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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

Profiling model T-cell metagenomes with short reads.

René L Warren1, Brad H Nelson, Robert A Holt

  • 1BC Cancer Agency, Michael Smith Genome Sciences Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada. rwarren@bcgsc.ca

Bioinformatics (Oxford, England)
|January 13, 2009
PubMed
Summary

We developed immuno-SSAKE (iSSAKE) software to profile T-cell receptor (TCR) diversity using short-read sequencing. This approach enables comprehensive TCR repertoire analysis, even for rare clonotypes.

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11:22

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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
11:23

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

Area of Science:

  • Immunology
  • Bioinformatics
  • Genomics

Background:

  • T-cell receptor (TCR) diversity in peripheral blood remains incompletely characterized at the sequence level.
  • The vast potential for T-cell diversity presents challenges for repertoire analysis.
  • Somatic recombination of TCR genes generates unique T-cell clonotypes.

Purpose of the Study:

  • To develop a sequencing approach and assembly software for profiling T-cell metagenomes.
  • To enable comprehensive analysis of T-cell receptor diversity using short reads from massively parallel sequencing platforms.

Main Methods:

  • Developed immuno-SSAKE (iSSAKE) software for de novo assembly of TCR CDR3 sequences.
  • Utilized simulated TCRbeta (sTCRbeta) sequences with varying read lengths and error models.
  • Employed reads aligning to TCR variable (V) genes to seed iSSAKE assemblies.

Main Results:

  • iSSAKE detected over 51% and 63% of rare (1 p.p.m.) clonotypes using 36 nt reads with random or modeled errors, respectively.
  • Detection rates for abundant clonotypes (≥6 p.p.m.) exceeded 99%.
  • Sensitivity increased with read length, with 42 nt and 50 nt reads identifying 82.0% and 94.7% of rare clonotypes, respectively.

Conclusions:

  • The developed sequencing approach and iSSAKE software demonstrate the feasibility of complete TCR repertoire profiling.
  • Massively parallel short read sequencing technology can be effectively utilized for detailed TCR repertoire analysis.