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Publications

Date Revised: March 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 March 2025, Simons Searchlight has contributed to 117 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Please be aware that papers posted on medRxiv (pronounced med-archive) or bioRxiv (pronounced bio-archive) are not peer-reviewed or edited before online publication.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
117 Publications
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

The general impact of haploinsufficiency on brain connectivity underlies the pleiotropic effect of neuropsychiatric CNVs
  • The researchers looked at several copy number variants (CNV) to study how the brain forms when a person has a CNV. A CNV happens when the number of copies of a gene region is affected, a set of genes are removed/deleted, or are extra/duplicated in a region of the DNA. 16p11.2 deletion is an example of a CNV.Show More
  • The researchers used magnetic resonance imaging (MRI) scans from people with 1q21.1 and 16p11.2 CNVs in Simons Searchlight. They included people with 15q11.2, 17q12, and 22q11.2 CNVs from other research studies.
  • They found brain changes in all genetic conditions studied in various regions of the brain. They also looked at the features of IQ, autism, schizophrenia, and ADHD within the groups and looked at brain connectivity patterns. This was the first time that MRIs were studied for 1q21.1 and 15q11.2 CNVs.
  • The researchers found that a region of the brain called the thalamus was a common region affected by these CNVs. Changes in the thalamus are linked to neuropsychiatric conditions. The thalamus region of the brain is needed to process the body's senses (except smell), and it plays a role in sleep, wakefulness, consciousness, learning, and memory.
  • This research was supported by a grant from the Simons Foundation Autism Research Initiative (SFARI).Show Less
Bio Psy 89, S40 (2021)
Moreau et al.
Full Article

16p11.2 deletion
16p11.2 duplication
1q21.1 deletion
1q21.1 duplication
2021

A genetics-first approach to dissecting the heterogeneity of autism: Phenotypic comparison of autism risk copy number variants
  • To understand the autism profile of people with a 16p11.2 or 22q11.2 deletion or duplication, researchers studied the features of autism in these individuals.Show More
  • This study included people from the following seven research studies: Simons Searchlight, ExperienCes of people witH cOpy number variants (ECHO study), Intellectual Disability and Mental Health: Assessing Genomic Impact on Neurodevelopment, Hospital Neurodevelopmental CNV Cohort at Belgrade University Children’s Hospital, International 22q11.2 Deletion Syndrome Brain Behavior Consortium, Center for Autism Research at Children’s Hospital of Philadelphia, and 16p11.2 European Consortium.
  • There were 82 participants with a 16p11.2 deletion, 50 with a 16p11.2 duplication, 370 with a 22q11.2 deletion, and 45 with a 22q11.2 duplication.
  • About half of the participants with a 16p11.2 deletion, 16p11.2 duplication, and 22q11.2 duplication met the clinical criteria for an autism diagnosis. Participants with a 22q11.2 deletion had the lowest rate, with only 1 out of 5 meeting the criteria. The researchers stated that the autism rates were for the number of people found in the clinic with these genetic conditions, which does not include people who were not found because they had no symptoms of the genetic condition.
  • Of the participants who did not meet the clinical definition of autism, most with a 16p11.2 deletion or duplication had issues in at least one area of the autism measurement.
  • Participants with a 16p11.2 deletion or 22q11.2 deletion had less severe features of autism than people with autism in the general population. Participants with a 16p11.2 duplication or 22q11.2 duplication had autism features that were similar to people with autism in the general population.
  • The researchers stated that there was a large amount of variability between each of the genetic conditions. In addition, there were more males than females in all four of the genetic conditions that had an autism diagnosis. Show Less
Am J Psychiatry 178, 77-86 (2021)
Chawner et al.
Full Article

16p11.2 deletion
16p11.2 duplication
2021

Detailed clinical and psychological phenotype of the X-linked HNRNPH2-related neurodevelopmental disorder
  • This is the first publication on HNRNPH2 that includes Simons Searchlight data. HNRNPH2 stands for heterogeneous nuclear ribonucleoprotein H2, and it is important for cell function and helps brain cells to make connections.Show More
  • The researchers studied people with a genetic change in HNRNPH2. With consent from the participants’ family, their information was shared with Simons Searchlight. This information was linked to information already provided by people who participate in Simons Searchlight.
  • The researchers studied 33 people with a pathogenic, or likely pathogenic, genetic change in HNRNPH2. The paper includes a large table of the participants’ medical features, as well as photos of the participants smiling.
  • Nearly half the participants had had a seizure at some point. Most children had hypotonia, difficultly coordinating, and issues with balance.
  • When children had a brain MRI, the most common findings were a change in the bundle of brain cells that connect the left and right sides of the brain, delayed development of the protective covering of brain cells, and decreased brain size in the region that controls coordination and balance.
  • Feeding and stomach issues were a concern for most children, and many parents said that their children had chronic constipation.
  • This paper has many more details on the medical findings in both males and females with genetic changes in HNRNPH2.Show Less
Neurol Genet 7, e551 (2021)
Bain et al.
Full Article

HNRNPH2
2021