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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
EGAS00001005274 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 bam 11.9 GB
EGAF00005308874 bam 9.9 GB
EGAF00005308875 bam 11.0 GB
EGAF00005308876 bam 10.1 GB
EGAF00005308877 bam 9.1 GB
EGAF00005308878 bam 10.1 GB
EGAF00005308879 bam 11.3 GB
EGAF00005308880 bam 9.4 GB
EGAF00005308881 bam 9.6 GB
EGAF00005308882 bam 11.4 GB
EGAF00005308883 bam 9.3 GB
EGAF00005308884 bam 10.2 GB
EGAF00005308885 bam 10.1 GB
EGAF00005308886 bam 9.0 GB
EGAF00005308887 bam 10.8 GB
EGAF00005308888 bam 9.1 GB
EGAF00005308889 bam 12.8 GB
EGAF00005308890 bam 9.2 GB
EGAF00005308891 bam 10.9 GB
EGAF00005308892 bam 11.1 GB
EGAF00005308893 bam 9.5 GB
EGAF00005308894 bam 11.1 GB
EGAF00005308895 bam 9.8 GB
EGAF00005308896 bam 10.3 GB
EGAF00005308897 bam 11.4 GB
EGAF00005308898 bam 11.7 GB
EGAF00005308899 bam 10.6 GB
EGAF00005308900 bam 12.4 GB
EGAF00005308901 bam 10.1 GB
EGAF00005308902 bam 9.3 GB
EGAF00005308903 bam 11.9 GB
EGAF00005308904 bam 9.7 GB
EGAF00005308905 bam 9.7 GB
EGAF00005308906 bam 11.6 GB
EGAF00005308907 bam 13.2 GB
EGAF00005308908 bam 9.3 GB
EGAF00005308909 bam 13.7 GB
EGAF00005308910 bam 11.8 GB
EGAF00005308911 bam 13.3 GB
EGAF00005309049 bam 11.7 GB
EGAF00005309050 bam 9.5 GB
EGAF00005309051 bam 9.7 GB
EGAF00005309052 bam 12.8 GB
EGAF00005309053 bam 10.1 GB
EGAF00005309054 bam 10.8 GB
EGAF00005309055 bam 9.6 GB
EGAF00005309056 bam 10.6 GB
EGAF00005309057 bam 10.9 GB
EGAF00005309058 bam 9.3 GB
EGAF00005309059 bam 11.1 GB
EGAF00005309060 bam 10.1 GB
EGAF00005309061 bam 9.0 GB
EGAF00005309062 bam 11.4 GB
EGAF00005309063 bam 12.4 GB
EGAF00005309064 bam 11.9 GB
EGAF00005309065 bam 11.6 GB
EGAF00005309066 bam 10.3 GB
EGAF00005309067 bam 11.8 GB
EGAF00005309068 bam 9.1 GB
EGAF00005309069 bam 9.4 GB
EGAF00005309070 bam 11.9 GB
EGAF00005309071 bam 9.8 GB
EGAF00005309072 bam 9.2 GB
EGAF00005309073 bam 11.3 GB
EGAF00005309074 bam 13.3 GB
EGAF00005309075 bam 9.3 GB
EGAF00005309076 bam 10.2 GB
EGAF00005309077 bam 11.1 GB
EGAF00005309078 bam 13.2 GB
EGAF00005309079 bam 13.7 GB
EGAF00005309081 bam 9.1 GB
EGAF00005309082 bam 11.4 GB
EGAF00005309083 bam 10.1 GB
EGAF00005309084 bam 9.7 GB
EGAF00005309085 bam 9.3 GB
EGAF00005309086 bam 9.9 GB
EGAF00005309087 bam 10.1 GB
EGAF00005309088 bam 11.0 GB
78 Files (833.7 GB)