Whole genome analyses reveal no pathogenetic single nucleotide or structural differences between monozygotic twins discordant for amyotrophic lateral sclerosis

References

• Graham AJ, Macdonald AM, Hawkes CH. British motor neuron disease twin study. J Neurol Neurosurg Psychiatry. 1997;62:562–9.
   PubMed Web of Science ®Google Scholar
• Dellefave L, Bangash MA, Siddique T. Pairwise concordance rates are similar in monozygotic and dizygotic twins for amyotrophic lateral sclerosis. Amyotroph Lateral Scler Other Motor Neuron Disord. 2003;4 (Suppl 1):47.
   Google Scholar
• Al-Chalabi A, Fang F, Hanby MF, Leigh PN, Shaw CE, Ye W, et al. An estimate of amyotrophic lateral sclerosis heritability using twin data. J Neurol Neurosurg Psychiatry. 2010;81:1324–6.
   PubMed Web of Science ®Google Scholar
• Razzaghian HR, Shahi MH, Forsberg LA, de Stahl TD, Absher D, Dahl N, et al. Somatic mosaicism for chromosome X and Y aneuploidies in monozygotic twins heterozygous for sickle cell disease mutation. Am J Med Genet A. 2010;152A:2595–8.
   PubMed Web of Science ®Google Scholar
• Dahoun S, Gagos S, Gagnebin M, Gehrig C, Burgi C, Simon F, et al. Monozygotic twins discordant for trisomy 21 and maternal 21q inheritance: a complex series of events. Am J Med Genet A. 2008;146A:2086–93.
   PubMed Web of Science ®Google Scholar
• Ramsey KW, Slavin TP, Graham G, Hirata GI, Balaraman V, Seaver LH. Monozygotic twins discordant for trisomy 13. J Perinatol. 2012;32:306–8.
   PubMed Web of Science ®Google Scholar
• Pauli S, Schmidt T, Funke R, Zoll B, Burfeind P, Dybowski U, et al. Discordant phenotype in monozygotic twins with mosaic trisomy 12p in lymphocytes. Eur J Med Genet. 2012;55:480–4.
   PubMed Web of Science ®Google Scholar
• Campbell CD, Chong JX, Malig M, Ko A, Dumont BL, Han LD, et al. Estimating the human mutation rate using autozygosity in a founder population. Nat Genet. 2012;44: 1277–81.
   PubMed Web of Science ®Google Scholar
• Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, Magnusson G, et al. Rate of de novo mutations and the importance of father’s age to disease risk. Nature. 2012;488: 471–5.
   PubMed Web of Science ®Google Scholar
• Vogt J, Kohlhase J, Morlot S, Kluwe L, Mautner VF, Cooper DN, et al. Monozygotic twins discordant for neurofibromatosis type 1 due to a post zygotic NF1 gene mutation. Hum Mutat. 2011;32:E2134–47.
   PubMed Web of Science ®Google Scholar
• Robertson SP, Jenkins ZA, Morgan T, Ades L, Aftimos S, Boute O, et al. Frontometaphyseal dysplasia: mutations in FLNA and phenotypic diversity. Am J Med Genet A. 2006;140:1726–36.
   PubMed Web of Science ®Google Scholar
• Rio M, Royer G, Gobin S, de Blois MC, Ozilou C, Bernheim A, et al. Monozygotic twins discordant for submicroscopic chromosomal anomalies in 2p25.3 region detected by array CGH. Clin Genet. 2013;84:31–6.
   PubMed Web of Science ®Google Scholar
• Breckpot J, Thienpont B, Bauters M, Tranchevent LC, Gewillig M, Allegaert K, et al. Congenital heart defects in a novel recurrent 22q11.2 deletion harbouring the genes CRKL and MAPK1. Am J Med Genet A. 2012;158A:574–80.
   PubMed Web of Science ®Google Scholar
• Bruder CE, Piotrowski A, Gijsbers AA, Andersson R, Erickson S, Diaz de Stahl T, et al. Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles. Am J Hum Genet. 2008;82: 763–71.
   PubMed Web of Science ®Google Scholar
• Kimani JW, Yoshiura K, Shi M, Jugessur A, Moretti-Ferreira D, Christensen K, et al. Search for genomic alterations in monozygotic twins discordant for cleft lip and/or palate. Twin Res Hum Genet. 2009;12:462–8.
   PubMed Web of Science ®Google Scholar
• Baranzini SE, Mudge J, van Velkinburgh JC, Khankhanian P, Khrebtukova I, Miller NA, et al. Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature. 2010;464:1351–6.
   PubMed Web of Science ®Google Scholar
• Solomon BD, Pineda-Alvarez DE, Hadley DW, Hansen NF, Kamat A, Donovan FX, et al. Exome sequencing and high-density microarray testing in monozygotic twin pairs discordant for features of VACTERL association. Mol Syndromol. 2013;4:27–31.
   PubMedGoogle Scholar
• Al-Chalabi A, Hardiman O. The epidemiology of ALS: a conspiracy of genes, environment and time. Nat Rev Neurol. 2013;9:617–28.
   PubMed Web of Science ®Google Scholar
• Blauw HM, Veldink JH, van Es MA, van Vught PW, Saris CG, van der Zwaag B, et al. Copy number variation in sporadic amyotrophic lateral sclerosis: a genome-wide screen. Lancet Neurol. 2008;7:319–26.
   PubMed Web of Science ®Google Scholar
• Cronin S, Tomik B, Bradley DG, Slowik A, Hardiman O. Screening for replication of genome-wide SNP associations in sporadic ALS. Eur J Hum Genet. 2009;17:213–8.
   PubMed Web of Science ®Google Scholar
• Shoichet SA, Waibel S, Endruhn S, Sperfeld AD, Vorwerk B, Muller I, et al. Identification of candidate genes for sporadic amyotrophic lateral sclerosis by array comparative genomic hybridization. Amyotroph Lateral Scler. 2009;10:162–9.
   PubMed Web of Science ®Google Scholar
• Pamphlett R, Morahan JM. Copy number imbalances in blood and hair in monozygotic twins discordant for amyotrophic lateral sclerosis. J Clin Neurosci. 2011;18: 1231–4.
   PubMed Web of Science ®Google Scholar
• Pamphlett R, Cheong PL, Trent RJ, Yu B. Can ALS- associated C9orf72 repeat expansions be diagnosed on a blood DNA test alone? PLoS One. 2013;8:e70007.
   PubMed Web of Science ®Google Scholar
• Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics. 2012;28:311–7.
   PubMed Web of Science ®Google Scholar
• Saunders CT, Wong WS, Swamy S, Becq J, Murray LJ, Cheetham RK. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics. 2012;28:1811–7.
   PubMed Web of Science ®Google Scholar
• Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22:568–76.
   PubMed Web of Science ®Google Scholar
• Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009;25:2865–71.
   PubMed Web of Science ®Google Scholar
• Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, et al. Recurring mutations found by sequencing an acute myeloid leukaemia genome. N Engl J Med. 2009;361: 1058–66.
   PubMed Web of Science ®Google Scholar
• Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24–6.
   PubMed Web of Science ®Google Scholar
• Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14:178–92.
   PubMed Web of Science ®Google Scholar
• Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, et al. BreakDancer: an algorithm for high resolution mapping of genomic structural variation. Nat Methods. 2009;6:677–81.
   PubMed Web of Science ®Google Scholar
• McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics. 2010;26:2069–70.
   PubMed Web of Science ®Google Scholar
• Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011;21:974–84.
   PubMed Web of Science ®Google Scholar
• Michaelson JJ, Sebat J. forestSV: structural variant discovery through statistical learning. Nat Methods. 2012;9: 819–21.
   PubMed Web of Science ®Google Scholar
• Abel O, Powell JF, Andersen PM, Al-Chalabi A. ALSoD: a user-friendly online bioinformatics tool for amyotrophic lateral sclerosis genetics. Hum Mutat. 2012;33:1345–51.
   PubMed Web of Science ®Google Scholar
• Doi K, Monjo T, Hoang PH, Yoshimura J, Yurino H, Mitsui J, et al. Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing. Bioinformatics. 2014;30:815–22.
   PubMed Web of Science ®Google Scholar
• Petersen BS, Spehlmann ME, Raedler A, Stade B, Thomsen I, Rabionet R, et al. Whole genome and exome sequencing of monozygotic twins discordant for Crohn’s disease. BMC Genomics. 2014;15:564.
   PubMed Web of Science ®Google Scholar
• Magne F, Serpa R, van Vliet G, Samuels ME, Deladoey J. Somatic mutations are not observed by exome sequencing of lymphocyte DNA from monozygotic twins discordant for congenital hypothyroidism due to thyroid dysgenesis. Horm Res Paediatr. 2014;83:79–85.
   PubMed Web of Science ®Google Scholar
• Chaiyasap P, Kulawonganunchai S, Srichomthong C, Tongsima S, Suphapeetiporn K, Shotelersuk V. Whole genome and exome sequencing of monozygotic twins with trisomy 21, discordant for a congenital heart defect and epilepsy. PLoS One. 2014;9:e100191.
   PubMed Web of Science ®Google Scholar
• Armon C. Smoking may be considered an established risk factor for sporadic ALS. Neurology. 2009;73:1693–8.
   PubMed Web of Science ®Google Scholar
• Pamphlett R. Exposure to environmental toxins and the risk of sporadic motor neuron disease: an expanded Australian case-control study. Eur J Neurol. 2012;19:1343–8.
   PubMed Web of Science ®Google Scholar
• Pamphlett R, Rikard-Bell A. Different occupations associated with amyotrophic lateral sclerosis: is diesel exhaust the link? PLoS One. 2013;8:e80993.
   PubMed Web of Science ®Google Scholar
• Pamphlett R, Kum Jew S. Heavy metals in locus ceruleus and motor neurons in motor neuron disease. Acta Neuropathol Commun 2013;1:81.
   PubMed Web of Science ®Google Scholar
• Al-Chalabi A, Calvo A, Chio A, Colville S, Ellis CM, Hardiman O, et al. Analysis of amyotrophic lateral sclerosis as a multistep process: a population-based modeling study. Lancet Neurol. 2014;13:1108–13.
   PubMed Web of Science ®Google Scholar
• Kaminsky ZA, Tang T, Wang SC, Ptak C, Oh GH, Wong AH, et al. DNA methylation profiles in monozygotic and dizygotic twins. Nat Genet. 2009;41:240–5.
   PubMed Web of Science ®Google Scholar
• Oates N, Pamphlett R. An epigenetic analysis of SOD1 and VEGF in ALS. Amyotroph Lateral Scler. 2007;8:83–6.
   PubMed Web of Science ®Google Scholar
• Morahan JM, Yu B, Trent RJ, Pamphlett R. Are metallothionein genes silenced in ALS? Toxicol Let. 2007;168:83–7.
   PubMed Web of Science ®Google Scholar
• Morahan JM, Yu B, Trent RJ, Pamphlett R. A genome-wide analysis of brain DNA methylation identifies new candidate genes for sporadic amyotrophic lateral sclerosis. Amyotroph Lateral Scler. 2009;10:418–29.
   PubMed Web of Science ®Google Scholar
• Gordon L, Joo JE, Powell JE, Ollikainen M, Novakovic B, Li X, et al. Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence. Genome Res. 2012;22:1395–406.
   PubMed Web of Science ®Google Scholar
• Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, et al. Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci U S A. 2005;102:10604–9.
   PubMed Web of Science ®Google Scholar
• Gervin K, Vigeland MD, Mattingsdal M, Hammero M, Nygard H, Olsen AO, et al. DNA methylation and gene expression changes in monozygotic twins discordant for psoriasis: identification of epigenetically dysregulated genes. PLoS Genet. 2012;8:e1002454.
   PubMed Web of Science ®Google Scholar
• Pamphlett R, Morahan JM, Luquin N, Yu B. Looking for differences in copy number between blood and brain in sporadic amyotrophic lateral sclerosis. Muscle Nerve. 2011;44:492–8.
   PubMed Web of Science ®Google Scholar
• Xi Z, Yunusova Y, van Blitterswijk M, Dib S, Ghani M, Moreno D, et al. Identical twins with the C9orf72 repeat expansion are discordant for ALS. Neurology. 2014;83:1476–8.
   PubMed Web of Science ®Google Scholar
• Arlotta P, Molyneaux BJ, Chen J, Inoue J, Kominami R, Macklis JD. Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo. Neuron. 2005;45:207–21.
   PubMed Web of Science ®Google Scholar
• Daoud H, Valdmanis PN, Gros-Louis F, Belzil V, Spiegelman D, Henrion E, et al. Resequencing of 29 candidate genes in patients with familial and sporadic amyotrophic lateral sclerosis. Arch Neurol. 2011;68:587–93.
   PubMed Web of Science ®Google Scholar
• Couthouis J, Hart MP, Erion R, King OD, Diaz Z, Nakaya T, et al. Evaluating the role of the FUS/TLS-related gene EWSR1 in amyotrophic lateral sclerosis. Hum Mol Genet. 2012;21: 2899–911.
   PubMed Web of Science ®Google Scholar