The architecture of gene regulatory variation across multiple human tissues: the MuTHER study.

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Fältnamn	Indikatorer	Metadata
000		04335naa a2200697 4500
001		oai:DiVA.org:uu-275702
003		SwePub
008		160204s2011 \| \|\|\|\|\|\|\|\|\|\|\|000 \|\|eng\|
024	7	a https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-2757022 URI
024	7	a https://doi.org/10.1371/journal.pgen.10020032 DOI
040		a (SwePub)uu
041		a engb eng
042		9 SwePub
072	7	a ref2 swepub-contenttype
072	7	a art2 swepub-publicationtype
100	1	a Nica, Alexandra C4 aut
245	1 0	a The architecture of gene regulatory variation across multiple human tissues :b the MuTHER study.
264		c 2011-02-03
264	1	b Public Library of Science (PLoS),c 2011
338		a print2 rdacarrier
520		a While there have been studies exploring regulatory variation in one or more tissues, the complexity of tissue-specificity in multiple primary tissues is not yet well understood. We explore in depth the role of cis-regulatory variation in three human tissues: lymphoblastoid cell lines (LCL), skin, and fat. The samples (156 LCL, 160 skin, 166 fat) were derived simultaneously from a subset of well-phenotyped healthy female twins of the MuTHER resource. We discover an abundance of cis-eQTLs in each tissue similar to previous estimates (858 or 4.7% of genes). In addition, we apply factor analysis (FA) to remove effects of latent variables, thus more than doubling the number of our discoveries (1,822 eQTL genes). The unique study design (Matched Co-Twin Analysis--MCTA) permits immediate replication of eQTLs using co-twins (93%-98%) and validation of the considerable gain in eQTL discovery after FA correction. We highlight the challenges of comparing eQTLs between tissues. After verifying previous significance threshold-based estimates of tissue-specificity, we show their limitations given their dependency on statistical power. We propose that continuous estimates of the proportion of tissue-shared signals and direct comparison of the magnitude of effect on the fold change in expression are essential properties that jointly provide a biologically realistic view of tissue-specificity. Under this framework we demonstrate that 30% of eQTLs are shared among the three tissues studied, while another 29% appear exclusively tissue-specific. However, even among the shared eQTLs, a substantial proportion (10%-20%) have significant differences in the magnitude of fold change between genotypic classes across tissues. Our results underline the need to account for the complexity of eQTL tissue-specificity in an effort to assess consequences of such variants for complex traits.
650	7	a NATURVETENSKAPx Biologi0 (SwePub)1062 hsv//swe
650	7	a NATURAL SCIENCESx Biological Sciences0 (SwePub)1062 hsv//eng
700	1	a Parts, Leopold4 aut
700	1	a Glass, Daniel4 aut
700	1	a Nisbet, James4 aut
700	1	a Barrett, Amy4 aut
700	1	a Sekowska, Magdalena4 aut
700	1	a Travers, Mary4 aut
700	1	a Potter, Simon4 aut
700	1	a Grundberg, Elin4 aut
700	1	a Small, Kerrin4 aut
700	1	a Hedman, Asa K4 aut
700	1	a Bataille, Veronique4 aut
700	1	a Tzenova Bell, Jordana4 aut
700	1	a Surdulescu, Gabriela4 aut
700	1	a Dimas, Antigone S4 aut
700	1	a Ingle, Catherine4 aut
700	1	a Nestle, Frank O4 aut
700	1	a di Meglio, Paola4 aut
700	1	a Min, Josine L4 aut
700	1	a Wilk, Alicja4 aut
700	1	a Hammond, Christopher J4 aut
700	1	a Hassanali, Neelam4 aut
700	1	a Yang, Tsun-Po4 aut
700	1	a Montgomery, Stephen B4 aut
700	1	a O'Rahilly, Steve4 aut
700	1	a Lindgren, Cecilia M4 aut
700	1	a Zondervan, Krina T4 aut
700	1	a Soranzo, Nicole4 aut
700	1	a Barroso, Inês4 aut
700	1	a Durbin, Richard4 aut
700	1	a Ahmadi, Kourosh4 aut
700	1	a Deloukas, Panos4 aut
700	1	a McCarthy, Mark I4 aut
700	1	a Dermitzakis, Emmanouil T4 aut
700	1	a Spector, Timothy D4 aut
773	0	t PLOS Geneticsd : Public Library of Science (PLoS)g 7:2q 7:2x 1553-7390x 1553-7404
856	4	u https://doi.org/10.1371/journal.pgen.1002003
856	4 8	u https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-275702
856	4 8	u https://doi.org/10.1371/journal.pgen.1002003

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