Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • PubMed: Profiling model T cell metagenomes with short reads.

    Syndicated from PubMed RSS Feeds

    Related Articles Profiling model T cell metagenomes with short reads.

    Bioinformatics. 2009 Jan 9;

    Authors: Warren RL, Nelson BH, Holt RA

    MOTIVATION: T cell receptor (TCR) diversity in peripheral blood has not yet been fully profiled with sequence level resolution. Each T cell clonotype expresses a unique receptor, generated by somatic recombination of TCR genes and the enormous potential for T cell diversity makes repertoire analysis challenging. We developed a sequencing approach and assembly software (immuno-SSAKE or iSSAKE) for profiling T cell metagenomes using short reads from the massively parallel sequencing platforms. RESULTS: Models of sequence diversity for the TCR beta-chain CDR3 region were built using empirical data and used to simulate, at random, distinct TCR clonotypes at 1-20 parts per million. Using simulated TCRbeta (sTCRbeta) sequences, we randomly created 20 million 36nt reads having 1%-2% random error, 20 million 42nt or 50nt reads having 1% random error and 20 million 36nt reads with 1% error modeled on real short read data. Reads aligning to the end of known TCR variable (V) genes and having consecutive unmatched bases in the adjacent CDR3 were used to seed iSSAKE de novo assemblies of CDR3. With assembled 36nt reads we detect over 51% and 63% of rare (1 ppm) clonotypes using a random or modeled error distribution, respectively. We detect over 99% of more abundant clonotypes (6 ppm or higher) using either error distribution. Longer reads improve sensitivity, with assembled 42nt and 50nt reads identifying 82.0% and 94.7% of rare 1 ppm clonotypes, respectively. Our approach illustrates the feasibility of complete profiling of the TCR repertoire using new massively parallel short read sequencing technology. AVAILABILITY: ftp://ftp.bcgsc.ca/supplementary/iSSAKE. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary methods and data available at Bioinformatics online and at ftp://ftp.bcgsc.ca/supplementary/iSSAKE.

    PMID: 19136549 [PubMed - as supplied by publisher]



    More...

Latest Articles

Collapse

  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM
  • seqadmin
    The Impact of AI in Genomic Medicine
    by seqadmin



    Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
    02-26-2024, 02:07 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-14-2024, 06:13 AM
0 responses
34 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-08-2024, 08:03 AM
0 responses
72 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-07-2024, 08:13 AM
0 responses
81 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-06-2024, 09:51 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X