@article {142,
	title = {Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics.},
	journal = {Nat Genet},
	volume = {53},
	year = {2021},
	month = {2021 03},
	pages = {313-321},
	abstract = {<p>Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental contexts. However, in their pluripotent state, the disease impact of genetic variants is less well known. Here, we integrate data from 1,367 human iPSC lines to comprehensively map common and rare regulatory variants in human pluripotent cells. Using this population-scale resource, we report hundreds of new colocalization events for human traits specific to iPSCs, and find increased power to identify rare regulatory variants compared with somatic tissues. Finally, we demonstrate how iPSCs enable the identification of causal genes for rare diseases.</p>},
	keywords = {Bardet-Biedl Syndrome, Calcium Channels, Cell Line, Cerebellar Ataxia, DNA Methylation, Gene Expression, Genetic Variation, Humans, Induced Pluripotent Stem Cells, Polymorphism, Single Nucleotide, Proteins, Quantitative Trait Loci, Rare Diseases, Regulatory Sequences, Nucleic Acid, Sequence Analysis, RNA, Whole Genome Sequencing},
	issn = {1546-1718},
	doi = {10.1038/s41588-021-00800-7},
	author = {Bonder, Marc Jan and Smail, Craig and Gloudemans, Michael J and Fr{\'e}sard, Laure and Jakubosky, David and D{\textquoteright}Antonio, Matteo and Li, Xin and Ferraro, Nicole M and Carcamo-Orive, Ivan and Mirauta, Bogdan and Seaton, Daniel D and Cai, Na and Vakili, Dara and Horta, Danilo and Zhao, Chunli and Zastrow, Diane B and Bonner, Devon E and Wheeler, Matthew T and Kilpinen, Helena and Knowles, Joshua W and Smith, Erin N and Frazer, Kelly A and Montgomery, Stephen B and Stegle, Oliver}
}
@article {120,
	title = {Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy.},
	journal = {Nat Genet},
	volume = {52},
	year = {2020},
	month = {2020 11},
	pages = {1145-1150},
	abstract = {<p>The influence of genetic background on driver mutations is well established; however, the mechanisms by which the background interacts with Mendelian loci remain unclear. We performed a systematic secondary-variant burden analysis of two independent cohorts of patients with Bardet-Biedl syndrome (BBS) with known recessive biallelic pathogenic mutations in one of 17 BBS genes for each individual. We observed a significant enrichment of trans-acting rare nonsynonymous secondary variants in patients with BBS compared with either population controls or a cohort of individuals with a non-BBS diagnosis and recessive variants in the same gene set. Strikingly, we found a significant over-representation of secondary alleles in chaperonin-encoding genes-a finding corroborated by the observation of epistatic interactions involving this complex in vivo. These data indicate a complex genetic architecture for BBS that informs the biological properties of disease modules and presents a model for secondary-variant burden analysis in recessive disorders.</p>},
	keywords = {Alleles, Bardet-Biedl Syndrome, Cohort Studies, Exome, Genetic Variation, Humans},
	issn = {1546-1718},
	doi = {10.1038/s41588-020-0707-1},
	author = {Kousi, Maria and S{\"o}ylemez, Onuralp and Ozanturk, Ayseg{\"u}l and Mourtzi, Niki and Akle, Sebastian and Jungreis, Irwin and Muller, Jean and Cassa, Christopher A and Brand, Harrison and Mokry, Jill Anne and Wolf, Maxim Y and Sadeghpour, Azita and McFadden, Kelsey and Lewis, Richard A and Talkowski, Michael E and Dollfus, H{\'e}l{\`e}ne and Kellis, Manolis and Davis, Erica E and Sunyaev, Shamil R and Katsanis, Nicholas}
}
