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Related Concept Videos

Genomics02:02

Genomics

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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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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.
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Genetic Material01:20

Genetic Material

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Within the human body, a complex and detailed system of trillions of cells works in unison to sustain life. Each cell houses a nucleus, which contains 46 chromosomes divided into 23 pairs. Chromosomes are highly coiled structures made of the genetic material DNA. These chromosomes are essential carriers of genetic information, with half inherited from the mother through her egg and the other half from the father's sperm, combining to create the unique genetic makeup of an individual.
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Evolutionary Relationships through Genome Comparisons02:54

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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...
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Genetic Screens02:46

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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
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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.
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PGsim: A Comprehensive and Highly Customizable Personal Genome Simulator.

Liran Juan1, Yongtian Wang2, Jingyi Jiang1

  • 1School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.

Frontiers in Bioengineering and Biotechnology
|February 13, 2020
PubMed
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PGsim is a new genome simulator that creates realistic individual genomes using known data and customizable parameters. This tool aids research by overcoming the cost and privacy limitations of real genome sequencing.

Keywords:
computational toolsgenome simulationgenome variationpersonal genomevariant simulation

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Individual genome sequencing is costly and faces privacy/legal barriers.
  • Existing sequencing data provides deep human genome understanding but lacks simulation tools.
  • Simulating genomes with extreme conditions or rare variants is challenging.

Purpose of the Study:

  • To develop PGsim, a comprehensive and customizable individual genome simulator.
  • To leverage existing genomic knowledge for realistic genome simulation.
  • To provide a tool that overcomes limitations of real genome data.

Main Methods:

  • PGsim utilizes known data including variant allele frequencies, mutation probabilities, Ti/Tv ratios, Indel characteristics, structural variations, and pathogenic sites.
  • Users can control proportions of known, common, novel, and special variants in coding/non-coding regions.
  • The simulator employs large background databases without requiring SQL support and is easily adaptable to different variant databases.

Main Results:

  • PGsim generates realistic and reliable simulated genomes with controlled randomness.
  • Simulated variants exhibit accurate distribution, proportion, and population characteristics.
  • The tool is implemented as a standalone Perl script, ensuring cross-platform compatibility (MAC OS, Linux) without external dependencies.

Conclusions:

  • PGsim offers a flexible and powerful solution for simulating individual genomes.
  • The simulator enhances genomic research by providing a cost-effective and privacy-preserving alternative to real sequencing data.
  • PGsim is publicly available, promoting accessibility and further development in the field.