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Ligation-anchored PCR unveils immune repertoire of TCR-beta from whole blood

Overview of attention for article published in BMC Biotechnology, May 2015
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  • Above-average Attention Score compared to outputs of the same age (51st percentile)

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Title
Ligation-anchored PCR unveils immune repertoire of TCR-beta from whole blood
Published in
BMC Biotechnology, May 2015
DOI 10.1186/s12896-015-0153-9
Pubmed ID
Authors

Fan Gao, Kai Wang

Abstract

As one of the genetic mechanisms for adaptive immunity, V(D)J recombination generates an enormous repertoire of T-cell receptors (TCRs). With the development of high-throughput sequencing techniques, systematic exploration of V(D)J recombination becomes possible. Multiplex PCR has been previously developed to assay immune repertoire; however, the use of primer pools leads to inherent biases in target amplification. In our study, we developed a "single-primer" ligation-anchored PCR method that may amplify the repertoire with much less biases. By utilizing a universal primer paired with a single primer targeting the conserved constant region, we amplified TCR-beta (TRB) variable regions from total RNA extracted from blood. Next-generation sequencing libraries were then prepared for Illumina HiSeq 2500 sequencer, which generates 151-bp read length to cover the entire V(D)J recombination region. We evaluated this approach on blood samples from healthy donors and from patients with malignant and benign meningiomas. Mapping of sequencing data showed that 64% to 96% of mapped TCRV-containing reads belong to TRB subtype. An increased usage of specific V segments and V-J pairing were observed in malignant meningiomas samples. The CDR3 sequences of the expanded V-J pairs were distinct in each malignant individual, even for pairing of TRBV7-3 with TRBJ2-2 that showed increased usage in both cases. We demonstrated the technical feasibility and effectiveness of ligation-anchored PCR approach in capturing the TCR-beta landscapes. Further development of this technology may enable a comprehensive delineation of immune repertoire, including other forms of TCRs as well as immunoglobulins.

Twitter Demographics

The data shown below were collected from the profiles of 3 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 23 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
China 1 4%
Unknown 22 96%

Demographic breakdown

Readers by professional status Count As %
Researcher 5 22%
Student > Ph. D. Student 4 17%
Student > Master 4 17%
Professor > Associate Professor 3 13%
Other 2 9%
Other 4 17%
Unknown 1 4%
Readers by discipline Count As %
Agricultural and Biological Sciences 9 39%
Medicine and Dentistry 7 30%
Immunology and Microbiology 3 13%
Biochemistry, Genetics and Molecular Biology 2 9%
Chemical Engineering 1 4%
Other 0 0%
Unknown 1 4%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 11 March 2016.
All research outputs
#3,351,733
of 7,380,153 outputs
Outputs from BMC Biotechnology
#229
of 461 outputs
Outputs of similar age
#96,763
of 214,820 outputs
Outputs of similar age from BMC Biotechnology
#32
of 39 outputs
Altmetric has tracked 7,380,153 research outputs across all sources so far. This one has received more attention than most of these and is in the 52nd percentile.
So far Altmetric has tracked 461 research outputs from this source. They receive a mean Attention Score of 4.6. This one is in the 45th percentile – i.e., 45% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 214,820 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 51% of its contemporaries.
We're also able to compare this research output to 39 others from the same source and published within six weeks on either side of this one. This one is in the 12th percentile – i.e., 12% of its contemporaries scored the same or lower than it.