HipSci HumanExome BeadChip analysis-Healthy volunteers

The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies from healthy volunteers.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

5 Datasets 11 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00010000566	HipSci - Healthy Normals - Genotyping Array - May 2014		120
EGAD00010000768	Replication data for HipSci normal samples using both HumanCoreExome-12_v1 and HumanOmni2.5-8 BeadChips		-
EGAD00010000773	HipSci - Healthy Normals - Genotyping Array - November 2014	Illumina	580
EGAD00010001147	HipSci - Healthy Normals - Genotyping Array - September 2016	Illumina	613
EGAD00010001328	HipSci - Healthy Normals - Genotyping Array - July 2017	Illumina	-

Publications	Citations
A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data. Danecek P, McCarthy SA, HipSci Consortium, Durbin R. PLoS One 11: 2016 e0155014	26
Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response. Alasoo K, Rodrigues J, Mukhopadhyay S, Knights AJ, Mann AL, Kundu K, HIPSCI Consortium, Hale C, Dougan G, Gaffney DJ. Nat Genet 50: 2018 424-431	286
Genetic effects on promoter usage are highly context-specific and contribute to complex traits. Alasoo K, Rodrigues J, Danesh J, Freitag DF, Paul DS, Gaffney DJ. Elife 8: 2019 e41673	62
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation. Jerber J, Seaton DD, Cuomo ASE, Kumasaka N, Haldane J, Steer J, Patel M, Pearce D, Andersson M, Bonder MJ, Mountjoy E, Ghoussaini M, Lancaster MA, HipSci Consortium, Marioni JC, Merkle FT, Gaffney DJ, Stegle O. Nat Genet 53: 2021 304-312	245
Optimizing expression quantitative trait locus mapping workflows for single-cell studies. Cuomo ASE, Alvari G, Azodi CB, single-cell eQTLGen consortium, McCarthy DJ, Bonder MJ. Genome Biol 22: 2021 188	60
A compendium of uniformly processed human gene expression and splicing quantitative trait loci. Kerimov N, Hayhurst JD, Peikova K, Manning JR, Walter P, Kolberg L, Samoviča M, Sakthivel MP, Kuzmin I, Trevanion SJ, Burdett T, Jupp S, Parkinson H, Papatheodorou I, Yates AD, Zerbino DR, Alasoo K. Nat Genet 53: 2021 1290-1299	350
Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation. Merkle FT, Ghosh S, Genovese G, Handsaker RE, Kashin S, Meyer D, Karczewski KJ, O'Dushlaine C, Pato C, Pato M, MacArthur DG, McCarroll SA, Eggan K. Cell Stem Cell 29: 2022 472-486.e7	41
Feasibility and application of polygenic score analysis to the morphology of human-induced pluripotent stem cells. Coleman JRI. Mol Genet Genomics 297: 2022 1111-1122	3
Somatic mutations alter the differentiation outcomes of iPSC-derived neurons. Puigdevall P, Jerber J, Danecek P, Castellano S, Kilpinen H. Cell Genom 3: 2023 100280	16
Gene expression QTL mapping in stimulated iPSC-derived macrophages provides insights into common complex diseases. Panousis NI, El Garwany O, Knights A, Rop JC, Kumasaka N, Imaz M, Boquete Vilarino L, Tsingene A, Tokolyi A, Barnett A, Gomez C, Anderson CA, Gaffney DJ. Nat Commun 16: 2025 7204	2
Splicing QTL mapping in stimulated macrophages associates low-usage splice junctions with immune-mediated disease risk. El Garwany O, Panousis NI, Knights A, Kumasaka N, Imaz M, Vilarino LB, Tsingene A, Tokolyi A, Martin CC, Alegbe T, Krzak M, Raine T, Barnett A, Gomez C, Gaffney DJ, Anderson CA. Nat Commun 16: 2025 7205	1