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Simons Searchlight

Simons Searchlight is a Simons Foundation Autism Research Initiative (SFARI) program that aims to better understand rare genetic neurodevelopmental conditions.

Previously named Simons Variation in Individuals Project (Simons VIP), the name change better reflects the program’s mission of shedding light on these conditions by collecting natural history data.

Simons Searchlight is an international research program that gathers family, medical, developmental and behavioral information through online surveys and phone interviews with families and individuals. Details on surveys administered can be found in the Researcher welcome packet. Biospecimen collection is performed either remotely or at in-person family conferences. Today, over 164 genes and more than 24 CNVs are part of the Simons Searchlight community, with the list always expanding.

Joining such a community enables families to find and engage with others with the same genetic condition, as well as providing opportunities to connect with researchers. Participants can also be invited to additional research studies aimed at better understanding these disorders and, in some cases, clinical trials to advance treatments.

Over 3,600 individuals with rare genetic neurodevelopmental disorders and their families are currently registered in Simons Searchlight and more than 85 research publications or preprints have resulted from data collected. Interested investigators can request access to the database through SFARI Base. The database is divided into two phases. The initial phase of Simons Searchlight (Simons VIP Phase 1) ended in early 2014 and involved in-person evaluations of 16p11.2 and 1q21.1 deletion or duplication carriers at clinical centers. 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. Phase 2 data collection includes online-only measures.

Inclusion list

The Simons Searchlight inclusion list contains 24 copy number variants (orange) and 162 monogenic conditions (blue) that are associated with autism and other neurodevelopmental disorders.

A list of all the genes for Simons Searchlight updated in May 2024.

Genetic variants

A list of genetic variants observed in Simons Searchlight participants can be found in the “genetic variants” spreadsheet . Where variants are found in more than one participant, counts are indicated. Variants included are classified as pathogenic, likely pathogenic, or variants of uncertain significance (VUS).

For more details, see data sets available through SFARI Base.

Phenotypic data

Phenotypic data from the following individuals are currently available to approved researchers via SFARI Base. A summary of the number of carriers per genetic community that have contributed data for each phenotypic measure can be found in the “Carrier Count by Measure” spreadsheet.

Copy number variants (individuals enrolled in Phase 1 and/or Phase 2):

  • 56 carriers of the 15q11.2 BP1-BP2 deletion
  • 12 carriers of the 15q13.3 deletion
  • 362 carriers of the 16p11.2 deletion
  • 64 carriers of the Distal 16p11.2 deletion
  • 265 carriers of the 16p11.2 duplication
  • 25 carriers of the Distal 16p11.2 duplication
  • 8 carriers of the 16p12.1 deletion
  • 5 carriers of the 16p12.2 deletion
  • 15 carriers of the 16p13.11 deletion
  • 8 carriers of the 17q12 duplication
  • 97 carriers of the 1q21.1 deletion
  • 118 carriers of the 1q21.1 duplication
  • 15 carriers of the 2p16.3 deletion
  • 18 carriers of the 5p deletion
  • 28 carriers of the 7q11.23 duplication

Monogenic Conditions (all individuals enrolled in Phase 2):

  • 33 individuals with ADNP mutations
  • 13 individuals with ANK2 mutations
  • 34 individuals with ANKRD11  mutations
  • 28 individuals with ARID1B  mutations
  • 10 individuals with ASH1L mutations
  • 85 individuals with ASXL3 mutations
  • 20 individuals with ATRX mutations
  • 18 individuals with AUTS2 mutations
  • 5 individuals with BCL11A mutations
  • 9 individuals with BRSK2 mutations
  • 5 individuals with CACNA1C mutations
  • 5 individuals with CASK mutations
  • 46 individuals with CHAMP1 mutations
  • 21 individuals with CHD2 mutations
  • 6 individuals with CHD3 mutations
  • 29 individuals with CHD8 mutations
  • 28 individuals with CLCN4 mutations
  • 5 individuals with CNOT3 mutations
  • 9 individuals with CSDE1 mutations
  • 90 individuals with CSNK2A1 mutations
  • 28 individuals with CSNK2B mutations
  • 6 individuals with CTBP1 mutations
  • 185 individuals with CTNNB1 mutations
  • 25 individuals with CUL3 mutations
  • 10 individuals with DDX3X mutations
  • 19 individuals with DEAF1 mutations
  • 42 individuals with DLG4 mutations
  • 13 individuals with DNMT3A mutations
  • 28 individuals with DYNC1H1 mutations
  • 61 individuals with DYRK1A mutations
  • 12 individuals with EHMT1 mutations
  • 17 individuals with EIF3F mutations
  • 6 individuals with EP300 mutations
  • 23 individuals with FOXP1 mutations
  • 7 individuals with GIGYF1 mutations
  • 18 individuals with GRIN1 mutations
  • 15 individuals with GRIN2A mutations
  • 112 individuals with GRIN2B mutations
  • 10 individuals with HECW2 mutations
  • 45 individuals with HIVEP2 mutations
  • 53 individuals with HNRNPH2 mutations
  • 13 individuals with HNRNPU mutations
  • 5 individuals with IQSEC2 mutations
  • 31 individuals with IRF2BPL mutations
  • 17 individuals with KDM6B mutations
  • 32 individuals with 17q21.31 deletion or KANSL1 mutation
  • 8 individuals with KMT2A mutations
  • 13 individuals with KMT2C mutations
  • 13 individuals with KMT2E mutations
  • 13 individuals with KMT5B mutations
  • 12 individuals with MBD5 mutations
  • 15 individuals with MED13 mutations
  • 108 individuals with MED13L mutations
  • 40 individuals with MEF2C mutations
  • 16 individuals with MYT1L mutations
  • 5 individuals with NAA15 mutations
  • 8 individuals with NBEA mutations
  • 5 individuals with NCKAP1 mutations
  • 9 individuals with NEXMIF mutations
  • 11 individuals with NR4A2 mutations
  • 6 individuals with NRXN1 mutations
  • 36 individuals with PACS1 mutations
  • 8 individuals with PHIP mutations
  • 23 individuals with PPP2R1A mutations
  • 165 individuals with PPP2R5D mutations
  • 26 individuals with PPP3CA mutations
  • 12 individuals with PTCHD1 mutations
  • 7 individuals with SCN1A mutations
  • 5 individuals with SCN1B mutations
  • 224 individuals with SCN2A mutations
  • 66 individuals with SETBP1 mutations
  • 6 individuals with SETD2 mutations
  • 23 individuals with SETD5 mutations
  • 9 individuals with SIN3A mutations
  • 132 individuals with SLC6A1 mutations
  • 7 individuals with SMARCA4 mutations
  • 6 individuals with SMARCC2 mutations
  • 5 individuals with SON mutations
  • 5 individuals with SOX5 mutations
  • 211 individuals with STXBP1 mutations
  • 134 individuals with SYNGAP1 mutations
  • 15 individuals with TANC2 mutations
  • 12 individuals with TAOK1 mutations
  • 20 individuals with TBR1 mutations
  • 15 individuals with TCF20 mutations
  • 12 individuals with TLK2 mutations
  • 16 individuals with TRIO mutations
  • 21 individuals with TRIP12 mutations
  • 7 individuals with UPF3B mutations
  • 9 individuals with USP9X mutations
  • 21 individuals with VPS13B mutations
  • 6 individuals with WAC mutations
  • 24 individuals with WDFY3 mutations
  • 10 individuals with ZNF292 mutations

Biospecimens

The following biospecimens are currently available for request via SFARI Base. Please note that not every sample type listed here is available for each donor.

Associated costs for obtaining and shipping these samples can be found here.

Induced pluripotent stem cells (iPSCs) that are available from SFARI Data and Biospecimen Repository (SDBR) can be found here.

  • 15q13.3 deletion 0 0 0 0 0 2 2
    16p11.2 deletion 59 29 14 19 27 148 195
    16p11.2 duplication 44 34 5 10 33 110 155
    16p11.2 triplication 0 0 0 0 0 3 3
    16p12.1 deletion 0 0 0 0 0 1 2
    17q21.3 deletion 0 0 0 0 0 3 16
    17q12 duplication 0 0 0 0 0 3 4
    1q21.1 deletion 11 5 2 7 5 25 44
    1q21.1 duplication 8 10 3 6 9 29 43
    5p deletion 0 0 0 0 0 0 4
    7q11.23 duplication 0 1 0 0 1 4 7
    ADNP 0 2 3 3 2 4 9
    ANK2 0 0 0 0 0 1 2
    ANKRD11 0 0 0 1 0 5 9
    ARID1B 0 2 0 0 2 2 4
    ASXL3 0 15 6 4 12 15 30
    ATRX 0 0 0 0 0 1 3
    BCL11A 0 0 0 0 0 1 1
    BRSK2 0 0 0 0 0 2 3
    CACNA1C 0 0 0 0 0 0 1
    CASK 0 0 0 0 0 0 1
    CHAMP1 0 0 7 0 0 1 9
    CHD2 0 1 0 0 1 3 3
    CHD3 0 0 0 0 0 3 3
    CHD8 0 0 0 1 0 2 3
    CLCN4 0 0 0 0 0 2 6
    CNOT3 0 0 0 0 0 1 1
    CSDE1 0 0 0 0 0 2 2
    CSNK2A1 0 6 9 2 4 12 22
    CSNK2B 0 0 0 0 0 3 8
    CTNNB1 0 0 6 0 0 11 39
    Distal 16p11.2 deletion 0 0 0 0 0 3 4
    Distal 16p11.2 duplication 0 0 0 0 0 4 5
    CUL3 0 0 0 0 0 5 7
    DEAF1 0 0 0 0 0 0 2
    DLG4 0 0 0 0 0 6 9
    DNMT3A 0 0 0 0 0 1 1
    DYNC1H1 0 0 0 0 0 2 3
    DYRK1A 0 1 6 4 1 11 29
    EHMT1 0 0 0 0 0 1 1
    EIF3F 0 0 0 0 0 3 3
    FOXP1 0 0 0 1 0 0 1
    GIGYF1 0 0 0 0 0 2 2
    GRIN1 0 0 0 0 0 3 6
    GRIN2A 0 1 0 0 0 3 4
    GRIN2B 0 8 11 3 8 18 35
    HECW2 0 0 0 0 0 1 1
    HIVEP2 0 2 3 1 2 13 19
    HNRNPH2 3 3 5 0 3 6 15
    HNRNPU 0 0 0 0 0 0 6
    IQSEC2 0 0 0 0 0 0 1
    IRF2BPL 0 0 0 0 0 2 5
    KANSL1 0 0 0 0 0 1 5
    KDM6B 0 0 0 0 0 1 1
    KMT5B 0 0 0 1 0 1 2
    MBD5 0 0 0 1 0 5 6
    MED13 0 0 1 0 0 4 4
    MED13L 0 2 5 2 2 15 25
    MEF2C 0 0 0 0 0 2 6
    MYT1L 0 0 0 0 0 2 2
    NR4A2 0 0 0 0 0 2 2
    NRXN1 0 0 2 0 0 2 2
    PACS1 0 2 2 2 2 9 13
    PPP2R1A 0 1 0 0 0 0 3
    PPP2R5D 5 16 17 0 15 43 72
    PPP3CA 0 0 0 0 0 3 5
    PTCHD1 0 0 0 0 0 1 1
    SCN1A 0 0 0 0 0 3 3
    SCN2A 0 20 12 10 20 37 75
    SETBP1 0 0 4 1 0 14 19
    SETD2 0 0 0 0 0 1 1
    SETD5 0 1 0 1 1 2 4
    SLC6A1 0 1 3 0 1 11 19
    SMARCA4 0 0 0 0 0 1 2
    STXBP1 0 6 13 4 4 25 63
    SYNGAP1 0 1 3 3 1 18 38
    TAOK1 0 0 0 0 0 1 1
    TBR1 0 0 0 0 0 3 4
    TLK2 0 0 0 0 0 1 2
    TRIP12 0 0 0 0 0 0 1
    UPF3B 0 0 0 0 0 1 1
    VPS13B 0 0 0 0 0 2 4
    WDFY3 0 0 0 0 0 1 1

Genetic data

Genomic 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

Targeted sequencing data

  1. Nuttle X. et al. Nature 536, 205-209 (2016) PubMed, Data available through SFARI Base (targeted sequencing around the 16p11.2 rearrangement breakpoints; please reference accession SFARI_SVIP_MIPS_1)
  2.  Fiddes I.T. et al. Cell 173, 1356-1369 (2018) PubMed (targeted sequencing around the 1q21.1 rearrangement breakpoints; please reference accession SFARI_SVIP_VSV_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)

Research Match

SFARI launched the Research Match program in 2017. Research Match is a free service that enables approved researchers to re-contact participants from SFARI autism cohorts, including SPARK (Simons Foundation Powering Autism Research), Simons Searchlight and Simons Simplex Collection (SSC), for recruitment into new research studies.

Since Research Match launched, more than 180 projects have been conducted with participants recruited through this service, of which more than 70 projects are currently in progress. In addition, 34 papers and preprints have been published based on these studies.

To date, 2,588 families participating in Simons Searchlight have been invited to join a study; 1,435 of these families have agreed to join studies through Research Match.

Researchers interested in recruiting Simons Searchlight participants into their studies can submit an application through SFARI Base. Approved researchers will receive further information about how to contact families.

Learn more about Research Match by visiting the SFARI website and by reviewing the Simons Searchlight Research Match Recruitment Process Document.

Induced pluripotent stem cell lines from Simons Searchlight participants

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