Dataset

NG00077 - Genetic analyses of patients with CTE

Overview

This dataset includes whole-genome sequncing of cases with CTE. Sequencing libraries were prepared from 100 ng high quality genomic DNA from cerebellum using the Illumina Nextera DNA Flex Library Prep Kit, and assessed using a Qubit and Agilent Bioanalyzer. High-throughput sequencing was carried out on multiple libraries pooled in equal molarity using a NovaSeq6000 (150 bp paired end configuration, Illumina) and aligned to the human reference genome GRCh38 using BWA and Bwakit (v0.7.15). ExpansionHunter was applied to estimate expansion numbers of short tandem repeats (v2.5.5) and germline variants were identified with Strelka2 (v2.9.9), with default parameters for whole genome sequence data. The variants were annotated for their effects with ANNOVAR.

Access to Whole Genome sequencing data is available through an approved NIAGADS application. Once approved, the dataset will be transferred via FTP, as the size exceeds 160GB.

Molecular Data Type

Type

WGS

Disease

CTE
Submission date: 
1/24/2019
Samples

2018-011 (Case 1 in article) male, CTE, retired professional American football player who died aged 67. Suffered from memory problems, irritable mood and behavioural outbursts. He also reported muscle weakness and was mostly reliant on a wheelchair.

2017-036 (Case 2 in article) male, CTE, former professional boxer who died at age 67. A heterozygous hexanucleotide GGGGCC repeat expansion mutation in intron 1 of C9orf72 was detected. He suffered from inherited frontotemporal lobar degeneration (FTLD)/ALS, in addition to CTE.

2017-036 (Case 3 in article), male, CTE, former professional boxer who died aged 78. This individual had Parkinson’s disease as well as CTE.

PI Information