title	author	date	output
Nicoya - Preprocessing & Normalization	Lisa M. McEwen	January 9, 2017	html_document

CRELES Study

Please email: [email protected] if you have any questions about this code.

Publication details (accepted at Epigenetics and Chromatin on April 12, 2017):

Title: Differential DNA methylation and lymphocyte proportions in a Costa Rican high longevity region

Authors: Lisa M. McEwen, BSc; Alexander M. Morin, BSc.; Rachel D. Edgar, MSc.; Julia L. MacIsaac, PhD; Meaghan J. Jones, PhD.; William H. Dow, PhD.; Luis Rosero-Bixby, PhD.; Michael S. Kobor, PhD.; David H. Rehkopf, ScD., MPH.

Date: April 2017

Paper Link: Click here

Overview

This R script is to preprocess and normalize data generated with the Infinium HumanMethylation450 Array (450K).

Whole blood was collected from 95 individuals from the Costa Rican Berkeley CRELES cohort. We sampled from the Nicoyan population ('Nicoyans',n=47) and from other regions of Costa Rica('Controls' or 'non-Nicoyans',n=47). The Nicoya peninsula hosts a population of Costa Rica that exceed expected life expectancy, see Luis Rosero-Bixby et al., 2013. The goal of this study was to explore the epigenetics (DNA methylation) of Nicoyan individuals as compared to non-Nicoyans, considering that DNA methylation is closely related to biological aging.

Study Design: 95 samples + 1 technical replicate, randomly distributed across 12 arrays ("chips", as each chip has 12 samples) run in one batch.

All R objects and files are located:

1. Kobor Server: big_data/lmcewen/Rehkopf (locally saved)
2. Stanford Server: please email [email protected] or [email protected] to request access

LINKS TO CODE:

Preprocessing & Normalization

DNAm Age Analysis

Cell Type Analysis

DMRcate Analysis

DNAm Variability Analysis

GLINT Analysis

Pyro verification