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Prediction of HLA genotypes using NGS data

High-precision human leukocyte antigen (HLA) genotyping is crucial for anti-cancer immunotherapy, but existing tools predicting HLA genotypes using next-generation sequencing (NGS) data are insufficiently accurate. We compared the availability and accuracy of eight HLA genotyping tools (OptiType, HLA-HD, PHLAT, seq2HLA, arcasHLA, HLAscan, HLA*LA, and Kourami) using 1,275 cases from the 1000 Genomes Project data and created a new HLA-genotyping algorithm combining tools. Then, we assessed the new algorithm’s performance in 39 in-house samples with normal whole-exome sequencing (WES) data and polymerase chain reaction–sequencing-based typing (PCR-SBT) results.

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Asan Medical Center Data Access Committee policy

1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Research Purposes. The User Institution further agrees that it will only use these Data for Research Purposes which are within the limitations (if any) set out in Appendix I. 2. The User Institution agrees to preserve, at all times, the confidentiality of these Data. In particular, it undertakes not to use, or attempt to use these Data to compromise or otherwise infringe the confidentiality of information on Research Participants. Without prejudice to the generality of the foregoing, the User Institution agrees to use at least the measures set out in Appendix I to protect these Data. 3. The User Institution agrees to protect the confidentiality of Research Participants in any research papers or publications that they prepare by taking all reasonable care to limit the possibility of identification. 4. The User Institution agrees not to link or combine these Data to other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been formally granted to the User Institution or is freely available without restriction. 5. The User Institution agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorised Personnel. Should the User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete a separate application for access to these Data. 6. The User Institution agrees that the Data Producers, and all other parties involved in the creation, funding or protection of these Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of these Data; b) exclude to the fullest extent permitted by law all liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards damages and payments made by the Recipient that may arise (whether directly or indirectly) in any way whatsoever from the Recipient’s use of these Data or from the unavailability of, or break in access to, these Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of these Data. 7. The User Institution agrees to follow the Fort Lauderdale Guidelines (http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtd003207.pdf ) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). This includes but is not limited to recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 8. The User Institution agrees to follow the Publication Policy in Appendix III. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 9. The User Institution agrees not to make intellectual property claims on these Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of these Data, or conclusion drawn directly from these Data. 10. The User Institution can elect to perform further research that would add intellectual and resource capital to these data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User Institution agrees to implement licensing policies that will not obstruct further research and to follow the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) (https://www.icgc.org/files/daco/NIH_BestPracticesLicensingGenomicInventions_2005_en.pdf ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (http://www.oecd.org/science/biotech/36198812.pdf ). 11. The User Institution agrees to destroy/discard the Data held, once it is no longer used for the Project, unless obliged to retain the data for archival purposes in conformity with audit or legal requirements. 12. The User Institution will notify Asan Medical Center within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Asan Medical Center prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Asan Medical Center as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Asan Medical Center may terminate this agreement by written notice to the User Institution. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User Institution from retaining these data for archival purpose in conformity with audit or legal requirements. 16. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. As an example, this may include specific provisions relating to the Data required by Data Producers other than Asan Medical Center. In the event that changes are required, the Data Producers or their appointed agent will contact the User Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. 17. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 18. The User Institution agrees to distribute a copy of these terms to the Authorised Personnel. The User Institution will procure that the Authorised Personnel comply with the terms of this agreement. 19. This agreement (and any dispute, controversy, proceedings or claim of whatever nature arising out of this agreement or its formation) shall be construed, interpreted and governed by the laws of England and Wales and shall be subject to the exclusive jurisdiction of the English courts.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00005308873 1622534957377 11.9 GB
EGAF00005308874 1622535852441 9.9 GB
EGAF00005308875 1622540892671 11.0 GB
EGAF00005308876 1622537292918 10.1 GB
EGAF00005308877 1622533984706 9.1 GB
EGAF00005308878 1622535674737 10.1 GB
EGAF00005308879 1622536941060 11.3 GB
EGAF00005308880 1622539327769 9.4 GB
EGAF00005308881 1622535610924 9.6 GB
EGAF00005308882 1622534957378 11.4 GB
EGAF00005308883 1622533984706 9.3 GB
EGAF00005308884 1622537177279 10.2 GB
EGAF00005308885 1622541948668 10.1 GB
EGAF00005308886 1622535065795 9.0 GB
EGAF00005308887 1622538605261 10.8 GB
EGAF00005308888 1622533685142 9.1 GB
EGAF00005308889 1622535972869 12.8 GB
EGAF00005308890 1622535004503 9.2 GB
EGAF00005308891 1622536697965 10.9 GB
EGAF00005308892 1622538907155 11.1 GB
EGAF00005308893 1622538907155 9.5 GB
EGAF00005308894 1622539745996 11.1 GB
EGAF00005308895 1622537773472 9.8 GB
EGAF00005308896 1622533685142 10.3 GB
EGAF00005308897 1622566578900 11.4 GB
EGAF00005308898 1622534957379 11.7 GB
EGAF00005308899 1622535852441 10.6 GB
EGAF00005308900 1622566578900 12.4 GB
EGAF00005308901 1622541948668 10.1 GB
EGAF00005308902 1622536514948 9.3 GB
EGAF00005308903 1622537833748 11.9 GB
EGAF00005308904 1622534107269 9.7 GB
EGAF00005308905 1622535792843 9.7 GB
EGAF00005308906 1622535915213 11.6 GB
EGAF00005308907 1622534224481 13.2 GB
EGAF00005308908 1622538545727 9.3 GB
EGAF00005308909 1622535004503 13.7 GB
EGAF00005308910 1622534957379 11.8 GB
EGAF00005308911 1622566578900 13.3 GB
EGAF00005309049 1623872087409 11.7 GB
EGAF00005309050 1623871203125 9.5 GB
EGAF00005309051 1623868852290 9.7 GB
EGAF00005309052 1623874357058 12.8 GB
EGAF00005309053 1623883634977 10.1 GB
EGAF00005309054 1623873179354 10.8 GB
EGAF00005309055 1623874909611 9.6 GB
EGAF00005309056 1623872809215 10.6 GB
EGAF00005309057 1623873535011 10.9 GB
EGAF00005309058 1623874357058 9.3 GB
EGAF00005309059 1623876530779 11.1 GB
EGAF00005309060 1623869742035 10.1 GB
EGAF00005309061 1623870786134 9.0 GB
EGAF00005309062 1623875452763 11.4 GB
EGAF00005309063 1623874357058 12.4 GB
EGAF00005309064 1623867225896 11.9 GB
EGAF00005309065 1623885978017 11.6 GB
EGAF00005309066 1623872087409 10.3 GB
EGAF00005309067 1623873717851 11.8 GB
EGAF00005309068 1623873179354 9.1 GB
EGAF00005309069 1623874357058 9.4 GB
EGAF00005309070 1623887655860 11.9 GB
EGAF00005309071 1623872991307 9.8 GB
EGAF00005309072 1623870786134 9.2 GB
EGAF00005309073 1623876881237 11.3 GB
EGAF00005309074 1622569475582 13.3 GB
EGAF00005309075 1623869202339 9.3 GB
EGAF00005309076 1623869202339 10.2 GB
EGAF00005309077 1622569002286 11.1 GB
EGAF00005309078 1623870601423 13.2 GB
EGAF00005309079 1623872991307 13.7 GB
EGAF00005309081 1623872809215 9.1 GB
EGAF00005309082 1622569717706 11.4 GB
EGAF00005309083 1623870601423 10.1 GB
EGAF00005309084 1623870601423 9.7 GB
EGAF00005309085 1623865084795 9.3 GB
EGAF00005309086 1623870601423 9.9 GB
EGAF00005309087 1623875268545 10.1 GB
EGAF00005309088 1623874557905 11.0 GB
78 Files (833.7 GB)