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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.
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Gene Duplication and Divergence02:37

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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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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

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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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Peptide Identification Using Tandem Mass Spectrometry01:33

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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
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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. 
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Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
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ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data.

Navin Rustagi1,2, Oliver A Hampton3,4, Jie Li3,5

  • 1Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA. Rustagi@bcm.edu.

BMC Bioinformatics
|April 29, 2016
PubMed
Summary
This summary is machine-generated.

ITD Assembler efficiently detects internal tandem duplications (ITDs) in cancer genomes by analyzing next-generation sequencing data. This novel method improves the identification of these critical mutations for better cancer research.

Keywords:
AMLAssemblyCancer geneticsClusteringData miningDe Bruijn graphsFLT3Somatic mutationsTandem duplication

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • Detecting internal tandem duplications (ITDs) in coding exons is difficult due to read alignment challenges.
  • Efficient methods are needed to identify these crucial mutational events.

Purpose of the Study:

  • Introduce ITD Assembler, a novel computational approach for detecting ITDs.
  • Improve the recovery of internal tandem duplications from next-generation sequencing data.

Main Methods:

  • ITD Assembler utilizes De Bruijn graphs to identify reads with cycles indicative of ITDs.
  • Overlap-layout-consensus is employed for the assembly of these reads.
  • The method was tested on The Cancer Genome Atlas AML dataset.

Main Results:

  • ITD Assembler achieved the highest detection rate for FLT3-ITDs compared to existing algorithms.
  • The tool identified novel ITDs in FLT3, KIT, CEBPA, WT1, and other genes.
  • Polymorphic ITDs were discovered in 54 genes and validated using RNA sequencing data.

Conclusions:

  • ITD Assembler is a sensitive tool capable of detecting various types of tandem duplications.
  • The findings underscore the importance of investigating ITDs in other cancers and Mendelian diseases.