MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation

Hermida, Leandro; Schaad, Olivier; Demougin, Philippe; Descombes, Patrick; Primig, Michael

doi:10.1186/1471-2105-7-190

Cited by 15 publications

(5 citation statements)

References 48 publications

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“…Quality control filtering of variants was based on coverage, strand bias, mapping quality, and base quality custom Perl scripts were used to annotate variants as previously described [13]. Multiple metrics for prediction of potential functional consequences of variants were applied: CADD [14], SIFT [15] and PolyPhen2 [16], Genomic Evolutionary Rate Profiling (GERP) [17,18], and PhyloP [19]. Filtering of variants included five criteria: 1.…”

Section: Methodsmentioning

confidence: 99%

Successful diagnosis of HIBCH deficiency from exome sequencing and positive retrospective analysis of newborn screening cards in two siblings presenting with Leigh's disease

Stiles

Ferdinandusse

Besse

et al. 2015

Molecular Genetics and Metabolism

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Purpose 3-hydroxyisobutryl-CoA hydrolase (HIBCH) deficiency is a rare disorder of valine metabolism. We present a family with the oldest reported subjects with HIBCH deficiency and provide support that HIBCH deficiency should be included in the differential for elevated hydroxy-C4-carnitine in newborn screening (NBS). Methods Whole exome sequencing (WES) was performed on one affected sibling. HIBCH enzymatic activity was measured in patient fibroblasts. Acylcarnitines were measured by electrospray ionization tandem mass spectrometry (ESI-MS/MS). Disease incidence was estimated using a cohort of 61,434 individuals. Results Two siblings presented with infantile-onset, progressive neurodegenerative disease. WES identified a novel homozygous variant in HIBCH c.196C>T; p.Arg66Trp. HIBCH enzymatic activity was significantly reduced in patients’ fibroblasts. Acylcarnitine analysis showed elevated hydroxy-C4-carnitine in blood spots of both affected siblings, including in their NBS cards, while plasma acylcarnitines were normal. Estimates show HIBCH deficiency incidence as high as 1 in ~130,000 individuals. Conclusion We describe a novel family with HIBCH deficiency at the biochemical, enzymatic and molecular level. Disease incidence estimates indicate HIBCH deficiency may be under-diagnosed. This together with the elevated hydroxy-C4-carnitine found in the retrospective analysis of our patient’s NBS cards suggests that this disorder could be screened by NBS programs and should be added to the differential diagnosis for elevated hydroxy-C4-carnitine which is already measured in most NBS programs using MS/MS.

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Section: Methodsmentioning

confidence: 99%

Successful diagnosis of HIBCH deficiency from exome sequencing and positive retrospective analysis of newborn screening cards in two siblings presenting with Leigh's disease

Stiles

Ferdinandusse

Besse

et al. 2015

Molecular Genetics and Metabolism

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show abstract

“…However, they do not integrate their data in a framework that allows scalable and detailed querying (e.g., quickly extracting all water table and temperature data from multiple sites into a single table, for scaling of water table-temperature relationships from individual sites to a broader geographical range). The field of bioinformatics is further along in this regard: for molecular meta-omic data, numerous databases (e.g., MIGS/MIMS, MIMAS, IMG/M, GeneLab) (Hermida et al, 2006;Field et al, 2008;Gattiker et al, 2009;Chen et al, 2019;Ray et al, 2019) and integrative data management platforms (e.g., KBase, MOD-CO, ODG, GeNNet, BioKNO, MGV, OMMS, mixOmics) (Sujansky, 2001;Symons & Nieselt, 2011;Perez-Arriaga et al, 2015;Yoon, Kim & Kim, 2017;Costa et al, 2017;Rohart et al, 2017;Guhlin et al, 2017;Manzoni et al, 2018;Arkin et al, 2018;Brandizi et al, 2018;Rambold et al, 2019) have been developed, and often include standardization of sample metadata to enable efficient data integration. Notable among these are KBase (https://kbase.us/) (Arkin et al, 2018), which provides "apps" through which users can process their data in a framework that tracks processing steps ("provenance") in an accessible format, and MOD-CO (Rambold et al, 2019), a bioinformatics data processing tool that includes a conceptual schema and data model to track metadata and workflows.…”

Section: Introductionmentioning

confidence: 99%

The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research

Bolduc¹,

Hodgkins²,

Varner³

et al. 2020

PeerJ

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Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project’s interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team’s modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB’s expandability and flexible architecture allow it to serve as an example ecosystems database.

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“…However, they do not integrate their data in a framework that allows scalable and detailed querying (for example, quickly extracting all water table and temperature data from multiple sites into a single table, for scaling of water table-temperature relationships from individual sites to a broader geographical range). The field of bioinformatics is further along in this regard: for molecular meta-omic data, numerous databases (e.g., MIGS/MIMS, MIMAS, IMG/M, GeneLab) (Hermida et al, 2006;Field et al, 2008;Gattiker et al, 2009;Chen et al, 2019;Ray et al, 2019) and integrative data management platforms (e.g., KBase, MOD-CO, ODG, GeNNet, BioKNO, MGV, OMMS, mixOmics) (Sujansky, 2001;Symons & Nieselt, 2011;Perez-Arriaga et al, 2015;Yoon, Kim & Kim, 2017;Costa et al, 2017;Rohart et al, 2017;Guhlin et al, 2017;Manzoni et al, 2018;Arkin et al, 2018;Brandizi et al, 2018;Rambold et al, 2019) have been developed, and often include standardization of sample metadata to enable efficient data integration. Notable among these are KBase (https://kbase.us/) (Arkin et al, 2018), which provides "apps" through which users can process their data in a framework that tracks processing steps ("provenance") in an accessible format, and MOD-CO (Rambold et al, PeerJ reviewing PDF | (2019:10:42335:1:1:NEW 22 May 2020)…”

Section: Introductionmentioning

confidence: 99%

Peer Review #1 of "The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research (v0.2)"

2020

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Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in 'speaking' to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10-year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project's interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team's modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB's expandability and flexible architecture allow it to serve as an example

show abstract

MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation

Cited by 15 publications

References 48 publications

Successful diagnosis of HIBCH deficiency from exome sequencing and positive retrospective analysis of newborn screening cards in two siblings presenting with Leigh's disease

Successful diagnosis of HIBCH deficiency from exome sequencing and positive retrospective analysis of newborn screening cards in two siblings presenting with Leigh's disease

The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research

Peer Review #1 of "The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research (v0.2)"

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