Publications

  1. Ingham D, Diggle CP, Berry I, Bristow CA, Hayward BE, Rahman N, Markham AF, Sheridan EG, Bonthron DT, Carr IM. Simple Detection of Germline Microsatellite Instability for Diagnosis Of Constitutional Mismatch Repair Cancer Syndrome. Hum Mutat. 2013 Mar 8. doi: 10.1002/humu.22311. [Epub ahead of print]
  2. Parry DA, Poulter JA, Logan CV, Brookes SJ, Jafri H, Ferguson CH, Anwari BM,Rashid Y, Zhao H, Johnson CA, Inglehearn CF, Mighell AJ.
    Identification of Mutations in SLC24A4, Encoding a Potassium-Dependent Sodium/Calcium Exchanger, asa Cause of Amelogenesis Imperfecta.
    Am J Hum Genet. 2013 Feb 7;92(2):307-12. doi:10.1016/j.ajhg.2013.01.003. Epub 2013 Jan 31. PubMed PMID: 23375655.
  3. Carr IM, Bhaskar S, O'Sullivan J, Aldahmesh MA, Shamseldin HE, Markham AF,Bonthron DT, Black G, Alkuraya FS.
    Autozygosity mapping with exome sequence data.
    Hum Mutat. 2013 Jan;34(1):50-6. doi: 10.1002/humu.22220. Epub 2012 Oct 22. PubMedPMID: 23090942.
  4. Ali H, Daser A, Dear P, Wood H, Rabbitts P, Rabbitts T.
    Nonreciprocal chromosomal translocations in renal cancer involve multiple DSBs and NHEJ associated with breakpoint inversion but not necessarily with transcription.
    Genes Chromosomes Cancer. 2013 Apr;52(4):402-9. doi: 10.1002/gcc.22038. Epub 2013Jan 23. PubMed PMID: 23341332.
  5. Chambers PA, Stead LF, Morgan JE, Carr IM, Sutton KM, Watson CM, Crowe V,Dickinson H, Roberts P, Mulatero C, Seymour M, Markham AF, Waring PM, Quirke P,Taylor GR.
    Mutation detection by clonal sequencing of PCR amplicons and grouped read typing is applicable to clinical diagnostics.
    Hum Mutat. 2013Jan;34(1):248-54. doi: 10.1002/humu.22207. Epub 2012 Oct 11. PubMed PMID:22915446.
  6. Parry DA, Brookes SJ, Logan CV, Poulter JA, El-Sayed W, Al-Bahlani S, AlHarasi S, Sayed J, Raif el M, Shore RC, Dashash M, Barron M, Morgan JE, Carr IM, Taylor GR, Johnson CA, Aldred MJ, Dixon MJ, Wright JT, Kirkham J, Inglehearn CF, Mighell AJ.
    Mutations in C4orf26, encoding a peptide with in vitro hydroxyapatite crystal nucleation and growth activity, cause amelogenesis imperfecta.
    Am J HumGenet. 2012 Sep 7;91(3):565-71. doi: 10.1016/j.ajhg.2012.07.020. Epub 2012 Aug16. PubMed PMID: 22901946; PubMed Central PMCID: PMC3511980.
  7. Koenekoop RK, Wang H, Majewski J, Wang X, Lopez I, Ren H, Chen Y, Li Y,Fishman GA, Genead M, Schwartzentruber J, Solanki N, Traboulsi EI, Cheng J, LoganCV, McKibbin M, Hayward BE, Parry DA, Johnson CA, Nageeb M;
    Finding of Rare Disease Genes (FORGE) Canada Consortium, Poulter JA, Mohamed MD, Jafri H, Rashid Y, Taylor GR, Keser V, Mardon G, Xu H, Inglehearn CF, Fu Q, Toomes C, Chen R.
    Mutations in NMNAT1 cause Leber congenital amaurosis and identify a new disease pathway for retinal degeneration. Nat Genet. 2012 Sep;44(9):1035-9. doi:10.1038/ng.2356. Epub 2012 Jul 29. PubMed PMID: 22842230.
  8. Diggle CP, Parry DA, Logan CV, Laissue P, Rivera C, Restrepo CM, Fonseca DJ,Morgan JE, Allanore Y, Fontenay M, Wipff J, Varret M, Gibault L, Dalantaeva N,Korbonits M, Zhou B, Yuan G, Harifi G, Cefle K, Palanduz S, Akoglu H, ZwijnenburgPJ, Lichtenbelt KD, Aubry-Rozier B, Superti-Furga A, Dallapiccola B, Accadia M,Brancati F, Sheridan EG, Taylor GR, Carr IM, Johnson CA, Markham AF, Bonthron DT.
    Prostaglandin transporter mutations cause pachydermoperiostosis with myelofibrosis.
    Hum Mutat. 2012 Aug;33(8):1175-81. doi: 10.1002/humu.22111. Epub 2012 May 29. PubMed PMID: 22553128.
  9. Poulter JA, Davidson AE, Ali M, Gilmour DF, Parry DA, Mintz-Hittner HA, CarrIM, Bottomley HM, Long VW, Downey LM, Sergouniotis PI, Wright GA, MacLaren RE,Moore AT, Webster AR, Inglehearn CF, Toomes C.
    Recessive mutations in TSPAN12 cause retinal dysplasia and severe familial exudative vitreoretinopathy (FEVR).
    Invest Ophthalmol Vis Sci. 2012 May 14;53(6):2873-9. doi: 10.1167/iovs.11-8629.PubMed PMID: 22427576.
  10. Robinson JI, Carr IM, Cooper DL, Rashid LH, Martin SG, Emery P, Isaacs JD,Barton A; BRAGGSS, Wilson AG, Barrett JH, Morgan AW.
    Confirmation of association of FCGR3B but not FCGR3A copy number with susceptibility to autoantibody positive rheumatoid arthritis.
    Hum Mutat. 2012 Apr;33(4):741-9. doi: 10.1002/humu.22031.Epub 2012 Feb 28. PubMed PMID: 22290871.
  11. Conway C, Chalkley R, High A, Maclennan K, Berri S, Chengot P, Alsop M, EganP, Morgan J, Taylor GR, Chester J, Sen M, Rabbitts P, Wood HM.
    Next-generationsequencing for simultaneous determination of human papillomavirus load, subtype, and associated genomic copy number changes in tumors.
    J Mol Diagn. 2012Mar-Apr;14(2):104-11. doi: 10.1016/j.jmoldx.2011.10.003. Epub 2012 Jan 10. PubMedPMID: 22240447.
  12. Khan K, Logan CV, McKibbin M, Sheridan E, Elçioglu NH, Yenice O, Parry DA, Fernandez-Fuentes N, Abdelhamed ZI, Al-Maskari A, Poulter JA, Mohamed MD, CarrIM, Morgan JE, Jafri H, Raashid Y, Taylor GR, Johnson CA, Inglehearn CF, ToomesC, Ali M.
    Next generation sequencing identifies mutations in Atonal homolog 7(ATOH7) in families with global eye developmental defects.
    Hum Mol Genet. 2012Feb 15;21(4):776-83. doi: 10.1093/hmg/ddr509. Epub 2011 Nov 7. PubMed PMID:22068589; PubMed Central PMCID: PMC3263993.
  13. Carr IM, Diggle CP, Touqan N, Anwar R, Sheridan EG, Bonthron DT, Johnson CA, Ali M, Markham AF.
    Identification of autosomal recessive disease loci using out-bred nuclear families.
    Hum Mutat. 2012 Feb;33(2):338-42. doi:10.1002/humu.21645. Epub 2011 Nov 28. PubMed PMID: 22052625.
  14. Conway C, Chalkley R, High A, Maclennan K, Berri S, Chengot P, Alsop M, EganP, Morgan J, Taylor GR, Chester J, Sen M, Rabbitts P, Wood HM.
    Next-generation sequencing for simultaneous determination of human papilloma virus load, subtype, and associated genomic copy number changes in tumors.
    J Mol Diagn. 2012Mar-Apr;14(2):104-11. doi: 10.1016/j.jmoldx.2011.10.003. Epub 2012 Jan 10. PubMedPMID: 22240447
  15. Belvedere O, Berri S, Chalkley R, Conway C, Barbone F, Pisa F, MacLennan K,Daly C, Alsop M, Morgan J, Menis J, Tcherveniakov P, Papagiannopoulos K, RabbittsP, Wood HM.
    A computational index derived from whole-genome copy number analysis is a novel tool for prognosis in early stage lung squamous cell carcinoma.
    Genomics. 2012 Jan;99(1):18-24. doi: 10.1016/j.ygeno.2011.10.006. Epub 2011 Oct25. PubMed PMID: 22050995.
  16. Carr IM, Diggle CP, Khan K, Inglehearn C, McKibbin M, Bonthron DT, MarkhamAF, Anwar R, Dobbie A, Pena SD, Ali M.
    Rapid visualisation of microarray copy number data for the detection of structural variations linked to a diseasephenotype.
    PLoS One. 2012;7(8):e43466. doi: 10.1371/journal.pone.0043466. Epub2012 Aug 17. PubMed PMID: 22912880; PubMed Central PMCID: PMC3422275.
  17. Carr IM, Johnson CA, Markham AF, Toomes C, Bonthron DT, Sheridan EG.
    DominantMapper: rule-based analysis of SNP data for rapid mapping of dominant diseases in related nuclear families.
    Hum Mutat. 2011 Dec;32(12):1359-66. doi:10.1002/humu.21597. Epub 2011 Sep 19. PubMed PMID: 21905167.
  18. Carr IM, Markham SA, Pena SD.
    Estimating the degree of identity by descent inconsanguineous couples.
    Hum Mutat. 2011 Dec;32(12):1350-8. doi:10.1002/humu.21584. Epub 2011 Sep 23. PubMed PMID: 21901788.
  19. Logan CV, Lucke B, Pottinger C, Abdelhamed ZA, Parry DA, Szymanska K, Diggle CP, van Riesen A, Morgan JE, Markham G, Ellis I, Manzur AY, Markham AF, Shires M,Helliwell T, Scoto M, Hübner C, Bonthron DT, Taylor GR, Sheridan E, Muntoni F,Carr IM, Schuelke M, Johnson CA.
    Mutations in MEGF10, a regulator of satellite cell myogenesis, cause early onset myopathy, areflexia, respiratory distress and dysphagia (EMARDD).
    Nat Genet. 2011 Nov 20;43(12):1189-92. doi: 10.1038/ng.995.PubMed PMID: 22101682.
  20. Carr IM, Morgan JE, Diggle CP, Sheridan E, Markham AF, Logan CV, InglehearnCF, Taylor GR, Bonthron DT.
    Illuminator, a desktop program for mutation detectionusing short-read clonal sequencing.
    Genomics. 2011 Oct;98(4):302-9. doi:10.1016/j.ygeno.2011.05.004. Epub 2011 May 19. PubMed PMID: 21621601.
  21. Melnik S, Deng B, Papantonis A, Baboo S, Carr IM, Cook PR.
    The proteomes oftranscription factories containing RNA polymerases I, II or III.
    Nat Methods.2011 Sep 25;8(11):963-8. doi: 10.1038/nmeth.1705. PubMed PMID: 21946667; PubMedCentral PMCID: PMC3324775.
  22. Gusnanto A, Wood HM, Pawitan Y, Rabbitts P, Berri S.
    Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data.
    Bioinformatics. 2012 Jan1;28(1):40-7. doi: 10.1093/bioinformatics/btr593. Epub 2011 Oct 28. PubMed PMID: 22039209.
  23. Khan K, Rudkin A, Parry DA, Burdon KP, McKibbin M, Logan CV, Abdelhamed ZI,Muecke JS, Fernandez-Fuentes N, Laurie KJ, Shires M, Fogarty R, Carr IM, Poulter JA, Morgan JE, Mohamed MD, Jafri H, Raashid Y, Meng N, Piseth H, Toomes C, CassonRJ, Taylor GR, Hammerton M, Sheridan E, Johnson CA, Inglehearn CF, Craig JE, Ali M.
    Homozygous mutations in PXDN cause congenital cataract, corneal opacity, anddevelopmental glaucoma.
    Am J Hum Genet. 2011 Sep 9;89(3):464-73. doi:10.1016/j.ajhg.2011.08.005. PubMed PMID: 21907015; PubMed Central PMCID:PMC3169830.
  24. Parry DA, Logan CV, Hayward BE, Shires M, Landolsi H, Diggle C, Carr I,Rittore C, Touitou I, Philibert L, Fisher RA, Fallahian M, Huntriss JD, PictonHM, Malik S, Taylor GR, Johnson CA, Bonthron DT, Sheridan EG.
    Mutations causing familial biparental hydatidiform mole implicate c6orf221 as a possible regulator of genomic imprinting in the human oocyte.
    Am J Hum Genet. 2011 Sep9;89(3):451-8. doi: 10.1016/j.ajhg.2011.08.002. Epub 2011 Sep 1. PubMed PMID:21885028; PubMed Central PMCID: PMC3169823.
  25. Khan K, Al-Maskari A, McKibbin M, Carr IM, Booth A, Mohamed M, Siddiqui S,Poulter JA, Parry DA, Logan CV, Hashmi A, Sahi T, Jafri H, Raashid Y, Johnson CA,Markham AF, Toomes C, Rice A, Sheridan E, Inglehearn CF, Ali M.
    Genetic heterogeneity for recessively inherited congenital cataract microcornea withcorneal opacity.
    Invest Ophthalmol Vis Sci. 2011 Jun 16;52(7):4294-9. doi:10.1167/iovs.10-6776. PubMed PMID: 21474777; PubMed Central PMCID: PMC3175982.
  26. Yang Y, Cochran DA, Gargano MD, King I, Samhat NK, Burger BP, Sabourin KR,Hou Y, Awata J, Parry DA, Marshall WF, Witman GB, Lu X.
    Regulation of flagellar motility by the conserved flagellar protein CG34110/Ccdc135/FAP50.
    Mol Biol Cell.2011 Apr;22(7):976-87. doi: 10.1091/mbc.E10-04-0331. Epub 2011 Feb 2. PubMedPMID: 21289096; PubMed Central PMCID: PMC3069022.
  27. Carr IM, Camm N, Taylor GR, Charlton R, Ellard S, Sheridan EG, Markham AF,Bonthron DT.
    GeneScreen: a program for high-throughput mutation detection in DNA sequence electropherograms.
    J Med Genet. 2011 Feb;48(2):123-30. doi:10.1136/jmg.2010.082081. Epub 2010 Oct 30. PubMed PMID: 21037276.
  28. El-Sayed W, Shore RC, Parry DA, Inglehearn CF, Mighell AJ.
    Hypomaturation amelogenesis imperfecta due to WDR72 mutations: a novel mutation andultrastructural analyses of deciduous teeth.
    Cells Tissues Organs.2011;194(1):60-6. doi: 10.1159/000322036. Epub 2010 Dec 29. PubMed PMID:21196691; PubMed Central PMCID: PMC3128158.
  29. Pardo CE, Carr IM, Hoffman CJ, Darst RP, Markham AF, Bonthron DT, Kladde MP.
    MethylViewer: computational analysis and editing for bisulfite sequencing andmethyltransferase accessibility protocol for individual templates (MAPit)projects.
    Nucleic Acids Res. 2011 Jan;39(1):e5. doi: 10.1093/nar/gkq716. Epub2010 Oct 19. PubMed PMID: 20959287; PubMed Central PMCID: PMC3017589.
  30. Diggle CP, Carr IM, Zitt E, Wusik K, Hopkin RJ, Prada CE, Calabrese O,Rittinger O, Punaro MG, Markham AF, Bonthron DT.
    Common and recurrent HPGDmutations in Caucasian individuals with primary hypertrophic osteoarthropathy.
    Rheumatology (Oxford). 2010 Jun;49(6):1056-62. doi: 10.1093/rheumatology/keq048. Epub 2010 Mar 18. PubMed PMID: 20299379.
  31. Wood HM, Belvedere O, Conway C, Daly C, Chalkley R, Bickerdike M, McKinley C, Egan P, Ross L, Hayward B, Morgan J, Davidson L, MacLennan K, Ong TK,Papagiannopoulos K, Cook I, Adams DJ, Taylor GR, Rabbitts P.
    Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embeddedspecimens.
    Nucleic Acids Res. 2010 Aug;38(14):e151. doi: 10.1093/nar/gkq510. Epub2010 Jun 4. PubMed PMID: 20525786; PubMed Central PMCID: PMC2919738.
  32. Morgan JE, Carr IM, Sheridan E, Chu CE, Hayward B, Camm N, Lindsay HA,Mattocks CJ, Markham AF, Bonthron DT, Taylor GR.
    Genetic diagnosis of familial breast cancer using clonal sequencing.
    Hum Mutat. 2010 Apr;31(4):484-91. doi:10.1002/humu.21216. PubMed PMID: 20127978.
  33. Carr IM, Robinson JI, Dimitriou R, Markham AF, Morgan AW, Bonthron DT.
    Inferring relative proportions of DNA variants from sequencing electropherograms.
    Bioinformatics. 2009 Dec 15;25(24):3244-50. doi: 10.1093/bioinformatics/btp583.Epub 2009 Oct 9. PubMed PMID: 19819885.
  34. Carr IM, Szymanska K, Sheridan E, Markham AF, Bonthron DT, Johnson CA.
    Shadow autozygosity mapping by linkage exclusion (SAMPLE): a simple strategy to identifythe genetic basis of lethal autosomal recessive disorders.
    Hum Mutat. 2009Dec;30(12):1642-9. doi: 10.1002/humu.21105. PubMed PMID: 19842213.
  35. Abdollahi MR, Morrison E, Sirey T, Molnar Z, Hayward BE, Carr IM, SpringellK, Woods CG, Ahmed M, Hattingh L, Corry P, Pilz DT, Stoodley N, Crow Y, TaylorGR, Bonthron DT, Sheridan E.
    Mutation of the variant alpha-tubulin TUBA8 results in polymicrogyria with optic nerve hypoplasia.
    Am J Hum Genet. 2009Nov;85(5):737-44. doi: 10.1016/j.ajhg.2009.10.007. Epub 2009 Nov 5. PubMed PMID: 19896110; PubMed Central PMCID: PMC2775839.
  36. El-Sayed W, Parry DA, Shore RC, Ahmed M, Jafri H, Rashid Y, Al-Bahlani S, Al Harasi S, Kirkham J, Inglehearn CF, Mighell AJ.
    Mutations in the beta propeller WDR72 cause autosomal-recessive hypomaturation amelogenesis imperfecta.
    Am J Hum Genet. 2009 Nov;85(5):699-705. doi: 10.1016/j.ajhg.2009.09.014. Epub 2009 Oct 22.PubMed PMID: 19853237; PubMed Central PMCID: PMC2775821.
  37. Rice GI, Bond J, Asipu A, Brunette RL, Manfield IW, Carr IM, Fuller JC,Jackson RM, Lamb T, Briggs TA, Ali M, Gornall H, Couthard LR, Aeby A,Attard-Montalto SP, Bertini E, Bodemer C, Brockmann K, Brueton LA, Corry PC,Desguerre I, Fazzi E, Cazorla AG, Gener B, Hamel BC, Heiberg A, Hunter M, van derKnaap MS, Kumar R, Lagae L, Landrieu PG, Lourenco CM, Marom D, McDermott MF, van der Merwe W, Orcesi S, Prendiville JS, Rasmussen M, Shalev SA, Soler DM, Shinawi M, Spiegel R, Tan TY, Vanderver A, Wakeling EL, Wassmer E, Whittaker E, Lebon P, Stetson DB, Bonthron DT, Crow YJ.
    Mutations involved in Aicardi-Goutièressyndrome implicate SAMHD1 as regulator of the innate immune response.
    Nat Genet. 2009 Jul;41(7):829-32. doi: 10.1038/ng.373. Epub 2009 Jun 14. PubMed PMID:19525956.
  38. Carr IM, Sheridan E, Hayward BE, Markham AF, Bonthron DT.
    IBDfinder andSNPsetter: tools for pedigree-independent identification of autozygous regions inindividuals with recessive inherited disease. H
    um Mutat. 2009 Jun;30(6):960-7.doi: 10.1002/humu.20974. PubMed PMID: 19405095.
  39. Parry DA, Toomes C, Bida L, Danciger M, Towns KV, McKibbin M, Jacobson SG,Logan CV, Ali M, Bond J, Chance R, Swendeman S, Daniele LL, Springell K, Adams M,Johnson CA, Booth AP, Jafri H, Rashid Y, Banin E, Strom TM, Farber DB, Sharon D, Blobel CP, Pugh EN Jr, Pierce EA, Inglehearn CF.
    Loss of the metalloproteaseADAM9 leads to cone-rod dystrophy in humans and retinal degeneration in mice.
    Am J Hum Genet. 2009 May;84(5):683-91. doi: 10.1016/j.ajhg.2009.04.005. Epub 2009Apr 30. PubMed PMID: 19409519; PubMed Central PMCID: PMC2681008.
  40. Ali M, McKibbin M, Booth A, Parry DA, Jain P, Riazuddin SA, Hejtmancik JF,Khan SN, Firasat S, Shires M, Gilmour DF, Towns K, Murphy AL, Azmanov D, Tournev I, Cherninkova S, Jafri H, Raashid Y, Toomes C, Craig J, Mackey DA, KalaydjievaL, Riazuddin S, Inglehearn CF.
    Null mutations in LTBP2 cause primary congenital glaucoma.
    Am J Hum Genet. 2009 May;84(5):664-71. doi: 10.1016/j.ajhg.2009.03.017.Epub 2009 Apr 9. PubMed PMID: 19361779; PubMed Central PMCID: PMC2680998.