---
title: "NG00183 – Diverse somatic genomic alterations in single neurons in chronic traumatic encephalopathy"
id: "8530"
type: "dataset"
slug: "ng00183"
published_at: "2025-10-27T17:45:52+00:00"
modified_at: "2026-03-19T15:10:58+00:00"
url: "https://dss.niagads.org/datasets/ng00183/"
markdown_url: "https://dss.niagads.org/datasets/ng00183.md"
excerpt: "To access this data, please log into DSS and submit an application.Within the application, add this dataset (accession NG00183) in the “Choose a Dataset” section.Once approved, you will be able to log in and access the data within the DARM..."
taxonomy_dataset_categories:
  - "Controlled Access"
  - "CTE"
  - "Data Type"
  - "Disease"
  - "Illumina HiSeq X"
  - "Illumina NovaSeq 6000"
  - "Illumina NovaSeq X"
  - "Open and Controlled Access Data"
  - "Platform"
  - "Single-neuron WGS"
---

## Overview

To access this data, please log into DSS and submit an application.  
Within the application, add this dataset (accession NG00183) in the “Choose a Dataset” section.  
Once approved, you will be able to log in and access the data within the DARM portal.

#### Description

This study characterized somatic mutations in chronic traumatic encephalopathy (CTE) and performed whole-genome sequencing of single neurons isolated from prefrontal cortex (PFC) of postmortem human brain of individuals with CTE, repetitive head impacts but without CTE (RHI), or non-disease control, along with bulk whole-genome sequencing performed on each individual as a reference genome for variant calling. Single neuron genomes were amplified using primary template-directed amplification (PTA) or multiplexed end-tagging amplification of complementary strands (META-CS).

Single-neuron amplified genome libraries were sequenced (WGS) on Illumina instruments and aligned to the human reference genome GRCh37. Two sequencing modalities were used, including PTA and META-CS, which is a duplex consensus sequencing method, to perform somatic mutation calling in single neurons with the matched bulk. The single-cell dataset includes a total of 349 single-neuron genome sequences (88 PTA, 261 META-CS). Sequence files are in either .bam (PTA) or .fastq.gz (META-CS) format.

#### Sample Summary per Data Type

| Sample Set | Accession | Data Type | Number of Samples |
| --- | --- | --- | --- |
| Diverse somatic genomic alterations in single neurons in chronic traumatic encephalopathy | snd10128 | Single-neuron WGS | 370 |

#### Available Filesets

| Name | Accession | Latest Release | Description |
| --- | --- | --- | --- |
| CTE sn-WGS: META-CS Single-neuron WGS | fsa000151 | NG00183.v1 | META-CS Single-neuron WGS |
| CTE sn-WGS: PTA Single-neuron WGS | fsa000152 | NG00183.v1 | PTA Single-neuron WGS |
| CTE sn-WGS: Bulk WGS | fsa000153 | NG00183.v1 | Bulk WGS |
| CTE sn-WGS: Phenotypes, Sample Information, README | fsa000154 | NG00183.v1 | Phenotypes, Sample Information, README |

View the [File Manifest](https://st1.niagads.org/portal/download-public/NG00183.v1/fm)
 for a full list of files released in this dataset.

## Participant Information

For a breakdown of the study population characteristics, navigate to the individual sample sets below.

| Sample Set | Accession Number | Number of Participants | Number of Samples |
| --- | --- | --- | --- |
| Diverse somatic genomic alterations in single neurons in chronic traumatic encephalopathy | snd10128 | 35 | 370 |

## Related Studies

- [sa000075 - Diverse somatic genomic alterations in single neurons in chronic traumatic encephalopathy](https://dss.niagads.org/studies/sa000075/) This study characterized somatic mutations in chronic traumatic encephalopathy (CTE) and performed whole-genome sequencing of single neurons isolated from prefrontal cortex (PFC) of postmortem human brain of individuals with CTE,… [Learn more](https://dss.niagads.org/studies/sa000075/)

## Cohorts

| Cohort | Number of Participants | Number of Samples |
| --- | --- | --- |
| NIH Neurobiobank/University of Maryland (UMB-BTB) | 14 | 128 |
| UNITE - Understanding Neurologic Injury and Traumatic Encephalopathy Brain Bank (BU-CTE Center) | 21 | 242 |

## Consent Levels

| Consent Level | Number of Participants | Number of Samples |
| --- | --- | --- |
| HMB-IRB-PUB | 35 | 370 |

Visit the [Data Use Limitations page](/documentation/policies-and-guidelines/data-use-limitations/)
 for definitions of the consent levels above.

## Acknowledgement

### Acknowledgment statement for any data distributed by NIAGADS:

Data for this study were prepared, archived, and distributed by the National Institute on Aging Alzheimer's Disease Data Storage Site (NIAGADS) at the University of Pennsylvania (U24-AG041689), funded by the National Institute on Aging.

Use the study-specific acknowledgement statements below (as applicable):

### For investigators using any data from this dataset:

Please cite/reference the use of NIAGADS data by including the accession [NG00183](https://archive.niagads.org/datasets/NG00183)
.

### For investigators using Diverse somatic genomic alterations in single neurons in chronic traumatic encephalopathy (sa000075) data:

This work was supported by the National Institute on Aging (R01 AG082346, R01 AG088082, R01 AG070921, K08 AG065502, DP2 AG086138) and the Doris Duke Charitable Foundation Clinical Scientist Development Award (2021183), as part of Dong et al., “Diverse somatic genomic alterations in single neurons in chronic traumatic encephalopathy.”

## Publications

- Dong G. **Diverse somatic genomic alterations in single neurons in chronic traumatic encephalopathy.***Science (New York, N.Y.). 2025 Oct 30.*[PubMed link](https://pubmed.ncbi.nlm.nih.gov/41166474/)

## Approved Users

**Total number of approved DARs:** 1

[JSON Export](https://st1.niagads.org/portal/v1/adars/NG00183)
|[CSV Export](https://dss.niagads.org/wp-admin/admin-post.php?action=niagads_export_dars_csv&accession=NG00183)

- Investigator: Kamboh, M. Ilyas Institution: University of Pittsburgh Project Title: Genetics of Alzheimer's Disease and Endophenotypes Date of Approval: March 31, 2026 Request status: Approved Publications: None Reported Research use statements: Show statements Technical Research Use Statement: Objectives: We are requesting access to the NIAGADS datasets to augment our ongoing studies on the genetics of Alzheimer’s disease (AD) and AD-related endophenotypes being carried out by Kamboh and his group since 1995. We are doing GWAS using array genotypes, whole-exome sequencing and whole-genome sequencing on datasets derived from University of Pittsburgh ADRC and ancillary population-based longitudinal studies on dementia and biomarkers. Different available phenotypes include AD and non-AD dementia, age-at-set, disease progression and survival, neuroimaging, cognitive decline, plasma biomarkers for the core ATN and non-ATN pathologies. We also plan to expand on gene-gene interaction and sex-stratified analyses which require the actual genotype data. The NIAGADS datasets will be used for replication and meta-analysis, and for gene-gene interaction and sex-stratified analyses. Study Design: A case-control design will incorporate a diverse cohort of individuals with AD and age-matched controls. For quantitative traits (neuroimaging and plasma biomarkers, cognitive performance measures, indicators of disease progression), linear regression analyses will be performed to identify genetic loci. To ensure the findings are robust and inclusive, participants from diverse demographic backgrounds will be included, enabling the exploration of potential genetic variations across populations. Analysis Plan: We will conduct GWAS and targeted analyses on candidate genes on different AD and AD-related phenotypes. Primary phenotypic variables include AD disease status, age-at-onset, last age for controls, APOE genotype, cognitive decline trajectories, sex, and race. Analyses will evaluate the influence of specific genetic variants on disease risk, cognitive performance, and biomarker levels, considering both individual and interactive effects of the APOE genotype. Results will be adjusted for potential confounders, such as demographic factors, to ensure valid associations. Detail analytical methods are described in our published papers for case-control (PMID: 32651314;35694926), quantitative traits (PMID: 30361487;37666928), and cognitive decline (PMID: 37089073; 30954325). Non-Technical Research Use Statement: Our research group at the University of Pittsburgh (Pitt), has been working on the genetics of Alzheimer’s disease (AD) and AD-related endophenotypes for almost three decades, on data derived largely from the University of Pittsburgh Alzheimer’s Disease Research Center and ancillary dementia studies. We are requesting access to the NIAGADS genotype and phenotype datasets to augment our sample size to increase power to detect novel genetic associations with AD and related endophenotypes.

### Total number of participants: 35

SexRaceEthnicityDiagnosisAPOE

Female720.0 %

Male2880.0 %

| NA | 35 |
| --- | --- |

- NA35 (100.0%)

| CTE |  |  |
| --- | --- | --- |
| Control | 16 | 45.7% |
| Case | 15 | 42.9% |
| Other | 4 | 11.4% |

Not Applicable/Not Available

35

100.0%