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Publications

Date Revised: August 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 August 2025, Simons Searchlight has contributed to 125 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Please be aware that papers posted on medRxiv (pronounced med-archive) or bioRxiv (pronounced bio-archive) are not peer-reviewed or edited before online publication.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
125 Publications
Analysis of mitochondrial DNA replisome in autism spectrum disorder: Exploring the role of replisome genes
  • The researchers investigated how energy production in the cells might be different in autistic people. In cells, energy is transferred from food molecules to the molecules that the cell can use to do work. This process happens inside a structure called the mitochondria.Show More
  • The researchers used a Simons Searchlight 16p11.2 deletion induced pluripotent stem cell (iPSC) line from a person who had an autism diagnosis.
  • From cheek swab samples of children with autism, the researchers found that children with autism had a different number of mitochondrial DNA. This finding suggests that the production of mitochondria is different in children with autism.
  • The researchers tested for oxidative stress, which is a byproduct of turning food into energy. Children with autism had a higher amount of oxidative stress and an inflammation marker in their cheek samples. The researchers suggested that oxidative stress might contribute to mitochondria dysfunction and inflammation might play a role in immune dysregulation in autistic people.
  • The researchers also found that the iPSCs of a person with autism were more prone to mitochondrial errors under a stressed condition (induced by a drug) compared with cells from a person without autism.
  • The researchers did not find links between mitochondrial gene regulation and brain volume, other genetic variants in certain mitochondrial genes, or the development of autistic features.Show Less
Autism Res Epub ahead of print, (2024)
Rojas et al.
Full Article

16p11.2 deletion
2024

Rare CNVs and phenome-wide profiling highlight brain structural divergence and phenotypical convergence
  • These researchers compared the brain structures of people with copy number variants (CNVs) and people in the UK Biobank that were from the general population. This study included eight CNVs: deletions or duplications of 1q21.1, 15p11.2, 16p11.2, and 22q11.2.Show More
  • This study included participants from several research studies or universities: Simons Searchlight; Cardiff University; 16p11.2 European Consortium; University of Montreal; and University of California, Los Angeles. There were 548 people with a CNV and 312 people with no genetic condition.
  • The researchers used computer analytics to study the brain features of each of the CNVs and created one of the largest brain imaging studies to date.
  • They made a comparison between brain structures and medical features in order to find links between the two. They aimed to understand how brain structure can lead to behaviors.
  • Brain volumes were smaller in participants with a 1q21.1 deletion, 15p11.2 duplication, 16p11.2 duplication, and 22q11.2 deletion. Brain volumes were bigger in people with a 1q21.1 duplication, 15p11.2 deletion, 16p11.2 deletion, and 22q11.2 duplication.
  • They found that people with a 16p11.2 deletion or 22q11.2 deletion had unique brain patterns, whereas people with a 15p11.2 duplication had brain structures that were similar to the general population.
  • People with a 16p11.2 deletion had the highest number of brain regions affected, whereas people with a 15p11.2 duplication had the lowest number of regions affected.
  • The researchers created a graph showing the large-scale network of each CNV, and they studied characteristics of people with a CNV, such as body size, lifestyle, and blood factors. All eight CNVs had strong associations with diastolic blood pressure, a protein called alkaline phosphatase, and red blood cell count.
  • This research was supported by a grant from the Simons Foundation Autism Research Initiative (SFARI).Show Less
Nat Hum Behav Epub ahead of print, (2023)
Kopal et al.
Full Article

16p11.2 deletion
16p11.2 duplication
1q21 deletion
1q21 duplication
2023

Subcortical brain alterations in carriers of genomic copy number variants
  • Researchers know that copy number variants (CNV) can contribute to neurodevelopmental and psychiatric disorders, such as autism and schizophrenia. 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
  • The goal of this study was to compare the sizes and patterns of regions of the brain for 11 different CNVs.
  • The researchers studied the following deletions and duplications: 1q21.1, 13q12.12, 15q11.2, 16p11.2, 16p13.11, and 22q11.2. They also studied duplications within chromosome 1, including the TAR region. This study included 675 participants. Brain MRI images for 1q21.1 and 16p11.2 CNVs came from Simons Searchlight participants.
  • The researchers found that CNVs with more genes deleted or duplicated within that region, such as 16p11.2, resulted in more structural changes on magnetic resonance imaging (MRI). All 11 CNVs had changes in the thickness of the brain region that affects cognitive, affective, and social functions. The researchers did not find a link between overall brain volume and the cognition of the person with these CNVs, but, the shape/structure of the brain regions were linked to a person’s cognition.
  • People with 16p11.2 duplications had brain structure changes that were different than those seen in people with autism, and people with no genetic diagnosis. This suggests that there may be several different brain changes that could lead to autism.
  • This research was supported by a grant from the Simons Foundation Autism Research Initiative (SFARI).Show Less
Am J Psychiatry 180, 685-698 (2023)
Kumar et al.
Full Article

16p11.2 deletion
16p11.2 duplication
16p13.11 deletion
1q21.1 deletion
1q21.1 duplication
2023

Caregiver-reported dental manifestations in individuals with genetic neurodevelopmental disorders
  • Children with neurodevelopmental disorders (NDDs) are more likely to have dental health issues than children without an NDD. Often these dental hygiene issues are due to a lack of cooperation during brushing or dental visits.Show More
  • To learn whether people with NDDs have unique dental issues, the researchers surveyed Simons Searchlight caregivers to ask about dental features found in their dependents. This question was raised by a parent in a Simons Searchlight community.
  • The researchers studied 39 genetic conditions, which included 620 people with a genetic NDD, and they compared the findings with those of 145 siblings with no genetic finding.
  • In general, people within the NDD group had more issues with drooling, late first teeth appearance, and abnormal shape of first and second teeth.
  • This is the first time that researchers found genetic variations in CSNK2A1, DYRK1A, and PPP2R5D were each associated with specific dental features.
  • About half of children with a CSNK2A1-related NDD had defects in their first teeth, such as longer than average front teeth, cracked teeth, missing enamel, small teeth, or fused teeth.
  • About half of children with a damaging DYRK1A genetic variant had delayed appearance of the first teeth.
  • Finally, about 2 out of 3 children with a pathogenic PPP2R5D genetic variant had excessive drooling.Show Less
Int J Paediatr Dent Epub ahead of print, (2023)
Ming et al.
Full Article

All Genes
CSNK2A1
DYRK1A
PPP2R5D
2023

Development of webcam-collected and artificial-intelligence-derived social and cognitive performance measures for neurodevelopmental genetic syndromes
  • Studying social and cognitive ability in people with neurodevelopmental genetic syndromes is hard not only because the conditions are rare, but also because it requires the detection of subtle differences. Being able to see even small changes in social and cognitive ability in a person is important to assess the effectiveness of a drug or personalized medicine.Show More
  • In this study, the researchers created a webcam-based eye tracking method that uses the camera on the participants' home computer or laptop to detect where participants look when shown videos and images. This was the first time that researchers tried to develop a multi-condition wide method for use remotely without a clinician, and for use in people with intellectual disability.
  • The researchers recruited participants through patient advocacy organizations and Simons Searchlight, and they used participant information within the Simons Searchlight database. Participants were between the ages of 3 and 45 years old. Genetic communities that participated through Simons Searchlight included GRIN2B, CSNK2A1, HIVEP2, SCN2A, MED13L, and STXBP1.
  • The study included 375 participants, including 163 with a neurodevelopmental genetic syndrome, 56 with a neurodevelopmental condition but no genetic diagnosis, and 156 without any neurodevelopmental issues. The researchers used artificial intelligence to analyze the participant recordings, and they collected caregiver-reported surveys.
  • Participants were surveyed with this new measure at 3 different times. The survey looked at various parts of social attention, how much vocabulary was understood, how fast information was processed, and single-word reading.
  • The researchers found that in all areas evaluated, there was strong evidence of validity, suggesting that this method could be consistent and reliable for this community. One exception was within the social domain that measures positive and negative emotional expression.
  • Participants with intellectual disability had lower levels in all of the following measures: attention, intentionally reviewing the screen, social attention and preference, single-word reading, speed of recognizing images on screen, and understanding vocabulary.
  • In general, participants with a neurodevelopmental genetic syndrome showed a more impaired neurobehavioral condition, including lower attention, higher nonsocial preference, worse ability to understand vocabulary and single-word reading, and slower speed to faces and objects.
  • Some genetic conditions were found to have group patterns. For example, the participants with SYNGAP1 had higher scores for negative emotional expressiveness.
  • The researchers suggested that this new method could be used consistently for people with mild to moderate cognitive disability, but that consistency could be lower for people with severe cognitive disability.
  • This research was supported by a grant from the Simons Foundation Autism Research Initiative (SFARI).Show Less
Am J Med Genet C Semin Med Genet. 193, e32058 (2023)
Frazier et al.
Full Article

CSNK2A1
GRIN2B
HIVEP2
MED13L
SCN2A
STXBP1
2023

Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles
  • Many people with autism also have gastrointestinal issues, such as constipation, diarrhea, or abdominal bloating. To understand why this might be, researchers have focused on the gut-brain connection by studying the links between hormones, the immune system, and the nervous system.Show More
  • The gut microbiome is the set of bacteria, archaea, fungi, and viruses that live within a person’s intestine and help with digestion.
  • A disruption in the gut-brain connection (also called the gut-brain axis) has been suggested to play a role in neurodevelopmental disorders. Studies on the microbiome in autism have not had consistent findings.
  • In this study, the researchers compared 25 different studies and datasets to identify patterns in people with autism. These studies had 1,193 samples, including blood, urine, and fecal samples. The researchers used 16p11.2 deletion data from Simons Searchlight.
  • The researchers had difficulty in identifying a pattern between studies because the findings were more consistent within studies than between studies. They suggested that this might be due to age, sex, or global location of the participants in each study.
  • In age- and sex-matched analyses, the researchers found a difference between the microbiome of children with autism and children without autism. The researchers called this an autism microbiome signal.
  • There may be a link between the microbiome and diet. The researchers found that autistic people have a lower intake of food enriched for certain amino acids that are important for helping the body to make neurotransmitters. Neurotransmitters are biological messengers that carry chemical signals from one brain cell to the next.
  • The researchers found that a core microbiome made up of Bacteroides, Prevotella, Bifidobacteria, Desulfovibrio, and multiple butyrate producers is linked to autism. This finding suggests that that gut microbiome may play a role in shaping autism symptoms.
  • The researchers did not find any link between a specific genetic variation and a person’s microbiome.
  • The researchers concluded that our understanding of the link between the gut and the brain in autism is still very limited, and that more studies are needed for larger conclusions to be possible.Show Less
Nat Neurosci. 26, 1208-1217 (2023)
Morton et al.
Full Article

16p11.2 deletion
All Genes
2023

The immune status of patients with 16p11.2 deletion syndrome
  • Within the usual 16p11.2 deletion region, also known as the proximal deletion, there are several genes that are important for immune function. The immune genes within the 16p11.2 region are CORO1A, MAPK3, and SPN. There are a few other immune-associated genes just outside the region.Show More
  • The researchers wanted to know if there was an association between having a 16p11.2 deletion and immune issues.
  • In this study, the researchers used information provided by 170 Simons Searchlight participants with a 16p11.2 deletion.
  • Most participants, 138 out of 170 (81 percent) reported that they had a history of infections that were significant. The most common infection category was ear infections occurring more than 8 times, followed by respiratory infections and pneumonia. Eleven participants (6.5 percent) reported that they had a diagnosis of an immunodeficiency. These findings were similar to the findings in participants with a 16p11.2 deletion that were recruited by researchers at Children’s Hospital Colorado.
  • The researchers compared their findings to a group of participants who do not have a 16p11.2 deletion, and there were no reported concerns for a history of infection or autoimmune issues for that comparison group.
  • The article contains a detailed table of all reported infections for people with and without a 16p11.2 deletion.
  • The researchers suggested that people with a 16p11.2 deletion might benefit from extra immunological evaluation by their managing provider.Show Less
J Clin Immunol 43, 1792-1795 (2023)
Wang et al.
Full Article

16p11.2 deletion
2023