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2.7 million samples genotyped for HLA by next generation sequencing: lessons learned

Overview of attention for article published in BMC Genomics, February 2017
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (82nd percentile)
  • High Attention Score compared to outputs of the same age and source (85th percentile)

Mentioned by

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18 tweeters

Citations

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70 Dimensions

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78 Mendeley
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Title
2.7 million samples genotyped for HLA by next generation sequencing: lessons learned
Published in
BMC Genomics, February 2017
DOI 10.1186/s12864-017-3575-z
Pubmed ID
Authors

Gerhard Schöfl, Kathrin Lang, Philipp Quenzel, Irina Böhme, Jürgen Sauter, Jan A. Hofmann, Julia Pingel, Alexander H. Schmidt, Vinzenz Lange

Abstract

At the DKMS Life Science Lab, Next Generation Sequencing (NGS) has been used for ultra-high-volume high-resolution genotyping of HLA loci for the last three and a half years. Here, we report on our experiences in genotyping the HLA, CCR5, ABO, RHD and KIR genes using a direct amplicon sequencing approach on Illumina MiSeq and HiSeq 2500 instruments. Between January 2013 and June 2016, 2,714,110 samples largely from German, Polish and UK-based potential stem cell donors have been processed. 98.9% of all alleles for the targeted HLA loci (HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1) were typed at high resolution or better. Initially a simple three-step workflow based on nanofluidic chips in conjunction with 4-primer amplicon tagging was used. Over time, we found that this setup results in PCR artefacts such as primer dimers and PCR-mediated recombination, which may necessitate repeat typing. Split workflows for low- and high-DNA-concentration samples helped alleviate these problems and reduced average per-locus repeat rates from 3.1 to 1.3%. Further optimisations of the workflow included the use of phosphorothioate oligos to reduce primer degradation and primer dimer formation, and employing statistical models to predict read yield from initial template DNA concentration to avoid intermediate quantification of PCR products. Finally, despite the populations typed at DKMS Life Science Lab being relatively homogenous genetically, an analysis of 1.4 million donors processed between January 2015 and May 2016 led to the discovery of 1,919 distinct novel HLA alleles. Amplicon-based NGS HLA genotyping workflows have become the workhorse in high-volume tissue typing of registry donors. The optimisation of workflow practices over multiple years has led to insights and solutions that improve the efficiency and robustness of short amplicon based genotyping workflows.

Twitter Demographics

The data shown below were collected from the profiles of 18 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 78 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 1 1%
Unknown 77 99%

Demographic breakdown

Readers by professional status Count As %
Researcher 24 31%
Student > Ph. D. Student 9 12%
Other 8 10%
Student > Bachelor 6 8%
Student > Master 5 6%
Other 15 19%
Unknown 11 14%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 24 31%
Agricultural and Biological Sciences 13 17%
Medicine and Dentistry 9 12%
Immunology and Microbiology 6 8%
Computer Science 3 4%
Other 5 6%
Unknown 18 23%

Attention Score in Context

This research output has an Altmetric Attention Score of 10. 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 25 July 2018.
All research outputs
#2,144,095
of 15,922,193 outputs
Outputs from BMC Genomics
#982
of 8,861 outputs
Outputs of similar age
#64,044
of 363,182 outputs
Outputs of similar age from BMC Genomics
#4
of 28 outputs
Altmetric has tracked 15,922,193 research outputs across all sources so far. Compared to these this one has done well and is in the 86th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 8,861 research outputs from this source. They receive a mean Attention Score of 4.3. This one has done well, scoring higher than 88% 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 363,182 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 82% of its contemporaries.
We're also able to compare this research output to 28 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 85% of its contemporaries.