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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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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Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Locus Reference Genomic sequences: an improved basis for describing human DNA variants.

Raymond Dalgleish1, Paul Flicek, Fiona Cunningham

  • 1Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK. raymond.dalgleish@le.ac.uk.

Genome Medicine
|April 20, 2010
PubMed
Summary

The Locus Reference Genomic (LRG) sequence format offers a stable, single-file solution for reporting gene variants. Widespread adoption of LRGs and Human Genome Variation Society nomenclature aims to reduce errors and improve communication in genetic research.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Accurate description of disease-causing gene variants is challenged by complex gene architecture and expression.
  • Current reference DNA sequence formats are insufficient for comprehensive gene variant reporting.

Purpose of the Study:

  • Introduce the Locus Reference Genomic (LRG) sequence format for standardized gene variant reporting.
  • Provide a stable, single-file record for reference DNA, transcript, and protein sequences.

Main Methods:

  • Developed the Locus Reference Genomic (LRG) sequence format, building on the NCBI RefSeqGene project.
  • Ensured the LRG format accommodates any organism and respects legacy numbering systems for exons and amino acids.
  • Established that LRGs will be created and maintained by the NCBI and EBI.

Main Results:

  • The LRG format provides a uniquely stable reference DNA sequence.
  • Includes all relevant transcript and protein sequences necessary for gene variant description.
  • Designed to be applicable to any organism.

Conclusions:

  • Widespread adoption of LRGs and consistent use of Human Genome Variation Society (HGVS) nomenclature are expected to decrease reporting errors.
  • Improved communication regarding gene variants affecting human health is anticipated.
  • The LRG format aims to enhance the accuracy and reliability of genetic variant reporting in scientific literature.