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Genomic medicine holds great promise for improving health care, but integrating searchable and actionable genetic data into electronic health records (EHRs) remains a challenge. Here we describe Neptune, a system for managing the interaction between a clinical laboratory and an EHR system during the clinical reporting process. We developed Neptune and applied it to two clinical sequencing projects that required report customization, variant reanalysis, and EHR integration. Neptune has been applied for the generation and delivery of over 15,000 clinical genomic reports. This work spans two clinical tests based on targeted gene panels that contain 68 and 153 genes respectively. These projects demanded customizable clinical reports that contained a variety of genetic data types including single-nucleotide variants (SNVs), copy-number variants (CNVs), pharmacogenomics, and polygenic risk scores. Two variant reanalysis activities were also supported, highlighting this important workflow. Methods are needed for delivering structured genetic data to EHRs. This need extends beyond developing data formats to providing infrastructure that manages the reporting process itself. Neptune was successfully applied on two high-throughput clinical sequencing projects to build and deliver clinical reports to EHR systems. The software is open source and available at https://gitlab.com/bcm-hgsc/neptune .

PURPOSE: The Mayo-Baylor RIGHT 10K Study enabled preemptive, sequence-based pharmacogenomics (PGx)-driven drug prescribing practices in routine clinical care within a large cohort. We also generated the tools and resources necessary for clinical PGx implementation and identified challenges to be overcome. Furthermore, we measured the frequency of both common genetic variation for which clinical guidelines already exist and that of rare variation that could be detected by DNA sequencing, rather than genotyping. METHODS: Targeted oligonucleotide-capture sequencing of 77 “pharmacogenes” was performed using DNA from 10,077 consented Mayo Clinic Biobank volunteers. The resulting predicted drug response related phenotypes for 13 genes, including CYP2D6 and HLA, affecting 21 drug-gene pairs, were deposited preemptively in the Mayo electronic health record (EHR). RESULTS: For the 13 pharmacogenes of interest, the genomes of 79% of participants carried clinically actionable variants in 3 or more genes and DNA sequencing identified an average of 3.3 additional conservatively predicted deleterious variants that would not have been evident using genotyping. CONCLUSIONS: Implementation of preemptive rather than reactive, sequence-based rather than genotype-based PGx prescribing revealed nearly universal patient applicability and required integrated institution-wide resources to fully realize individualized drug therapy and to demonstrate more efficient use of health care resources.

The advancement of precision medicine requires new methods to coordinate and deliver genetic data from heterogeneous sources to physicians and patients. The eMERGE III Network enrolled >25,000 participants from biobank and prospective cohorts of predominantly healthy individuals for clinical genetic testing to determine clinically actionable findings. The network developed protocols linking together the 11 participant collection sites and 2 clinical genetic testing laboratories. DNA capture panels targeting 109 genes were used for testing of DNA and sample collection, data generation, interpretation, reporting, delivery, and storage were each harmonized. A compliant and secure network enabled ongoing review and reconciliation of clinical interpretations, while maintaining communication and data sharing between clinicians and investigators. A total of 202 individuals had positive diagnostic findings relevant to the indication for testing and 1,294 had additional/secondary findings of medical significance deemed to be returnable, establishing data return rates for other testing endeavors. This study accomplished integration of structured genomic results into multiple electronic health record (EHR) systems, setting the stage for clinical decision support to enable genomic medicine. Further, the established processes enable different sequencing sites to harmonize technical and interpretive aspects of sequencing tests, a critical achievement toward global standardization of genomic testing. The eMERGE protocols and tools are available for widespread dissemination.

Mutational processes can cause driver mutations and are considered the primary cause of tumorigenesis. Cosmic signatures classify environmental or intrinsic mutational processes. Identification of signatures including DNA Damage Response (DDR) signatures enables research into the origin of cancer mutagenesis and into treatment optimization. Typically, Mutation signatures are identified using Whole Genome Sequencing or Whole Exome Sequencing. We demonstrate signature prediction of mutation signatures with two amplification-based targeted panels, which have a high sequencing success rate for FFPE samples. ~2000 FFPE Samples from a pan-solid tumor cohort were sequenced with either of two AmpliSeq panels (OCAplus and OTMLA), sizes 1.4 Mb and 1.7 Mb, to optimize a method to identify mutation signatures. First, we identified somatic SNVs by filtering out likely population germline mutations, and used these to construct the single base change substitution (SBS) matrix. The COSMIC cancer signatures use properties of the whole genome: we normalized to extend signature detection to targeted panel data. We adjusted the mutation frequencies observed using the ratio of trinucleotide counts in the genome and the ratio in the panel. Next, we measured the cosine similarity between the normalized sample and the COSMIC signatures. We selected the signatures with a strong match (>0.7) to the normalized sample. We further impute the signatures using a reduced candidate set, to assess the signature fit in the sample and reduce false positives. These steps provide the optimized signatures. We detected optimized signatures in 33% of the samples. A single signature was detected in 9% of the samples, 2 signatures in 6%, and >2 signatures in 17% of the samples. ~3% of samples showed at least one MMR signatures (SBS6, SBS14, SBS15, SBS20, SBS21, SBS26 and SBS44). In all 10 OCAPlus samples with MMR signatures, we also detected mutation(s) in an MMR gene. APOBEC signatures, SBS2 and SBS13, were observed in 3% of samples sequenced with OCAPlus panel and TML panel. We found 3 samples showing HRR signature SBS3. We successfully identified the putative causal DDR mutation in a number of samples. For example, of 62 samples with NTHL1 mutations, 60 had NTHL1 related signature SBS30. A sample with MUTYH mutations was assigned the SBS36 signature. We sequenced matched Tumor/Normal pairs; in most cases, the tumor sample showed a stronger mutational signature, with their corresponding normal sample showing either no signature or a weaker matching signature. We assessed reproducibility of the mutational signature. Looking at duplicate and triplicate replicates, we found that replicates consistently displayed the same mutational signatures. We show identification of mutation signatures using targeted panels designed for FFPE samples. Citation Format: Fiona Hyland, Ajithavalli Chellappan, Chintan Vora, Shilpa Nair, Jagannath Patro, Ritika Raj, Rushikesh Kanap. Prediction of DDR and other mutation signatures using targeted panels for FFPE samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2079.

Nowadays SCADA systems are used for Home automation, Greenhouse automation, E-agriculture etc. Basically these SCADA applications include Level Monitoring, Light & Climate Control, Security & Surveillance, control and manage spatially separated utility sites and Control of Shutters & Doors and so on. With the arrival of new hardware and software technologies here a system is proposed which can perform the similar SCADA applications at lower cost and lower maintenances. This paper proposes a viable solution for SCADA like applications which include Water level monitoring, Oil level monitoring & Displacement control by using a microcontroller board and .NET interfacing. This system can not only perform these industrial applications but also proposes fine web based solution to access all these acquired data and equipments. Here a remote based application is used which will allow the user to access the data/equipments in industries via internet, it also overcome the problem of weak encryption used by the SCADA. In future this system using .NET platform may replace these SCADA solutions.

The interrelationship of the helminthes have attracted attention from both phylogeneticists restricting their attention to morphological characters and those relying solely on molecular data. The phylogenic relationships exsisting among four monogenoideans belonging to genus Dactylogyroides found on two species of freshwater cypriniformes Puntius as P.sophore and P.chola in the River Gomti, India. These relationships were investigated via the use of the partial 28S ribosomal DNA (rDNA). characters for the differentiation of closely related genera or species group are usually selected based on practical purposes, taking no account of the evolutionary values of the characters. It is really difficult to establish a criterion for genus erection for the diversified monogenoideans. Analyses of 28S region in this study revealed that this gene is a very good molecular marker for inferring a relationship between closely related species. The aim of this paper is to describe the phylogenetic relationships between the monogenoidean parasites (genus Dactylogyroides) infesting genus Puntius, using DNA sequence data from nuclear ribosomal clusters.

Objective To observe their specificity, speciation and ecological equivalence by using previous and present records, from freshwater fish from Tanakpur to Sultanpur areas, during 2009 & 2010. Methods Data is gathered from the published records to compare it with the present records and entered into a computer database. The taxonomy of monogenoideans follows and those of fish follows. The worms were gently scrapped from the gills of fish and counted manually. They were studied mostly live, under a phase contrast microscope (Olympus CX 41 U-DA 4E 03365 Japan) or fixed in 3% formalin, after being relaxed in lukewarm water. Results These monogenoids have perfect ecological equivalence, as their macro habitat is geologically connected. They exhibit specificity at different taxonomic levels of the parasites and the hosts. Sympatric speciation of parasites and their host is evident in the present study. Conclusions The monogenoidean fauna, in this region, has its species integrity in the past sixty to sixty five years. From this important body of study, it seems likely that host specificity among monogenoids from the fresh water fish is more widely spread than previously thought. Seasonal variations, probable controlling factor of infection, determine the intensity.