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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 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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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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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.
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Next-generation Sequencing03:00

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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A population is composed of members of the same species that simultaneously live and interact in the same area. When individuals in a population breed, they pass down their genes to their offspring. Many of these genes are polymorphic, meaning that they occur in multiple variants. Such variations of a gene are referred to as alleles. The collective set of all the alleles within a population is known as the gene pool.
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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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ATAV: a comprehensive platform for population-scale genomic analyses.

Zhong Ren1, Gundula Povysil2, Joseph A Hostyk2

  • 1Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA. zhong.ren@hotmail.com.

BMC Bioinformatics
|March 24, 2021
PubMed
Summary
This summary is machine-generated.

The ATAV platform streamlines large-scale sequencing analysis by centralizing variant data, reducing costs and enabling real-time discovery of disease-associated variants and genes. It provides public access to a vast database for enhanced genetic research.

Keywords:
Association testingDiagnosticGene discoveryGenome analysisWeb platform

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Area of Science:

  • Genomics and Bioinformatics
  • Computational Biology
  • Medical Genetics

Background:

  • Traditional joint-calling for sequencing studies becomes prohibitive with continually added samples or reused controls.
  • Efficiently managing and analyzing large-scale variant data is a significant challenge in genomic research.

Purpose of the Study:

  • To present ATAV, an analysis platform designed for large-scale whole-exome and whole-genome sequencing projects.
  • To provide a scalable and reproducible framework for variant analysis and disease gene discovery.

Main Methods:

  • ATAV centralizes variant and coverage data in a database for efficient querying.
  • The platform supports diagnostic analyses for trios and singletons, and rare-variant collapsing for complex diseases.
  • Runtime logs ensure reproducibility, and a modular framework allows extensibility.

Main Results:

  • ATAV has enabled the discovery of disease-genes in datasets exceeding 20,000 samples.
  • Analyses have been performed on over 110,000 individuals, demonstrating scalability.
  • A web-based data browser provides real-time access to variant data for over 40,000 samples.

Conclusions:

  • ATAV offers public access to one of the largest variant databases from a tertiary care center.
  • The freely available code facilitates deployment by other research groups to build custom platforms and databases.