Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SudanMitoSeq: Sudanese mitochondrial sequencing

ABSTRACT: In various contexts, mitochondrial function or dysfunction can be linked to mitochondrial genome variations. The use of mitochondrial genetics thus promises personalized diagnostics and treatments. In order to devise specific precision medicine approaches based on mitochondrial genetic variation and to test them within clinical studies, control data is indispensable. Such control data needs to comprehensively cover genetic variation commonly observed and thus expected. In the context of this study we assessed whether current, world-wide mitochondrial data sufficiently represents the region of North and East Africa, that is, whether current reference data is ready for precision medicine in this region. Towards this, we sequenced mitochondrial genomes of 159 Sudanese individuals provided as part of this EGA study and analyzed them together with various other, publicly available data concerning mitochondrial variation. For details, please refer to the publication.

PROVIDER: EGAS00001005669 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Impact of Exercise on Mitochondria in Cancer Patients.

Project description:The aim is to investigate the impact of prostate and colorectal cancer on mitochondrial quantity and quality along with muscle mass and function and whether this can be modified through the use of a home-based short-term exercise training program. The investigators aim to recruit participants awaiting curative surgery for colorectal and prostate cancer and to assess the variation in baseline mitochondrial activity between them. Participants from both cancer types will then carry out a 4 week home exercise program, this will be randomly allocated to either resistance-based or high-intensity interval training based. Participants will then be re-assessed on the day of their planned surgical procedure to assess the changes effected by the training program. The investigators hypothesize that there will be variation in mitochondrial activity linked to muscle mass across the two cancer types and that home-based exercise programs have the ability to improve mitochondrial activity along with muscle mass.

| 2352291 | ecrin-mdr-crc

Intergrative Multi-Omics of Asian Pregnant Mother

Project description:As Asians are underrepresented across many omics databases limiting the potential of precision medicine of the global population. It is thus important for multi-omics derived quantitative trait loci (QTLs) to fill the knowledge gap of complex traits in the Asian ancestry. Integrating omics data from genomics and epigenomics (including DNA methylation and RNA-seq from blood), we developed iMOMdb, an open-acesss database to enhance disease prediction models and precision medicine outcomes in Asian pregnant women.

2022-10-04 | GSE182409 | GEO

DNA-seq of mitochondrial DNA from mouse heart that is both heart SOD2 knockout and deficient for mitochondrial DNA repair

Project description:To study whether increase in mitochondrial oxidative stress (SOD2 removal) and decrease in mitochondrial DNA repair (Ogg1 dMTS) results into increase in mitochondrial DNA mutation load. Oxidative stress has been suggested to induce mutations in mtDNA. To verify this, we extracted and sequenced (Illumina) mitochondrial DNA from heart Sod2 knockout animals that were also deficient for mitochondrial base-excision repair. The repair deficiency was induced by removing the genomic region encoding for the predicted mitochondrial targeting sequence from endogenous OGG1 (L2 to W23) called Ogg1 dMTS mice, thus excluding the protein from mitochondria. OGG1 is a DNA glycosylase that recognizes and repairs 8-oxo-dG damage from DNA. Oxidative stress can induce 8-oxo-dG lesions, thus we removed the mitochondrial matrix localized superoxide dismutase (SOD2) from these mice to increase the level of oxidative stress. 8-oxo-dG lesion can be mutagenic because some DNA repair polymerases are known to erroneously incorporate adenosine opposite to 8-oxo-dG during replication leading to GC>TA transversion mutations.

2018-07-13 | E-MTAB-6533 | biostudies-arrayexpress

Aberrant circTMEM45A Facilitates ESCC Inflammatory Progression by upregulating the NLRP3/Caspase1/IL-1β pathway through m5C-mediated NLRP3 Activation

Project description:Esophageal squamous cell carcinoma (ESCC) is a highly invasive, metastatic upper gastrointestinal malignancy. With the continuous deepening of personalized precision medicine, targeted therapy and immunotherapy have greatly improved the current treatment dilemma of esophageal cancer, but not all patients can benefit from them, and the overall efficacy is still poor. Circular RNA (circRNA) has become a key regulator of cancer development and progression and is expected to become a biomarker for the diagnosis and prediction of various cancers. Our goal is to find effective early diagnostic markers and therapeutic intervention targets by identifying the circRNA expression pattern of ESCC.

2025-04-02 | GSE293235 | GEO

Homo sapiens

Project description:ctDNA Panel sequencing for precision medicine

| PRJNA415870 | ENA

Precision Medicine for Inherited Retinal Degenerations

Project description:Precision Medicine for Inherited Retinal Degenerations

| PRJNA736120 | ENA

Precision Medicine for Inherited Retinal Degenerations

Project description:Precision Medicine for Inherited Retinal Degenerations

| PRJNA736121 | ENA

Using human genetic variation to improve red blood cell production from stem cells

Project description:Multipotent and pluripotent stem cells have significant potential as sources for cell replacement therapies. However, the low yield and quality of in vitro differentiated cells produced from various stem cell sources presents a significant limitation for therapeutic applications. The most mature use of these stem cell products is in the field of transfusion medicine, where stem cell-derived red blood cells (RBCs) have clinically-proven potential as alternative transfusion products. To improve upon current approaches for RBC production, we used insight from both common and rare human genetic variation of blood counts to focus on the SH2B3 gene. By producing loss of function of SH2B3 using targeted knockdown and genome editing approaches in human hematopoietic stem and progenitor cells, as well as human pluripotent stem cells, we are able to significantly improve both the quality and yield of in vitro derived RBCs. We illustrate how insight from human genetic variation can assist in the development of broadly applicable approaches that have tremendous value for regenerative medicine.

2015-10-22 | GSE67219 | GEO

Signaling network diversification during differentiation sensitizes AML cells to PAK and MEK inhibitors

Project description:A main requirement for precision medicine is the identification of patients that are more likely to respond to a particular drug. AML is a heterogeneous disease in which molecules associated to kinase signaling are frequently mutated. However, no kinase inhibitor has been approved for the treatment of this malignancy. Thus, patient stratification requires new molecular profiling techniques in addition of to the current sequencing strategies. We have used a multiomics approach that combines proteomics, phosphoproteomics, mass cytometry and DNA sequencing to classify primary AML cells derived from 36 patients. Comprehensive integrative analysis identified molecular signatures based on phosphopeptide abundance or surface marker expression that separate AML cases according to their differentiation status. Differentiated cells presented a particular pattern of protein phosphorylation, an enrichment in the activity of several kinases and a higher sensitivity to PAK, MEK and PKC/FLT3 inhibitors. In addition, mutations in proteins closely linked to kinase signaling were more frequent on differentiated cells. Interestingly the set of patients with differentiated cells as clustered by marker expression signatures showed an increased overall survival in our set of patients and in the TCGA database registered cohort. Thus, molecular differentiation signatures could be used as prognosis and drug response markers in order to implement the application of precision medicine in AML patients.

2020-04-15 | PXD005978 | Pride

RNA-seq of mouse heart that is both heart SOD2 knockout and deficient for mitochondrial DNA repair

Project description:To study whether increase in mitochondrial oxidative stress (SOD2 removal) and decrease in mitochondrial DNA repair (Ogg1 dMTS) results into increase in mutations in mitochondrial RNA (mtRNA). Oxidative stress has been suggested to induce mutations in mtDNA and as DNA is used as a template in transcription, mutations or 8-oxo-dG on DNA can induce GC>TA transversion accumulation in mtRNA. To verify this, we extracted and sequenced (Illumina) total RNA from heart Sod2 knockout mice alone and mice that were also deficient for mitochondrial base-excision repair. The repair deficiency was induced by removing the genomic region encoding for the predicted mitochondrial targeting sequence from endogenous OGG1 (L2 to W23) called Ogg1 dMTS mice, thus excluding the protein from mitochondria. OGG1 is a DNA glycosylase that recognizes and repairs 8-oxo-dG damage from DNA. Oxidative stress can induce 8-oxo-dG lesions, thus we removed the mitochondrial matrix localized superoxide dismutase (SOD2) from these mice to increase the level of oxidative stress. 8-oxo-dG lesion can be mutagenic because some DNA repair polymerases are known to erroneously incorporate adenosine opposite to 8-oxo-dG during replication leading to GC>TA transversion mutations.

2018-07-13 | E-MTAB-6534 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data