Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR

Nat Neurosci. 2016 Mar;19(3):517-22. doi: 10.1038/nn.4235. Epub 2016 Feb 1.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Autistic Disorder / genetics*
  • CRISPR-Cas Systems / genetics*
  • Chromosome Deletion
  • Chromosome Disorders / genetics*
  • Chromosomes, Human, Pair 15 / genetics
  • Chromosomes, Human, Pair 16 / genetics
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics
  • DNA Copy Number Variations / genetics*
  • Genetic Engineering / methods*
  • Humans
  • Intellectual Disability / genetics*
  • Segmental Duplications, Genomic / genetics*
  • Seizures / genetics*
  • Sequence Deletion / genetics*

Supplementary concepts

  • 16p11.2 Deletion Syndrome
  • Chromosome 15q13.3 Microdeletion Syndrome