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Publications

Date Revised: September 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 September 2025, Simons Searchlight has contributed to 128 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Please be aware that papers posted on medRxiv (pronounced med-archive) or bioRxiv (pronounced bio-archive) are not peer-reviewed or edited before online publication.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
128 Publications
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

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

Spontaneous neural activity relates to psychiatric traits in 16p11.2 CNV carriers: An analysis of EEG spectral power and multiscale entropy
  • These researchers studied electroencephalograms (EEGs) from Simons Searchlight participants to learn about resting brain activity in people with a 16p11.2 deletion or duplication. An EEG measures electrical activity in the brain. Show More
  • The researchers focused on the front region of the brain that is important for movement, language, and skills called executive functions. Executive function skills include being able to have self-control, flexible thinking, and working memory.
  • This research included 25 people with a 16p11.2 deletion, 14 people with a 16p11.2 duplication, and 14 people with none of these genetic changes.
  • The paper includes a summary table of the different altered brain functions in people with a 16p11.2 deletion or duplication from other published papers.
  • In the front region of the brain, the researchers found increased brain dynamics in participants with a 16p11.2 deletion or duplication. Participants with a 16p11.2 duplication had brain patterns that are associated with sleepiness. Participants with a 16p11.2 deletion had an association between irregular brain patterns and anxiety issues, as well as pervasive developmental issues.
  • The researchers suggested that abnormal frontal brain activity seems to strongly reflect certain psychiatric traits. Show Less
J Psychiatr Res 136, 610-618 (2021)
Al-Jawahiri et al.
Full Article

16p11.2 deletion
16p11.2 duplication
2021

Overexpression of CD47 is associated with brain overgrowth and 16p11.2 deletion syndrome
  • People with a 16p11.2 deletion often have a large head size, and MRIs show that they have an enlargement in brain matter volume. Show More
  • The researchers got induced pluripotent stem cells (iPSCs) from Simons Searchlight to study why brain matter is larger for people with a 16p11.2 deletion.
  • 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.
  • The researchers got iPSCs from six people with a 16p11.2 deletion, two people with a 16p11.2 duplication, and three people with no genetic change. They also got medical data on the people who donated the cells from Simons Searchlight. Four of the six people with a 16p11.2 deletion had much larger head sizes than the average population.
  • The researchers turned the iPSCs into brain cells and studied changes in gene expression and cell communication. They found that the 16p11.2 deletion cells had an increase in a cell signal called CD47. CD47 stands for cluster of differentiation 47, and it acts like a ‘don’t eat me’ signal to the immune system.
  • The researchers showed that immune cells were less likely to eat the 16p11.2 deletion cells than the 16p11.2 duplication cells or regular brain cells. In similar studies done in mice, the researchers showed that brain cells with extra CD47 were less likely to be eaten by immune cells.
  • The researchers suggested that brain growth and enlargement in people with a 16p11.2 deletion could be due to cell communication factors. Show Less
Proc Natl Acad Sci USA 118, e2005483118 (2021)
Li et al.
Full Article

16p11.2 deletion
2021