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RNA-Seq in Patients with Primordial Dwarfism

Transcriptome studies in patients with rare genetic diseases can potentially aid in the interpretation of likely causal genetic variation through identification of altered transcript abundance and/or structure. RNA-Seq is the most sensitive assay for both investigating transcript structure and abundance The primary aim of this pilot project is to investigate to what degree integrating exome-Seq and RNA-Seq data on the same individual can accelerate the identification of causal alleles for rare genetic diseases. There are two main strands to this: (i) identifying which variants discovered in exome-seq appear to be having a functional impact on transcripts, and (ii) identifying transcript outliers, especially among known causal genes, that may not necessarily have a causal variant identified from exome sequencing. The latter may identify the presence of causal variants that lie far from coding regions (e.g. the formation of cryptic splice sites deep within introns, or loss of long range regulatory elements), which can be confirmed with further targeted genetic assays. Just over 50% of all disease-causing variants recorded in the Human Gene Mutation Database (HGMD) affect transcript structure and abundance (e.g. nonsense SNVs, essential splice site SNVs, frameshifting indels, CNVs). This pilot project will study RNA from lymphoblastoid cell-lines from 12 patients with primordial dwarfism syndromes, for 10 of these samples we have previously generate exome data as part of our collaboration with the group of Prof Andrew Jackson. The two remaining samples are positive controls where the causal mutation is known, and is known to affect transcript structure and/or abundance. Primordial dwarfism is a prime candidate for these RNA-seq studies because all known causal mutations to date have key roles in DNA replication and thus, unsurprisingly, the products of the causal genes are typically ubiquitously expressed. Each RNA will be sequenced, with two technical replicates (independent RT-PCR and libraries) per sample, and each replicate run in 1/2 of a HiSeq lane using 100bp paired reads. Samples preparation was as follows :The cells were grown to confluency, then pellets frozen at -80. RNA samples were prepared using the Qiagen RNeasy kit, then nanodropped and analyzed using the bioanalyzer to determine concentration and purity. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see

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Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001000283 Transcriptome Analysis

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00000151624 bam 1.1 GB
EGAF00000151625 bam 1.0 GB
EGAF00000151626 bam 1.0 GB
EGAF00000151627 bam 997.8 MB
EGAF00000151628 bam 1.0 GB
EGAF00000151629 bam 1.1 GB
EGAF00000151630 bam 1.2 GB
EGAF00000151631 bam 1.2 GB
EGAF00000151632 bam 975.5 MB
EGAF00000151633 bam 1.2 GB
EGAF00000151634 bam 850.7 MB
EGAF00000151635 bam 1.2 GB
EGAF00000151636 bam 992.6 MB
EGAF00000151637 bam 931.7 MB
EGAF00000151638 bam 1.1 GB
EGAF00000151639 bam 1.0 GB
EGAF00000151640 bam 921.0 MB
EGAF00000151641 bam 923.4 MB
EGAF00000151642 bam 1.2 GB
EGAF00000151643 bam 1.0 GB
EGAF00000151644 bam 1.1 GB
EGAF00000151645 bam 1.1 GB
EGAF00000151646 bam 1.2 GB
EGAF00000151647 bam 1.2 GB
EGAF00000151648 bam 1.4 GB
EGAF00000151649 bam 1.4 GB
EGAF00000151650 bam 1.3 GB
EGAF00000151651 bam 1.3 GB
EGAF00000151652 bam 1.4 GB
EGAF00000151653 bam 1.4 GB
EGAF00000151654 bam 1.6 GB
EGAF00000151655 bam 1.5 GB
EGAF00000151656 bam 1.3 GB
EGAF00000151657 bam 1.5 GB
EGAF00000151658 bam 1.1 GB
EGAF00000151659 bam 1.5 GB
EGAF00000151660 bam 1.3 GB
EGAF00000151661 bam 1.2 GB
EGAF00000151662 bam 1.4 GB
EGAF00000151663 bam 1.3 GB
EGAF00000151664 bam 1.2 GB
EGAF00000151665 bam 1.2 GB
EGAF00000151666 bam 1.5 GB
EGAF00000151667 bam 1.4 GB
EGAF00000151668 bam 1.5 GB
EGAF00000151669 bam 1.4 GB
EGAF00000151670 bam 1.6 GB
EGAF00000151671 bam 1.6 GB
EGAF00000151672 bam 1.4 GB
EGAF00000151673 bam 1.3 GB
EGAF00000151674 bam 1.3 GB
EGAF00000151675 bam 1.3 GB
EGAF00000151676 bam 1.3 GB
EGAF00000151677 bam 1.4 GB
EGAF00000151678 bam 1.5 GB
EGAF00000151679 bam 1.5 GB
EGAF00000151680 bam 1.3 GB
EGAF00000151681 bam 1.5 GB
EGAF00000151682 bam 1.1 GB
EGAF00000151683 bam 1.5 GB
EGAF00000151684 bam 1.3 GB
EGAF00000151685 bam 1.2 GB
EGAF00000151686 bam 1.4 GB
EGAF00000151687 bam 1.3 GB
EGAF00000151688 bam 1.2 GB
EGAF00000151689 bam 1.2 GB
EGAF00000151690 bam 1.5 GB
EGAF00000151691 bam 1.3 GB
EGAF00000151692 bam 1.5 GB
EGAF00000151693 bam 1.4 GB
EGAF00000151694 bam 1.6 GB
EGAF00000151695 bam 1.6 GB
EGAF00000151696 bam 1.4 GB
EGAF00000151697 bam 1.4 GB
EGAF00000151698 bam 1.3 GB
EGAF00000151699 bam 1.3 GB
EGAF00000151700 bam 1.4 GB
EGAF00000151701 bam 1.4 GB
EGAF00000151702 bam 1.6 GB
EGAF00000151703 bam 1.5 GB
EGAF00000151704 bam 1.3 GB
EGAF00000151705 bam 1.5 GB
EGAF00000151706 bam 1.1 GB
EGAF00000151707 bam 1.5 GB
EGAF00000151708 bam 1.3 GB
EGAF00000151709 bam 1.2 GB
EGAF00000151710 bam 1.4 GB
EGAF00000151711 bam 1.3 GB
EGAF00000151712 bam 1.2 GB
EGAF00000151713 bam 1.2 GB
EGAF00000151714 bam 1.5 GB
EGAF00000151715 bam 1.4 GB
EGAF00000151716 bam 1.5 GB
EGAF00000151717 bam 1.4 GB
EGAF00000151718 bam 1.6 GB
EGAF00000151719 bam 1.6 GB
EGAF00000151720 bam 1.3 GB
EGAF00000151721 bam 1.3 GB
EGAF00000151722 bam 1.2 GB
EGAF00000151723 bam 1.2 GB
EGAF00000151724 bam 1.2 GB
EGAF00000151725 bam 1.3 GB
EGAF00000151726 bam 1.4 GB
EGAF00000151727 bam 1.4 GB
EGAF00000151728 bam 1.2 GB
EGAF00000151729 bam 1.4 GB
EGAF00000151730 bam 1.0 GB
EGAF00000151731 bam 1.4 GB
EGAF00000151732 bam 1.2 GB
EGAF00000151733 bam 1.1 GB
EGAF00000151734 bam 1.3 GB
EGAF00000151735 bam 1.2 GB
EGAF00000151736 bam 1.1 GB
EGAF00000151737 bam 1.1 GB
EGAF00000151738 bam 1.4 GB
EGAF00000151739 bam 1.3 GB
EGAF00000151740 bam 1.4 GB
EGAF00000151741 bam 1.3 GB
EGAF00000151742 bam 1.5 GB
EGAF00000151743 bam 1.5 GB
EGAF00000151744 bam 1.3 GB
EGAF00000151745 bam 1.3 GB
EGAF00000151746 bam 1.2 GB
EGAF00000151747 bam 1.2 GB
EGAF00000151748 bam 1.3 GB
EGAF00000151749 bam 1.3 GB
EGAF00000151750 bam 1.5 GB
EGAF00000151751 bam 1.4 GB
EGAF00000151752 bam 1.2 GB
EGAF00000151753 bam 1.4 GB
EGAF00000151754 bam 1.0 GB
EGAF00000151755 bam 1.4 GB
EGAF00000151756 bam 1.2 GB
EGAF00000151757 bam 1.1 GB
EGAF00000151758 bam 1.3 GB
EGAF00000151759 bam 1.2 GB
EGAF00000151760 bam 1.1 GB
EGAF00000151761 bam 1.1 GB
EGAF00000151762 bam 1.4 GB
EGAF00000151763 bam 1.3 GB
EGAF00000151764 bam 1.4 GB
EGAF00000151765 bam 1.3 GB
EGAF00000151766 bam 1.5 GB
EGAF00000151767 bam 1.5 GB
EGAF00000151768 bam 1.2 GB
EGAF00000151769 bam 1.2 GB
EGAF00000151770 bam 1.1 GB
EGAF00000151771 bam 1.1 GB
EGAF00000151772 bam 1.2 GB
EGAF00000151773 bam 1.2 GB
EGAF00000151774 bam 1.4 GB
EGAF00000151775 bam 1.3 GB
EGAF00000151776 bam 1.1 GB
EGAF00000151777 bam 1.3 GB
EGAF00000151778 bam 1.0 GB
EGAF00000151779 bam 1.3 GB
EGAF00000151780 bam 1.1 GB
EGAF00000151781 bam 1.1 GB
EGAF00000151782 bam 1.2 GB
EGAF00000151783 bam 1.1 GB
EGAF00000151784 bam 1.1 GB
EGAF00000151785 bam 1.0 GB
EGAF00000151786 bam 1.3 GB
EGAF00000151787 bam 1.2 GB
EGAF00000151788 bam 1.3 GB
EGAF00000151789 bam 1.2 GB
EGAF00000151790 bam 1.4 GB
EGAF00000151791 bam 1.4 GB
EGAF00000151792 bam 1.3 GB
EGAF00000151793 bam 1.2 GB
EGAF00000151794 bam 1.2 GB
EGAF00000151795 bam 1.2 GB
EGAF00000151796 bam 1.2 GB
EGAF00000151797 bam 1.3 GB
EGAF00000151798 bam 1.4 GB
EGAF00000151799 bam 1.4 GB
EGAF00000151800 bam 1.2 GB
EGAF00000151801 bam 1.4 GB
EGAF00000151802 bam 1.0 GB
EGAF00000151803 bam 1.4 GB
EGAF00000151804 bam 1.2 GB
EGAF00000151805 bam 1.1 GB
EGAF00000151806 bam 1.3 GB
EGAF00000151807 bam 1.2 GB
EGAF00000151808 bam 1.1 GB
EGAF00000151809 bam 1.1 GB
EGAF00000151810 bam 1.4 GB
EGAF00000151811 bam 1.2 GB
EGAF00000151812 bam 1.4 GB
EGAF00000151813 bam 1.3 GB
EGAF00000151814 bam 1.5 GB
EGAF00000151815 bam 1.5 GB
EGAF00000151816 bam 1.3 GB
EGAF00000151817 bam 1.2 GB
EGAF00000151818 bam 1.2 GB
EGAF00000151819 bam 1.2 GB
EGAF00000151820 bam 1.2 GB
EGAF00000151821 bam 1.3 GB
EGAF00000151822 bam 1.4 GB
EGAF00000151823 bam 1.4 GB
EGAF00000151824 bam 1.2 GB
EGAF00000151825 bam 1.4 GB
EGAF00000151826 bam 1.0 GB
EGAF00000151827 bam 1.3 GB
EGAF00000151828 bam 1.2 GB
EGAF00000151829 bam 1.1 GB
EGAF00000151830 bam 1.2 GB
EGAF00000151831 bam 1.2 GB
EGAF00000151832 bam 1.1 GB
EGAF00000151833 bam 1.1 GB
EGAF00000151834 bam 1.4 GB
EGAF00000151835 bam 1.2 GB
EGAF00000151836 bam 1.4 GB
EGAF00000151837 bam 1.3 GB
EGAF00000151838 bam 1.4 GB
EGAF00000151839 bam 1.4 GB
EGAF00000151840 bam 1.3 GB
EGAF00000151841 bam 1.2 GB
EGAF00000151842 bam 1.2 GB
EGAF00000151843 bam 1.2 GB
EGAF00000151844 bam 1.2 GB
EGAF00000151845 bam 1.3 GB
EGAF00000151846 bam 1.4 GB
EGAF00000151847 bam 1.4 GB
EGAF00000151848 bam 1.2 GB
EGAF00000151849 bam 1.4 GB
EGAF00000151850 bam 1.0 GB
EGAF00000151851 bam 1.4 GB
EGAF00000151852 bam 1.2 GB
EGAF00000151853 bam 1.1 GB
EGAF00000151854 bam 1.3 GB
EGAF00000151855 bam 1.2 GB
EGAF00000151856 bam 1.1 GB
EGAF00000151857 bam 1.1 GB
EGAF00000151858 bam 1.4 GB
EGAF00000151859 bam 1.2 GB
EGAF00000151860 bam 1.4 GB
EGAF00000151861 bam 1.3 GB
EGAF00000151862 bam 1.5 GB
EGAF00000151863 bam 1.5 GB
EGAF00000151864 bam 1.3 GB
EGAF00000151865 bam 1.2 GB
EGAF00000151866 bam 1.2 GB
EGAF00000151867 bam 1.2 GB
EGAF00000151868 bam 1.2 GB
EGAF00000151869 bam 1.3 GB
EGAF00000151870 bam 1.4 GB
EGAF00000151871 bam 1.4 GB
EGAF00000151872 bam 1.1 GB
EGAF00000151873 bam 1.4 GB
EGAF00000151874 bam 1.0 GB
EGAF00000151875 bam 1.3 GB
EGAF00000151876 bam 1.2 GB
EGAF00000151877 bam 1.1 GB
EGAF00000151878 bam 1.2 GB
EGAF00000151879 bam 1.2 GB
EGAF00000151880 bam 1.1 GB
EGAF00000151881 bam 1.1 GB
EGAF00000151882 bam 1.4 GB
EGAF00000151883 bam 1.2 GB
EGAF00000151884 bam 1.4 GB
EGAF00000151885 bam 1.3 GB
EGAF00000151886 bam 1.4 GB
EGAF00000151887 bam 1.4 GB
EGAF00000151888 bam 1.3 GB
EGAF00000151889 bam 1.3 GB
EGAF00000151890 bam 1.2 GB
EGAF00000151891 bam 1.2 GB
EGAF00000151892 bam 1.3 GB
EGAF00000151893 bam 1.3 GB
EGAF00000151894 bam 1.5 GB
EGAF00000151895 bam 1.4 GB
EGAF00000151896 bam 1.2 GB
EGAF00000151897 bam 1.4 GB
EGAF00000151898 bam 1.1 GB
EGAF00000151899 bam 1.4 GB
EGAF00000151900 bam 1.2 GB
EGAF00000151901 bam 1.2 GB
EGAF00000151902 bam 1.3 GB
EGAF00000151903 bam 1.3 GB
EGAF00000151904 bam 1.1 GB
EGAF00000151905 bam 1.1 GB
EGAF00000151906 bam 1.5 GB
EGAF00000151907 bam 1.3 GB
EGAF00000151908 bam 1.4 GB
EGAF00000151909 bam 1.3 GB
EGAF00000151910 bam 1.5 GB
EGAF00000151911 bam 1.5 GB
288 Files (367.5 GB)