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--- dag3 [2019/10/11 14:11]
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+++ dag3 [2022/05/13 09:41]
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 ===== Background =====
-There is increasing insight into the role of bacterial composition in the intestine and upon the occurrence of (chronic) diseases. Previous research in DAG1 ([[DEEP]]) demonstrated the relation of the microbiome and lipids, but also many other diseases and intrinsic and extrinsic factors.
+There is increasing insight into the role of bacterial composition in the intestine and upon the occurrence of (chronic) diseases. Previous research in DAG1 ([[DEEP]]) demonstrated the relation of the microbiome and lipids, but also many other diseases and intrinsic and extrinsic factors. The purpose of DAG3 was to gather additional data and biological samples from Lifelines participants to answer research questions such as:
+  * ‘What is the role of the microbiome in the occurrence of chronic diseases?’
+  * ‘What is the relation between  genetic variants, methylation, gene expression and metabolite levels?’
-The purpose of DAG3 is to gather additional data and biological samples from Lifelines participants to answer  research questions such as: ‘What is the role of the microbiome in the occurrence of chronic diseases?’, and ‘What is the relation between  genetic variants, methylation, gene expression and metabolite levels?’
+===== Subcohort =====
+A total of +-9500 participants were included in the DAG3 dataset:
+  * 700 were [[children]] aged 8-17 years
+  * 400 participants were also included in the ([[DEEP]]) dataset
+  * microbiome collection sites were more diverse
+  * ~9000 participants were genotyped in the [[UGLI]] project.
+Metagenomic sequencing of the Lifelines DAG3 samples was performed to assess taxonomy, strain diversity and functionality. Uniquely, not only are all individuals fully genotyped but glycerol aliquots of their microbiota are also stored to enable bacterial culture for further functional studies. Lifelines DAG3 will have the power to study host-microbe interactions and will also allow studies to move from association to causality ((Doestzada, M., Vich Vila, A., Zhernakova, A., Koonen, D. P. Y., Weersma, R. K., Touw, D. J., ... Fu, J.
+(2018). Pharmacomicrobiomics: A novel route towards personalized medicine? Protein & cell, 9(5).)).
+Besides the samples used to generate the microbiome data, questionnaires were also sent to participants to gather phenotypic data on GI health symptoms by means of [[Functional bowel symptoms (Rome III)|Rome III]] criteria questionnaire (Longstreth etal 2006) and the Bristol Stool Form Scale (O’Donnell etal 1990).
-===== Subcohort =====
+===== Study protocol =====
+Participants who were invited for assessment [[2A]] according to the regular Lifelines invitation process were asked to also participate in this study. In addition to the regular [[2A]] measurements, DAG3 participants underwent the following steps:
-Previously we collected additional biological samples from almost 1500 Lifelines participants to allow analysis of the microbiome, (epi)genome, transcriptome, metabolome and other biological levels. This sub-cohort Lifelines-DEEP allows for new insights into disease mechanisms and future potential therapeutic prevention methods. In DAG3 we increaesd the number of participants as well as the number of microbiome sample sites. We have collected these extra biological samples from nearly 10,000 Lifelines participants, from a wide age range (8 - 91 years). Metagenomic sequencing of the Lifelines DAG3 samples is underway to assess taxonomy, strain diversity and functionality. Uniquely, not only are all individuals fully genotyped but glycerol aliquots of their microbiota are also stored to enable bacterial culture for further functional studies. Lifelines DAG3 will have the power to study host-microbe interactions and will also allow studies to move from association to causality ((Doestzada, M., Vich Vila, A., Zhernakova, A., Koonen, D. P. Y., Weersma, R. K., Touw, D. J., ... Fu, J.
+[[2A Visit 1]]
-(2018). Pharmacomicrobiomics: A novel route towards personalized medicine? Protein & cell, 9(5).)).
+  * Signed DAG3 IC available
+  * Registration of participant
+  * 1 x throat and 1 x nose swab with amysmedium
+  * 1 x throat and 1 x nose e-nat-swab with presercation solution for DNA-isolation
+  * Swabs are stored in refrigerator at the visit location and processed/frozen within 48h
+  * Face-to-face instruction of stool collection
+  * Hand over written stool collection instructions and collection material
+[[2A Visit 2]]
+  * (Additional) puncture blood in PAXgene and registered, stored at room temperature at visit location
-Besides the samples used to generate the microbiome data, questionnaires were also sent to participants to gather phenotypic data on GI health symptoms by means of Rome III criteria questionnaire (Longstreth etal 2006) and the Bristol Stool Form Scale (O’Donnell etal 1990). A total of 9500 participants were included in the DAG3 dataset, of which 9300 are Dutch Caucasians and 700 are children aged 8-17 years. Approximately 400 participants were included in the ([[DEEP]]) dataset. ~9000 DAG3 participants will be included in the [[ugli|UGLI]] dataset.
+===== Stool collection =====
+Participants received a package with the following materials:
+  * 3 precoded cups to put stool in by means of a provided pipet
+  * 2 tubes with amysmedium and glycerol to put stool in with provided e-swabs, and two barcoded labels for the tubes
+  * a nontransparent bag to store the samples in the home freezer immediately after collection
+  * participants were instructed to fill in a questionnaire and stool diary in the week of stool collection
-The selection criteria were the following:
+===== Sample processing =====
-===== Variables =====
+  * Swabs containing amysmedium were processed into 3 aliquots, containing glycerol. The processing of swabs to aliquots was performed in a flow chamber to prevent contamination. Aliquots were be stored at -80C.
+  * Stool samples were taken in between 16:30 and 19:00 by hired personnel and transported to the Lifelines lab in cool boxes containing cooling elements. Collectors asked participants at home if they filled all three cups and two tubes and if not, the reason for an incomplete collection. At the Lifelines lab all cups and tubes are stored at -80C.
+  * blood samples were collected in a PAXgene tube, by means of a ‘butterfly needle’. An empty dummy tube preceded the Paxgene tube. The Paxgene tube was transported to the Lifelines lab, registered and stored in -80C freezers.
-The following variables were collected:
+===== Collected samples =====
+The following additional samples have been collected for DAG3 from +- 9500 participants:
+  * 9535 e-nat nose samples
+  * 9540 nose swab samples
+  * 28612 nose swab aliquots (glycerol)*
+  * 9425 throat e-nat samples
+  * 9421 throat swab samples
+  * 28245 throat swab aliquots (glycerol)*
+  * 16827 feces swab samples*
+  * 25376 feces cryo samples*
+  * 8931 paxgene samples
+  * 5400 complete diaries
+  * 2482 incomplete diaries (i.e. may miss one or more days)
+*Multiple samples from a single participant
+===== Papers based on DAG3 =====
+  * Gacesa, R et al. (2022) Environmental factors shaping the gut microbiome in a Dutch population. Nature 604, 732–739

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