references.bib

@article{cardona2014,
    author = {Cardona, Alexia AND Pagani, Luca AND Antao, Tiago AND Lawson, Daniel J. AND Eichstaedt, Christina A. AND Yngvadottir, Bryndis AND Shwe, Ma Than Than AND Wee, Joseph AND Romero, Irene Gallego AND Raj, Srilakshmi AND Metspalu, Mait AND Villems, Richard AND Willerslev, Eske AND Tyler-Smith, Chris AND Malyarchuk, Boris A. AND Derenko, Miroslava V. AND Kivisild, Toomas},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    title = {Genome-Wide Analysis of Cold Adaptation in Indigenous Siberian Populations},
    year = {2014},
    month = {05},
    volume = {9},
    url = {https://doi.org/10.1371/journal.pone.0098076},
    pages = {1-11},
    abstract = {Following the dispersal out of Africa, where hominins evolved in warm environments for millions of years, our species has colonised different climate zones of the world, including high latitudes and cold environments. The extent to which human habitation in (sub-)Arctic regions has been enabled by cultural buffering, short-term acclimatization and genetic adaptations is not clearly understood. Present day indigenous populations of Siberia show a number of phenotypic features, such as increased basal metabolic rate, low serum lipid levels and increased blood pressure that have been attributed to adaptation to the extreme cold climate. In this study we introduce a dataset of 200 individuals from ten indigenous Siberian populations that were genotyped for 730,525 SNPs across the genome to identify genes and non-coding regions that have undergone unusually rapid allele frequency and long-range haplotype homozygosity change in the recent past. At least three distinct population clusters could be identified among the Siberians, each of which showed a number of unique signals of selection. A region on chromosome 11 (chr11:66–69 Mb) contained the largest amount of clustering of significant signals and also the strongest signals in all the different selection tests performed. We present a list of candidate cold adaption genes that showed significant signals of positive selection with our strongest signals associated with genes involved in energy regulation and metabolism (CPT1A, LRP5, THADA) and vascular smooth muscle contraction (PRKG1). By employing a new method that paints phased chromosome chunks by their ancestry we distinguish local Siberian-specific long-range haplotype signals from those introduced by admixture.},
    number = {5},
    doi = {10.1371/journal.pone.0098076}
}

@article {cardona2019,
	author = {Cardona, Alexia and Day, Felix R. and Perry, John R.B. and Loh, Marie and Chu, Audrey Y. and Lehne, Benjamin and Paul, Dirk S. and Lotta, Luca A. and Stewart, Isobel D. and Kerrison, Nicola D. and Scott, Robert A. and Khaw, Kay-Tee and Forouhi, Nita G. and Langenberg, Claudia and Liu, Chunyu and Mendelson, Michael M. and Levy, Daniel and Beck, Stephan and Leslie, R. David and Dupuis, Jos{\'e}e and Meigs, James B. and Kooner, Jaspal S and Pihlajam{\"a}ki, Jussi and Vaag, Allan and Perfilyev, Alexander and Ling, Charlotte and Hivert, Marie-France and Chambers, John C and Wareham, Nicholas J. and Ong, Ken K.},
	title = {Epigenome-Wide Association Study of Incident Type 2 Diabetes in a British Population: EPIC-Norfolk Study},
	elocation-id = {db180290},
	year = {2019},
	doi = {10.2337/db18-0290},
	publisher = {American Diabetes Association},
	abstract = {Epigenetic changes may contribute substantially to risks of diseases of ageing. Previous studies reported seven methylation variable positions (MVPs) robustly associated with incident type 2 diabetes mellitus (T2DM). However, their causal roles in T2DM are unclear. In an incident T2DM case-cohort study nested within the population-based EPIC-Norfolk cohort, we used whole blood DNA collected at baseline, up to 11 years before T2DM onset to investigate the role of methylation in the aetiology of T2DM. We identified 15 novel MVPs with robust associations with incident T2DM, and robustly confirmed three MVPs identified previously (near to TXNIP, ABCG1 and SREBF1). All 18 MVPs showed directionally consistent associations with incident and prevalent T2DM in independent studies. Further conditional analyses suggested that the identified epigenetic signals appear related to T2DM via glucose and obesity-related pathways acting before the collection of baseline samples. We integrated genome-wide genetic data to identify methylation-associated quantitative trait loci robustly associated with 16 of the 18 MVPs, and found one MVP, cg00574958 at CPT1A, with a possible direct causal role on T2DM. None of the implicated genes was previously highlighted by genetic association studies, suggesting that DNA methylation studies may reveal novel biological mechanisms involved in tissue responses to glycemia.},
	issn = {0012-1797},
	URL = {https://diabetes.diabetesjournals.org/content/early/2019/09/09/db18-0290},
	eprint = {https://diabetes.diabetesjournals.org/content/early/2019/09/09/db18-0290.full.pdf},
	journal = {Diabetes}
}