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Immunoseq : the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells

Morin Andréanne, Kwan Tony, Ge Bing, Letourneau Louis, Ban Maria, Tandre Karolina, Caron Maxime, Sandling Johanna K., Carlsson Jonas, Bourque Guillaume, Laprise Catherine, Montpetit Alexandre, Syvanen Ann-Christine, Ronnblom Lars, Sawcer Stephen J., Lathrop Mark G. et Pastinen Tomi. (2016). Immunoseq : the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells. BMC Medical Genomics, 9, (1), p. 1-12.

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URL officielle: http://dx.doi.org/doi:10.1186/s12920-016-0220-7

Résumé

Background: The observation that the genetic variants identified in genome-wide association studies (GWAS) frequently lie in non-coding regions of the genome that contain cis-regulatory elements suggests that altered gene expression underlies the development of many complex traits. In order to efficiently make a comprehensive assessment of the impact of non-coding genetic variation in immune related diseases we emulated the whole-exome sequencing paradigm and developed a custom capture panel for the known DNase I hypersensitive site (DHS) in immune cells - "Immunoseq". Results: We performed Immunoseq in 30 healthy individuals where we had existing transcriptome data from T cells. We identified a large number of novel non-coding variants in these samples. Relying on allele specific expression measurements, we also showed that our selected capture regions are enriched for functional variants that have an impact on differential allelic gene expression. The results from a replication set with 180 samples confirmed our observations. Conclusions: We show that Immunoseq is a powerful approach to detect novel rare variants in regulatory regions. We also demonstrate that these novel variants have a potential functional role in immune cells.

Type de document:Article publié dans une revue avec comité d'évaluation
ISSN:1755-8794
Volume:9
Numéro:1
Pages:p. 1-12
Version évaluée par les pairs:Oui
Date:2016
Sujets:Sciences de la santé > Sciences médicales > Biologie moléculaire
Sciences de la santé > Sciences médicales > Génétique
Sciences de la santé > Sciences médicales > Immunologie
Département, module, service et unité de recherche:Départements et modules > Département des sciences fondamentales
Mots-clés:rare variants, immune disease, gene expression, next-generation sequencing, capture
Informations complémentaires:Creative Commons Attribution 4.0
Déposé le:05 avr. 2017 21:05
Dernière modification:05 avr. 2017 21:05
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