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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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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.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Sanger Sequencing01:57

Sanger Sequencing

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

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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.
Challenges of the Maxam-Gilbert Method
The...
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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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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Next-Generation Sequencing Informatic Architecture Considerations.

W Bailey Glen1, Cynthia A Schandl2

  • 1Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA. glen@musc.edu.

Methods in Molecular Biology (Clifton, N.J.)
|April 11, 2023
PubMed
Summary
This summary is machine-generated.

Implementing robust bioinformatics pipelines is crucial for managing the increasing complexity of clinical sequencing tests. This ensures reliable and repeatable analysis as new technologies and data emerge.

Keywords:
Bioinformatics pipelineData storageDisaster recoveryInformatic architectureNGSValidationVerification

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Area of Science:

  • Clinical bioinformatics
  • Genomic data analysis
  • Next-generation sequencing (NGS) informatics

Background:

  • Clinical sequencing methodologies are rapidly expanding in diversity, complexity, and scale.
  • This evolution necessitates specialized implementations across wet bench, bioinformatics, and reporting.
  • Ongoing updates to software, annotation sources, guidelines, and IT infrastructure impact test informatics over time.

Purpose of the Study:

  • To discuss key principles for implementing informatics in new clinical tests.
  • To address the challenges of managing evolving bioinformatics needs in clinical labs.
  • To highlight the importance of adaptable and reliable informatics solutions for clinical sequencing.

Main Methods:

  • Discussion of informatics issues spanning all next-generation sequencing (NGS) applications.
  • Emphasis on implementing reliable, repeatable, redundant, and version-controlled bioinformatics pipelines and architectures.
  • Exploration of common methodologies to manage informatics updates and changes.

Main Results:

  • Identification of critical informatics principles for handling evolving clinical sequencing tests.
  • Demonstration of how robust pipeline implementation aids rapid and reliable updates.
  • Highlighting the need for adaptable bioinformatics architectures to accommodate changes.

Conclusions:

  • Implementing a version-controlled, reliable, and redundant bioinformatics pipeline is essential for clinical labs.
  • Key principles can significantly improve a lab's capacity to manage informatics updates for clinical tests.
  • Adaptable bioinformatics strategies are vital for sustained clinical relevance in sequencing.