Variation

BioCodeKb - Bioinformatics Knowledgebase

In biology, variation means any difference between cells, individual organisms, or groups of organisms of any species caused either by genetic differences (genotypic variation) or by the effect of environmental factors on the expression of the genetic potentials (phenotypic variation). Basically, the differences in characteristics between individuals of the same species is called variation.


Examples of genetic variation include eye color, blood type, camouflage in animals, and leaf modification in plants. Variation helps a species to survive, by causing individuals of a species to be genetically and physically different. Variation can be measured at the individual level, for example, differences between individual people, or at the population level, such as differences between populations living in different regions.


Some variation is passed on from parents to offspring, via genes, during reproduction. This is inherited variation.


Some variation is the result of differences in the surroundings, or what an individual does. This is called environmental variation.


Importance of Genetic Variation

  • Genetic variation is necessary in natural selection.

  • Major causes of variation include mutations, gene flow, and sexual reproduction.

  • DNA mutation causes genetic variation by altering the genes of individuals in a population.

  • Gene flow leads to genetic variation as new individuals with different gene combinations migrate into a population.

  • Sexual reproduction promotes variable gene combinations in a population leading to genetic variation.


Variation Viewer tools

  • The Variant Effect Predictor (VEP)

  • SNPs3D

  • Sorting Intolerant From Tolerant (SIFT)

  • SNPnexus

  • HaploReg

  • RSAT (Regulatory Sequence Analysis Tools)

  • SNP (Single Nucleotide Polymorphism)

  • TF (Transcription Factor)

  • TFBS (Transcription Factor Binding Site)

  • PSSM (Position Specific Scoring Matrix)

  • MPRA (Massively Parallel Reporter Assays)

  • LD (Linkage Disequilibrium)

  • rsID (Reference SNP Identifier)

  • SOIs (SNPs of Interest)

  • GWAS (Genome Wide Association Studies)

  • CRM (Cis-Regulatory Module)

  • eQTL

  • Expression Quantitative Trait Loci

  • ROC (Receiver Operating Characteristic)


Variation Databases

  • dbSNP is the NCBI database of single nucleotide polymorphisms (SNPs) and also includes information on insertions/deletions, microsatellites, and non-polymorphic variants.

  • The database of Genotypes and Phenotypes (dbGaP) archive data that resulted from the interaction of genotype and phenotype; e.g. genome-wide association studies, medical sequencing, molecular diagnostic assays.

  • ClinVar provides is an archive of reports of relationships among medically important variants and phenotypes.

  • ALFRED  is a database that provides allele frequencies and DNA polymorphisms.

  • Allele Frequency Net Immunogenetic gene frequencies in worldwide populations.

  • Findbase is an online resource documenting frequencies of pathogenic genetic variations leading to inherited disorders in various populations worldwide.

  • The Online Mendelian Inheritance in Man (OMIM) is a freely available compendium of human genes and genetic phenotypes.

  • The Genetic Testing Registry (GTR) provides a central location for voluntary submission of genetic test information by providers.

  • dbVar is NCBI's database of human genomic Structural Variation , large variants >50 bp including insertions, deletions, duplications, inversions, mobile elements, translocations, and complex variants.

  • The Ensembl Variation database stores areas of the genome that differ between individual genomes and, where available, associated disease and phenotype information.

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