---
title: "Diverse somatic genomic alterations in single neurons in chronic traumatic encephalopathy"
id: "8536"
type: "sample_set"
slug: "snd10128"
published_at: "2025-10-27T17:46:31+00:00"
modified_at: "2025-10-27T17:46:32+00:00"
url: "https://dss.niagads.org/sample-sets/snd10128/"
markdown_url: "https://dss.niagads.org/sample-sets/snd10128.md"
excerpt: "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,..."
---

## 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.

## Cohorts

- [NIH Neurobiobank/University of Maryland (UMB-BTB)](https://dss.niagads.org/cohorts/nih-neurobiobank-university-of-maryland/)
- [UNITE - Understanding Neurologic Injury and Traumatic Encephalopathy Brain Bank (BU-CTE Center)](https://dss.niagads.org/cohorts/understanding-neurologic-injury-and-traumatic-encephalopathy-brain-bank-bu-cte-center/)

## Sex

### Total number of samples: 370

Female6617.8 %

Male30482.2 %

## Diagnosis

### Total number of samples: 370

| CTE |  |  |
| --- | --- | --- |
| Control | 152 | 41.1% |
| Case | 198 | 53.5% |
| Other | 20 | 5.4% |