Q&A [Utilization/Submission of Specimens and Data]

You are required to have a Repository Portal account to view the showcase. Please click here for preliminary registration of your account, and use the link sent to your registered e-mail address to enter personal details such as your name. An official account will be issued within seven days after completing this step. Once you are issued an official account, log in and take the e-learning courses in “Application Information.”

We ask that the principal investigators, along with persons responsible for handling specimens, pathogens, and information related to the specimens and data to be utilized, all take the e-learning courses. Please note that it is necessary to take an e-learning course to create an account in the Repository Portal.

Researchers who plan to conduct studies, whether based in hospitals, research institutions, government organizations, or companies, may apply for access to the specimens and data in the iCROWN Repository. After application, access is granted once approved by the utilization subcommittee.

There is no application deadline. The utilization subcommittee is held approximately once every month, and applications are reviewed at the meetings closest to the application date. For further details, please refer to 5) Research consultation and 6) Utilization application on this page.

The utilization subcommittee is held approximately once every month, and applications are reviewed at the meetings closest to the application date. Once approved, the data will be prepared in approximately one month. For this reason, it will take approximately two months from the submission of the application to the commencement of data utilization. Please note that a few more weeks may be necessary for human genome data, according to the data type and number of cases applied for. For further details, please refer to “Timeline and review flow for specimen and data utilization” on this page.

The utilization subcommittee is held approximately once every month, and applications are reviewed at the meetings closest to the application date. Once approved, specimens will be prepared in approximately one month. For this reason, it will take approximately two months from the submission of the application to the commencement of specimen utilization. For further details, please refer to “Timeline and review flow for specimen and data utilization” on this page.

Please provide the iCROWN Utilization Desk with the ID for the specimen found in the showcase. After consultation, we will provide guidance on the application process if you wish to utilize the specimen.

Although there is a necessity to state in the utilization application form that the variant will be used for research and approval is required by the utilization subcommittee, once approved, additional variants may be provided without creating new applications as long as they are within the scope of the approved application.

A “Declaration of Exemption from Ethics Review” of the user’s affiliated institution or “Report of Exemption from Research Ethics Review” as prepared by the iCROWN Repository should be submitted in place of the research plan and the ethics review committee approval notice that are submitted when applying for utilization of specimens and data.

There are no fees incurred if the intended use aligns with the purposes specified by the iCROWN Repository. However, actual costs necessary for the provision of specimens and data, such as shipping fees, will be the responsibility of the applicant. Furthermore, from the perspective of personal information protection, primary data may only be analyzed in the analysis room of the Japan Institute for Health Security in Tokyo. Travel and other related expenses for this will be the responsibility of the applicant.

The Access Regulations state that use is permitted within the approximate scope of the numbers and quantities shown below. However, use may exceed the published guidelines if approved by the utilization subcommittee. For further details, please refer to the Access Regulations within the public documents.

• Guideline for number of cases: 50 cases
• Guidelines for quantities per collection:
  • 　Plasma sample: 200 μL
  • 　PBMC sample: 5-50×10^5 cells (Count at the time of storage)
  • 　DNA sample: approximately 2 μg
  • 　Nasopharyngeal swab sample: approximately 200 μL
  • 　Saliva sample: approximately 200 μL
  • 　Stool sample: approximately 1 g

There are no limits to the number of cases regarding clinical and genome information to be provided. Once approved by the utilization subcommittee, you may access all available data within the scope of the approved application.
Please note that 50 cases is used as a guideline, as there is a limit to the stored specimens. Larger quantities required for research may be available upon application and approval from the utilization subcommittee.

Clinical information is provided in a format (such as CSV) that can be analyzed on the terminal installed at the Japan Institute for Health Security in Tokyo, which is the lead research institution.
No data collected in the iCROWN Repository, including clinical information, may be taken outside of the Japan Institute for Health Security in Tokyo, where the iCROWN Administrative Office is located.

Unfortunately, we are not able to make data definition documents available prior to the conclusion of a Material Transfer Agreement (MTA) for Specimens and Related Materials. We will be able to provide data definition documents once your application is approved and an MTA is concluded. Please consult with the iCROWN Utilization Desk if you require such data.

As of April 2025, the diseases covered by the iCROWN Repository include Severe Acute Respiratory Infection (SARI), including COVID-19; Mpox; Pediatric Hepatitis of Unknown Etiology; and, among the Priority Infectious Diseases, arthropod-borne infectious diseases (dengue fever, chikungunya fever, and Zika virus infection). Specimens collected through the Entry Screening Genome Surveillance Program are also included.

The types of specimens currently collected and stored include plasma, DNA, peripheral blood mononuclear cells (PBMCs), swab specimens, saliva, stool samples, and isolated pathogens.

The time periods depend on the disease. It is possible to review cases in the showcase, which features overviews of individual cases. For the latest information that has not been updated in the showcase, or diseases that are not publicly disclosed, please submit an inquiry to the iCROWN Utilization Desk.

In principle, there is clinical information available for each specimen. However, please note that not all cases have this information.

PBMCs use 1.5 ml Azenta tubes. Items such as plasma samples, DNA, nasopharyngeal swab samples, saliva samples, and stool samples use 1.0 ml Azenta tubes.

At present, these specimens are not eligible for secondary use through the repository. Residual clinical serum specimens collected from cases of arthropod-borne infectious diseases are being collected specifically for pathogen genome analysis and pathogen isolation, and the necessary framework for making serum specimens available for secondary use has not yet been established.

Whole-genome sequencing is conducted using the next-generation sequencer NovaSeq 6000 System, with two-color florescence detection.

An ultrasonic method with the DNA Shearing System from Covaris is used.

It is generally at 550 bp, but for a small number of samples with issues such as DNA concentration, fragmentation is conducted at 350 bp.

More than 90 billion bases (90 G bases) of data are obtained, excluding duplicate reads.

gVCF files for each sample, along with VCF files for samples that have already been joint-called are available. Furthermore, a certain number of specimens that feature HLA polymorphism information obtained by next-generation sequencers are also available for use.

The genome reference version is GRCh38/hg38.

For cases in which the same patient is newly registered at another location, the iCROWN Repository assigns a unique ID for management. Consequently, in theory, there is a possibility that data from the same sample could be included. Furthermore, there is a possibility of the existence of specimens from the same family.

Items regarding QC are evaluated, and specimens with an average coverage value of 25 or under, or with an unmapped read ratio that exceeds 8E-4 are excluded from specimens that are available for utilization.

The clinical data is based on medical records from various medical institutions. This information is reported by individuals involved in patient care, such as physicians and nurses. The medical records are reviewed and entered into electronic data capture (EDC) reports by research collaborators (such as physicians and CRCs).

Unfortunately, CRFs are not available for viewing. If you are considering using this information, please consult with the iCROWN Utilization Desk regarding the specific information you require. Based on your inquiry, we will determine whether the information you have requested is available.

Utilization of receipt information is currently under preparation.

Staff from various medical institutions who have completed the required e-learning courses for iCROWN review medical records and enter data into the electronic data capture (EDC) reports.

Data checks are conducted for missing values, missing measurements, unentered data, and consistency, based on a data checklist created beforehand. Queries are issued for any suspected items, and data corrections are made at each medical institution. Valid data are locked to ensure consistency and reliability.