the length of staining improved karyotype resolution particularly for larger chromosomes and reduced the presence of chromosome fragments (debris). However, the most interesting and surprising finding was that the exclusion of NaCl in PAB buffer improved the yield and resolution of larger chromosomes.
Cytometry. Part A : the journal of the International Society for Analytical Cytology 2006;69;9;1028-36
PUBMED: 16969800; DOI: 10.1002/cyto.a.20330
-
BRCTx is a novel, highly conserved RAD18-interacting protein.
The Wellcome Trust Sanger Institute Hinxton, Cambs CB10 1SA, United Kingdom.
The BRCT domain is a highly conserved module found in many proteins that participate in DNA damage checkpoint regulation, DNA repair, and cell cycle control. Here we describe the cloning, characterization, and targeted mutagenesis of Brctx, a novel gene with a BRCT motif. Brctx was found to be expressed ubiquitously in adult tissues and during development, with the highest levels found in testis. Brctx-deficient mice develop normally, show no pathological abnormalities, and are fertile. BRCTx binds to the C terminus of hRAD18 in yeast two-hybrid and immunoprecipitation assays and colocalizes with this protein in the nucleus. Despite this, Brctx-deficient murine embryonic fibroblasts (MEFs) do not show overt sensitivity to DNA-damaging agents. MEFs from Brctx-deficient embryos grow at a similar rate to wild-type MEF CD4/CD8 expressions, and the cell cycle parameters of thymocytes from wild-type and Brctx knockout animals are indistinguishable. Intriguingly, the BRCT domain of BRCTx is responsible for mediating its localization to the nucleus and centrosome in interphase cells. We conclude that, although highly conserved, Brctx is not essential for the above-mentioned processes and may be redundant.
Molecular and cellular biology 2005;25;2;779-88
PUBMED: 15632077; PMC: 543416; DOI: 10.1128/MCB.25.2.779-788.2005
-
Applications of combined DNA microarray and chromosome sorting technologies.
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
The sequencing of the human genome has led to the availability of an extensive mapped clone resource that is ideal for the construction of DNA microarrays. These genomic clone microarrays have largely been used for comparative genomic hybridisation studies of tumours to enable accurate measurement of copy number changes (array-CGH) at increased resolution. We have utilised these microarrays as the target for chromosome painting and reverse chromosome painting to provide a similar improvement in analysis resolution for these studies in a process we have termed array painting. In array painting, chromosomes are flow sorted, fluorescently labelled and hybridised to the microarray. The complete composition and the breakpoints of aberrant chromosomes can be analysed at high resolution in this way with a considerable reduction in time, effort and cytogenetic expertise required for conventional analysis using fluorescence in situ hybridisation. In a similar way, the resolution of cross-species chromosome painting can be improved and we present preliminary observations of the organisation of homologous DNA blocks between the white cheeked gibbon chromosome 14 and human chromosomes 2 and 17.
Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 2004;12;1;35-43
PUBMED: 14984100
-
Chromosome paints from single copies of chromosomes.
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
We have used OmniPlex library technology to construct chromosome painting probes from single copies of flow sorted chromosomes. We show that this whole genome amplification technology is particularly efficient at amplifying single copies of chromosomes for the production of paints and that single aberrant chromosomes can be analysed in this way using reverse chromosome painting. The efficient generation of painting probes from single copies of sorted chromosomes has the advantage that the probe must be specific for the chromosome sorted and will not suffer from contamination from other chromosomes particularly in situations where flow karyotype peaks are poorly resolved. These initial results suggest that OmniPlex whole genome amplification will be equally effective in other cytogenetic applications where only small amounts of DNA are available, i.e. from single cells or from small pieces of microdissected tissue.
Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 2004;12;2;143-51
PUBMED: 15053484
Caroline Wright
- Senior Scientific Manager
I completed my undergraduate degree in natural sciences and a masters in chemistry at the University of Cambridge, where I stayed to do a PhD in biological chemistry focused on protein folding and aggregation. Following graduation, I worked as a research analyst in the diagnostics industry and then as Head of Science at the PHG Foundation, an independent genetics think-tank focused on developing policy around the use of new molecular technologies in health care. Since joining the Sanger Institute, I have remained an Associate at the Foundation, working on the implications of whole genome sequencing for the NHS.
Research
I currently manage the DDD project, which involves interacting with multiple teams within the Sanger Institute as well as across the NHS to keep the project on track. I'm particularly interested in the biological mechanisms underlying developmental disorders, defining a methodology to feedback diagnostically useful findings to participants in the study, and the broader ethical implications of genome-wide testing for society.
References
-
Strengthening the reporting of genetic risk prediction studies (GRIPS): explanation and elaboration.
Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands. a.janssens@erasmusmc.nl
The rapid and continuing progress in gene discovery for complex diseases is fueling interest in the potential application of genetic risk models for clinical and public health practice. The number of studies assessing the predictive ability is steadily increasing, but they vary widely in completeness of reporting and apparent quality. Transparent reporting of the strengths and weaknesses of these studies is important to facilitate the accumulation of evidence on genetic risk prediction. A multidisciplinary workshop sponsored by the Human Genome Epidemiology Network developed a checklist of 25 items recommended for strengthening the reporting of Genetic RIsk Prediction Studies (GRIPS), building on the principles established by previous reporting guidelines. These recommendations aim to enhance the transparency, quality and completeness of study reporting, and thereby to improve the synthesis and application of information from multiple studies that might differ in design, conduct or analysis.
European journal of human genetics : EJHG 2011;19;5;18 p preceding 494
PUBMED: 21407270; PMC: 3083630; DOI: 10.1038/ejhg.2011.27
-
Regulating direct-to-consumer genetic tests: what is all the fuss about?
PHG Foundation, Cambridge, United Kingdom. caroline.wright@phgfoundation.org
The number of genetic tests available direct-to-consumer has burgeoned over the last few years, prompting numerous calls for tighter regulation of these services. However, there is a lack of consensus about the most appropriate and achievable level of regulation, particularly given the global nature of the market. By consideration of potential for direct and indirect harms caused by genetic susceptibility or genomic profiling tests, in this study we offer an overarching framework that we believe to be feasible for the regulation of direct-to-consumer genetic tests and likely to be relevant to other forms of predictive testing. We suggest that just five key requirements would adequately protect the consumer: a proportionate set of consent procedures; formal laboratory accreditation; evidence of a valid gene-disease association; appropriately qualified staff to interpret the test result; and consumer protection legislation to prevent false or misleading claims.
Genetics in medicine : official journal of the American College of Medical Genetics 2011;13;4;295-300
PUBMED: 20921893; DOI: 10.1097/GIM.0b013e3181f69dd2
-
Extending the reach of public health genomics: what should be the agenda for public health in an era of genome-based and “personalized” medicine?
Department of Bioethics & Humanities, University of Washington, Seattle, Washington, USA. alison.hall@phgfoundation.org
The decade following the completion of the Human Genome Project has been marked by divergent claims about the utility of genomics for improving population health. On the one hand, genomics is viewed as the harbinger of a brave new world in which novel treatments rectify known causes of disease. On the other hand, genomics may have little practical relevance to the principal causes or remedies of diseases which are predominantly social or environmental in origin, particularly in low- and middle-income countries. Those supportive of a role for public health genomics argue that increasing knowledge of genomics and molecular pathology could unlock effective diagnostic techniques and treatments, and better target public health interventions. To resolve some of these tensions, an international multidisciplinary meeting was held in May 2010 in Ickworth, United Kingdom, with the aim of setting an agenda for the development of public health in an era of genome-based and "personalized" medicine. A number of key themes emerged, suggesting a need to reconfigure both the focus for existing genomic research and the stage at which funding is targeted, so that priority is given to areas of greatest potential health impact and that translation from basic science to implementation is given greater emphasis. To support these developments, there should be an immediate, sustained and systematic effort to provide an evidence base. These deliberations formed the basis for six key recommendations, which could guide the practice of public health in an era of genomics and personalized medicine.
Genetics in medicine : official journal of the American College of Medical Genetics 2010;12;12;785-91
PUBMED: 21189494; DOI: 10.1097/GIM.0b013e3182011222
-
Realising the benefits of genetics for health.
PHG Foundation, Strangeways Research Laboratory, Cambridge CB1 8RN, UK. caroline.wright@phgfoundation.org
Lancet 2010;376;9750;1370-1
PUBMED: 20971348; DOI: 10.1016/S0140-6736(10)61310-4
-
Evaluation of genetic tests for susceptibility to common complex diseases: why, when and how?
PHG Foundation, 2 Worts Causeway, Cambridge CB1 8RN, UK. caroline.wright@phgfoundation.org
Recent research into the human genome has generated a wealth of scientific knowledge and increased both public and professional interest in the concept of personalised medicine. Somewhat unexpectedly, in addition to increasing our understanding about the genetic basis for numerous diseases, these new discoveries have also spawned a burgeoning new industry of 'consumer genetic testing'. In this paper, we present the principles learnt though the evaluation of tests for single gene disorders and suggest a comparable framework for the evaluation of genetic tests for susceptibility to common complex diseases. Both physicians and the general public will need to be able to assess the claims made by providers of genetic testing services, and ultimately policy-makers will need to decide if and when such tests should be offered through state funded healthcare systems.
Human genetics 2010;127;2;125-34
PUBMED: 19936793; DOI: 10.1007/s00439-009-0767-x
-
Non-invasive prenatal diagnosis using cell-free fetal DNA technology: applications and implications.
PHG Foundation, Cambridge, UK. alison.hall@phgfoundation.org
Cell-free fetal DNA and RNA circulating in maternal blood can be used for the early non-invasive prenatal diagnosis (NIPD) of an increasing number of genetic conditions, both for pregnancy management and to aid reproductive decision-making. Here we present a brief review of the scientific and clinical status of the technology, and an overview of key ethical, legal and social issues raised by the analysis of cell-free fetal DNA for NIPD. We suggest that the less invasive nature of the technology brings some distinctive issues into focus, such as the possibility of broader uptake of prenatal diagnosis and access to the technology directly by the consumer via the internet, which have not been emphasised in previous work in this area. We also revisit significant issues that are familiar from previous debates about prenatal testing. Since the technology seems to transect existing distinctions between screening and diagnostic tests, there are important implications for the form and process involved in obtaining informed consent or choice. This analysis forms part of the work undertaken by a multidisciplinary group of experts which made recommendations about the implementation of this technology within the UK National Health Service.
Public health genomics 2010;13;4;246-55
PUBMED: 20395693; DOI: 10.1159/000279626
-
Biomarkers, dementia, and public health.
PHG Foundation, Cambridge, United Kingdom.
Public health is defined as the organized efforts of society to improve health. This is often framed in terms of prevention, with primary, secondary, and tertiary prevention representing, respectively, fundamental prevention through understanding of causation, to alteration of natural history, through understanding of pathophysiological mechanisms and palliation. Biomarkers play a role in all of these levels of prevention of dementias. The clearest application of biomarkers from a public health perspective is in the setting of screening. Screening has particular meaning for public health and includes early detection as a core element, coupled with treatments or preventative actions to reduce the burden of disease. Here, we will cover the range of evidence required if biomarkers are to play a part in population prevention of dementia, including scientific and technical aspects together with ethical, legal, and social considerations. Ensuring research activity that addresses these wider perspectives is essential.
Annals of the New York Academy of Sciences 2009;1180;11-9
PUBMED: 19906256; DOI: 10.1111/j.1749-6632.2009.04942.x
-
Cell-free fetal DNA and RNA in maternal blood: implications for safer antenatal testing.
PHG Foundation, Strangeways Research Laboratory, Cambridge CB1 8RN. caroline.wright@phgfoundation.org
BMJ (Clinical research ed.) 2009;339;b2451
PUBMED: 19581324
-
The importance of sequence diversity in the aggregation and evolution of proteins.
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
Incorrect folding of proteins, leading to aggregation and amyloid formation, is associated with a group of highly debilitating medical conditions including Alzheimer's disease and late-onset diabetes. The issue of how unwanted protein association is normally avoided in a living system is particularly significant in the context of the evolution of multidomain proteins, which account for over 70% of all eukaryotic proteins, where the effective local protein concentration in the vicinity of each domain is very high. Here we describe the aggregation kinetics of multidomain protein constructs of immunoglobulin domains and the ability of different homologous domains to aggregate together. We show that aggregation of these proteins is a specific process and that the efficiency of coaggregation between different domains decreases markedly with decreasing sequence identity. Thus, whereas immunoglobulin domains with more than about 70% identity are highly prone to coaggregation, those with less than 30-40% sequence identity do not detectably interact. A bioinformatics analysis of consecutive homologous domains in large multidomain proteins shows that such domains almost exclusively have sequence identities of less than 40%, in other words below the level at which coaggregation is likely to be efficient. We propose that such low sequence identities could have a crucial and general role in safeguarding proteins against misfolding and aggregation.
Funded by: Wellcome Trust
Nature 2005;438;7069;878-81
PUBMED: 16341018; DOI: 10.1038/nature04195
-
Parallel protein-unfolding pathways revealed and mapped.
Department of Chemistry, University of Cambridge, MRC Centre for Protein Engineering, Lensfield Road, Cambridge CB2 1EW, UK.
Theoretical studies of protein folding suggest that multiple folding pathways should exist, but there is little experimental evidence to support this. Here we demonstrate changes in the flux between different transition states on parallel folding pathways, resulting in unprecedented upward curvature in the denaturant-dependent unfolding kinetics of a beta-sandwich protein. As denaturant concentration increases, the highly compact transition state of one pathway becomes destabilized and the dominant flux of protein molecules shifts toward another pathway with a less structured transition state. Furthermore, point mutations alter the relative accessibility of the pathways, allowing the structure of two transition states on separate, direct folding pathways to be mapped by systematic Phi-value analysis. It has been suggested that pathways with diffuse rather than localized transition states are evolutionarily selected to prevent misfolding, and indeed we find that the transition state favored at high concentrations of denaturant is more polarized than the physiologically relevant one.
Nature structural biology 2003;10;8;658-62
PUBMED: 12833152; DOI: 10.1038/nsb947
Dr Matthew Hurles is leading this group after the retirement of Dr Nigel Carter.