GenoVault: A Cloud Based Genomics Repository

Abstract GenoVault is a cloud-based repository for handling Next Generation Sequencing (NGS) data. It is developed using OpenStack based private cloud with various services like keystone for authentication, cinder for block storage, neutron for networking and nova for managing compute instances for the Cloud. GenoVault uses object-based storage, which enables data to be stored as objects instead of files or blocks for faster retrieval from different distributed object nodes. Along with a web-based interface JavaFX-based desktop client has also been developed to meet the requirements of large file uploads ( > 5 GB) that is usually seen in NGS datasets. Users can store as many as one million files in their respective object based storage areas and the metadata provided by the user during file uploads is used for querying the database. GenoVault repository is designed taking into account future needs and hence can scale both vertically and horizontally without any need for modification in the design. Users have an option to make the data shareable to the public or restrict the access as private. Data security is ensured as every container is a separate entity in object-based storage architecture also supported by secured file transfer protocol during data upload and download. The data is uploaded by the user in their individual containers that include raw read files (fastq), processed alignment files (bam, sam, bed) and output of variation detection (vcf). GenoVault architecture allows verification of the data in terms of integrity and authentication before making it available to collaborators as per user permissions. GenoVault is useful for maintaining the organization wide NGS data generated by experiments in various labs which is not yet published and submitted to public repositories like NCBI. GenoVault also provides support to share NGS data among the collaborating institutions. GenoVault can thus manage vast volumes of NGS data on any OpenStack-based private cloud.

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GenoVault: a cloud based genomics repository

BioData Mining ◽

10.1186/s13040-021-00268-5 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Sankalp Jain ◽

Amit Saxena ◽

Suprit Hesarur ◽

Kirti Bhadhadhara ◽

Neeraj Bharti ◽

...

Keyword(s):

Private Cloud ◽

File Transfer ◽

Web Based ◽

The Public ◽

Private Data ◽

Object Based ◽

Block Storage ◽

Public Repositories ◽

Next Generation Sequencing Ngs ◽

Ngs Data

AbstractGenoVault is a cloud-based repository for handling Next Generation Sequencing (NGS) data. It is developed using OpenStack-based private cloud with various services like keystone for authentication, cinder for block storage, neutron for networking and nova for managing compute instances for the Cloud. GenoVault uses object-based storage, which enables data to be stored as objects instead of files or blocks for faster retrieval from different distributed object nodes. Along with a web-based interface, a JavaFX-based desktop client has also been developed to meet the requirements of large file uploads that are usually seen in NGS datasets. Users can store files in their respective object-based storage areas and the metadata provided by the user during file uploads is used for querying the database. GenoVault repository is designed taking into account future needs and hence can scale both vertically and horizontally using OpenStack-based cloud features. Users have an option to make the data shareable to the public or restrict the access as private. Data security is ensured as every container is a separate entity in object-based storage architecture which is also supported by Secure File Transfer Protocol (SFTP) for data upload and download. The data is uploaded by the user in individual containers that include raw read files (fastq), processed alignment files (bam, sam, bed) and the output of variation detection (vcf). GenoVault architecture allows verification of the data in terms of integrity and authentication before making it available to collaborators as per the user’s permissions. GenoVault is useful for maintaining the organization-wide NGS data generated in various labs which is not yet published and submitted to public repositories like NCBI. GenoVault also provides support to share NGS data among the collaborating institutions. GenoVault can thus manage vast volumes of NGS data on any OpenStack-based private cloud.

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TACITuS: transcriptomic data collector, integrator, and selector on big data platform

BMC Bioinformatics ◽

10.1186/s12859-019-2912-4 ◽

2019 ◽

Vol 20 (S9) ◽

Author(s):

Salvatore Alaimo ◽

Antonio Di Maria ◽

Dennis Shasha ◽

Alfredo Ferro ◽

Alfredo Pulvirenti

Keyword(s):

High Throughput ◽

Rna Seq ◽

Web Based ◽

Large Bandwidth ◽

Specific Analysis ◽

Galaxy Environment ◽

Public Repositories ◽

Microarray Datasets ◽

User Friendly ◽

Ngs Data

Abstract Background Several large public repositories of microarray datasets and RNA-seq data are available. Two prominent examples include ArrayExpress and NCBI GEO. Unfortunately, there is no easy way to import and manipulate data from such resources, because the data is stored in large files, requiring large bandwidth to download and special purpose data manipulation tools to extract subsets relevant for the specific analysis. Results TACITuS is a web-based system that supports rapid query access to high-throughput microarray and NGS repositories. The system is equipped with modules capable of managing large files, storing them in a cloud environment and extracting subsets of data in an easy and efficient way. The system also supports the ability to import data into Galaxy for further analysis. Conclusions TACITuS automates most of the pre-processing needed to analyze high-throughput microarray and NGS data from large publicly-available repositories. The system implements several modules to manage large files in an easy and efficient way. Furthermore, it is capable deal with Galaxy environment allowing users to analyze data through a user-friendly interface.

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PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation

Journal of Personalized Medicine ◽

10.3390/jpm11111230 ◽

2021 ◽

Vol 11 (11) ◽

pp. 1230

Author(s):

Jittima Piriyapongsa ◽

Chanathip Sukritha ◽

Pavita Kaewprommal ◽

Chalermpong Intarat ◽

Kwankom Triparn ◽

...

Keyword(s):

Human Leukocyte ◽

Web Based ◽

Leukocyte Antigen ◽

Genome Wide ◽

Immune Mediated ◽

Hla Genotypes ◽

One Stop ◽

Potential Risks ◽

Next Generation Sequencing Ngs ◽

Ngs Data

The increasing availability of next generation sequencing (NGS) for personal genomics could promote pharmacogenomics (PGx) discovery and application. However, current tools for analysis and interpretation of pharmacogenomic variants from NGS data are inadequate, as none offer comprehensive analytic functions in a simple, web-based platform. In addition, no tools exist to analyze human leukocyte antigen (HLA) genes for determining potential risks of immune-mediated adverse drug reaction (IM-ADR). We describe PharmVIP, a web-based PGx tool, for one-stop comprehensive analysis and interpretation of genome-wide variants obtained from NGS platforms. PharmVIP comprises three main interpretation modules covering analyses of pharmacogenes involved in pharmacokinetics, pharmacodynamics and IM-ADR. The Guideline module provides Clinical Pharmacogenetics Implementation Consortium (CPIC) drug guideline recommendations based on the translation of genotypic data in genes having guidelines. The HLA module reports HLA genotypes, potential adverse drug reactions, and the relevant drug guidelines. The Pharmacogenes module is employed for prioritizing variants according to variant effect on gene function. Detailed, customizable reports are provided as exportable files and as an interactive web version. PharmVIP is a new integrated NGS workflow for the PGx community to facilitate discovery and clinical application.

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DESIGN AND DEVELOPMENT OF POPULATION SERVICE ADMINISTRATION SYSTEM WITH PIECES METHOD IN KEMIRI VILLAGE HEAD OFFICE BANTEN

ADI Journal on Recent Innovation (AJRI) ◽

10.34306/ajri.v1i1.98 ◽

2019 ◽

Vol 1 (1) ◽

pp. 33-45

Author(s):

Rosdiana Rosdiana ◽

Padeli Padeli ◽

Revi Sajidah Sri Handayani ◽

Rifky Alfian

Keyword(s):

Human Error ◽

Unified Modeling Language ◽

Integrated System ◽

Web Based ◽

Administration System ◽

Unified Modeling ◽

The Public ◽

File Storage ◽

The Government ◽

The Village

The public service administration system at the government offices of the Kemiri village office in the Kemiri District currently does not have a computerized and integrated system. Because the system runs, residents who submit letters for administrative completeness, still use the Ms.Word / Ms.Excel application. of course has many weaknesses including human error, not neat in file storage, resulting in the lengthy process of searching and making a cover letter and required reports. The analytical method used in this study is to use PIECES (Performance, Informance, Economy, Control, Efficiency, Service) analysis, the design of the model uses UML (Unified Modeling Language). The results of this study are web-based letter information systems at the Office of the Village Chief of Kemiri that can accessed using a local computer browser. Thus the information letter needed by the Kemiri Village community and more effective and efficient in making the letter.

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DELIVERING KENTUCKY GEOLOGIC MAP INFORMATION TO THE PUBLIC: FIFTEEN YEARS OF AN EVOLVING WEB-BASED MAP SERVICE

10.1130/abs/2020am-357196 ◽

2020 ◽

Author(s):

Douglas C. Curl ◽

Keyword(s):

Web Based ◽

The Public ◽

Geologic Map ◽

Map Service

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Quantifying Media Effects, Its Content, and Role in Promoting Community Awareness of Chikungunya Epidemic in Bangladesh

Epidemiologia ◽

10.3390/epidemiologia2010008 ◽

2021 ◽

Vol 2 (1) ◽

pp. 84-94

Author(s):

Mst. Marium Begum ◽

Osman Ulvi ◽

Ajlina Karamehic-Muratovic ◽

Mallory R. Walsh ◽

Hasan Tarek ◽

...

Keyword(s):

Social Media ◽

Web Based ◽

Study Objective ◽

The Public ◽

Mainstream Media ◽

Related Information ◽

Vector Borne ◽

Media Outlet ◽

And Control

Background: Chikungunya is a vector-borne disease, mostly present in tropical and subtropical regions. The virus is spread by Ae. aegypti and Ae. albopictus mosquitos and symptoms include high fever to severe joint pain. Dhaka, Bangladesh, suffered an outbreak of chikungunya in 2017 lasting from April to September. With the goal of reducing cases, social media was at the forefront during this outbreak and educated the public about symptoms, prevention, and control of the virus. Popular web-based sources such as the top dailies in Bangladesh, local news outlets, and Facebook spread awareness of the outbreak. Objective: This study sought to investigate the role of social and mainstream media during the chikungunya epidemic. The study objective was to determine if social media can improve awareness of and practice associated with reducing cases of chikungunya. Methods: We collected chikungunya-related information circulated from the top nine television channels in Dhaka, Bangladesh, airing from 1st April–20th August 2017. All the news published in the top six dailies in Bangladesh were also compiled. The 50 most viewed chikungunya-related Bengali videos were manually coded and analyzed. Other social media outlets, such as Facebook, were also analyzed to determine the number of chikungunya-related posts and responses to these posts. Results: Our study showed that media outlets were associated with reducing cases of chikungunya, indicating that media has the potential to impact future outbreaks of these alpha viruses. Each media outlet (e.g., web, television) had an impact on the human response to an individual’s healthcare during this outbreak. Conclusions: To prevent future outbreaks of chikungunya, media outlets and social media can be used to educate the public regarding prevention strategies such as encouraging safe travel, removing stagnant water sources, and assisting with tracking cases globally to determine where future outbreaks may occur.

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Patient Derived Xenografts for Genome-Driven Therapy of Osteosarcoma

Cells ◽

10.3390/cells10020416 ◽

2021 ◽

Vol 10 (2) ◽

pp. 416

Author(s):

Lorena Landuzzi ◽

Maria Cristina Manara ◽

Pier-Luigi Lollini ◽

Katia Scotlandi

Keyword(s):

Clinical Trials ◽

Tumor Heterogeneity ◽

Functional Studies ◽

Ngs Data Analysis ◽

The Many ◽

Orthotopic Xenografts ◽

Next Generation Sequencing Ngs ◽

Ngs Data ◽

Generation Sequencing ◽

Somatic Copy Number Alterations

Osteosarcoma (OS) is a rare malignant primary tumor of mesenchymal origin affecting bone. It is characterized by a complex genotype, mainly due to the high frequency of chromothripsis, which leads to multiple somatic copy number alterations and structural rearrangements. Any effort to design genome-driven therapies must therefore consider such high inter- and intra-tumor heterogeneity. Therefore, many laboratories and international networks are developing and sharing OS patient-derived xenografts (OS PDX) to broaden the availability of models that reproduce OS complex clinical heterogeneity. OS PDXs, and new cell lines derived from PDXs, faithfully preserve tumor heterogeneity, genetic, and epigenetic features and are thus valuable tools for predicting drug responses. Here, we review recent achievements concerning OS PDXs, summarizing the methods used to obtain ectopic and orthotopic xenografts and to fully characterize these models. The availability of OS PDXs across the many international PDX platforms and their possible use in PDX clinical trials are also described. We recommend the coupling of next-generation sequencing (NGS) data analysis with functional studies in OS PDXs, as well as the setup of OS PDX clinical trials and co-clinical trials, to enhance the predictive power of experimental evidence and to accelerate the clinical translation of effective genome-guided therapies for this aggressive disease.

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Perceptions Regarding the Academic and Cognitive Performance of Individuals With Cleft Lip and/or Palate

The Cleft Palate-Craniofacial Journal ◽

10.1177/1055665621995308 ◽

2021 ◽

pp. 105566562199530

Author(s):

İlkem Kara ◽

Aydan Baştuğ Dumbak ◽

Maviş Emel Kulak Kayıkcı

Keyword(s):

Academic Performance ◽

Cognitive Performance ◽

General Public ◽

Cleft Lip ◽

Group Differences ◽

Web Based ◽

The Public ◽

Adverse Impacts ◽

Facial Difference ◽

Self Administered Questionnaire

Introduction: Factors such as teachers’ appropriate support and social interactions have an impact on the academic performance of children with cleft lip and/or palate (CL/P). This study was designed to investigate the perceptions of the teachers and the general public about the academic and cognitive performance of individuals with CL/P. Methods: This study was included 360 (male/female = 102/258) teachers and 640 (male/female = 259/381) participants that represent the general public. Anonymized web-based and paper-and-pencil self-administered questionnaire that included multiple-choice and yes/no questions were administered. Within-group differences and intergroup differences were analyzed in terms of academic and cognitive performance. Results: Most of the teachers and the general public indicated that the academic and cognitive performance of individuals with CL/P is the same as their unaffected peers. A significantly higher proportion of the teachers indicated that the academic performance of children with CL/P is the same as their unaffected peers than the general public. Conclusion: Considering that the general public’s attitudes and appropriate teacher support are crucial to prevent adverse impacts on the lives of individuals with CL/P, it is important to support teachers with the appropriate information and to encourage the public to recognize that everybody with a facial difference should be treated as an individual rather than a disability.

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HGG-21. GERMLINE MUTATIONS IN MSH2 GENE IN PEDIATRIC PATIENTS WITH CONGENITAL AND SPORADIC GLIOBLASTOMA

Neuro-Oncology ◽

10.1093/neuonc/noaa222.308 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii348-iii348

Author(s):

Maria Ejmont ◽

Małgorzata Rydzanicz ◽

Wiesława Grajkowska ◽

Marta Perek-Polnik ◽

Agnieszka Sowińska ◽

...

Keyword(s):

Germline Mutations ◽

Response To Therapy ◽

Msh2 Gene ◽

Illumina Hiseq ◽

Adult Type ◽

Targeted Next Generation Sequencing ◽

Pathogenic Variants ◽

New Treatment ◽

Next Generation Sequencing Ngs ◽

Ngs Data

Abstract INTRODUCTION Glioblastoma (GBM) remains one of the biggest therapeutic challenges in neuro-oncology. In spite of multimodal treatment approaches the prognosis of GBM is extremely poor, median survival is estimated about 12–16 months. Although GBM is one of the most common and malignant primary brain tumors, pediatric glioblastoma, including congenital is a very rare tumor, with an incidence of about 1.1–3.4 per million live births. Moreover, the mode of presentation, behavior, response to therapy and molecular background of pediatric glioblastomas differs from adult type of GBM. Until now, about ten patients with congenital glioblastoma have been described and in none of them germline markers were examined. Here we report two patients with GBM, one with congenital tumor with germline mutations in MSH2 gene. METHODS Targeted Next-Generation Sequencing (NGS) of the probands DNA extracted from leucocytes was performed using the TruSight One sequencing panel on an Illumina HiSeq 1500. Applied gene panel investigated the coding sequence and splice sites of 4813 genes associated with known disease phenotypes. The NGS data were analyzed using an in-house procedure. Identified variants were validated by Sanger sequencing. RESULTS NGS analysis of patients constitutional DNA revealed know, pathogenic variants c.940C>T and c.942 + 3A>T in MSH2 gene (NM_000251.3) associated with MMR-dependent hereditary cancer syndromes. CONCLUSION Molecular analysis are heavily needed for better understanding of pediatric GBM etiology and new treatment modality implementation. Identification of this oncogenic driver may provide insight into the pathogenesis of GBM, including congenital cases. Funded by National Science Centre, Poland (2016/23/B/NZ2/03064 and 2016/21/B/NZ2/01785).

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