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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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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Genomic DNA in Prokaryotes00:46

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
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Fast and accurate genomic analyses using genome graphs.

Goran Rakocevic1,2, Vladimir Semenyuk1,2, Wan-Ping Lee1

  • 1Seven Bridges Genomics, Inc, Cambridge, MA, USA.

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|January 16, 2019
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Summary
This summary is machine-generated.

This study introduces a graph reference genome for improved genomic analysis. This new approach enhances sequencing read alignment and variant calling accuracy across diverse human genomes.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • The standard human reference genome is a single consensus haplotype, limiting genomic analysis accuracy.
  • Accurate alignment of sequencing reads and variant calling are crucial for understanding human genetic variation.

Purpose of the Study:

  • To develop and evaluate a graph reference genome implementation for enhanced genomic analysis.
  • To assess the impact of a graph genome on read alignment, variant calling, and structural variation genotyping.

Main Methods:

  • Implemented a graph reference genome encompassing 2,800 diploid genomes, 12.6 million SNPs, and 4.0 million indels.
  • Developed a computational pipeline for whole-genome sequencing sample processing.
  • Evaluated read mapping sensitivity, variant calling recall and specificity, and structural variation genotyping.

Main Results:

  • The graph genome reference improved read mapping sensitivity and increased variant calling recall by 0.5% with unaffected specificity.
  • Accurate genotyping of structural variations was achieved within a unified framework.
  • Iterative augmentation of graph genomes demonstrated incremental gains in variant calling accuracy.

Conclusions:

  • Graph reference genomes significantly enhance the accuracy and scalability of genomic analyses.
  • This implementation represents a key advancement toward realizing the potential of graph genomes in personalized medicine and research.
  • The developed pipeline offers a practical solution for processing large-scale genomic datasets.