Molecular cytogenetics

The Molecular cytogenetics team is investigating 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. The team was led by Dr Nigel Carter, who retired from the Institute on 1 May 2012. His research group is now led by Dr Matthew Hurles.

For more information on the Cytogenetics Facility, please contact Fengtang Yang.

The observable differences are so small and rare that they are difficult to find and to prove cause and effect, and so the team works together with a large international consortium of researchers investigating inherited disorders. The team has also developed microarray technologies to reveal changes in copy number of individual genes in single cells, as well as a technique known as arraypainting that allows the rapid detection of large changes in chromosome structure associated with a variety of human disorders.

The team are also responsible for setting up the resource known as DECIPHER, which is a clinical database open to physicians all over the world into which information concerning rare genetic disorders can be entered with the purpose of sharing research findings to further the understanding of genetic diseases in man.

[Genome Research Limited]

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.

    Gribble SM, Kalaitzopoulos D, Burford DC, Prigmore E, Selzer RR, Ng BL, Matthews NS, Porter KM, Curley R, Lindsay SJ, Baptista J, Richmond TA and Carter NP

    Journal of medical genetics 2007;44;1;51-8

  • High resolution array-CGH analysis of single cells.

    Fiegler H, Geigl JB, Langer S, Rigler D, Porter K, Unger K, Carter NP and Speicher MR

    Nucleic acids research 2007;35;3;e15

  • Global variation in copy number in the human genome.

    Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, González JR, Gratacòs M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW and Hurles ME

    Nature 2006;444;7118;444-54

Team

Team members

Nigel Carter
Consultant
Tomas Fitzgerald
Senior Bioinformatician
Anna Middleton
am33@sanger.ac.ukEthics Researcher
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.

    Papageorgiou EA, Karagrigoriou A, Tsaliki E, Velissariou V, Carter NP and Patsalis PC

    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

  • Laser excitation power and the flow cytometric resolution of complex karyotypes.

    Ng BL and Carter NP

    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

  • Origins and functional impact of copy number variation in the human genome.

    Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, Macdonald JR, Onyiah I, Pang AW, Robson S, Stirrups K, Valsesia A, Walter K, Wei J, Wellcome Trust Case Control Consortium, Tyler-Smith C, Carter NP, Lee C, Scherer SW and Hurles ME

    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

  • DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.

    Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM and Carter NP

    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

  • Array painting: a protocol for the rapid analysis of aberrant chromosomes using DNA microarrays.

    Gribble SM, Ng BL, Prigmore E, Fitzgerald T and Carter NP

    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

  • Copy number variation and evolution in humans and chimpanzees.

    Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, Lee AS, Hyland C, Stone AC, Hurles ME, Tyler-Smith C, Eichler EE, Carter NP, Lee C and Redon R

    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

  • Global variation in copy number in the human genome.

    Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, González JR, Gratacòs M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW and Hurles ME

    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: NHLBI NIH HHS: T32 HL007627; Wellcome Trust: 077008, 077009, 077014

    Nature 2006;444;7118;444-54

Tomas Fitzgerald

- Senior 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.

    Koumbaris G, Hatzisevastou-Loukidou H, Alexandrou A, Ioannides M, Christodoulou C, Fitzgerald T, Rajan D, Clayton S, Kitsiou-Tzeli S, Vermeesch JR, Skordis N, Antoniou P, Kurg A, Georgiou I, Carter NP and Patsalis PC

    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

  • aCGH.Spline--an R package for aCGH dye bias normalization.

    Fitzgerald TW, Larcombe LD, Le Scouarnec S, Clayton S, Rajan D, Carter NP and Redon R

    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

  • High incidence of recurrent copy number variants in patients with isolated and syndromic Müllerian aplasia.

    Nik-Zainal S, Strick R, Storer M, Huang N, Rad R, Willatt L, Fitzgerald T, Martin V, Sandford R, Carter NP, Janecke AR, Renner SP, Oppelt PG, Oppelt P, Schulze C, Brucker S, Hurles M, Beckmann MW, Strissel PL and Shaw-Smith C

    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

  • Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls.

    Wellcome Trust Case Control Consortium, Craddock N, Hurles ME, Cardin N, Pearson RD, Plagnol V, Robson S, Vukcevic D, Barnes C, Conrad DF, Giannoulatou E, Holmes C, Marchini JL, Stirrups K, Tobin MD, Wain LV, Yau C, Aerts J, Ahmad T, Andrews TD, Arbury H, Attwood A, Auton A, Ball SG, Balmforth AJ, Barrett JC, Barroso I, Barton A, Bennett AJ, Bhaskar S, Blaszczyk K, Bowes J, Brand OJ, Braund PS, Bredin F, Breen G, Brown MJ, Bruce IN, Bull J, Burren OS, Burton J, Byrnes J, Caesar S, Clee CM, Coffey AJ, Connell JM, Cooper JD, Dominiczak AF, Downes K, Drummond HE, Dudakia D, Dunham A, Ebbs B, Eccles D, Edkins S, Edwards C, Elliot A, Emery P, Evans DM, Evans G, Eyre S, Farmer A, Ferrier IN, Feuk L, Fitzgerald T, Flynn E, Forbes A, Forty L, Franklyn JA, Freathy RM, Gibbs P, Gilbert P, Gokumen O, Gordon-Smith K, Gray E, Green E, Groves CJ, Grozeva D, Gwilliam R, Hall A, Hammond N, Hardy M, Harrison P, Hassanali N, Hebaishi H, Hines S, Hinks A, Hitman GA, Hocking L, Howard E, Howard P, Howson JM, Hughes D, Hunt S, Isaacs JD, Jain M, Jewell DP, Johnson T, Jolley JD, Jones IR, Jones LA, Kirov G, Langford CF, Lango-Allen H, Lathrop GM, Lee J, Lee KL, Lees C, Lewis K, Lindgren CM, Maisuria-Armer M, Maller J, Mansfield J, Martin P, Massey DC, McArdle WL, McGuffin P, McLay KE, Mentzer A, Mimmack ML, Morgan AE, Morris AP, Mowat C, Myers S, Newman W, Nimmo ER, O'Donovan MC, Onipinla A, Onyiah I, Ovington NR, Owen MJ, Palin K, Parnell K, Pernet D, Perry JR, Phillips A, Pinto D, Prescott NJ, Prokopenko I, Quail MA, Rafelt S, Rayner NW, Redon R, Reid DM, Renwick, Ring SM, Robertson N, Russell E, St Clair D, Sambrook JG, Sanderson JD, Schuilenburg H, Scott CE, Scott R, Seal S, Shaw-Hawkins S, Shields BM, Simmonds MJ, Smyth DJ, Somaskantharajah E, Spanova K, Steer S, Stephens J, Stevens HE, Stone MA, Su Z, Symmons DP, Thompson JR, Thomson W, Travers ME, Turnbull C, Valsesia A, Walker M, Walker NM, Wallace C, Warren-Perry M, Watkins NA, Webster J, Weedon MN, Wilson AG, Woodburn M, Wordsworth BP, Young AH, Zeggini E, Carter NP, Frayling TM, Lee C, McVean G, Munroe PB, Palotie A, Sawcer SJ, Scherer SW, Strachan DP, Tyler-Smith C, Brown MA, Burton PR, Caulfield MJ, Compston A, Farrall M, Gough SC, Hall AS, Hattersley AT, Hill AV, Mathew CG, Pembrey M, Satsangi J, Stratton MR, Worthington J, Deloukas P, Duncanson A, Kwiatkowski DP, McCarthy MI, Ouwehand W, Parkes M, Rahman N, Todd JA, Samani NJ and Donnelly P

    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; Chief Scientist Office: CZB/4/540, ETM/137, ETM/75; Medical Research Council: G0000934, G0400874, G0500115, G0501942, G0600329, G0600705, G0700491, G0701003, G0701420, G0701810, G0701810(85517), G0800383, G0800759, G19/9, G90/106, G9521010, MC_UP_A390_1107; Wellcome Trust: 061858, 083948, 089989

    Nature 2010;464;7289;713-20

  • Origins and functional impact of copy number variation in the human genome.

    Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, Macdonald JR, Onyiah I, Pang AW, Robson S, Stirrups K, Valsesia A, Walter K, Wei J, Wellcome Trust Case Control Consortium, Tyler-Smith C, Carter NP, Lee C, Scherer SW and Hurles ME

    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

  • Reduced TFAP2A function causes variable optic fissure closure and retinal defects and sensitizes eye development to mutations in other morphogenetic regulators.

    Gestri G, Osborne RJ, Wyatt AW, Gerrelli D, Gribble S, Stewart H, Fryer A, Bunyan DJ, Prescott K, Collin JR, Fitzgerald T, Robinson D, Carter NP, Wilson SW and Ragge NK

    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: Medical Research Council: G0501487, G0700089; Wellcome Trust: 074376, 078047, WT077008

    Human genetics 2009;126;6;791-803

  • Genomic and genic deletions of the FOX gene cluster on 16q24.1 and inactivating mutations of FOXF1 cause alveolar capillary dysplasia and other malformations.

    Stankiewicz P, Sen P, Bhatt SS, Storer M, Xia Z, Bejjani BA, Ou Z, Wiszniewska J, Driscoll DJ, Maisenbacher MK, Bolivar J, Bauer M, Zackai EH, McDonald-McGinn D, Nowaczyk MM, Murray M, Hustead V, Mascotti K, Schultz R, Hallam L, McRae D, Nicholson AG, Newbury R, Durham-O'Donnell J, Knight G, Kini U, Shaikh TH, Martin V, Tyreman M, Simonic I, Willatt L, Paterson J, Mehta S, Rajan D, Fitzgerald T, Gribble S, Prigmore E, Patel A, Shaffer LG, Carter NP, Cheung SW, Langston C and Shaw-Smith C

    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

  • Array painting: a protocol for the rapid analysis of aberrant chromosomes using DNA microarrays.

    Gribble SM, Ng BL, Prigmore E, Fitzgerald T and Carter NP

    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

  • A robust statistical method for case-control association testing with copy number variation.

    Barnes C, Plagnol V, Fitzgerald T, Redon R, Marchini J, Clayton D and Hurles ME

    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

  • Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.

    Marioni JC, Thorne NP, Valsesia A, Fitzgerald T, Redon R, Fiegler H, Andrews TD, Stranger BE, Lynch AG, Dermitzakis ET, Carter NP, Tavaré S and Hurles ME

    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

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'.

    Middleton A

    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

  • Preferences for communication in clinic from deaf people: a cross-sectional study.

    Middleton A, Turner GH, Bitner-Glindzicz M, Lewis P, Richards M, Clarke A and Stephens D

    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

  • Communicating in a healthcare setting with people who have hearing loss.

    Middleton A, Niruban A, Girling G and Myint PK

    Institute of Medical Genetics, Cardiff University, Cardiff CF14 4XN, UK.

    BMJ (Clinical research ed.) 2010;341;c4672

  • Reproductive liberty and deafness: Clause 14(4)(9) of embryo bill should be amended or deleted.

    Emery S, Burke TB, Middleton A, Belk R and Turner G

    BMJ (Clinical research ed.) 2008;336;7651;976

  • Providing a transcultural genetic counseling service in the UK.

    Middleton A, Robson F, Burnell L and Ahmed M

    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

  • Editorial on supervision.

    Middleton A, Cowley L and Clarke A

    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

  • Reflections on the experience of counseling supervision by a team of genetic counselors from the UK.

    Middleton A, Wiles V, Kershaw A, Everest S, Downing S, Burton H, Robathan S and Landy A

    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

  • Report from the UK and Eire Association of Genetic Nurses and Counsellors (AGNC) supervision working group on genetic counselling supervision.

    Clarke A, Middleton A, Cowley L, Guilbert P, Macleod R, Clarke A, Tran V and AGNC Supervision Working Group

    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

  • Prenatal diagnosis for inherited deafness--what is the potential demand?

    Middleton A, Hewison J and Mueller R

    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

  • Attitudes of deaf adults toward genetic testing for hereditary deafness.

    Middleton A, Hewison J and Mueller RF

    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

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.

    Janssens AC, Ioannidis JP, Bedrosian S, Boffetta P, Dolan SM, Dowling N, Fortier I, Freedman AN, Grimshaw JM, Gulcher J, Gwinn M, Hlatky MA, Janes H, Kraft P, Melillo S, O'Donnell CJ, Pencina MJ, Ransohoff D, Schully SD, Seminara D, Winn DM, Wright CF, van Duijn CM, Little J and Khoury MJ

    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

  • Regulating direct-to-consumer genetic tests: what is all the fuss about?

    Wright CF, Hall A and Zimmern RL

    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

  • Extending the reach of public health genomics: what should be the agenda for public health in an era of genome-based and “personalized” medicine?

    Burke W, Burton H, Hall AE, Karmali M, Khoury MJ, Knoppers B, Meslin EM, Stanley F, Wright CF, Zimmern RL and Ickworth Group

    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

  • Realising the benefits of genetics for health.

    Wright CF, Brice P, Stewart A and Burton H

    PHG Foundation, Strangeways Research Laboratory, Cambridge CB1 8RN, UK. caroline.wright@phgfoundation.org

    Lancet 2010;376;9750;1370-1

  • Evaluation of genetic tests for susceptibility to common complex diseases: why, when and how?

    Wright CF and Kroese M

    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

  • Non-invasive prenatal diagnosis using cell-free fetal DNA technology: applications and implications.

    Hall A, Bostanci A and Wright CF

    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

  • Biomarkers, dementia, and public health.

    Wright CF, Hall A, Matthews FE and Brayne C

    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.

    Funded by: Medical Research Council: MC_U105292687

    Annals of the New York Academy of Sciences 2009;1180;11-9

  • Cell-free fetal DNA and RNA in maternal blood: implications for safer antenatal testing.

    Wright CF and Chitty LS

    PHG Foundation, Strangeways Research Laboratory, Cambridge CB1 8RN. caroline.wright@phgfoundation.org

    BMJ (Clinical research ed.) 2009;339;b2451

  • The importance of sequence diversity in the aggregation and evolution of proteins.

    Wright CF, Teichmann SA, Clarke J and Dobson CM

    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

  • Parallel protein-unfolding pathways revealed and mapped.

    Wright CF, Lindorff-Larsen K, Randles LG and Clarke J

    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

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