Abstract
One challenge in conducting DNA methylation-based epigenome-wide association study (EWAS) is the appropriate cleaning and quality-checking of data to minimize biases and experimental artifacts, while simultaneously retaining potential biological signals. These issues are compounded in studies that include multiple tissue types, and/or tissues for which reference data are unavailable to assist in adjusting for cell-type mixture, for example cerebral spinal fluid (CSF). For our study that evaluated blood and CSF taken from aneurysmal subarachnoid hemorrhage (aSAH) patients, we developed a protocol to clean and quality-check genome-wide methylation levels and compared the methylomic profiles of the two tissues to determine whether blood is a suitable surrogate for CSF. CSF samples were collected from 279 aSAH patients longitudinally during the first 14 days of hospitalization, and a subset of 88 of these patients also provided blood samples within the first 2 days. Quality control (QC) procedures included identification and exclusion of poor performing samples and low-quality probes, functional normalization, and correction for cell-type heterogeneity via surrogate variable analysis (SVA). Significant differences in rates of poor ...Continue Reading
References
Jan 1, 1968·Journal of Neurosurgery·W E Hunt, R M Hess
Jan 1, 1980·Neurosurgery·C M FisherJ M Davis
Dec 1, 1995·Journal of Neuroimmunology·A SvenningssonS Stemme
Jan 18, 2007·Neurosurgery·Marieke J H WermerUNKNOWN Aneurysm Screening after Treatment for Ruptured Aneurysms Study Group
Jan 11, 2008·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Erika D NelsonLisa M Monteggia
Mar 4, 2010·Science Signaling·Martha StapelsAn Zhou
Jul 16, 2010·Cytometry. Part B, Clinical Cytometry·Marieke T de GraafJan W Gratama
May 14, 2011·Cytometry. Part B, Clinical Cytometry·Marieke T de GraafJan W Gratama
Jan 20, 2012·Bioinformatics·Jeffrey T LeekJohn D Storey
May 10, 2012·BMC Bioinformatics·Eugene Andres HousemanKarl T Kelsey
Feb 21, 2013·Epigenetics : Official Journal of the DNA Methylation Society·Francesco MarabitaDavid Gomez-Cabrero
Aug 31, 2013·Annual Review of Pathology·Suping Zhang, Thomas J Kipps
Nov 26, 2013·Critical Care Nursing Clinics of North America·Edythe M Lyn Greenberg, Alexandra Probst
Jan 22, 2014·Nucleic Acids Research·Baoshan MaLiming Liang
Jan 31, 2014·Bioinformatics·Martin J AryeeRafael A Irizarry
Jun 2, 2014·Haematologica·Paolo Ghia, Michael Hallek
Sep 23, 2014·Methods : a Companion to Methods in Enzymology·Tiffany J Morris, Stephan Beck
Dec 18, 2014·Cancer Cell·Maria CicconeGeorge A Calin
Jan 20, 2015·Genome Biology·Jean-Philippe FortinKasper D Hansen
Apr 25, 2015·American Journal of Hematology·Michael Hallek
Sep 19, 2015·Nucleic Acids Research·Zongli XuJack A Taylor
Jan 5, 2017·BMC Genomics·Zongli XuLiang Niu