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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Genome-wide Association Studies-GWAS01:11

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
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Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Genomics02:02

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genetic Variation01:25

Genetic Variation

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Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles,...
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Genome Copying Errors02:46

Genome Copying Errors

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DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
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Related Experiment Video

Updated: Jul 12, 2025

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

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Sync for Genes Phase 5: Computable artifacts for sharing dynamically annotated FHIR-formatted genomic variants.

Robert Dolin1, Bret S E Heale2, Rohan Gupta3

  • 1Elimu Informatics El Cerrito California USA.

Learning Health Systems
|October 20, 2023
PubMed
Summary

Dynamically annotating genetic variants ensures clinicians have up-to-date information for decision-making. This approach standardizes genomic knowledge sharing for improved clinical decision support (CDS).

Keywords:
EHRclinical decision supportgenomics

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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

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Area of Science:

  • Genomics
  • Bioinformatics
  • Clinical Decision Support

Background:

  • Variant annotation is crucial for interpreting next-generation sequencing data.
  • Genomic knowledge rapidly evolves, making static annotations outdated.
  • Clinical decision-making requires current and accurate variant context.

Purpose of the Study:

  • To standardize the sharing of dynamically annotated variants.
  • To enable clinical decision support (CDS) applications to provide real-time variant annotations.
  • To develop computable biomedical knowledge artifacts for on-demand annotation.

Main Methods:

  • Utilized Health Level 7 Fast Healthcare Interoperability Resources (FHIR) Genomics and Global Alliance for Genomics and Health (GA4GH) Variant Annotation (VA) standards.
  • Developed a CDS pipeline for dynamic variant annotation using ClinVar, CIViC, and PharmGKB as knowledge sources.
  • Encoded knowledge sources according to the GA4GH VA specification and served annotations via FHIR Genomics Operations.

Main Results:

  • Created a GitHub repository with source code, a Swagger interface for interaction, and a database for synthetic/anonymized data.
  • Demonstrated that bioinformatics strategies enhance automated annotation fidelity.
  • Showcased a feasible ecosystem for standardized genomic knowledge bases and dynamic CDS.

Conclusions:

  • Variant annotation complexity varies by variant type.
  • Standardized genomic knowledge bases and dynamic CDS applications can provide real-time, up-to-date clinical decision support.
  • This approach facilitates an ecosystem for leveraging current genomic knowledge at the point of care.