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Dr Pilar Cacheiro

Pilar

Lecturer in Computational Biology

Centre: Centre for Translational Bioinformatics

Email: p.cacheiro@qmul.ac.uk

Profile

Pilar is a Lecturer in Computational Biology with extensive expertise in the analysis and interpretation of phenotypic data from rare disease patients and model organisms to inform on human disease. Pilar is involved in several projects aimed at deciphering the full spectrum of gene intolerance to variation and developing new machine learning and network approaches to prioritise candidate variants and genes in large scale sequencing studies, with a particular emphasis on neurodevelopmental disorders. Her interests include gene essentiality, phenotype ontologies, statistics and R. 

Pilar is involved in different activities to improve other researcher's statistical an programming skills, including teaching the Introduction to Statistics and R course within the Researcher Development Program and coordinating a Code Review Clinic to enable data sharing and reproducible research in collaboration with members of the ITSR team. She supervises students from the MSc in Bioinformatics and MSc in Genomic Medicine programs.

Research

Publications

  • Cacheiro P, Smedley D. Essential genes: a cross-species perspective. Mamm Genome. 2023;10.1007/s00335-023-09984-1. doi:10.1007/s00335-023-09984-1. PMID: 3689735.
  • Cacheiro P, Spielmann N, Mashhadi HH, et al. Knockout mice are an important tool for human monogenic heart disease studies. Dis Model Mech. 2023;16(5):dmm049770. doi:10.1242/dmm.049770. PMID: 3682546.
  • Groza T, Gomez FL, Mashhadi HH, Muñoz-Fuentes V, Gunes O, Wilson R, Cacheiro P, Frost A, Keskivali-Bond P, Vardal B, McCoy A, Cheng TK, Santos L, Wells S, Smedley D, Mallon AM, Parkinson H. The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease. Nucleic Acids Res. 2023;51(D1):D1038-D1045. doi:10.1093/nar/gkac972. PMID: 36305825. 
  • Vetro A, Balestrini B, Pelorosso C, Masi A, Hambleton S, Argilli E, Conti V, Giubbolini S, Barrick R, Bergant G, Writzl K, Bijlsma EK, Brunet T, Cacheiro P, Mei D, Devlin A, Hoffer MJV, Machol K, Mannaioni G, Sakamoto M, Menezes MP, Courtin T, Sherr E, Parra R, Richardson R, Roscioli T, Scala M, von Stülpnagel C, Smedley D, TMEM63B collaborators, The Genomics England Research Consortium, Torella A, Tohyama J, Koichihara R, Hamada K, Ogata K, Suzuki T, Sugie A, van der Smagt JJ, van Gassen K, Valence S, Vittery E, Kato M, Matsumoto N, Ratto GM, Guerrini R. Stretch-activated ion channel TMEM63B associates with developmental and epileptic encephalopathies and progressive neurodegeneration. medRxiv 2022.11.22.22282283. doi: https://doi.org/10.1101/2022.11.22.22282283
  • Cacheiro P, Westerberg CH, Mager J, Dickinson ME, Nutter LMJ, Muñoz-Fuentes V, Hsu CW, Van den Veyver IB, Flenniken AM, McKerlie C, Murray SA, Teboul L, Heaney JD, Lloyd KCK, Lanoue L, Braun RE, White JK, Creighton AK, Laurin V, Guo R, Qu D, Wells S, Cleak J, Bunton-Stasyshyn R, Stewart M, Harrisson J, Mason J, Haseli Mashhadi H, Parkinson H, Mallon AM; International Mouse Phenotyping Consortium; Genomics England Research Consortium, Smedley D. Mendelian gene identification through mouse embryo viability screening. Genome Med. 2022 Oct 13;14(1):119. doi: 10.1186/s13073-022-01118-7. PMID: 36229886; PMCID: PMC9563108. 
  • Dhombres F, Morgan P, Chaudhari BP, Filges I, Sparks TN, Lapunzina P, Roscioli T, Agarwal U, Aggarwal S, Beneteau C, Cacheiro P, Carmody LC, Collardeau-Frachon S, Dempsey EA, Dufke A, Duyzend MH, El Ghosh M, Giordano JL, Glad R, Grinfelde I, Iliescu DG, Ladewig MS, Munoz-Torres MC, Pollazzon M, Radio FC, Rodo C, Silva RG, Smedley D, Sundaramurthi JC, Toro S, Valenzuela I, Vasilevsky NA, Wapner RJ, Zemet R, Haendel MA, Robinson PN. Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology. Am J Med Genet C Semin Med Genet. 2022 Jun;190(2):231-242. doi: 10.1002/ajmg.c.31989. Epub 2022 Jul 24. PMID: 35872606; PMCID: PMC9588534. 
  • 100,000 Genomes Project Pilot Investigators, Smedley D, Smith KR, Martin A, Thomas EA, McDonagh EM, Cipriani V, Ellingford JM, Arno G, Tucci A, Vandrovcova J, Chan G, Williams HJ, Ratnaike T, Wei W, Stirrups K, Ibanez K, Moutsianas L, Wielscher M, Need A, Barnes MR, Vestito L, Buchanan J, Wordsworth S, Ashford S, Rehmström K, Li E, Fuller G, Twiss P, Spasic-Boskovic O, Halsall S, Floto RA, Poole K, Wagner A, Mehta SG, Gurnell M, Burrows N, James R, Penkett C, Dewhurst E, Gräf S, Mapeta R, Kasanicki M, Haworth A, Savage H, Babcock M, Reese MG, Bale M, Baple E, Boustred C, Brittain H, de Burca A, Bleda M, Devereau A, Halai D, Haraldsdottir E, Hyder Z, Kasperaviciute D, Patch C, Polychronopoulos D, Matchan A, Sultana R, Ryten M, Tavares ALT, Tregidgo C, Turnbull C, Welland M, Wood S, Snow C, Williams E, Leigh S, Foulger RE, Daugherty LC, Niblock O, Leong IUS, Wright CF, Davies J, Crichton C, Welch J, Woods K, Abulhoul L, Aurora P, Bockenhauer D, Broomfield A, Cleary MA, Lam T, Dattani M, Footitt E, Ganesan V, Grunewald S, Compeyrot-Lacassagne S, Muntoni F, Pilkington C, Quinlivan R, Thapar N, Wallis C, Wedderburn LR, Worth A, Bueser T, Compton C, Deshpande C, Fassihi H, Haque E, Izatt L, Josifova D, Mohammed S, Robert L, Rose S, Ruddy D, Sarkany R, Say G, Shaw AC, Wolejko A, Habib B, Burns G, Hunter S, Grocock RJ, Humphray SJ, Robinson PN, Haendel M, Simpson MA, Banka S, Clayton-Smith J, Douzgou S, Hall G, Thomas HB, O'Keefe RT, Michaelides M, Moore AT, Malka S, Pontikos N, Browning AC, Straub V, Gorman GS, Horvath R, Quinton R, Schaefer AM, Yu-Wai-Man P, Turnbull DM, McFarland R, Taylor RW, O'Connor E, Yip J, Newland K, Morris HR, Polke J, Wood NW, Campbell C, Camps C, Gibson K, Koelling N, Lester T, Németh AH, Palles C, Patel S, Roy NBA, Sen A, Taylor J, Cacheiro P, Jacobsen JO, Seaby EG, Davison V, Chitty L, Douglas A, Naresh K, McMullan D, Ellard S, Temple IK, Mumford AD, Wilson G, Beales P, Bitner-Glindzicz M, Black G, Bradley JR, Brennan P, Burn J, Chinnery PF, Elliott P, Flinter F, Houlden H, Irving M, Newman W, Rahman S, Sayer JA, Taylor JC, Webster AR, Wilkie AOM, Ouwehand WH, Raymond FL, Chisholm J, Hill S, Bentley D, Scott RH, Fowler T, Rendon A, Caulfield M. 100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care - Preliminary Report. N Engl J Med. 2021 Nov 11;385(20):1868-1880. doi: 10.1056/NEJMoa2035790. PMID: 34758253; PMCID: PMC7613219.  
  • Cousin MA, Creighton BA, Breau KA, Spillmann RC, Torti E, Dontu S, Tripathi S, Ajit D, Edwards RJ, Afriyie S, Bay JC, Harper KM, Beltran AA, Munoz LJ, Falcon Rodriguez L, Stankewich MC, Person RE, Si Y, Normand EA, Blevins A, May AS, Bier L, Aggarwal V, Mancini GMS, van Slegtenhorst MA, Cremer K, Becker J, Engels H, Aretz S, MacKenzie JJ, Brilstra E, van Gassen KLI, van Jaarsveld RH, Oegema R, Parsons GM, Mark P, Helbig I, McKeown SE, Stratton R, Cogne B, Isidor B, Cacheiro P, Smedley D, Firth HV, Bierhals T, Kloth K, Weiss D, Fairley C, Shieh JT, Kritzer A, Jayakar P, Kurtz-Nelson E, Bernier RA, Wang T, Eichler EE, van de Laar IMBH, McConkie-Rosell A, McDonald MT, Kemppainen J, Lanpher BC, Schultz-Rogers LE, Gunderson LB, Pichurin PN, Yoon G, Zech M, Jech R, Winkelmann J; Undiagnosed Diseases Network; Genomics England Research Consortium, Beltran AS, Zimmermann MT, Temple B, Moy SS, Klee EW, Tan QK, Lorenzo DN. Pathogenic SPTBN1 variants cause an autosomal dominant neurodevelopmental syndrome. Nat Genet. 2021 Jul;53(7):1006-1021. doi: 10.1038/s41588-021-00886-z. Epub 2021 Jul 1. PMID: 34211179; PMCID: PMC8273149. 
  • Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LMJ, Peterson KA, Haselimashhadi H, Flenniken AM, Morgan H, Westerberg H, Konopka T, Hsu CW, Christiansen A, Lanza DG, Beaudet AL, Heaney JD, Fuchs H, Gailus-Durner V, Sorg T, Prochazka J, Novosadova V, Lelliott CJ, Wardle-Jones H, Wells S, Teboul L, Cater H, Stewart M, Hough T, Wurst W, Sedlacek R, Adams DJ, Seavitt JR, Tocchini-Valentini G, Mammano F, Braun RE, McKerlie C, Herault Y, de Angelis MH, Mallon AM, Lloyd KCK, Brown SDM, Parkinson H, Meehan TF, Smedley D; Genomics England Research Consortium; International Mouse Phenotyping Consortium. Human and mouse essentiality screens as a resource for disease gene discovery. Nat Commun. 2020 Jan 31;11(1):655. doi: 10.1038/s41467-020-14284-2. PMID: 32005800; PMCID: PMC6994715.  
  • Cacheiro P, Haendel MA, Smedley D; International Mouse Phenotyping Consortium and the Monarch Initiative. New models for human disease from the International Mouse Phenotyping Consortium. Mamm Genome. 2019 Jun;30(5-6):143-150. doi: 10.1007/s00335-019-09804-5. Epub 2019 May 24. PMID: 31127358; PMCID: PMC6606664.  
  • Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Brown SDM, Flenniken AM, Flicek P, Galli A, Mashhadi HH, Hrabě de Angelis M, Kim JK, Lloyd KCK, McKerlie C, Morgan H, Murray SA, Nutter LMJ, Reilly PT, Seavitt JR, Seong JK, Simon M, Wardle-Jones H, Mallon AM, Smedley D, Parkinson HE; IMPC consortium. The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation. Conserv Genet. 2018;19(4):995-1005. doi: 10.1007/s10592-018-1072-9. Epub 2018 May 19. PMID: 30100824; PMCID: PMC6061128.
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