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Simons Variation in Individuals Project (Simons VIP)

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The genetics of autism is complex and involves mutations in hundreds of genes, each of which accounts for a small percentage of autism.

To probe the phenotype of genetically well-defined subtypes of autism more deeply, SFARI launched the Simons Variation in Individuals Project (Simons VIP). The project aims to identify and study large numbers of individuals sharing recurrent genetic variants known to increase the risk of developing autism spectrum and other neurodevelopmental disorders. Longer-term goals are to use these data to develop targeted interventions and focused clinical care.

The Simons VIP first studied individuals with a deletion or duplication of chromosomal segment 16p11.2, the study’s immediate goal being to identify medical, cognitive, neural and behavioral profiles shared by those in this group.

Phase 1 of this project, which ended in early 2014, involved in-person evaluations at clinical study sites. There, participants underwent extensive psychological and neurological testing, along with neuroimaging — including magnetic resonance imaging (MRI), functional MRI, and magnetoencephalography (MEG) — with a uniform protocol and collection of biospecimens. DNA was extracted from whole-blood for genetic experiments. Fibroblasts were cultured and cryopreserved for distribution to researchers interested in making induced pluripotent stem cells (iPSCs) or for other experiments. As a pilot project, Phase 1 also included testing a small number of 1q21.1 deletion and duplication carriers using the identical protocol (see Table 1).

Phase 2 – currently recruiting – involves the collection of family, medical, developmental and behavioral information through online surveys and phone interviews with families. Phase 2 permits expansion of the study by obviating the need for family travel and by enabling collection of longitudinal data. Importantly, this new phase permits the rapid integration and study of new groups with recurrent genetic changes other than 16p11.2 and 1q21.1 deletions and duplications. To date, 52 single genes associated with neurodevelopmental differences and features of autism have been incorporated into Phase 2 of the study (see Table 1).

Table 1. Individuals with copy number variants (CNVs) in 16p11.2 or 1q21.1 are being studied in Phases 1 and 2 of the Simons VIP. Phase 2 also includes individuals with mutations in 52 single genes.

Phases 1 and 2: Copy number variants

16p11.2 deletions

16p11.2 duplications

1q21.1 deletions

1q21.1 duplications

Phase 2: Genes associated with features of autism

ACTL6B

CTBP1

KAT6A

PTEN

ADNP

CTNNB1

KATNAL2

PURA

AHDC1

CUL3

KDM5B

REST

ANK2

DDX3X

KDM6B

SCN2A

ANKRD11

DNMT3A

KMT2C

SETBP1

ARID1B

DSCAM

KMT2E

SETD5

ASH1L

DST

MBD5

SMARCC1

ASXL3

DYRK1A

MED13L

SMARCC2

BCL11A

FOXP1

PACS1

SMARCA4

CHAMP1

GRIN2A

PBRM1

STXBP1

CHD2

GRIN2B

POGZ

SUV420H1

CHD8

HIVEP2

PPP2R5D

SYNGAP1

CSNK2A1

HNRNPH2

PTCHD1

TBR1


Simons VIP data:

Data from the following individuals are currently available to approved researchers via SFARI Base:

  • 187 carriers of the 16p11.2 deletion (enrolled in Phase 1 and/or Phase 2)
  • 143 carriers of the 16p11.2 duplication (enrolled in Phase 1 and/or Phase 2)
  • 45 carriers of the 1q21.1 deletion (enrolled in Phase 1 and/or Phase 2)
  • 35 carriers of the 1q21.1 duplication (enrolled in Phase 1 and/or Phase 2)
  • 37 individuals with SCN2A mutations (enrolled in Phase 2)
  • 17 individuals with GRIN2B mutations (enrolled in Phase 2)
  • 6 individuals with ADNP mutations (enrolled in Phase 2)
  • 5 individuals with HIVEP2 mutations (enrolled in Phase 2)

Genetic data are available for a subset of individuals and their families enrolled in Phase 1. More information is available in SFARI Base and in the publications listed below:

Single nucleotide polymorphism (SNP) genotype data

  1. Duyzend M.H. et al. Am. J. Hum. Genet. 98, 45-57 (2016) PubMed, Data available through SFARI Base and NDAR

Molecular inversion probe (MIP) sequencing data

  1. Nuttle X. et al. Nature 536, 205-209 (2016) PubMed, Data available through SFARI Base (please reference accession SFARI_SVIP_MIPS_1)

Whole-exome sequencing data

  1. Daly M.J. et al. (in preparation) Data available through SFARI Base

Whole-genome sequencing data

  1. Nuttle X. et al. Nature 536, 205-209 (2016) PubMed, Data available through SFARI Base (please reference accession SFARI_SVIP_WGS_1)


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