The DOI matches its Crossref record; 17 of the 17 references it cites were found in a registry or an index.
Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing
Open accessAbstract
Background: A close match of the HLA alleles between donor and recipient is an important prerequisite for successful unrelated hematopoietic stem cell transplantation. To increase the chances of finding an unrelated donor, registries recruit many hundred thousands of volunteers each year. Many registries with limited resources have had to find a trade-off between cost and resolution and extent of typing for newly recruited donors in the past. Therefore, we have taken advantage of recent improvements in NGS to develop a workflow for low-cost, high-resolution HLA typing. Results: We have established a straightforward three-step workflow for high-throughput HLA typing: Exons 2 and 3 of HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 are amplified by PCR on Fluidigm Access Array microfluidic chips. Illumina sequencing adapters and sample specific tags are directly incorporated during PCR. Upon pooling and cleanup, 384 samples are sequenced in a single Illumina MiSeq run. We developed “neXtype” for streamlined data analysis and HLA allele assignment. The workflow was validated with 1140 samples typed at 6 loci. All neXtype results were concordant with the Sanger sequences, demonstrating error-free typing of more than 6000 HLA loci. Current capacity in routine operation is 12,000 samples per week. Conclusions: The workflow presented proved to be a cost-efficient alternative to Sanger sequencing for high-throughput HLA typing. Despite the focus on cost efficiency, resolution exceeds the current standards of Sanger typing for donor registration.
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Cites
Nomenclature for factors of the HLA system, 2010
Marsh, S. G. E., Albert, E. D., Bodmer, W. F., Bontrop, R. E., Dupont, B., Erlich, H. A., Fernández‐Viña, M., Geraghty, D. E., Holdsworth, R., Hurley, C. K., et al. (2010) · Tissue Antigens · doi:10.1111/j.1399-0039.2010.01466.x · Cited by 4,222
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
Haas, B. J., Gevers, D., Earl, A. M., Feldgarden, M., Ward, D. V., Giannoukos, G., Ciulla, D., Tabbaa, D., Highlander, S. K., Sodergren, E., et al. (2011) · Genome Research · doi:10.1101/gr.112730.110 · Cited by 3,473
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
Kircher, M., Sawyer, S., & Meyer, M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr771 · Cited by 1,106 · cited 1×
“Therefore, 3 out of 4 index combinations are not used in a particular run, minimizing index mis-assignments [9].”
BackgroundNomenclature for Factors of the HLA System, 2004
Marsh, S. G. E., Albert, E. D., Bodmer, W. F., Bontrop, R. E., Dupont, B., Erlich, H. A., Geraghty, D. E., Hansen, J. A., Hurley, C. K., Mach, B., et al. (2005) · Human Immunology · doi:10.1016/j.humimm.2005.02.002 · Cited by 818
Robinson, J., Waller, M. J., Fail, S. C., McWilliam, H., Lopez, R., Parham, P., & Marsh, S. G. E. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn662 · Cited by 700
Robinson, J., Halliwell, J. A., McWilliam, H., Lopez, R., Parham, P., & Marsh, S. G. E. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks949 · Cited by 550
Limits of HLA mismatching in unrelated hematopoietic cell transplantation
Petersdorf, E. W., Anasetti, C., Martin, P. J., Gooley, T., Radich, J., Malkki, M., Woolfrey, A., Smith, A., Mickelson, E., & Hansen, J. A. (2004) · Blood · doi:10.1182/blood-2004-04-1674 · Cited by 263
Stimulation and suppression of PCR-mediated recombination
Judo, M. S. B., Wedel, A. B., & Wilson, C. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.7.1819 · Cited by 243
HLA DNA typing: past, present, and future
Erlich, H. (2012) · Tissue Antigens · doi:10.1111/j.1399-0039.2012.01881.x · Cited by 211
High‐resolution, high‐throughput HLA genotyping by next‐generation sequencing
Bentley, G., Higuchi, R., Hoglund, B., Goodridge, D., Sayer, D., Trachtenberg, E. A., & Erlich, H. A. (2009) · Tissue Antigens · doi:10.1111/j.1399-0039.2009.01345.x · Cited by 185
Cited by
The IPD and IMGT/HLA database: allele variant databases
Robinson, J., Halliwell, J. A., Hayhurst, J. D., Flicek, P., Parham, P., & Marsh, S. G. E. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1161 · Cited by 1,740
Hu, C., Hart, S. N., Polley, E. C., Gnanaolivu, R., Shimelis, H., Lee, K. Y., Lilyquist, J., Na, J., Moore, R., Antwi, S. O., et al. (2018) · JAMA · doi:10.1001/jama.2018.6228 · Cited by 577
A vaccine targeting mutant IDH1 in newly diagnosed glioma
Platten, M., Bunse, L., Wick, A., Bunse, T., Le Cornet, L., Harting, I., Sahm, F., Sanghvi, K., Tan, C. L., Poschke, I., et al. (2021) · Nature · doi:10.1038/s41586-021-03363-z · Cited by 432
Metadata
- Authors
- Lange, V., Böhme, I., Hofmann, J., Lang, K., Sauter, J., Schöne, B., Paul, P., Albrecht, V., Andreas, J. M., Baier, D. M., Nething, J., Ehninger, U., Schwarzelt, C., Pingel, J., Ehninger, G., & Schmidt, A. H.
- Venue
- BMC Genomics
- Published
- 2014-01-24
- Volume
- 15
- Issue
- 1
- Pages
- 63-63
- ISSN
- 1471-2164 (ISSN-L)
- OpenAlex
- W2068010299
- Cited by
- 271
- References
- 17
- FWCI
- 14.08
- Type
- journal article
- Language
- en
- Open access
- gold
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- Lange, V., Böhme, I., Hofmann, J., Lang, K., Sauter, J., Schöne, B., Paul, P., Albrecht, V., Andreas, J. M., Baier, D. M., Nething, J., Ehninger, U., Schwarzelt, C., Pingel, J., Ehninger, G., & Schmidt, A. H. (2014). Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing. BMC Genomics. https://doi.org/10.1186/1471-2164-15-63
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