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Related Concept Videos

Genetic Variation01:25

Genetic Variation

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, which...
Human Genetics01:28

Human Genetics

Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...
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,...
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...
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
Principles of Pharmacogenetics: Types of Genetic Variants01:27

Principles of Pharmacogenetics: Types of Genetic Variants

The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...

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In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila
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VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts.

Makoto K Shimada1, Ryuzou Matsumoto, Yosuke Hayakawa

  • 1Integrated Database and Systems Biology Team, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Japan Biological Informatics Consortium, Hitachi Software Engineering Co., Ltd., Tokyo, Japan.

Nucleic Acids Research
|October 28, 2008
PubMed
Summary

VarySysDB integrates genetic polymorphism and transcriptome data, offering a unified resource to study how human genetic variations impact alternative splicing transcripts. This database aids research into gene expression and phenotype alterations.

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Genetic variation and alternative splicing generate protein diversity.
  • Existing genetic and transcriptome data are fragmented and stored separately.
  • A unified resource is needed to link genetic polymorphisms to transcript variations.

Purpose of the Study:

  • To develop VarySysDB, a database integrating human genetic polymorphism data with annotated mRNA transcripts.
  • To provide a resource for analyzing the effects of genetic variations on alternative splicing.
  • To facilitate research on how polymorphisms influence gene expression and phenotypes.

Main Methods:

  • Utilized 187,156 annotated mRNA transcripts from H-InvDB.
  • Integrated polymorphism data including SNPs, CNVs, STRs, and LD regions from dbSNP, DGV, and H-InvDB.
  • Developed search functionalities based on polymorphism features, functions, effects, and keywords.
  • Incorporated GBrowse and Sequence View for visualization of genomic relationships.

Main Results:

  • VarySysDB provides comprehensive information on human genetic polymorphisms for individual transcripts.
  • Enables comparative analysis of polymorphism effects across different transcripts.
  • Offers integrated views of polymorphisms, genome, transcripts, loci, and functional domains.

Conclusions:

  • VarySysDB serves as a valuable research tool for understanding the functional impact of genetic polymorphisms on transcriptomes.
  • Facilitates discovery of novel genotype-phenotype relationships.
  • The database is accessible at http://h-invitational.jp/varygene/.