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Quality Control Metrics for Whole Blood Transcriptome Analysis in the Parkinson's Progression Markers Initiative (PPMI)

By Elizabeth Hutchins, David Craig, Ivo Violich, Eric Alsop, Bradford Casey, Samantha Hutten, Alyssa Reimer, Timothy G. Whitsett, Karen L. Crawford, Arthur W. Toga, Shawn Levy, Madison Robinson, Nripesh Prasad, J Raphel Gibbs, Mark R. Cookson, Kendall Van Keuren-Jensen, Parkinson Progression Marker Initiative

Posted 08 Jan 2021
medRxiv DOI: 10.1101/2021.01.05.21249278

The Michael J. Fox Foundations Parkinsons Progression Markers Initiative (PPMI) is an observational study to comprehensively evaluate Parkinsons disease (PD) patients using imaging, biologic sampling, clinical and behavioural assessments to identify biomarkers of PD progression. As part of this study, we obtained 4,756 whole blood samples from 1,570 subjects at baseline, 0.5, 1, 2, and 3 years from enrollment in the study. We isolated RNA and performed whole transcriptome sequencing in this longitudinal cohort. Here, we describe and quantify technical variability associated with this dataset through the use of pooled reference samples, including plate distribution, RNA quality, and outliers. This large, uniformly processed dataset is available to researchers at https://www.ppmi-info.org.

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