GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Series GSE72962

Query DataSets for GSE72962

Status

Public on Mar 16, 2016

Title

microRNA profiles in Parkinson’s disease prefrontal cortex

Organism

Homo sapiens

Experiment type

Non-coding RNA profiling by high throughput sequencing
Third-party reanalysis

Summary

Objective. The goal of this study was to examine the microRNA (miRNA) profile of Parkinson’s disease (PD) frontal cortex as compared to normal control brain, allowing for the identification of PD specific signatures as well as the study of disease-related phenotypes, such as onset age or dementia
Methods. Small RNA sequence analysis was performed from prefrontal cortex for 29 PD samples and 33 control samples. After sample QC, normalization and batch correction, linear regression was used to identify miRNAs altered in PD, and a PD classifier was developed using weighted voting class prediction. The relationship of miRNA levels to onset age and PD with dementia (PDD) was also characterized in case-only analyses.
Results. 125 miRNAs were differentially expressed in PD at a genome-wide level of significance (FDR q<0.05). A set of 29 miRNAs classified PD from non-diseased brain (93.9% specificity, 96.6% sensitivity). The majority of differentially expressed miRNAs (105/125) showed an ordinal relationship from control, to PD without dementia (PDN), to PDD. Among PD brains, 36 miRNAs classified PDD from PDN (sensitivity =81.2%, specificity =88.9%). Among differentially expressed miRNAs, miR-10b-5p had a positive association with onset age (q=4.7e-2).
Conclusions. Based on cortical miRNA levels, PD brains were accurately classified from non-diseased brains. Additionally, the PDD miRNA profile exhibited a more severe pattern of alteration among those differentially expressed in PD. To evaluate the clinical utility of miRNAs as potential clinical biomarkers, further characterization and testing of brain-related miRNA alterations in peripheral biofluids is justified.

Overall design

29 Parkinson's disease prefrontal cortex samples analyzed with 33 control samples from Series GSE64977. The adapter sequence from the sample prep TGGAATTCTCGGGTGCCAAGG.

Contributor(s)

Hoss AG, Myers RH, Labadorf A, Latourelle J

Citation(s)

26973511, 27716130

Submission date

Sep 11, 2015

Last update date

Jul 15, 2019

Contact name

Adam Labadorf

E-mail(s)

labadorf@bu.edu

Organization name

Boston University Medical School

Department

Neurology

Street address

72 East Concord Street E301

City

Boston

State/province

ZIP/Postal code

02118

Country

USA

Platforms (1)

GPL15433

Illumina HiSeq 1000 (Homo sapiens)

Samples (29)

More...

GSM1875443	P_0003
GSM1875444	P_0006
GSM1875445	P_0012

Relations

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

BioProject

SRA

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE72962_PD_C_DESeq2_norm_cnts_VST_batch_adj.csv.gz	435.8 Kb	(ftp)(http)	CSV
GSE72962_PD_miRNA_regression_results.csv.gz	43.2 Kb	(ftp)(http)	CSV
SRA Run Selector
Raw data are available in SRA
Processed data are available on Series record