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Dr Ernest Turro

Dr Ernest Turro

Senior Research Associate

NHS Blood and Transplant
Long Road
Cambridge CB2 0PT
United Kingdom

Email:
Office Phone: +44 (0)1223 588174

Biography:

Note: MRC-funded PhD studentships are currently available to work on integrative methods for identifying non-coding rare variants responsible for rare diseases, under the supervision of Prof Sylvia Richardson and myself.

I am a biostatistician with an interest in genome function and rare inherited disorders. My work focuses primarily on the development and application of statistical methods for interpreting genomic and phenotypic data.

I lead the analysis of the NIHR BioResource—Rare Diseases initiative to identify the genetic basis of unexplained bleeding and platelet disorders by genome sequencing and extensive phenotyping of over a thousand cases. This work has implicated variants in SRC, DIAPH1, TPM4 and TRPM7 in platelet disorders for the first time and has extended our understanding of rare variation in previously implicated genes, such as ETV6THBD and GP1BB

As part of this project, I have worked on statistical methods for identifying the genetic determinants of rare diseases, including:

  • BeviMed – statistical method for performing Bayesian evaluation of variant involvement in Mendelian disease (R package developed by Daniel Greene).
  • SimReg – Bayesian phenotype similarity regression for identifying associations between Human Phenotype Ontology (HPO)-coded patient phenotypes and genotypes at rare variant sites (R package developed by Daniel Greene).

The diagnostic counterpart to the rare disease research project on bleeding and platelet disorders is the ThromboGenomics project, for which I supervise the bioinformatics and statistical genetics.

Previously, I developed the first statistical methods for modelling haplotype and isoform specific expression using RNA sequencing data and have collaborated with research groups on their application to diverse biological questions. I also developed and applied the first statistical method for modelling isoform specific expression using Affymetrix microarray data. I am the main author of the following statistical software packages:

  • MMDIFF – software for flexible analysis of RNA-seq data using Bayesian mixed effects models.
  • MMSEQ – widely used software for Bayesian haplotype, isoform and gene specific expression estimation using multi-mapping RNA-seq reads.
  • MMBGX – a Bayesian method for estimating expression at the isoform and gene level and detecting differential splicing using whole-transcript Affymetrix arrays.
  • BGX – a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips.

I am a Visitor at the MRC Biostatistics Unit. Previously I was a postdoctoral researcher in the Computational Biology group at the CRUK Cambridge Institute and in the Department of Epidemiology and Biostatistics at Imperial College London. I hold a PhD (2011) in biostatistics (supervised by Prof Sylvia Richardson and Dr Alex Lewin) and a MSc with Distinction (2005) in Computing Science from Imperial College London.

Research Supervision

  • Daniel Greene (co-supervised by Prof Sylvia Richardson and Prof Willem H Ouwehand), PhD student, 2013–present.
  • Natasha Andressa (co-supervised by Dr Fabio Passetti), Visiting PhD student, 2015.
  • Mike Field (co-supervised by Dr Lucy Raymond), rotation project, MPhil in Computational Biology, 2014.
  • Jürgen Jänes, 1st year rotation project, Wellcome Trust PhD programme in Mathematics, Genomics and Medicine (MGM), 2012.

Teaching

I have been teaching part of the Functional Genomics module to students in the MPhil in Computational Biology since 2011. I wrote up many of the materials I developed for this course into a book chapter with Dr Alex Lewin.  

I also teach in specialised courses on analysis of high-throughput sequencing data, most recently:

  • TrainMALTA 2016 – HTS Bioinformatics Summer School. University of Malta, Malta. Sep 2016.
  • Advanced RNA-seq and ChIP-seq Data Analysis Course. European Bioinformatics Institute, UK. May 2012, Jun 2013, May 2014, May 2015, Apr 2016.
  • EMBO Practical Course on Analysis of High-Throughput Sequencing Data. European Bioinformatics Institute, UK. Oct-Nov 2012, Oct 2013, Oct 2015.
  • RNA-Seq analysis using Bioconductor. Park Hotel, Recife (PE), Brazil. Oct-Nov 2013.
  • Computational challenges and performance optimizations in NGS data analyses. Wellcome Trust Gibbs Building, UK. Sep 2013.
  • Winter School on Analysis of Massively-Parallel Sequencing Data. National Institute of Biomedical Genomics, India. Jan 2013.

Previously I have taught in courses on biostatistics and microarray analysis at Imperial College London.

Key Publications

(Full list of peer-reviewed articles on PubMed.)

High-throughput sequencing approaches for diagnosing hereditary bleeding and platelet disorders.
Freson K, Turro E.
Journal of Thrombosis and Haemostasis, 2017; to appear.

PIGO deficiency: palmoplantar keratoderma and novel mutations.
Morren MA*, Jaeken J*, Visser G, Salles I, van Geet C, NIHR BioResource, Simeoni I, Turro E, Freson K.
Orphanet Journal of Rare Diseases, 2017; to appear.

Mutations in tropomyosin 4 underlie a novel form of human macrothrombocytopenia.
Pleines I, Woods J, Chappaz S, Kew V, Foad N, Ballester-Beltr\'an J, Aurbach K, Lincetto C, Lane RM, Schevzov G, Alexander WS, Hilton DJ, Astle WJ, Downes K, Nurden P, Westbury SK, Mumford AD, Obaji SG, Collins PW, NIHR BioResource, Delerue F, Ittner LM, Bryce NS, Holliday M, Lucas CA, Hardeman EC, Ouwehand WH, Gunning PW, Turro E, Tijssen MR*, Kile BT*.
Journal of Clinical Investigation, 2017 Mar; 127(3):814–829.

ontologyX: A suite of R packages for working with ontological data.
Greene D, Richardson S, Turro E.
Bioinformatics, 2017 Jan; 1–3.

The Human Phenotype Ontology in 2017.
Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry, …, Turro E, …, Jacobsen JOB, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN.
Nucleic Acids Research, 2017 Jan; D865–D876.

Rare variants in GP1BB are responsible for autosomal dominant macrothrombocytopenia.
Sivapalaratnam S*, Westbury SK*, Stephens JC*, Greene D*, Downes K, Kelly AM, Lentaigne C, Astle WJ, Nurden P, Papadia S, Peerlinck K, Penkett CJ, Perry DJ, Roughley C, Simeoni I, Stirrups K, Hart DP, Tait RC, Mumford AD, NIHR BioResource, Laffan MA, Freson K§, Ouwehand WH§, Kunishima S§, Turro E§.
Blood, 2017 Jan; 129(4) 520–524. (Featured in This Week in Blood alongside Inside Blood Commentary).

Germline variants in ETV6 underlie reduced platelet formation, platelet dysfunction and increased levels of circulating CD34+ progenitors.
Poggi M*, Canault M*, Favier M*, Turro E*, Saultier P, Ghalloussi D, Baccini V, Vidal L, Mezzapesa A, Chelghoum N, Mohand-Oumoussa B, Falaise C, Favier R, Ouwehand WH, Fiore M, Peiretti F, Morange PE, Saut N, Bernot D, Greinacher A, NIHR BioResource, Nurden AT, Nurden P, Freson K§, Trégoüet D-A§, Raslova H§, Alessi M-C§.
Haematologica, 2017 Feb; 102(2):282–294.

Altered fibrinolysis in autosomal dominant thrombomodulin-associated coagulopathy.
Burley K, Whyte CS, Westbury SK, Walker M, Stirrups KE, Turro E, NIHR BioResource, Chapman OG, Reilly-Stitt C, Mutch NJ, and Mumford A.
Blood, 2016 Oct; 128(14) 1879–1883.

Inherited platelet disorders: towards DNA-based diagnosis.
Lentaigne C, Freson K, Laffan MA, Turro E, Ouwehand WH (on behalf of the BRIDGE-BPD Consortium and the ThromboGenomics Consortium).
Blood, 2016 Jun; 127(23) 2814–2823.

A gain-of-function variant in DIAPH1 causes dominant macrothrombocytopenia and hearing loss.
Stritt S*, Nurden P*, Turro E*, Greene D, Jansen SBG, Westbury SK, Petersen R, Astle WJ, Marlin S, Bariana TK, Kostadima M, Lentaigne C, Maiwald S, Papadia S, Kelly AM, Stephens JC, Penkett CJ, Ashford S, Tuna S, …, BRIDGE-BPD Consortium, Gomez K, Erber WN, Stirrups K, Rendon A, Bradley JR, Van Geet C, Raymond FL, Laffan MA, Nurden A, Nieswandt B, Richardson S, Freson K§, Ouwehand WH§, Mumford A§.
Blood, 2016 Jun; 127(23) 2903–2914. (Featured on cover.)

A high-throughput sequencing test for diagnosing inherited bleeding, thrombotic and platelet disorders.
Simeoni I, Stephens JC, Hu F, Deevi SVV, Megy K, Bariana TK, Lentaigne C, Schulman S, Sivapalaratnam S, Vries MJA, Westbury SK, Greene D, Papadia S, …, Ravel-Vilk S, Gresele P, Bellissimo D, Penkett CJ, Laffan MA, Mumford AD, Rendon A, Gomez K*, Freson K*, Ouwehand WH*, Turro E*.
Blood, 2016 Jun; 127(23) 2791–2803. (See also editorial: Platelet disorders: the next generation is in. Rao AK and Natthapol S. Blood, 2016 Jun; 127(23) 2781–2782.)

Defects in TRPM7 channel function result in deregulated thrombopoiesis through altered cellular Mg2+ homeostasis and cytoskeletal architecture.
Stritt S, Nurden P, Favier R, Favier M, Gotru SK, van Eeuwijk JMM, Schulze H, Nurden AT, Lambert MP, Turro E, Burger-Stritt S, Matsushita M, Ferioli S, Mittermeier L, Ballerini P, Zierler S, NIHR BioResource, Chubanov V, Laffan MA, Gudermann T, Nieswandt B*, Braun A*.
Nature Communications, 2016 Mar; 7:11097.

Phenotype similarity regression for identifying the genetic determinants of rare diseases.
Greene D, NIHR BioResource, Richardson S*, Turro E*.
American Journal of Human Genetics, 2016 Mar; 98:1–10.

A dominant gain-of-function mutation in universal tyrosine kinase SRC causes thrombocytopenia, myelofibrosis, bleeding and bone pathologies.
Turro E, Greene D, Wijgaerts A, Thys C, Lentaigne C, Bariana TK, Westbury SK, Kelly AM, Selleslag D, Stephens JC, Papadia S, Simeoni I, Penkett C, …, BRIDGE-BPD Consortium, De Maeyer M, Rendon A, Gomez K, Erber WN, Mumford AD, Nurden P, Stirrups K, Bradley J, Raymond FL, Laffan MA, Van Geet C, Richardson S, Freson K*, Ouwehand WH*.
Science Translational Medicine, 2016 Mar; 8:328. (Featured on cover.)

A multi-centre validation of recombinant β3 integrin-coupled beads to detect human platelet antigen-1 alloantibodies in 498 cases of fetomaternal alloimmune thrombocytopenia.
Chong W, Turro E, Metcalfe P, Yusuf R, Merieux Y, Rigal D, Porceljn L, Huiskes E, Lucas G, Bendukidze N, Green A, Fontão-Wendel R, Husebekk A, Dixey J, Guest A, Mushens R, Ouwehand WH, Navarrete C.
Transfusion, 2015 Nov; 55:2742–2751.

Fgf and Esrrb integrate epigenetic and transcriptional networks that regulate self-renewal of trophoblast stem cells.
Latos PA, Gonçalves Â, Oxley D, Mohammed H, Turro E, Hemberger M.
Nature Communications, 2015 Jul; 6:7776.

Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders.
Westbury S*, Turro E*, Greene D*, Kelly AM*, Lentaigne C*, Bariana T*, Simeoni I, Pillois X, …, Rendon A, Gomez K, Laffan M, Lambert M, Nurden P, Ouwehand WH§, Richardson S§, Mumford AD§, Freson K§ (on behalf of the BRIDGE-BPD Consortium).
Genome Medicine, 2015 Apr; 7:36.

A comparative study of RNA-seq analysis strategies.
Janes J*, Hu F*, Lewin AM, Turro E.
Briefings in Bioinformatics, 2015 Mar; 16(6):932–940.

The malignant phenotype in breast cancer is driven by eIF4A1-mediated changes in the translational landscape.
Modelska A, Turro E, Russell R, Beaton J, Sbarrato T, Spriggs K, Miller J, Gräf S, Provenzano E, Blows F, Pharoah P, Caldas C, Le Quesne J.
Cell Death & Disease, 2015 Jan, 6:e1603. (See also editorial: eIF4A1 is a promising new therapeutic target in ER-negative breast cancer. Stoneley M, Willis, A E. Cell Death & Differentiation, 2015 Jan; 22, 524–525.)

Hybrid mice reveal parent-of-origin and cis- and trans-regulatory effects in the retina.
Shen SQ, Turro E, Corbo JC.
PLoS ONE, 2014 Oct; 9(10):e109382.

Transcriptional diversity during lineage commitment of human blood progenitors.
Chen L*, Kostadima M*, Martens JHA*, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S, Farrow S, Poudel P, Burden F, Jansen SBG, …, Flicek P, Loos R, Goldman N, Bertone P, Read RJ, Richardson S, Cvejic A, Soranzo N§, Ouwehand WH§, Stunnenberg HG§, Frontini M§, Rendon A§.
Science, 2014 Sep; 345(6204):1251033.

The South Asian genome.
Chambers JC*, Abbott J*, Zhang W*, Turro E*, Scott WR, Tan S-T, Afzal U, Afaq S, Loh M, Lehne B, O’Reilly P, Gaulton KJ, Pearson RD, Li X, Lavery A, Vandrovcova J, Wass MS, Miller K, Sehmi J, Oozageer L, Kooner IK, Al-Hussaini A, Mills R, Grewal J, Panoulas V, Lewin AM, Northwood K, Wander GS, Geoghegan F, Li Y, Wang J, Aitman TJ, McCarthy MI, Scott J§, Butcher S§, Elliott P§ and Kooner JS§.
PLoS ONE, 2014 Aug; 9(8):e102645.

Flexible analysis of RNA-seq data using mixed effects models.
Turro E, Astle WJ, Tavaré S.
Bioinformatics, 2014 Jan; 30(2):180–188.

Statistical analysis of mapped reads from mRNA-seq data.
Turro E, Lewin A.
In: Do K-A, Qin ZS, Vannucci M, eds. Advances in Statistical Bioinformatics: Models and Integrative Inference for High-Throughput Data. Cambridge, England: Cambridge University Press; 2013:77–104.

Induction of p16INK4α is the major barrier to proliferation when Epstein-Barr virus (EBV) transforms primary B cells into lymphoblastoid cell lines.
Skalska L, White RE, Parker GA, Turro E, Sinclair AJ, Paschos K, Allday MJ.
PLoS Pathogens, 2013 Feb; 9(2):e1003187.

Extensive compensatory cis-trans regulation dominates the evolution of mouse gene expression.
Gonçalves Â*, Leigh-Brown S*, Thybert D§, Stefflova K§Turro E, Flicek P, Brazma A, Odom DT, Marioni JC.
Genome Research, 2012 Aug; 22(12):2376–84.

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.
Turro E, Su S-Y, Gonçalves  , Coin LJM, Richardson S, Lewin A.
Genome Biology, 2011 Feb; 12:R13.

Extensive cooperation between the Epstein-Barr virus EBNA3 proteins in the manipulation of host gene expression and epigenetic chromatin modification.
White RE, Groves IJ, Turro E, Yee J, Kremmer E, Allday MJ.
PLoS ONE, 2010 Nov; 5(11):e13979.

MMBGX: a method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays.
Turro E, Lewin A, Rose A, Dallman MJ, Richardson S.
Nucleic Acids Research, 2010 Jan; 38(1):e4.

BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips.
Turro E, Bochkina N, Hein A-MK, Richardson S.
BMC Bioinformatics, 2007 Nov; 8:439.

BGX: Bayesian Hierarchical analysis of 3’ GeneChip data.
Turro E.
In ISBA Bulletin, Ed. Gottardo R. International Society for Bayesian Analysis, 2007 Sep; 14(3).

* and § indicate equal contribution.

Other Publications

Interview for the Cambridge Biomedical Research Centre, 2 Feb 2016.

Statistical methods for gene expression analysis using microarray and RNA-Seq data.
Turro E.
PhD thesis. Imperial College London, 2011.

Parallelising the BGX bioinformatics package.
Turro E.
MSc thesis. Imperial College London, 2005.