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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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Genome Annotation and Assembly03:36

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Genomics

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In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
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Next generation sequence analysis and computational genomics using graphical pipeline workflows.

Federica Torri1, Ivo D Dinov, Alen Zamanyan

  • 1Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92617, USA ; Biomedical Informatics Research Network (BIRN), Information Sciences Institute, University of Southern California, Los Angeles, CA 90292, USA.

Genes
|November 10, 2012
PubMed
Summary
This summary is machine-generated.

Next-generation sequencing (NGS) analysis for complex genetic disorders, including psychiatric conditions, is challenging. The Graphical Pipeline for Computational Genomics (GPCG) offers a flexible solution for analyzing NGS data, from raw reads to variant annotation.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Whole-genome and exome sequencing are powerful for identifying genes in Mendelian disorders.
  • These methods are increasingly applied to complex disorders and population genetics.
  • Next-generation sequencing (NGS) technologies generate vast amounts of data requiring significant bioinformatics resources.

Purpose of the Study:

  • To review existing methods for processing NGS data.
  • To introduce the Graphical Pipeline for Computational Genomics (GPCG) as a computational resource for NGS data analysis.
  • To address the analytical bottleneck in publishing NGS studies, particularly in psychiatric genetics.

Main Methods:

  • The GPCG pipeline implements flexible workflows for NGS data analysis.
  • Includes steps for sequence alignment, quality control, and variant calling (SNPs, CNVs).
  • Covers variant annotation and results visualization, from raw reads to interpretation.

Main Results:

  • The GPCG pipeline provides a comprehensive solution for NGS data analysis.
  • It automates key computational steps, facilitating research in complex genetic disorders.
  • The pipeline is freely available, aiming to make NGS analysis more feasible.

Conclusions:

  • The GPCG pipeline streamlines NGS data analysis, potentially accelerating discoveries in psychiatric genetics.
  • Improved bioinformatics approaches are crucial for realizing the clinical utility of NGS, such as identifying disease-related miRNA signatures.
  • Annotation tools and strategies are vital for pinpointing genetic risk factors for psychiatric disorders.