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HLA typing from RNA-Seq sequence reads

Overview of attention for article published in Genome Medicine, January 2012
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (94th percentile)
  • Good Attention Score compared to outputs of the same age and source (74th percentile)

Mentioned by

2 blogs
10 tweeters
2 patents
1 Facebook page


144 Dimensions

Readers on

314 Mendeley
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HLA typing from RNA-Seq sequence reads
Published in
Genome Medicine, January 2012
DOI 10.1186/gm403
Pubmed ID

Sebastian Boegel, Martin Löwer, Michael Schäfer, Thomas Bukur, Jos de Graaf, Valesca Boisguérin, Özlem Türeci, Mustafa Diken, John C Castle, Ugur Sahin


ABSTRACT: We present a method, seq2HLA, for obtaining an individual's human leukocyte antigen (HLA) class I and II type and expression using standard next generation sequencing RNA-Seq data. RNA-Seq reads are mapped against a reference database of HLA alleles, and HLA type, confidence score and locus-specific expression level are determined. We successfully applied seq2HLA to 50 individuals included in the HapMap project, yielding 100% specificity and 94% sensitivity at a P-value of 0.1 for two-digit HLA types. We determined HLA type and expression for previously un-typed Illumina Body Map tissues and a cohort of Korean patients with lung cancer. Because the algorithm uses standard RNA-Seq reads and requires no change to laboratory protocols, it can be used for both existing datasets and future studies, thus adding a new dimension for HLA typing and biomarker studies.

Twitter Demographics

The data shown below were collected from the profiles of 10 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 314 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 5 2%
United States 4 1%
Brazil 4 1%
Germany 3 <1%
Hungary 2 <1%
Spain 2 <1%
Iran, Islamic Republic of 1 <1%
Denmark 1 <1%
Korea, Republic of 1 <1%
Other 0 0%
Unknown 291 93%

Demographic breakdown

Readers by professional status Count As %
Researcher 86 27%
Student > Ph. D. Student 71 23%
Student > Master 26 8%
Student > Bachelor 23 7%
Other 18 6%
Other 52 17%
Unknown 38 12%
Readers by discipline Count As %
Agricultural and Biological Sciences 108 34%
Biochemistry, Genetics and Molecular Biology 59 19%
Medicine and Dentistry 35 11%
Immunology and Microbiology 21 7%
Computer Science 17 5%
Other 22 7%
Unknown 52 17%

Attention Score in Context

This research output has an Altmetric Attention Score of 21. 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 2021.
All research outputs
of 18,823,067 outputs
Outputs from Genome Medicine
of 1,251 outputs
Outputs of similar age
of 272,981 outputs
Outputs of similar age from Genome Medicine
of 54 outputs
Altmetric has tracked 18,823,067 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 93rd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,251 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 23.2. This one has done well, scoring higher than 78% of its peers.
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 272,981 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 94% of its contemporaries.
We're also able to compare this research output to 54 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 74% of its contemporaries.