Analysis of Biomarkers in the Northern Ireland Cohort of Longitudinal study of Ageing (NICOLA)

Research output: Contribution to conferenceAbstract

Abstract

On behalf of the Northern Ireland COhort of Longitudinal Ageing collaborative group:The NICOLA study was formally launched as Northern Ireland’s largest ever public health research project in 2014. This collaborative initiative has finished fieldwork for WAVE 1, collating detailed information on 8,500 local residents over the age of 50 years, with follow-up interviews planned every two years and health assessments every four years. There is a particular focus on multi-omic biomarkers in this relatively early-stage, yet rich resource where additional health and social care information is linked by a unique identifier for each citizen.NICOLA created a powerful local biorepository including thirty-four biochemistry-based biomarkers linked to genetic-epigenetic-transcriptomic data. DNA was extracted from buffy coats, while RNA was extracted from PAXgene tubes for all individuals. Genotype data (n=551,839 markers) was generated using Illumina’s Infinium CoreExome-24 BeadChips for high-throughput screening on an iScan. Initial quality control was performed in GenomeStudio (v2) with association analysis conducted for a range of phenotypes using PLINK and R. SNPs are being imputed to the Haplotype Reference Consortium. Illumina’s Infinium MethylationEPIC BeadChips were employed to quantitatively interrogate >850,000 methylation sites across the genome for 2,000 samples. Data was analysed using GenomeStudio (v2011) with the distribution of methylation levels visualised; concordance rates was excellent (r>0.99), and standard quality control was employed prior to further data analysis. mEPIC data is comparable with Sequenom’s EpiTYPER results with a low false positive rate where Δβ≥0.2. RNA-seq data was generated using Ion Torrent’s S5XL™ system with both the whole transcriptome and AmpliSeq™ transcriptome (~21,000 targets) approaches; the AmpliSeq protocol has minimal hands on time for 10 ng of input RNA. Quantitative RNA-seq data was analysed using Torrent Suite and Partek Genomics Suite software, with expression compared to that from microarray and qPCR platforms.This robust approach for creating a biomarker repository and developing pipelines for analysis is feasible for larger multi-centre studies.
Original languageEnglish
Publication statusPublished - 2017
EventNIA Biomarker Network Meeting - Chicago, United States
Duration: 26 Apr 2017 → …

Conference

ConferenceNIA Biomarker Network Meeting
CountryUnited States
CityChicago
Period26/04/2017 → …

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    McKnight, A. (2017). Analysis of Biomarkers in the Northern Ireland Cohort of Longitudinal study of Ageing (NICOLA). Abstract from NIA Biomarker Network Meeting, Chicago, United States.