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• Diagnostic Exome Sequencing in Persons with Severe Intellectual Disability

  Intellectual disability is a common condition that carries lifelong severe medical and developmental consequences. The causes of intellectual disability (ID) remain unknown for the majority of patients due to the extensive clinical and genetic heterogeneity of this disorder. De novo mutations may play an important role in ID as most individuals with ID present as isolated cases without family history and/or clear syndromic indication. In addition, the involvement of such mutations have recently been demonstrated in a small number of individuals with ID. Here we evaluate the diagnostic potential and role of de novo mutations in a cohort of 100 patients with ID of unknown cause using family-based exome sequencing.

  Study EGAS00001000287

• Single-cell RNA sequence analysis of iPS cell-derived cardiomyocytes treated with S-RBD-sfGFP or GFP

  To determine the transcriptional response in human cardiomyocytes treated with SARS-CoV-2 spike receptor-binding domain (S-RBD-sfGFP), human cardiomyocytes differentiated from induced pluripotent stem cells (iPSC-CMs) were replated on day 21 after differentiation and treated with S-RBD-sfGFP or control-GFP for 48 hours on day 26-28. iPSC-CMs were dissociated and the single cell suspension was analyzed by single cell RNA-sequence.

  Study JGAS000620

• High-depth whole genome sequencing of paired ductal carcinoma in-situ (DCIS) and germline control samples from 26 individuals.

  Deposited here are whole-genome sequencing data for 26 paired breast cancer DCIS and matched-normal samples taken from the same individual. Average sequence coverage is 118x for DCIS samples and 41x for matched-normals. Matched-normal samples are from blood. Sequencing was performed on an Illumina HiseqX. Due to specific restrictions imposed by the ethical approval at sample collection, the use of the germline data is restricted to filtering of somatic mutation calls only and cannot be used outside this purpose.They are a part of a broader project that uses high-depth WGS to investigate the somatic mutation genomic landscape of DCIS in order to uncover biological insights into breast cancer progression as well as possible methods to stratify DCIS patients for individualised therapy or disease monitoring.

  Dataset EGAD50000002237

• RNA-Sequencing and Somatic Mutation Status of Adrenocortical Tumors: Novel Pathogenetic Insights

  To investigate the relationship between transcriptome profile and genetic background in a large series of adrenocortical tumors and to identify new potential pathogenetic mechanisms, we performed transcriptome profiling by high-throughput sequencing. We collected snap-frozen tissue from patients with adrenocortical tumors (n = 59) with known genetic background: 26 adenomas with Cushing syndrome, 17 adenomas with mild autonomous cortisol secretion, 9 endocrine-inactive adenomas, 7 adrenocortical carcinomas. Additionally, we sequenced 4 control samples.

  Study EGAS00001004533

• Breast Cancer Single-Cell RNA-Seq Dataset

  Single-cell RNA-Sequencing of 26 primary breast cancers from Wu et al. (2021) study. Data was generated using the Chromium controller (10X Genomics) and sequenced on the NextSeq 500 platform.

  Dataset EGAD00001007495

• Targeted capture ctDNA Library CRCQV34Run007-15

  Targeted capture ctDNA Library CRCQV34Run007-15 from patient PBC0001255, saliva sample

  Dataset EGAD00001010356

• Targeted capture ctDNA Library CRCQV42Run020-15

  Targeted capture ctDNA Library CRCQV42Run020-15 from patient PBC0001315, saliva sample

  Dataset EGAD00001010427

• Temporal Lobe Epilepsy and Retrotransposons

  Idiopathic (cryptogenic) epilepsy is a common, chronic group of brain disorders, affecting 1-2% of the US population, creating a significant public health problem because of the associated morbidity and mortality. One subtype of this complex group of brain disorders, temporal lobe epilepsy (TLE), is particularly burdensome, because a substantial fraction of patients do not respond to anticonvulsant medications. If the seizure focus can be localized by imaging and/or EEG, the TLE patient often elects to have a partial resection of the affected temporal lobe, because they have daily seizures, despite multiple pharmacotherapy regimens. Although genetic risk is thought to play a role in TLE, identification of common risk alleles has had limited success. In the past 5 years, data have accumulated to prove that neuronal embryogenesis is accompanied by activation of LINE1 (L1) retrotransposons (RTPs) to an unexpected degree, such that developing neurons may accumulate de novo L1 insertions. This results in a substantial mosaicism within populations of CNS neurons. While most of these somatic de novo L1s will have little effect on neuronal function (perhaps because they occur in gene deserts or in large introns or in genes not required for that cell's function), some may interfere with normal neuronal activity because they have inserted into a gene needed by that particular neuron for normal function. If one or more functional de novo L1s occur early in CNS development, all the daughter neurons that derive from that neuronal precursor will also carry the L1 insertion, perhaps leading to a dysfunctional population of neurons destined to become an epileptic focus. This study leveraged CNS tissue (obtained at craniotomy) from patients with intractable TLE, who have undergone a therapeutic partial resection of one temporal lobe. Using fluorescence-assisted cell sorting of temporal lobe neuronal nuclei, followed by high-throughput sequencing and alignment to the reference genome, detection of de novo L1s will be done. In this manner, it is expected that de-novo intragenic L1s, contributing to idiopathic TLE, will be discovered.

  Study phs002067

• DAC for study: "Circulating tumour DNA abundance and potential utility in de novo metastatic prostate cancer"

  Dac EGAC00001001099

• Targeted capture ctDNA Library CRCQV42Run046-15

  Targeted capture ctDNA Library CRCQV42Run046-15 from patient PBC0001183, plasma baseline sample

  Dataset EGAD00001010706

• Targeted capture ctDNA Library CRCQV42Run051-15

  Targeted capture ctDNA Library CRCQV42Run051-15 from patient PBC0001224, buffy coat sample

  Dataset EGAD00001010809

• Targeted capture ctDNA Library CRCQV42Run048-15

  Targeted capture ctDNA Library CRCQV42Run048-15 from patient PBC0001818, buffy coat sample

  Dataset EGAD00001010747

• Targeted capture ctDNA Library CRCQV42Run034-15

  Targeted capture ctDNA Library CRCQV42Run034-15 from patient PBC0004565, buffy coat sample

  Dataset EGAD00001010569

• Targeted capture ctDNA Library CRCQV42Run050-15

  Targeted capture ctDNA Library CRCQV42Run050-15 from patient PBC0001183, buffy coat sample

  Dataset EGAD00001010788

• Targeted capture ctDNA Library CRCQV34Run011-15

  Targeted capture ctDNA Library CRCQV34Run011-15 from patient PBC0002383, buffy coat sample

  Dataset EGAD00001010369

• Targeted capture ctDNA Library CRCQV42Run030-15

  Targeted capture ctDNA Library CRCQV42Run030-15 from patient PBC0003014, buffy coat sample

  Dataset EGAD00001010521

• Targeted capture ctDNA Library CRCQV42Run047-15

  Targeted capture ctDNA Library CRCQV42Run047-15 from patient PBC0002255, buffy coat sample

  Dataset EGAD00001010727

• Targeted capture ctDNA Library CRCQV42Run021-15

  Targeted capture ctDNA Library CRCQV42Run021-15 from patient PBC0001323, plasma baseline sample

  Dataset EGAD00001010437

• Targeted capture ctDNA Library CRCQV42Run049-15

  Targeted capture ctDNA Library CRCQV42Run049-15 from patient PBC0001782, buffy coat sample

  Dataset EGAD00001010768

• SweGen genetic variation from the Swedish Twin Registry

  The dataset contains files with single nucleotide variants in VCF format for a total of 942 DNA samples, selected to represent a cross-section of the Swedish population. The samples originate from the Swedish Twin Registry (STR) and have been obtained from different geographical regions. For each of the 942 individuals, DNA was extracted from a blood sample and subject to whole genome sequencing (WGS). The WGS was performed using 2x150 bp paired-end chemistry on Illumina HiSeq X Ten instrumentation at the SciLifeLab National Genomics Infrastructure (NGI) in Stockholm and Uppsala. FASTQ files generated by WGS were analyzed using the nf-core pipeline Sarek, which includes pre-processing, alignment to the human GRCh38 reference genome, and germline variant calling. All participants gave their written informed consent and the TwinGene study was approved by the regional ethics committee (Regionala Etikprövningsnämnden, Stockholm, dnr 2007-644-31, dnr 2014/521-32). Access to phenotypic information can be requested from the Swedish Twin Registry (http://ki.se/en/research/the-swedish-twin-registry).

  Dataset EGAD50000001323

• SweGen whole-genome sequencing from the Swedish Twin Registry

  The dataset contains whole-genome sequencing data (aligned read files) in CRAM-format (lossless compression) for a total of 942 DNA samples, selected to represent a cross-section of the Swedish population. The samples originate from the Swedish Twin Registry (STR) and have been obtained from different geographical regions. For each of the 942 individuals, DNA was extracted from a blood sample and subject to whole genome sequencing (WGS). The WGS was performed using 2x150 bp paired-end chemistry on Illumina HiSeq X Ten instrumentation at the SciLifeLab National Genomics Infrastructure (NGI) in Stockholm and Uppsala. FASTQ files generated by WGS were analyzed using the nf-core pipeline Sarek, which includes pre-processing, alignment to the human GRCh38 reference genome, and germline variant calling. All participants gave their written informed consent and the TwinGene study was approved by the regional ethics committee (Regionala Etikprövningsnämnden, Stockholm, dnr 2007-644-31, dnr 2014/521-32). Access to phenotypic information can be requested from the Swedish Twin Registry (http://ki.se/en/research/the-swedish-twin-registry).

  Dataset EGAD50000001326

• Targeted capture ctDNA Library CRCQV42Run044-15

  Targeted capture ctDNA Library CRCQV42Run044-15 from patient PBC0001818, plasma 3 month sample

  Dataset EGAD00001010665

• Targeted capture ctDNA Library CRCQV42Run017-15

  Targeted capture ctDNA Library CRCQV42Run017-15 from patient PBC0001673, plasma 24 month sample

  Dataset EGAD00001010407

• Targeted capture ctDNA Library CRCQV42Run039-15

  Targeted capture ctDNA Library CRCQV42Run039-15 from patient PBC0001432, plasma 6 month sample

  Dataset EGAD00001010610

• Targeted capture ctDNA Library CRCQV42Run043-15

  Targeted capture ctDNA Library CRCQV42Run043-15 from patient PBC0001470, plasma 3 month sample

  Dataset EGAD00001010644