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  • 1
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    Transcriptome genetics using second generation sequencing in a Caucasian population (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-03-12
    Description: Gene expression is an important phenotype that informs about genetic and environmental effects on cellular state. Many studies have previously identified genetic variants for gene expression phenotypes using custom and commercially available microarrays. Second generation sequencing technologies are now providing unprecedented access to the fine structure of the transcriptome. We have sequenced the mRNA fraction of the transcriptome in 60 extended HapMap individuals of European descent and have combined these data with genetic variants from the HapMap3 project. We have quantified exon abundance based on read depth and have also developed methods to quantify whole transcript abundance. We have found that approximately 10 million reads of sequencing can provide access to the same dynamic range as arrays with better quantification of alternative and highly abundant transcripts. Correlation with SNPs (small nucleotide polymorphisms) leads to a larger discovery of eQTLs (expression quantitative trait loci) than with arrays. We also detect a substantial number of variants that influence the structure of mature transcripts indicating variants responsible for alternative splicing. Finally, measures of allele-specific expression allowed the identification of rare eQTLs and allelic differences in transcript structure. This analysis shows that high throughput sequencing technologies reveal new properties of genetic effects on the transcriptome and allow the exploration of genetic effects in cellular processes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836232/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836232/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Montgomery, Stephen B -- Sammeth, Micha -- Gutierrez-Arcelus, Maria -- Lach, Radoslaw P -- Ingle, Catherine -- Nisbett, James -- Guigo, Roderic -- Dermitzakis, Emmanouil T -- 077046/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Apr 1;464(7289):773-7. doi: 10.1038/nature08903. Epub 2010 Mar 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, 1211 Switzerland. stephen.montgomery@unige.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20220756" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Alternative Splicing/genetics ; European Continental Ancestry Group/*genetics ; Exons/genetics ; Gene Expression Profiling/*methods ; Haplotypes/genetics ; Homozygote ; Humans ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci/genetics ; RNA, Messenger/*analysis/*genetics ; Sequence Analysis, DNA/*methods
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Transcriptome and genome sequencing uncovers functional variation in humans (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-09-17
    Description: Genome sequencing projects are discovering millions of genetic variants in humans, and interpretation of their functional effects is essential for understanding the genetic basis of variation in human traits. Here we report sequencing and deep analysis of messenger RNA and microRNA from lymphoblastoid cell lines of 462 individuals from the 1000 Genomes Project--the first uniformly processed high-throughput RNA-sequencing data from multiple human populations with high-quality genome sequences. We discover extremely widespread genetic variation affecting the regulation of most genes, with transcript structure and expression level variation being equally common but genetically largely independent. Our characterization of causal regulatory variation sheds light on the cellular mechanisms of regulatory and loss-of-function variation, and allows us to infer putative causal variants for dozens of disease-associated loci. Altogether, this study provides a deep understanding of the cellular mechanisms of transcriptome variation and of the landscape of functional variants in the human genome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3918453/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3918453/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lappalainen, Tuuli -- Sammeth, Michael -- Friedlander, Marc R -- 't Hoen, Peter A C -- Monlong, Jean -- Rivas, Manuel A -- Gonzalez-Porta, Mar -- Kurbatova, Natalja -- Griebel, Thasso -- Ferreira, Pedro G -- Barann, Matthias -- Wieland, Thomas -- Greger, Liliana -- van Iterson, Maarten -- Almlof, Jonas -- Ribeca, Paolo -- Pulyakhina, Irina -- Esser, Daniela -- Giger, Thomas -- Tikhonov, Andrew -- Sultan, Marc -- Bertier, Gabrielle -- MacArthur, Daniel G -- Lek, Monkol -- Lizano, Esther -- Buermans, Henk P J -- Padioleau, Ismael -- Schwarzmayr, Thomas -- Karlberg, Olof -- Ongen, Halit -- Kilpinen, Helena -- Beltran, Sergi -- Gut, Marta -- Kahlem, Katja -- Amstislavskiy, Vyacheslav -- Stegle, Oliver -- Pirinen, Matti -- Montgomery, Stephen B -- Donnelly, Peter -- McCarthy, Mark I -- Flicek, Paul -- Strom, Tim M -- Geuvadis Consortium -- Lehrach, Hans -- Schreiber, Stefan -- Sudbrak, Ralf -- Carracedo, Angel -- Antonarakis, Stylianos E -- Hasler, Robert -- Syvanen, Ann-Christine -- van Ommen, Gert-Jan -- Brazma, Alvis -- Meitinger, Thomas -- Rosenstiel, Philip -- Guigo, Roderic -- Gut, Ivo G -- Estivill, Xavier -- Dermitzakis, Emmanouil T -- 075491/Z/04/B/Wellcome Trust/United Kingdom -- 076113/Wellcome Trust/United Kingdom -- 081917/Wellcome Trust/United Kingdom -- 083270/Wellcome Trust/United Kingdom -- 085475/B/08/Z/Wellcome Trust/United Kingdom -- 085475/Z/08/Z/Wellcome Trust/United Kingdom -- 085532/Wellcome Trust/United Kingdom -- 090367/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 090532/Z/09/Z/Wellcome Trust/United Kingdom -- 095552/Wellcome Trust/United Kingdom -- 095552/Z/11/Z/Wellcome Trust/United Kingdom -- 098381/Wellcome Trust/United Kingdom -- G0601261/Medical Research Council/United Kingdom -- MH090941/MH/NIMH NIH HHS/ -- R01 GM104371/GM/NIGMS NIH HHS/ -- R01 MH090941/MH/NIMH NIH HHS/ -- WT085532/Wellcome Trust/United Kingdom -- England -- Nature. 2013 Sep 26;501(7468):506-11. doi: 10.1038/nature12531. Epub 2013 Sep 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland. tuuli.e.lappalainen@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24037378" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Cell Line, Transformed ; Exons/genetics ; Gene Expression Profiling ; Genetic Variation/*genetics ; Genome, Human/*genetics ; *High-Throughput Nucleotide Sequencing ; Humans ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci/genetics ; RNA, Messenger/analysis/genetics ; *Sequence Analysis, RNA ; Transcriptome/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
    Location Call Number Expected Availability
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