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Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR

Nature Neuroscience volume 19, pages 517522 (2016) | Download Citation


Recurrent, reciprocal genomic disorders resulting from non-allelic homologous recombination (NAHR) between near-identical segmental duplications (SDs) are a major cause of human disease, often producing phenotypically distinct syndromes. The genomic architecture of flanking SDs presents a challenge for modeling these syndromes; however, the capability to efficiently generate reciprocal copy number variants (CNVs) that mimic NAHR would represent a valuable modeling tool. We describe here a CRISPR/Cas9 genome engineering method, single-guide CRISPR/Cas targeting of repetitive elements (SCORE), to model reciprocal genomic disorders and demonstrate its capabilities by generating reciprocal CNVs of 16p11.2 and 15q13.3, including alteration of one copy-equivalent of the SDs that mediate NAHR in vivo. The method is reproducible, and RNA sequencing reliably clusters transcriptional signatures from human subjects with in vivo CNVs and their corresponding in vitro models. This new approach will provide broad applicability for the study of genomic disorders and, with further development, may also permit efficient correction of these defects.

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We thank S. Haggarty and S. Sheridan (Center for Human Genetic Research, Massachusetts General Hospital) for generously providing the control iPSC line. These studies were supported by funding from the Simons Foundation for Autism Research (SFARI 328656 and 346042 (M.E.T.) and SFARI 308955 (J.F.G.)), the Nancy Lurie Marks Family Foundation (J.F.G. and M.E.T.), the US National Institutes of Health (R01NS093200 (J.F.G. and M.E.T.), R00MH095867 (M.E.T.), P01GM061354 (J.F.G. and M.E.T.)), the March of Dimes (M.E.T.), NARSAD (M.E.T.) and Autism Speaks (J.F.G.). Research reported in this publication was also partially supported by US National Cancer Institute award P30CA034196 (C.L.) and National Human Genome Research Institute award U41HG007497 (C.L.). We gratefully acknowledge the resources provided by the AGRE consortium and the participating AGRE families. AGRE is a program of Autism Speaks and is supported, in part, by grant 1U24MH081810 from the US National Institute of Mental Health to C.M. Lajonchere. C.L. is supported by an Ewha Womans University Distinguished Professorship. D.J.C.T. is a recipient of the Postdoctoral Research Abroad Program sponsored by Ministry of Science and Technology of Taiwan (102-2917-I-564-012).

Author information


  1. Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA.

    • Derek J C Tai
    • , Ashok Ragavendran
    • , Poornima Manavalan
    • , Alexei Stortchevoi
    • , Catarina M Seabra
    • , Serkan Erdin
    • , Ryan L Collins
    • , Ian Blumenthal
    • , James F Gusella
    •  & Michael E Talkowski
  2. Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA.

    • Derek J C Tai
    • , Catarina M Seabra
    •  & Michael E Talkowski
  3. Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA.

    • Derek J C Tai
    • , Ashok Ragavendran
    • , Poornima Manavalan
    • , Alexei Stortchevoi
    • , Catarina M Seabra
    • , Serkan Erdin
    • , Ryan L Collins
    •  & Michael E Talkowski
  4. Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA.

    • Derek J C Tai
    • , Ashok Ragavendran
    • , Poornima Manavalan
    • , Alexei Stortchevoi
    • , Catarina M Seabra
    • , Serkan Erdin
    • , Ryan L Collins
    •  & Michael E Talkowski
  5. Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal.

    • Catarina M Seabra
  6. Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China.

    • Xiaoli Chen
  7. Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA.

    • Yiping Shen
  8. Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA.

    • Mustafa Sahin
  9. The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.

    • Chengsheng Zhang
    •  & Charles Lee
  10. Department of Graduate Studies – Life Sciences, Ewha Womans University, Seoul, Korea.

    • Charles Lee
  11. Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.

    • James F Gusella
    •  & Michael E Talkowski
  12. Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.

    • James F Gusella


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M.E.T., J.F.G., D.J.C.T., A.S. and I.B. conceived and designed the studies. D.J.C.T., P.M., C.M.S. and A.S. performed molecular studies. A.R., R.L.C. and S.E. performed computational and statistical analyses. X.C., Y.S. and M.S. obtained 16p11.2 family tissue samples. C.Z. and C.L. designed and performed microarray studies. D.J.C.T., J.F.G. and M.E.T. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to James F Gusella or Michael E Talkowski.

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