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--- dag2 [2019/10/11 11:51] – trynke
+++ dag2 [2025/02/05 13:49] (current) – external edit 127.0.0.1
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 ====== DAG2 ======
-DAG2 is one of Lifelines' [[additional assessments]] performed in collaboration with the UMCG [[https://www.systemsgenetics.nl/|department of genetics]] (see also: [[DEEP|DAG1]] and [[DAG3]]). DAG is the abbreviation of DArmGezondheid, or "Gastrointestinal health" in Dutch.
+DAG2 is one of [[start|Lifelines]]' [[additional assessments]] performed in collaboration with the UMCG [[https://www.systemsgenetics.nl/|department of genetics]] (see also: [[DEEP|DAG1]], [[DAG3]], [[DAG4]] and [[DAG5]]). DAG is the abbreviation of DArmGezondheid, or "Gastrointestinal health" in Dutch.\\
+DAG2 comprised of the collection and analyses of blood, breath, and faecal samples plus gastrointestinal questionnaire data following the same protocol as [[DEEP|DAG1]], in a small group of Lifelines participants that had previously been included in the [[http://www.nlgenome.nl/|GoNL]] project.
-DAG is the abbreviation of DArmGezondheid, which is Gastrointestinal health in Dutch. DAG2 is a in-depth data collection of ~100 Lifelines-GoNL participants including blood, exhaled air and faecal samples, and elicited responses to gastrointestinal health questionnaires by means of the Rome III criteria questionnaire (Longstreth etal 2006) and the Bristol Stool Form Scale (O’Donnell etal 1990). These data can be used for analyses of the genome, epigenome, transcriptome, microbiome, metabolome and other biological levels.
 =====Subcohort=====
-Approximately 100 Lifelines-GoNL participants where used for DAG2.
-====GoNL- The Genome of the Netherlands====
-In this consortium the whole genomes of 250 Dutch parent-offspring families are sequenced. Lifelines contributed samples of 55 trio’s (165 samples total) to the GoNL project.In total five biobanks contributed samples (Lifelines, Leiden Longevity Study, Netherlands Twin Registry, Rotterdam Study and Rucphen Study). Samples were sequenced on an Illumina HiSeq 2000 instrument (91-bp paired-end reads, 500-bp insert size), and reads were aligned on the UCSC human reference genome build 37 using Burrows-Wheeler Aligner (BWA) 0.5.9-r16 (Li and Durbin, 2010; Li and Durbin, 2009). Samples were also genotyped on the Illumina Immunochip as well as on at least one other genotyping chip. GoNL data can be requested through the GoNL website: www.nlgenome.nl.
-===== Sample and data analyses =====
-Sample and data analyses is similar to [[DEEP]] (a.k.a. DAG1) and [[DAG3]], except for the genetic data. Since whole genome sequences are available for the Lifelines-GoNL participants, SNP genotyping was not necessary for the DAG2 cohort.
+DAG2 included approximately 110 adult Lifelines participants from the 55 parent-parent-child trio’s whose blood samples (165 samples total) were donated to the [[http://www.nlgenome.nl/|GoNL]] project for [[https://en.wikipedia.org/wiki/Whole_genome_sequencing|whole genome sequencing]]((Francioli LC et al. (2014) Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nature Genetics 46(8): 818-825)).\\
+In this consortium project, a total of 250 Dutch parent-offspring families were sequenced. Five Dutch biobanks contributed samples: Lifelines, the [[http://www.leidenlangleven.nl/nl/home|Leiden Longevity Study]], the [[http://www.tweelingenregister.org/en/information/|Netherlands Twin Registry]], the [[http://www.ergo-onderzoek.nl/wp/|Rotterdam Study]] and the [[http://www.epib.nl/research/erf/erf_index.html|Rucphen Study]].\\