Publications

Date Revised: January 2024

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 chronologically, from oldest to newest. You can explore publications by specific genetic conditions using the categories below.

As of April 2024, Simons Searchlight has contributed to 98 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Please be aware that papers posted on medRxiv (pronounced med-archive) or bioRxiv (pronounced bio-archive) are not peer-reviewed or edited before online publication.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
98 Publications
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

Tags:

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 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, such as 16p11.2, had more structural changes on the MRI. All 11 CNVs had changes in the thickness of the brain region that affects cognitive, affective, and social functions. The large effects were seen in participants with a 16p11.2 or 1q21.1 CNVs.
  • 16p11.2 duplications had brain structure changes that were different than those seen in people with ASD and people with no genetic diagnosis. This suggests that there may be several different brain changes that may lead to autism.
  • This research was supported by a grant from the Simons Foundation Autism Research Initiative (SFARI).Show Less
medRxiv Preprint, (2023)
Kumar et al.
Full Article

Tags:

16p11.2 deletion
16p11.2 duplication
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

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All Genes
CSNK2A1
DYRK1A
PPP2R5D
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

Tags:

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

Tags:

16p11.2 deletion
2023
Receptive language and receptive-expressive discrepancy in minimally verbal autistic children and adolescents
  • Speaking communication is very difficult for about 30 percent of autistic people, and many will not be able to speak well into adulthood, also known as minimally verbal. The researchers aimed to learn how much people who are minimally verbal can understand when spoken to. This type of understanding is called receptive language.Show More
  • Using parent reported surveys and assessments, the researchers measured nonverbal cognitive abilities in the participants to understand their level of receptive language.
  • Children and adolescents between the ages of 5 and 18 with an autism diagnosis were included in this study. Participant data was used from Simons Searchlight, Simons Simplex Collection, and Autism Inpatient Collection, as well as the National Database for Autism Research. The study included 1,579 minimally verbal participants.
  • The researchers found that on average, children and adolescents who were minimally verbal had lower receptive language than age-matched peers. In addition, as children became older, the differences in receptive language were greater.
  • However, for the group, receptive language scores were higher than expressive language scores, suggesting that participants were able to understand more than they were able to express for themselves.
  • The researchers found that social skills, measured by a parent reported survey, was a high associated predictor of a person's receptive language ability within this study.
  • Finally, the researchers found that having better motor skills, measured by a developmental coordination disorder survey, was the highest predictor of having a discrepancy between spoken language and understood language. This suggests that the better the motor skills a minimally verbal child or adolescent has, the more they are likely to have better understanding of the language communicated to them.
  • The researchers suggested that the Vineland Adaptive Behavior Score, used as a standard for adaptive behaviors across many studies and within Simons Searchlight, was the most appropriate measure for minimally verbal people compared with some of the other measures used.
  • The researchers suggested that having better motor skills allows children better exposure to different activities and environments, which promotes language development.Show Less
Autism Res Epub ahead of print, (2023)
Chen et al.
Full Article

Tags:

All Genes
2023
Neurodevelopmental phenotypes associated with pathogenic variants in SLC6A1
  • This is the first publication on SLC6A1 that includes Simons Searchlight data.Show More
  • SLC6A1 stands for solute carrier 6 family member 1, and it is important for brain cells to receive signals from other brain cells. Changes in the SLC6A1 gene commonly result in a person having seizures. The most common seizures are absence seizures.
  • The researchers studied 28 Simons Searchlight participants with a pathogenic or likely pathogenic genetic variant in SLC6A1. This adds to the 116 people with SLC6A1 genetic variants that have been published to date in the medical literature.
  • In this study, most of the genetic variants were de novo, which is a random change that happens in the child. But, some of the genetic variants were inherited from a parent.
  • Most participants had seizures, low muscle tone, language problems or speech delay, intellectual disability or developmental delay, and issues with gross motor skills.
  • Less common medical features in the participants included autism, movement disorders, sleep issues, and a high pain tolerance.
  • This research was supported by a grant from the Simons Foundation Autism Research Initiative (SFARI).Show Less
J Med Genet 59, 536-543 (2022)
Kahen et al.
Full Article

Tags:

SLC6A1
2022