Biology subjects

Fedotov, A.

Publications and source records attributed to Fedotov, A..

3 recordsLinked to original sources

bioRxiv2021

Genomic Considerations for FHIR; eMERGE Implementation Lessons

Structured representation of clinical genetic results is necessary for advancing precision medicine. The Electronic Medical Records and Genomics (eMERGE) Networks Phase III program initially used a commercially developed XML message format for standardized and structured representation of genetic results for electronic health record (EHR) integration. In a desire to move towards a standard representation, the network created a new standardized format based upon Health Level Seven Fast Healthcare Interoperability Resources (HL7 FHIR), to represent clinical genomics results. These new standards improve the utility of HL7 FHIR as an international healthcare interoperability standard for management of genetic data from patients. This work advances the establishment of standards that are being designed for broad adoption in the current health information technology landscape.

genomics↗

bioRxiv2018

Atlas-CNV: a validated approach to call Single-Exon CNVs in the eMERGESeq gene panel

PurposeTo provide a validated method to confidently identify exon-containing copy number variants (CNVs), with a low false discovery rate (FDR), in targeted sequencing data from a clinical laboratory with particular focus on single-exon CNVs.\n\nMethodsDNA sequence coverage data are normalized within each sample and subsequently exonic CNVs are identified in a batch of samples (midpool), when the target log2 ratio of the sample to the batch median exceeds defined thresholds. The quality of exonic CNV calls is assessed by C-scores (Z-like scores) using thresholds derived from gold standard samples and simulation studies. We integrate an ExonQC threshold to lower FDR and compare performance with alternate software (VisCap).\n\nResultsThirteen CNVs were used as a truth set to validate Atlas-CNV and compared with VisCap. We demonstrated FDR reduction in validation, simulation and 10,926 eMERGESeq samples without sensitivity loss. Sixty-four multi-exon and 29 single-exon CNVs with high C-scores were assessed by MLPA.\n\nConclusionsAtlas-CNV is validated as a method to identify exonic CNVs in targeted sequencing data generated in the clinical laboratory. The ExonQC and C-score assignment can reduce FDR (identification of targets with high variance) and improve calling accuracy of single-exon CNVs respectively. We proposed guidelines and criteria to identify high confidence single-exon CNVs.

genomics↗

bioRxiv2018

Water motion as a transformation mechanism of algal communities structure in Lake Baikal

The diversity of algal communities of phytoplankton and meio-and macrophytes was investigated in Lake Baikal. Fragments of Spirogyra thallomes were recorded in the phytoplankton community of Southern Baikal, which had never been recorded before in its composition. It was also established that the structure of benthic algal communities changed in comparison with that in 2000 due to intense development of filamentous algae, particularly Spirogyra. Its lowest biomass was recorded in the surf zone and wave breaking, whereas the highest biomass was registered in the area of weakened effect of waves on the bottom. The cover percent of the bottom with filamentous algae in different areas of the coastal zone varied from 0 to 100%. Hydraulic characteristics of Spirogyra were the same as those of planktonic diatoms. The circulation currents and wave effect on the bottom favoured transfer and distribution of Spirogyra from the location of its intense development into the coastal area of Lake Baikal.

ecology↗