Version: 1.0.0 | Published: 24 Sep 2026 | Updated: 0 days ago
Documentation
Description:
**Please contact support@alzheimersdata.org to request this dataset.**
Published findings now available: [Radiogenomics of C9orf72 Expansion Carriers Reveals Global Transposable Element Derepression and Enables Prediction of Thalamic Atrophy and Clinical Impairment ](https://www.jneurosci.org/content/43/2/333). We generated a novel, whole-blood RNA-seq dataset to determine the relationships between peripheral C9orf72 expression, TE activation, thalamic atrophy, and clinical severity (n = 114). For whole-blood donors, ADRC participants carrying a pathogenic hexanucleotide repeat expansion (HRE) in C9orf72, defined as more than 30 repeats (n = 49; C9orf72+) (Renton et al., 2011), were assessed and clinically diagnosed at the UCSF MAC. No participants in this study carried other known neurodegenerative disease-causing pathogenic variants. Participants with mild cognitive or behavioral symptoms were classified as having MCI, while C9orf72+ participants who did not display any symptoms were classified as pre-symptomatic. Cognitively normal, healthy older adult controls (n = 65; mean age = 61.3 ± 6.7 years) were recruited to the UCSF MAC as part of ongoing longitudinal studies of aging. RNA Sequencing. For whole-blood analyses, blood was drawn from participants at UCSF within 90 days of clinical assessment and stored in PAXgene blood RNA tubes (Qiagen) in liquid nitrogen. The TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina) was used per the manufacturer’s protocol to prepare RNA for sequencing. Samples were sequenced in two batches: batch 1 (25 C9orf72 HRE carriers, 29 controls) was sequenced on a HiSeq 2500 generating 50 base pair paired-end reads, while batch 2 (24 C9orf72 HRE carriers, 36 controls) was sequenced on a HiSeq 4000 generating 75 base pair paired-end reads. Samples in both batches were sequenced over multiple lanes and at an average depth of 50-60 M paired reads per sample. Sequencing Data Processing. Gene and transposable element (TE) abundance was determined in RNA-seq data as previously described (Jin and Hammell, 2018) using TEcount from the TEToolkit suite (Jin et al., 2015) (http://hammelllab.labsites.cshl.edu/software/). Reads were aligned to the GRCh38 build of the human reference genome using STAR v2.7.3a (Dobin et al., 2013) and a prebuilt GTF file of gene and TE annotation provided with TEtranscripts. Gene and TE abundance were estimated from the resulting BAM files using TEcount, a comprehensive gene annotation GTF file from GENCODE release 34, and a prebuilt TE annotation index provided with TEtranscripts.
Published findings now available: [Radiogenomics of C9orf72 Expansion Carriers Reveals Global Transposable Element Derepression and Enables Prediction of Thalamic Atrophy and Clinical Impairment ](https://www.jneurosci.org/content/43/2/333). We generated a novel, whole-blood RNA-seq dataset to determine the relationships between peripheral C9orf72 expression, TE activation, thalamic atrophy, and clinical severity (n = 114). For whole-blood donors, ADRC participants carrying a pathogenic hexanucleotide repeat expansion (HRE) in C9orf72, defined as more than 30 repeats (n = 49; C9orf72+) (Renton et al., 2011), were assessed and clinically diagnosed at the UCSF MAC. No participants in this study carried other known neurodegenerative disease-causing pathogenic variants. Participants with mild cognitive or behavioral symptoms were classified as having MCI, while C9orf72+ participants who did not display any symptoms were classified as pre-symptomatic. Cognitively normal, healthy older adult controls (n = 65; mean age = 61.3 ± 6.7 years) were recruited to the UCSF MAC as part of ongoing longitudinal studies of aging. RNA Sequencing. For whole-blood analyses, blood was drawn from participants at UCSF within 90 days of clinical assessment and stored in PAXgene blood RNA tubes (Qiagen) in liquid nitrogen. The TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina) was used per the manufacturer’s protocol to prepare RNA for sequencing. Samples were sequenced in two batches: batch 1 (25 C9orf72 HRE carriers, 29 controls) was sequenced on a HiSeq 2500 generating 50 base pair paired-end reads, while batch 2 (24 C9orf72 HRE carriers, 36 controls) was sequenced on a HiSeq 4000 generating 75 base pair paired-end reads. Samples in both batches were sequenced over multiple lanes and at an average depth of 50-60 M paired reads per sample. Sequencing Data Processing. Gene and transposable element (TE) abundance was determined in RNA-seq data as previously described (Jin and Hammell, 2018) using TEcount from the TEToolkit suite (Jin et al., 2015) (http://hammelllab.labsites.cshl.edu/software/). Reads were aligned to the GRCh38 build of the human reference genome using STAR v2.7.3a (Dobin et al., 2013) and a prebuilt GTF file of gene and TE annotation provided with TEtranscripts. Gene and TE abundance were estimated from the resulting BAM files using TEcount, a comprehensive gene annotation GTF file from GENCODE release 34, and a prebuilt TE annotation index provided with TEtranscripts.
Coverage
Spatial:
US
Follow Up:
Unknown
Provenance
Temporal
Accrual Periodicity:
Static
Start Date:
01 January 2026
Time Lag:
Not applicable
Accessibility
Access
Access Rights:
See dataset for details. Access data at:
Usage
Resource Creators:
Luke W. Bonham, Ethan G. Geier, Daniel W. Sirkis, Jennifer S. Yokoyama
Observations
Statistical Population
Population Description
Population Size
Measured Property
Observation Date
Persons
114
Count
01 January 2026