scholarly journals LocalVar: a local variant collection manager to asynchronously detect synonyms, HGVS expression changes, and variant interpretation changes from ClinVar

2021 ◽  
Author(s):  
Michael Watkins ◽  
Wendy Kohlmann ◽  
Therese Berry ◽  
Neetha Sama ◽  
Cathryn Koptiuch ◽  
...  
Keyword(s):  
Clinical Significance ◽  
Genetic Variants ◽  
Sequence Variation ◽  
Variant Interpretation ◽  
Biological Sequence ◽  
Local Variant ◽  
New Variant ◽  
Complete Search ◽  
Variation Data ◽  
Public Repositories

While there are several public repositories of biological sequence variation data and associated annotations, there is little open-source tooling designed specifically for the upkeep of local collections of variant data. Many clinics curate and maintain such local collections and are burdened by frequent changes in the representation of those variants and evolving interpretations of clinical significance. A dictionary of genetic variants from the Huntsman Cancer Institute was analyzed over a period of two years and used to inform the development of LocalVar. This tool is institution-agnostic and uses publicly available ClinVar files to provide the following functionality: auto-complete search bar to pre-empt duplicate entries; single or bulk new variant record entry; auto-detection and merge suggestions for duplicate variant records; auto-detection and merge suggestions for variant records with HGVS expressions that are marked as synonyms in ClinVar; asynchronous suggestion of HGVS expression or variant interpretation updates; history tracking of additions, merges, updates, or other manual edits made to variant records; and the easy export of the collection (.csv), edit history (.json), or HGVS synonym bins (.json).

scholarly journals A systematic approach to assessing the clinical significance of genetic variants

2013 ◽  
Vol 84 (5) ◽  
pp. 453-463 ◽  
Author(s):  
H Duzkale ◽  
J Shen ◽  
H McLaughlin ◽  
A Alfares ◽  
MA Kelly ◽  
...  
Keyword(s):  
Clinical Significance ◽  
Genetic Variants ◽  
Systematic Approach

scholarly journals VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer

2011 ◽  
Vol 28 (4) ◽  
pp. 599-600 ◽  
Author(s):  
Jamie K. Teer ◽  
Eric D. Green ◽  
James C. Mullikin ◽  
Leslie G. Biesecker
Keyword(s):  
Sequence Variation ◽  
Desktop Computer ◽  
Variation Data ◽  
Scale Sequence

scholarly journals Tumor characteristics as an analytic tool for classifying genetic variants of uncertain clinical significance

2008 ◽  
Vol 29 (11) ◽  
pp. 1292-1303 ◽  
Author(s):  
Robert M.W. Hofstra ◽  
Amanda B. Spurdle ◽  
Diana Eccles ◽  
William D. Foulkes ◽  
Niels de Wind ◽  
...  
Keyword(s):  
Clinical Significance ◽  
Genetic Variants ◽  
Tumor Characteristics ◽  
Analytic Tool

scholarly journals Bibliome Variant Database: Automated Identification and Annotation of Genetic Variants in Primary Literature

2020 ◽  
Author(s):  
Samuel W. Baker ◽  
Arupa Ganguly
Keyword(s):  
Human Genome ◽  
Genetic Variants ◽  
Gene Symbol ◽  
Reference Database ◽  
Variant Interpretation ◽  
Automated Identification ◽  
Primary Literature ◽  
Time Required ◽  
Variant Database ◽  
Gene Symbols

ABSTRACTThe Bibliome Variant Database (BVdb) is a freely available reference database containing over 1 million human genetic variants mapped to the human genome that have been mined from primary literature. The BVdb is designed to facilitate variant interpretation in clinical and research contexts by reducing or eliminating the time required to search for literature describing a given variant. Users can search the database using gene symbols, HGVS variant nomenclature, genomic positions, or rsIDs. Each variant page lists references in the database that describe the variant, as well as the exact gene symbol and variant text description identified in each reference.AVAILABILITY AND IMPLEMENTATIONThe BVdb is freely available at http://bibliome.ai

scholarly journals Clinical and molecular relevance of genetic variants in the non-coding transcriptome of patients with cytogenetically normal acute myeloid leukemia

Haematologica ◽  
2021 ◽  
Author(s):  
Dimitrios Papaioannou ◽  
Hatice G. Ozer ◽  
Deedra Nicolet ◽  
Amog P. Urs ◽  
Tobias Herold ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Clinical Outcome ◽  
Rna Sequencing ◽  
Clinical Significance ◽  
Genetic Variants ◽  
Myeloid Leukemia ◽  
Sequencing Data ◽  
Younger Adults ◽  
Non Coding Rnas ◽  
Acute Myeloid

Expression levels of long non-coding RNAs (lncRNAs) have been shown to associate with clinical outcome of patients with cytogenetically normal acute myeloid leukemia (CN-AML). However, the frequency and clinical significance of genetic variants in the nucleotide sequences of lncRNAs in AML patients is unknown. Herein, we analyzed total RNA sequencing data of 377 younger adults (aged

scholarly journals CoV-Seq, a New Tool for SARS-CoV-2 Genome Analysis and Visualization: Development and Usability Study

10.2196/22299 ◽  
2020 ◽  
Vol 22 (10) ◽  
pp. e22299
Author(s):  
Boxiang Liu ◽  
Kaibo Liu ◽  
He Zhang ◽  
Liang Zhang ◽  
Yuchen Bian ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Ad Hoc ◽  
Web Server ◽  
Data Sets ◽  
Global Pandemic ◽  
Global Initiative ◽  
Public Repositories ◽  
Downstream Analysis ◽  
Programming Knowledge ◽  
The Web

Background COVID-19 became a global pandemic not long after its identification in late 2019. The genomes of SARS-CoV-2 are being rapidly sequenced and shared on public repositories. To keep up with these updates, scientists need to frequently refresh and reclean data sets, which is an ad hoc and labor-intensive process. Further, scientists with limited bioinformatics or programming knowledge may find it difficult to analyze SARS-CoV-2 genomes. Objective To address these challenges, we developed CoV-Seq, an integrated web server that enables simple and rapid analysis of SARS-CoV-2 genomes. Methods CoV-Seq is implemented in Python and JavaScript. The web server and source code URLs are provided in this article. Results Given a new sequence, CoV-Seq automatically predicts gene boundaries and identifies genetic variants, which are displayed in an interactive genome visualizer and are downloadable for further analysis. A command-line interface is available for high-throughput processing. In addition, we aggregated all publicly available SARS-CoV-2 sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID), National Center for Biotechnology Information (NCBI), European Nucleotide Archive (ENA), and China National GeneBank (CNGB), and extracted genetic variants from these sequences for download and downstream analysis. The CoV-Seq database is updated weekly. Conclusions We have developed CoV-Seq, an integrated web service for fast and easy analysis of custom SARS-CoV-2 sequences. The web server provides an interactive module for the analysis of custom sequences and a weekly updated database of genetic variants of all publicly accessible SARS-CoV-2 sequences. We believe CoV-Seq will help improve our understanding of the genetic underpinnings of COVID-19.

scholarly journals Pathogenicity Reclassification of Genetic Variants Related to Early-Onset Breast Cancer among Buryat Women

2021 ◽  
Author(s):  
Polina Gervas ◽  
Aleksey Molokov ◽  
Artem Kiselev ◽  
Aleksei Zarubin ◽  
Evgeny Yumov ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Genetic Variants ◽  
Early Onset ◽  
Rare Variants ◽  
Early Onset Breast Cancer ◽  
Post Translational Modification ◽  
Molecular Tests ◽  
Asian Populations ◽  
New Variant ◽  
Brca1 Brca2

Abstract Background: Germline alterations in ATM, BRCA1, BRCA2, and other genes are responsible for early-onset breast cancer. However, up to 20% of molecular tests report genetic variant of unknown significance (VUS) or novel variants that have never been previously described and their clinical significance are unknown. An existing open access databases (ClinVar, BIC, and ENIGMA and other) play an important role in the interpretation of VUS, but in Asian populations the interpretation of VUS is still difficult due to restricted data. This study aimed to reclassify the genetic variants by using the ActiveDriveDB database that annotates variants through the lens of sites of post-translational modifications.Methods: Our study included young Buryat BC patients, anthropologically belonging to the Central Asia. Genomic DNA was used to prepare libraries. NGS sequencing was performed on a NextSeq 500 System. Results: We re-examined 135 rare variants (41 VUS, 25 conflicting, 64 benign and 5 new variants). We identified 10 out of 135 (7.4%) mutations that affected the sites of post-translational modification in proteins. Of 135 rare mutations, 1 benign variant was reclassified as network-rewiring - motif loss mutation, 3 VUS and 1 new variant were reclassified as distal PTM- mutations, 2 new and 1 benign variant were classified as proximal PTM- mutations and 1 benign and 1 conflicting variant were classified as direct PTM- mutations.Conclusions: For the first time, 7.4% (10 out of 135) of mutations that affected the sites of post-translational modification in proteins were identified among Buryat women with early-onset breast cancer.

Sign in / Sign up

Export Citation Format

Share Document