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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Please be aware that papers posted on medRxiv (pronounced med-archive) or bioRxiv (pronounced bio-archive) are not peer-reviewed or edited before online publication.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
Sensory processing in 16p11.2 deletion and 16p11.2 duplication
  • The researchers aimed to understand how people with a 16p11.2 copy number variant (CNV) process sensory information. A CNV happens when there is a change in a section of DNA that results in a gene or several genes being deleted or duplicated. 16p11.2 deletion is an example of a CNV. Show More
  • This study included 38 children with a 16p11.2 deletion, 31 children with a 16p11.2 duplication, and participants from the Simons Searchlight registry.
  • Challenges with sensory processing are common for people with autism. This includes having difficulty with stimulation from the senses, such as light, texture, taste, and sound.
  • Participants with either a 16p11.2 deletion or a 16p11.2 duplication were more likely to have sensory processing challenges than participants without a 16p11.2 deletion or duplication. The sensory processing challenges for participants with a 16p11.2 deletion or duplication were comparable to the sensory processing challenges for participants with autism.
  • Participants with a 16p11.2 deletion or duplication were most likely to have issues with registering sensory information. Participants with a 16p11.2 duplication were more likely to be sensitive to sensory information. Other patterns of sensory processing, such as seeking and avoiding sensory information, were not as common in these two groups.
  • Participants with a 16p11.2 deletion or duplication and autism were more likely to have issues with touch and oral sensations than participants who did not have autism.
  • These results suggest that a detailed breakdown of sensory processing in people with a 16p11.2 deletion or duplication could be used for clinical evaluations. Show Less
Autism Res 15, 2081-2098 (2022)
Smith et al.
Full Article

16p11.2 deletion
16p11.2 duplication
2022

Clinical, neuroimaging and molecular characteristics of PPP2R5D-related neurodevelopmental disorders: An expanded series with functional characterisation and genotype–phenotype analysis
  • This is the first publication on PPP2R5D that focuses on Simons Searchlight data. Show More
  • PPP2R5D stands for protein phosphatase 2 regulatory subunit B delta. In cells, PPP2R5D is an enzyme that adds a molecule called a phosphate to the amino acids serine and threonine.
  • This study includes 72 Simons Searchlight participants with a pathogenic or likely pathogenic genetic variant in PPP2R5D. This adds to the 31 people with PPP2R5D genetic variants that have been published to date in the medical literature.
  • The researchers studied the function PPP2R5D genetic variants and grouped the variants into three different categories.
  • Participants ranged in age from 1 to 45 years old. Most participants had low muscle tone and a larger-than-average head size. About half of the participants had seizures, with an average age of seizure onset at just over 2. Seizure activity varied between participants: some had more than 100 seizures a day, others had one a year.
  • Participants had the most difficulty with expressive communication and personal daily living skills. About 1 in 3 participants had acid reflux and constipation.
  • The researchers found that about 1 in 5 participants had developmental delay or intellectual disability, which is lower than what other studies have reported.
  • The researchers looked at if there was any link between genetic variants and medical features. Most people with a Glu198Lys and Trp207Arg had the most consistent set of medical features, both of these variants are in the same functional category.
  • This was the largest study to date of participants with a PPP2R5D genetic variant. For the first time, researchers were able to investigate on a large scale the function that genetic variants have in the cell in relation to clinical features. Show Less
J Med Genet Epub ahead of print, (2022)
Oyama et al.
Full Article

PPP2R5D
2022

ConVnet BiLSTM for ASD classification on EEG brain signal
  • The goal of this research was to develop and validate a new computer-based method to assist doctors in diagnosing autism. The method used a convolutional neural network (ConVnet) structure that merges two LSTM blocks (BiLSTM). This computational deep learning method identifies patterns in electroencephalogram (EEG) information to help with diagnoses. ConVnet BiLSTM has been used with high accuracy in recent research studies on other topics, such as seizure detection or human motor recognition. Show More
  • This study included Simons Searchlight participants with a 16p11.2 deletion or a 16p11.2 duplication, as well as people with no genetic conditions from Boston Children’s Hospital. Participants were age 10 and younger.
  • Using the ConVnet BiLSTM method, the researchers were able to classify participants as autistic in a quick, inexpensive, and noninvasive way. The researchers created a recognizable pattern from participant EEGs. This deep learning method predicted autism with over 97 percent accuracy.
  • The researchers suggested that this method could be used by doctors to assist in the diagnosis of autism as an alternative to the current behavioral criteria from the diagnostic manual. Show Less
iJOE 18, (2022)
Ali et al.
Full Article

16p11.2 deletion
16p11.2 duplication
2022

Clinical characteristics of seizures and epilepsy in individuals with recurrent deletions and duplications in the 16p11.2 region
  • The researchers aimed to review how many people with a 16p11.2 copy number variant (CNV) develop seizures or epilepsy. A CNV happens when there is a change in a section of DNA that results in a gene or several genes being deleted or duplicated. 16p11.2 deletion is an example of a CNV. Show More
  • This study included Simons Searchlight participants: 129 with a 16p11.2 deletion and 106 with a 16p11.2 duplication.
  • Of the 129 participants with a 16p11.2 deletion, 31 were found to have had at least one seizure (24 percent). When assessed for epilepsy, 23 out of 129 participants (18 percent) received an epilepsy diagnosis. Participants with a 16p11.2 deletion had their first seizure between birth and 14 years old. The most common seizure type was a focal seizure.
  • Of the 106 participants with a 16p11.2 duplication, 17 had at least one seizure (16 percent). Also, 12 participants received an epilepsy diagnosis (11 percent). Participants had their first seizure between 1 and 10 years old. The most common seizure type was also a focal seizure for participants with a 16p11.2 duplication.
  • Successful anti-seizure treatment varied among participants.
  • This paper includes summary tables with all the seizure types and epilepsy details for all participants.
  • This research confirmed that seizure occurrence is associated with the 16p11.2 CNV. MRI brain imaging, which was done in only a small number of participants, did not explain the presence of abnormal brain activity. Show Less
Neurol Genet 8, e200018 (2022)
Moufawad et al.
Full Article

16p11.2 deletion
16p11.2 duplication
2022

Autism NPCs from both idiopathic and CNV 16p11.2 deletion patients exhibit dysregulation of proliferation and mitogenic responses
  • The majority of people with an autism diagnosis have a known genetic cause for their autism, also called idiopathic autism. Only about 1 in 5 people receive a genetic diagnosis associated with their autism. Show More
  • The goal of this research was to understand why some people with idiopathic autism develop larger than average head size and others do not. To do this, researchers used induced pluripotent stem cells (iPSCs) made from participants with a 16p11.2 deletion, because people with this deletion tend to have a larger than average head size. iPSCs are a special type of cells that can be turned into other body cells, making it easier to study parts of the body that are difficult to study, such as brain cells.
  • Two of the iPSCs, from Simons Searchlight participants with a 16p11.2 deletion, were turned into brain cells in the laboratory. The researchers also studied iPSCs from three families participating in the New Jersey Language and Autism Genetics Study and two people without autism from the National Institutes of Health (NIH).
  • This paper summarized clinical and intellectual information on the participants.
  • In all participants with idiopathic autism, there were problems with cell growth control. Two participants had a decrease in the number of cells that were able to grow, and one participant had cell overgrowth. All participants with a 16p11.2 deletion had increased cell growth.
  • The researchers tested all the cells to see if there were similar genetic pathways causing the cell growth problems. They found that the cells from participants with idiopathic autism had different patterns of genetic markers. The cells from participants with a 16p11.2 deletion had some similar genetic patterns.
  • The researchers suggested that too much or too little neurodevelopmental mechanisms contributes to the development of autism. Show Less
Stem Cell Rep 17, 1380-1394 (2022)
Connacher et al.
Full Article

16p11.2 deletion
2022

Predictive functional, statistical and structural analysis of CSNK2A1 and CSNK2B variants linked to neurodevelopmental diseases
  • The researchers aimed to create a list of all the CSNK2A1 and CSNK2B genetic variants available in research articles and public datasets. The researchers accessed Simons Searchlight genetic data for CSNK2A1 for this study. Show More
  • The researchers included a total of 68 CSNK2A1 and 67 CSNK2B genetic variants.
  • They identified some hot spots, which are regions within each gene where genetic variants occur at a higher rate than other parts of the gene. This means that several people have the same variant in some parts of the gene.
  • They used computational prediction programs to understand if the variant is problematic for CSNK2A1 or CSNK2B. Experimental data for some variants were added to the results.
  • The researchers suggested that genetic variants result in different types of functional outcomes for the CSNK2A1 protein, also called CK2α: a) a genetic variant that results in some downstream pathway changes, b) a genetic variant that results in many downstream pathway changes, c) a genetic variant that is not able to properly activate other proteins, or d) a genetic variant that disrupts the folding of the CK2α protein. Show Less
Front Mol Biosci 13, 851547 (2022)
Unni et al.
Full Article

CSNK2A1
2022

Multi-site normative modeling of diffusion tensor imaging metrics using hierarchical Bayesian regression
  • The researchers used magnetic resonance imaging (MRI) images of people with a 16p11.2 deletion to test different models to see which works best to detect changes in brain white matter substructure. Show More
  • This study looked at data from 6 studies, one of which included Simons Searchlight participants with a 16p11.2 deletion. This study included 70 people with the deletion and 1,377 people without any known genetic condition.
  • The researchers identified patterns in the brain’s white matter at different ages in both people with a 16p11.2 deletion and people without any known genetic condition. The researchers studied how the different models performed and how much they overlapped with each other, as well as compared them to other methods previously used to study MRI images.
  • They suggested that changes in the brain structure of people with a 16p11.2 deletion may be associated with an atypical amount and distribution of axons, which are the parts of brain cells involved in sending messages from one brain cell to the next.
  • This research was supported by a grant from the Simons Foundation Autism Research Initiative (SFARI). Show Less
Med Image Comput Comput Assist Interv 13431, 207-217 (2022)
Villalón-Reina et al.
Full Article

16p11.2 deletion
2022