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Publications

Date Revised: December 2025

Thank you to all the families for participating in Simons Searchlight. Through your involvement, we aim to assist researchers and geneticists worldwide in understanding genetic disorders affecting you or your family.

The research conducted using Simons Searchlight data has resulted in numerous published papers. These papers undergo a peer-review process, where other scientists assess and validate the research before publication in scientific journals. Additionally, some findings are shared via preprints, allowing rapid dissemination of information to the scientific community.

Many of the publications feature the name “Simons Variation in Individuals Project” (SimonsVIP), which was the original name of our research program, now known as Simons Searchlight.

The listed articles are organized from newest to oldest. You can explore publications by specific genetic conditions using the categories below.

As of December 2025, Simons Searchlight has contributed to 135 publications and preprints, and we will continue to summarize new publications.

For accessibility, the Simons Foundation encourages researchers to make their publications open access. If you cannot access a journal article, we recommend reaching out to the last author listed on the paper to request a copy.

Understanding Publication Reference Titles:

-The article title is followed by publication details, including where and when it was published.
– If there are more than three authors, we use “et al.” to represent additional contributors.
– Journals are referenced using shorthand names.

Disclaimer: Please be aware that papers posted on medRxiv (pronounced med-archive) or bioRxiv (pronounced bio-archive) are not peer-reviewed or edited before online publication. In contrast, all other articles listed here have undergone review by fellow researchers to ensure quality and accuracy. While posting on medRxiv or bioRxiv allows researchers to share findings quickly, the final published results may differ after undergoing formal peer review for journal publication.

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Genetic Condition
Year of Publication
134 Publications
Seizures and functional deficits across Mendelian disorders of epigenetic machinery: Differential effects as a function of epigenetic modifications
  • The researchers studied neurodevelopmental conditions in Simons Searchlight that are known as Mendelian disorders of epigenetic machinery, also called chromatinopathies. Show More
  • Chromatin consists of DNA, RNA, and proteins that are arranged to help the DNA fit inside of cells. Different classes of proteins perform tasks on the chromatin to help modify access to the DNA. “Writer” proteins write or add chemical tags to the chromatin to turn a gene on or off. “Writer/reader” proteins (WRs) can write tags, but they also read the tags on the chromatin to carry out the instructions. “Chromatin remodeler/reader” proteins (CRRs) change the structure of chromatin and then read the tags to know what changes to make.
  • The goal of this study was to look at the behavior, development, and medical and diagnostic history in people with genetic variants in genes that code for and affect the function of chromatin writers, WRs, and CRRs.
  • The researchers analyzed online survey data from 71 Simons Searchlight participants with a genetically confirmed pathogenic or likely-pathogenic variant: 15 people with a writer genetic variant (includes variants in KMT5B, SETD5), 22 people with a writer/reader variant (includes variants in DNMT3A, EHMT1, KMT2A, KMT2C, KMT2E), and 34 people with a remodeler/reader variant (includes variants in ATRX, CHD2, CHD8, SMARCA4).
  • The researchers collected the following data: Simons Searchlight medical history, seizure history, previous diagnosis, medication history, and the online parent/caregiver Vineland Adaptive Behavior Scales (Vineland-3) form to evaluate adaptive functioning and development.
  • The researchers showed that adaptive functioning across most adaptive behavior skills was lowest in people with a CRR variant and highest in people with a writer variant. People with a WR variant typically scored in between those with a writer or CRR variant. People with a WR variant had significantly greater scores than those with a CRR variant, specifically in community daily living skills and play/leisure skills.
  • The researchers did not find any significant differences among the groups in diagnosis of most developmental diagnoses, history of seizures, or seizures in sleep.
  • More participants with a CRR variant reported having minimally verbal status, using rescue medication for seizures, and/or needing emergency intervention for seizures, compared with those with a writer or WR variant.
  • These results show that variants that affect chromatin remodeling are associated with more severe functional deficits across adaptive functioning domains, and that despite similar risk of seizures and other diagnoses, people with chromatin remodeling disorders have more severe seizure-related outcomes that require more intensive care. Show Less
Arch Clin Neuropsychol Epub ahead of print, (2025)
Ng
Full Article

ATRX
CHD2
CHD8
DNMT3A
EHMT1
KMT2A
KMT2C
KMT2E
KMT5B
SETD5
SMARCA4
2025

Motor impairment in children with 16p11.2-deletion and -duplication syndromes
  • The researchers analyzed Simons VIP (Simons Searchlight from 2010-2014) in-clinic assessments and caregiver-reported information to study motor function in people with 16p11.2 deletions and duplications. Show More
  • This study included data from 339 people: 121 people with a 16p11.2 deletion, 66 people with a 16p11.2 duplication, 91 people who were non-carrier siblings, and 61 unrelated people without a copy number variant (CNV).
  • The researchers analyzed doctor-administered assessments of motor skills and the ability to control and coordinate movements, including fine and gross motor skills.
  • Across all study participants, having a clinical autism spectrum disorder diagnosis, a higher severity score on the Autism Diagnostic Observation Schedule survey, and/or a clinical developmental coordination disorder diagnosis was associated with worse performance on motor assessments.
  • Across almost all motor performance assessments, people with a 16p11.2 copy number variant (CNV) had poorer motor function compared with people without a 16p11.2 CNV.
  • In most cases, there was no observed difference in motor performance between people with a 16p11.2 deletion and people with a 16p11.2 duplication. Two exceptions were that people who were deletion carriers (1) had worse motor performance on the assessment of manual dexterity, aiming and catching, and balance, and (2) had slightly higher rates of developmental coordination disorder compared with people who were duplication carriers.
  • Sex and age did not have any significant effect on motor performance and did not impact the effect of having a 16p11.2 CNV on motor performance.
  • The researchers used a nonverbal intelligence quotient (IQ) to account for any language-related difficulties. IQ was a large predictor of motor performance, but when controlling for this, 16p11.2 CNV carrier status still explained most of the motor performance effects.
  • These results taken together reveal that autism in general, and specific genetic conditions associated with autism such as 16p11.2 deletions and 16p11.2 duplications, are associated with motor impairments. Show Less
J Autism Dev Disord Epub ahead of print, (2025)
Soliman et al.
Full Article

16p11.2 deletion
16p11.2 duplication
2025

OCNDS core features are conserved across variants, with loop-region mutations driving greater symptom burden
  • The researchers examined whether the location of a genetic variant within a gene is linked to specific disease features. Show More
  • This study included 48 Simons Searchlight participants with a pathogenic or likely pathogenic missense CSNK2A1 variant.
  • The CSNK2A1 gene makes the protein casein kinase 2 alpha subunit 1 (CK2α). This protein is a subunit of the protein complex called casein kinase 2 (CK2). CK2 is a large protein complex formed by smaller proteins – two CK2α proteins and two CSNK2B (CK2β) proteins. Damaging genetic variants in the CSNK2A1 gene result in Okur-Chung neurodevelopmental syndrome (OCNDS).
  • The most commonly reported participant symptoms were speech/language disorder/delay; non-seizure neurological disorders, such as diminished muscle tone; sleep disorders; and gastrointestinal issues. Developmental patterns (based on Vineland-3 scores) were also universally delayed.
  • Most participants (83 percent) had serious sleep disturbances that qualify as a pediatric sleep disorder. Caregivers reported sleep disruption as one of the three most problematic symptoms.
  • To examine associations between a genetic variant and clinical outcomes, the researchers categorized the variants into one of 10 known protein domain segments. Currently, two subsegments of the CK2α protein have no known CSNK2A1 missense variants. The activation segment (region 175-200 of CK2α) had the highest number of participants in what is called the p + 1 loop, which includes the most common recurring variant, p.Lys198Arg. The second largest group was the Glycine (Gly)-rich binding loop, region 45-53 of CK2α.
  • CSNK2A1 variants found within ‘loop’ regions of the protein were compared with genetic variants in ‘non-loop’ regions of the protein.
  • Participants with genetic variants located within a loop region had a younger age of diagnosis, had a reported higher number of non-seizure neurological and gastrointestinal symptoms, and used more medications.
  • Participants with genetic variants located within a non-loop region were more likely to report an autism diagnosis.
  • The researchers noted that the participants with non-missense variants, such as CSNK2A1 deletions and splice site, nonsense, and frameshift variants, were more similar symptomatically to participants with variants in a non-loop region.
  • The researchers compared participants with missense variants in the Gly-rich loop to participants with all other types of missense variants. This is because the Gly-rich loop is important for CK2α’s ability to bind to CK2β, and an activating molecule called ATP. Participants with missense variants in the Gly-rich loop had a higher number of symptoms reported and an earlier age of diagnosis.
  • These findings, although limited by the number of study participants, are a first step in understanding whether variant location within the gene can affect symptom type, severity, and potential treatment strategies. Show Less
Front Hum Neurosci 19, 1589897 (2025)
Bagatelas et al.
Full Article

CSNK2A1
2025

Development and adaptive function in individuals with SCN2A-related disorders
  • The researchers aimed to describe the developmental and functional abilities of participants with SCN2A-related disorders based on different clinical groupings. Show More
  • The researchers studied 100 participants and assigned them to one of three groups: early onset SCN2A-related disorder, late onset SCN2A-related disorder, or a copy number variant (CNV) group that included SCN2A.
  • The early onset group (44 participants) was defined as having seizures that developed before 3 months old or developed between 3 months and 24 months (excluding a seizure type called epileptic spasms).
  • The late onset group (48 participants) included people who did not qualify for the early onset group.
  • The CNV group included 8 participants.
  • The researchers did not use variant function (loss of function or gain of function) to categorize SCN2A variants because not all variants have been functionally tested. But, they noted that for the variants that have been functionally tested, the participants with a gain of function variant were most often classified as early onset, and all participants in the early onset group had missense variants. Participants classified in the late onset group usually had variants that were considered to be loss of function. Of note, two participants with variants characterized as loss of function had seizures at birth.
  • Caregivers completed a comprehensive medical questionnaire and a medical interview either in-person or through a video call. Some caregivers provided additional medical records and completed a 1-year, follow-up medical questionnaire. The researchers also examined data from the Vineland Adaptive Behavior Scales-3 survey completed by Simons Searchlight participants.
  • Most participants (91 out of 100) had developmental delay and or intellectual disability, and 23 out of 80 participants over the age of 2 had an autism diagnosis, with a higher rate of people in the late onset group having autism.
  • Within the early onset group, the researchers observed three distinct phenotype sub-groups. 1) Early onset benign – self-limited infantile epilepsy that typically resolved by the age of 2, with no neurological symptoms after 2 years old. 2) Early onset intermediate – people with ongoing symptoms after 2 years, with one or more of the following: seizures, movement disorder, developmental delay/intellectual disability of up to moderate severity. 3) Early onset severe – people with severe to profound developmental impairments.
  • All participants in the early onset benign group attained their developmental milestones, whereas participants in the early onset intermediate group were often able to walk and run, but higher level skills were less often acquired, and participants in the early onset severe group had delays across all domains. Adaptive behavior scores followed a similar pattern – scores were highest (in the normal range) in the benign group, in a lower range in the intermediate group, and lowest in the severe group.
  • For the late onset group, people with seizures were less likely to be able to walk independently, and when studying this group, the researchers compared: 1) those without epilepsy, 2) those with late-onset epilepsy in childhood, and 3) those with late-onset epilepsy in mid-infancy.
  • Participants in the late onset group were more likely to experience a plateau or regression in development. This was less pronounced for participants without epilepsy. The presence of seizures had the highest association with the onset of a plateau or regression.
  • Many participants in the late onset group were able to sit and walk, and about 1 out of 5 were able to speak or follow 2-part commands. Most people without epilepsy were able to follow single commands. Adaptive behavior composite scores were similar among people in the late onset group (in the lower range), but scores were highest for participants without epilepsy.
  • This research will directly benefit families because it provides prognostic information in the absence of variant functional information. This research may also inform clinical care or the design of clinical studies. Show Less
Neurology 105, e213868 (2025)
Goad et al.
Full Article

SCN2A
2025

The Developmental Assessment of Social Communication Ability (DASCA): Initial creation and psychometric description
  • There was a need for more specific quantitative measures for social communication that are sensitive to the changes that a person undergoes over time. Show More
  • In this study, the researchers created the Developmental Assessment of Social Communication Ability (DASCA), a new survey developed as a clinical outcome tool for monitoring a person’s social and communication changes in response to treatment.
  • The researchers recruited through several studies, including 571 participants in Simons Searchlight.
  • The researchers used feedback from caregivers in the neurodevelopmental community to adjust their questions to effectively assess communication abilities for dependents in the neurodevelopmental community.
  • The researchers suggested that this new survey will be helpful in future clinical trials to measure the improvement in the social communication of children with neurodevelopmental disability. Show Less
Mol Autism 16, 52 (2025)
Kaat et al.
Full Article

All Genes
2025

Characterizing key correlates of sleep problems across rare neurodevelopmental genetic disorders
  • This study looked at sleep difficulties in rare genetic neurodevelopmental conditions. Show More
  • The researchers recruited through several patient advocacy organizations, including SYNGAP1, ADNP, CSNK2A1, GRIN2B, STXBP1, HIVEP2, SCN2A, and MED13L participants in Simons Searchlight.
  • Caregivers completed two surveys: the Children’s Sleep Habits Questionnaire and the Neurobehavioral Evaluation Tool. They also filled out a 7-day sleep diary.
  • Sleep issues were found in all the conditions studied. Participants in the SYNGAP1 group had the most disrupted sleep, as compared with the other genetic conditions, and the most problematic sleep areas were shorter time sleeping and a higher sleep anxiety.
  • The researchers suggested that people with SYNGAP1-related disorder might have more sleep disruption due to seizure activity.
  • Similar to other sleep research, the analysis found that emotion regulation challenges and depressive feelings were related to sleep initiation and maintenance issues. Emotional dysregulation likely makes it difficult for a child to fall asleep at night, but also to return to sleep on their own when they wake up during the night. Depressive feelings were also linked to feeling very sleepy in the morning and poor sleep quality.
  • Separation anxiety and not liking change to routine and/or rituals (insistence on sameness) were the biggest predictors of bedtime resistance. Children with sleep anxiety might have insistence on sameness behaviors to minimize their fears associated with sleep.
  • Anxiety and sensory sensitivities were also related to decreased sleep length, and they might contribute to insomnia symptoms.
  • The researchers suggested that sleep interventions for people with rare neurodevelopmental disorders should include the sleep disorder, the behavior, and emotional factors. This type of comprehensive approach is more likely to improve the quality of life for the person and their family. Show Less
J Autism Dev Disord 55, 4480-4491 (2025)
Baker et al.
Full Article

ADNP
CSNK2A1
GRIN2B
HIVEP2
MED13L
SCN2A
STXBP1
SYNGAP1
2025

Brief report: Differences in naturalistic attention to real-world scenes in adolescents with 16p.11.2 deletion
  • The goal of this research was to study the specific clinical manifestations in people with a 16p11.2 deletion. Show More
  • People with a 16p11.2 deletion have an increased rate of autism and autism-related traits.
  • The researchers did eye-tracking studies in 21 teenage and adult participants with a 16p11.2 deletion and 23 participants without a genetic condition. Participants with a 16p11.2 deletion were recruited from Simons Searchlight.
  • The researchers used a virtual reality headset to show the participants real-world scenes, with objects, people, or background scenery. The researchers created eye-tracking maps based on what the participant focused on.
  • The researchers found that sex, IQ, and autistic traits were not good predictors of what the participant focused on. Participants with a 16p11.2 deletion had less observing across each scene and fewer fixations. The researchers suggested studying younger participants with a 16p11.2 deletion to see if a more obvious pattern would emerge. Show Less
J Autism Dev Disord 54, 1078-1087 (2024)
Haskins et al.
Full Article

16p11.2 deletion
2024