Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis

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Monozygotic or ‘identical’ twins have been widely studied to dissect the relative contributions of genetics and environment in human diseases. In multiple sclerosis (MS), an autoimmune demyelinating disease and common cause of neurodegeneration and disability in young adults, disease discordance in monozygotic twins has been interpreted to indicate environmental importance in its pathogenesis1, 2, 3, 4, 5, 6, 7, 8. However, genetic and epigenetic differences between monozygotic twins have been described, challenging the accepted experimental model in disambiguating the effects of nature and nurture9, 10, 11, 12. Here we report the genome sequences of one MS-discordant monozygotic twin pair, and messenger RNA transcriptome and epigenome sequences of CD4+ lymphocytes from three MS-discordant, monozygotic twin pairs. No reproducible differences were detected between co-twins among ~3.6 million single nucleotide polymorphisms (SNPs) or ~0.2 million insertion-deletion polymorphisms. Nor were any reproducible differences observed between siblings of the three twin pairs in HLA haplotypes, confirmed MS-susceptibility SNPs, copy number variations, mRNA and genomic SNP and insertion-deletion genotypes, or the expression of ~19,000 genes in CD4+ T cells. Only 2 to 176 differences in the methylation of ~2million CpG dinucleotides were detected between siblings of the three twin pairs, in contrast to ~800 methylation differences between T cells of unrelated individuals and several thousand differences between tissues or between normal and cancerous tissues. In the first systematic effort to estimate sequence variation among monozygotic co-twins, we did not find evidence for genetic, epigenetic or transcriptome differences that explained disease discordance. These are the first, to our knowledge, female, twin and autoimmune disease individual genome sequences reported.

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  1. Comparison of the genomic locations of heterozygous cSNPs exhibiting imbalanced allelic expression in mRNA of twins 041896-001 and -101.
    Figure 1: Comparison of the genomic locations of heterozygous cSNPs exhibiting imbalanced allelic expression in mRNA of twins 041896-001 and -101.

    a, b, Allelic imbalance for 041896-001 (a) and 041896-101 (b) was detected in cSNPs called by≥10 gDNA reads with Q20 and where 20–80% of uniquely aligning gDNA reads called the SNP, together with detection in≥10 mRNA reads with Q20. Out of 14,461 heterozygous cSNPs, 268 (1.9%) showed significant allelic imbalance in expression (P<10-7), of which 153 (57%) were of the same magnitude and direction in both subjects. TCRVB is the T cell receptor beta locus, V (variable) segment, locus symbol TRB@. WDR40B is also known as DCAF12L1.

  2. Comparisons of methylation of genomic CpG sites in CD4+ lymphocytes and breast and lung tissue samples.
    Figure 2: Comparisons of methylation of genomic CpG sites in CD4+ lymphocytes and breast and lung tissue samples.

    a, Frequency distribution of CpG site methylation in 041896-001 (blue) and -101 (red) using ELAND-extended. bj, Pairwise comparisons of CpG site methylation using ELAND-extended in CD4+ lymphocytes from monozygotic twin siblings 041896-001 and -101 (b), 230178-001 and -101 (c) and 041907-001 and -101 (d); inter-individual differences between CD4+ lymphocytes from 041896-001 and 041907-001 (e) and 041896-001 and 230178-101 (f); neoplastic differences between breast tissue and breast cancer (g) and between normal lung tissue and lung cancer (h); and between-tissue differences between CD4+ lymphocytes and breast tissue (i) and lung tissue (j).


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Author information


  1. Department of Neurology, University of California at San Francisco, San Francisco, California 94143, USA

    • Sergio E. Baranzini,
    • Pouya Khankhanian,
    • Stacy J. Caillier,
    • Joseph P. McElroy,
    • Refujia Gomez,
    • Jorge R. Oksenberg &
    • Stephen L. Hauser
  2. National Center for Genome Resources, Santa Fe, New Mexico 87505, USA

    • Joann Mudge,
    • Jennifer C. van Velkinburgh,
    • Neil A. Miller,
    • Andrew D. Farmer,
    • Callum J. Bell,
    • Ryan W. Kim,
    • Gregory D. May,
    • Jimmy E. Woodward,
    • Leonda E. Clendenen,
    • Elena E. Ganusova,
    • Faye D. Schilkey,
    • Thiruvarangan Ramaraj &
    • Stephen F. Kingsmore
  3. Illumina Inc., Hayward, California 94545, USA

    • Irina Khrebtukova,
    • Lu Zhang,
    • Jim J. Huntley,
    • Shujun Luo &
    • Gary P. Schroth
  4. Stanford Medical School Blood Center, Palo Alto, California 94303, USA

    • Marcelo J. Pando
  5. Department of Neurology, Wayne State Medical School, Detroit, Michigan 48201, USA

    • Omar A. Khan
  6. Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94143, USA

    • Pui-yan Kwok
  7. Institute for Human Genetics, University of California at San Francisco, San Francisco, California 94143, USA

    • Pui-yan Kwok,
    • Jorge R. Oksenberg &
    • Stephen L. Hauser
  8. Department of Bioinformatics, Genentech Inc., South San Francisco, California 94080, USA

    • Thomas D. Wu


S.E.B., G.P.S., J.R.O., S.L.H. and S.F.K. designed the project. S.F.K., S.E.B., J.M. and J.R.O. wrote the paper with input from the other authors. S.E.B., J.M., J.C.v.V., L.Z., R.W.K., G.D.M., J.E.W., S.J.C., J.P.M., R.G., M.J.P., L.E.C., E.E.G., F.D.S., J.J.H. and S.L. performed the experiments. S.E.B., J.M., J.C.v.V., P.K., I.K., N.A.M., L.Z., A.D.F., C.J.B., T.R., S.L., P.K., T.D.W., G.P.S., J.R.O., S.L.H. and S.F.K. analysed the data. S.L.H., J.R.O. and O.A.K. supervised patient recruitment.

Competing financial interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to:

Data is deposited at dbGaP under accession phs000239.v1.p1.

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  1. Supplementary Information (21.9M)

    This file contains Supplementary Tables 1-16 and Supplementary Figures 1-18 with legends.


  1. Report this comment #10639

    Muy-Teck Teh said:

    Could mitochondria genome provide an answer for the discordant twins?

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