Integrated Database Project

Human Genome Variation Research Database (HGVRD) Sharing Policy

 

　At present, the volume of information concerning human genes is increasing at an astounding rate in the discovery of disease-associated genes, and efficient use of such a huge volume of data has become an urgent challenge. The Integrated Database Project, a research and development project commissioned by the Ministry of Education, Culture, Sports, Science and Technology, is aiming at extensive sharing of these data, and implementing measures to enable various data to be shared. This Policy defines the data-sharing policy of the "Integrated Database Project - Disease Analysis DB Group" (Lead by K. Tokunaga, University of Tokyo) (hereafter, “Disease Analysis DB Group”) concerning the genome-wide SNP and association study (GWAS) data and the resequencing data for disease-associated genes. These data are classified into six categories according to the data contents and further into three levels for data access, and a separate sharing policy is established for each level. The Data Sharing Review Board of Disease Analysis DB Group (“DSRB”) is established within the Disease Analysis DB Group to review deposit of the data to database and access to the data. Members of the Board include multiple members from outside the Disease Analysis DB Group, who will examine each case from scientific, ethical and other perspectives.

 

<Outline of This Sharing Policy>

Data Category/Level and Procedures for Data Use

Level		1	2	3
Type of Data	GWAS data	Category A (Frequency data and statistical values)	Category B (Individual- level copy number variation [CNV] information)	Category C (GWAS genotype data)
				Category D (GWAS raw data)
	Resequencing data	Category E (Publicly available resequencing and mutation data)	Category F (Resequencing data and mutation data)	(Not applicable)
Procedures for data use/access		Available for viewing at the website. However, the application for Level 2 Data is necessary if a large volume of Category A data is requested.	Apply for data use by providing the name, job title, contact address, intended use and e-mail address (generally the address issued by the institution).	Submit an Application Form for Data Access to obtain authorization. Submission of a Data Use Report is required according to the Period of Data Use.

 

About Secure Handling of Data

 

For Level 3 data, submit a Data Use Certification (DUC) (http://gwas.lifesciencedb.jp/gwasdb/db_form/db_duc_en.pdf) and securely handle the data you are authorized to access according to the Security Guideline (http://gwas.lifesciencedb.jp/gwasdb/gwas_secr_en.html).

　For large volume of Level 1 and Level 2 data, each user must agree to the Terms and Conditions of Data Access posted on the website (http://gwas.lifesciencedb.jp/gwasdb/db_term_en.html)

1. Data Category

Data are classified into three access levels: (1) Level 1, covering Categories A and E below, available for viewing at the website by the general public; (2) Level 2, covering Categories B and F, available for viewing by any registered investigator and personnel involved in operations in related fields; and (3) Level 3, covering Categories C and D, with controlled access.

 

<GWAS-Related Data>

A. Frequency Data and Statistical Values: Allele/Genotype frequency data, Hardy-Weinberg equilibrium test, association study results and other post-analysis data, collective information on genetic and genomic mutation (including SNP, CNV and microsatellite) and the clinical data that cannot identify an individual.

 

B. Individual-Level CNV Information: A list of individual-level CNV information including the strength for each SNP. However, only the following information is provided in addition to sequence information.

・ Position and direction on the chromosome (+/- strand)

・Age of onset or sample collection (Described as the 10-year age range. However, use of a shorter age range will be studied according to diseases.)

・Any description limited to clinical phenotype (i.e. disease type or the information equivalent to disease type, or the information necessary for disease type classification.)

・Gender 

C. GWAS Genotype Data: Anonymized personal genotyping results and clinical information. However, only the following information is provided in addition to sequence information.

・Position and direction on the chromosome (+/-strand)

・Age of onset or sample collection (Described as the 10-year age range. However, use of a shorter age range will be studied according to diseases.)

・Any description limited to clinical phenotype (i.e. disease type or the information equivalent to disease type, or the information necessary for disease type classification.)

・Gender

 (Any individualized data that have been published and become public are not included in this category.)

 

D. GWAS Raw Data: Anonymized personal raw data generated prior to genotyping and clinical information. However, only the following information is provided in addition to sequence information.

・Position and direction on the chromosome (+/-strand)

・Age of onset or sample collection (Described as the 10-year age range. However, use of a shorter age range will be studied according to diseases.)

・Any description limited to clinical phenotype (i.e. disease type or the information equivalent to disease type, or the information necessary for disease type classification.)

・Gender

 (Any individualized data that have been published and become public are not included in this category.)

 

<Resequencing-Related Data>

E. Publicly available Resequencing Data and Mutation Data: Anonymized personal resequencing data and mutation information in any specific gene region and the associated clinical information, which have been published in an article or presented at a conference and become public. If the existence of any particular mutation is known or becomes public through publications in this case, any gene region from the same individual other than the gene that contains this particular mutation may be released to the public without access restrictions to the extent specified by the data provider. However, the data must be posted for one gene at the maximum, and the data must be presented in such a way that the viewer cannot tell that two or more gene regions are derived from the same individual. Only the following information is provided in addition to sequence information.

・Position and direction on the chromosome (+/-strand)

・Age of onset or sample collection (Described as the 10-year age range. However, use of a shorter age range will be studied according to diseases.)

・Any description limited to clinical phenotype (i.e. disease type or the information equivalent to disease type, or the information necessary for disease type classification.)

・Gender

 

F. Resequencing Data and Mutation Data: Anonymized personal resequencing data and mutation information in any specific gene region and the associated clinical information, which have yet to become public. However, only the following information is provided in addition to sequence information.

・Position and direction on the chromosome (+/-strand)

・Age of onset or sample collection (Described as the 10-year age range. However, use of a shorter age range will be studied according to diseases.)

・Any description limited to clinical phenotype (i.e. disease type or the information equivalent to disease type, or the information necessary for disease type classification.)

・Gender

 

If more detailed clinical information is needed for the information in any category, conduct a joint research directly with the data provider.

2. About Level 1 Data (Categories A and E)

Level 1 Data do not contain individualized information or has partially become public. Posting of the Data may be considered publication of research results and the Data are available for viewing at the website without authentication..

 

1) Deposit of Data to Database

Any investigator or other personnel involved in operations in related fields wishing to deposit data must send the data to DSRB with the information including the name, institution, address (institution), e-mail address and outline of data. E-mail address: gwas@lifesciencedb.jp

 

2) Procedures for Application for Data Use

1. The user may view Data at the website without authentication. However, the user is not allowed to continuously download data or download a large volume of data, which may lead to identification of an individual, at the website. Any investigator or other personnel involved in operations in related fields requesting a large volume of Category A data (e.g. genome-wide data) is required to register in the same way as Level 2 Data. For registration, provide the name, job title, contact address, intended use and e-mail address (as a general rule, the e-mail address issued by the institution) at the website (http://gwas.lifesciencedb.jp/gwasdb/catA.html) and send the application to DSRB. The ID and password will be issued to the registered user.

2. The user must agree to comply with the Terms and Conditions of Data Access posted on the website (http://gwas.lifesciencedb.jp/gwasdb/db_term_en.html) when using Data.

 

3. About Level 2 Data (Categories B and F)

Level 2 Data contain information that cannot identify an individual, and viewing of the information by investigators and other personnel involved in operations in related fields is considered meaningful by the data provider. Any investigator or other such personnel may view these Data freely by registration to DSRB.

 

1) Deposit of Data to Database

Any investigator or other personnel involved in operations in related fields wishing to deposit data must send the data to DSRB with the information including the name, institution, address (institution), e-mail address and outline of data. E-mail address: gwas@lifesciencedb.jp

 

2) Procedures for Application for Data Use

1. To use Level 2 Data, registration is required. For registration, provide the name, job title, contact address, intended use and e-mail address (as a general rule, the e-mail address issued by the institution) at the website (http://gwas.lifesciencedb.jp/gwasdb/catB.html for Category B; https://reseq.lifesciencedb.jp/resequence/registration_e.html for Category F) and send the application to DSRB. The ID and password will be issued to the registered user.

2. The user must agree to comply with the Terms and Conditions of Data Access posted on the website (http://gwas.lifesciencedb.jp/gwasdb/db_term_en.html) when using Data.

 

4. About Level 3 Data (Categories C and D)

Level 3 Data contain individualized information. To protect the privacy of research participants (sample providers), especially careful procedures are required for data sharing. For the purpose of this Policy, the data in this category are called “Controlled Access Data”.

 

1) Deposit of Data to Database

1. Any investigator or other personnel involved in operations in related fields wishing to deposit data must send the Application Form for Data Deposit (at http://gwas.lifesciencedb.jp/gwasdb/db_form_en.html)to DSRB as a preliminary step ([i]). DSRB will review the submitted Application on the following points, and will notify a recommendation of the data deposit to the applicant if the Board finds the data deposit appropriate ([ii]).

・ Does the informed consent support data sharing?
・ Was the procedure for utilizing the data upon withdrawal of informed consent by a research participant explained before obtaining the informed consent?

(Example) If irretrievably unlinked anonymized data have been generated from an individual’s sample, these data cannot be deleted from the database even if the informed consent of the individual is withdrawn.

・ Is the research project carried out on the samples that are worthy of data sharing?

2. The applicant who has notified a recommendation of data deposit must submit the designated application form to the ethical review board of his/her research institution and the Application Form for Data Deposit to DSRB for review ([iii]).

3. The applicant who has obtained the approvals of the Institutional Review Board (IRB) of his/her research institution and DSRB ([iv]) must generate irretrievably unlinked anonymized data from the analysis data and provide the anonymized data to the database of Disease Analysis DB Group ([v]).

 

2) Procedures for Application for Data Use

1. Any investigator or other personnel involved in operations in related fields wishing to use Level 3 Data must submit the Application Form for Data Access　(at http://gwas.lifesciencedb.jp/gwasdb/db_form_en.html) to DSRB (E-mail address: gwas@lifesciencedb.jp) ([vi]) for review of authorizing the data use. If IRB review is required by the regulations of the applicant’s institution, the applicant must submit an application for research program to the IRB of his/her institution ([vi]) for review.

2. The applicant for Level 3 Data use who has obtained the approval of DSRB (and the IRB of the applicant’s institution if required) ([vii]) must submit the DUC (http://gwas.lifesciencedb.jp/gwasdb/db_form/db_duc_en.pdf) specifying such items as bans on provision of data to a third party and any act leading to identification of an individual to DSRB ([viii], E-mail address: gwas@lifesciencedb.jp).

3. DSRB will issue the ID and password to the applicant after checking the DUC ([ix]).

4. The applicant may access the database by using the ID and password ([x]). (Depending on the format and volume of the data to be used, some data may be provided by using data storage media. The applicant must prepare the necessary media as instructed by DSRB.

5. The person using the data must report the use status to DSRB at the end of each fiscal year during Period of Data Use ([xi]).

(Format of the report is at http://gwas.lifesciencedb.jp/gwasdb/db_form_en.html)

6. The user of the data must comply with the terms and conditions of the DUC and the Security Guideline (http://gwas.lifesciencedb.jp/gwasdb/gwas_secr_en.html) when using the data.

　

 

The above policy and the documents covering above procedures will be published on the web for widespread awareness. DSRB reviews the provisions of this Sharing Policy as needed at any time. Any change of this Policy will be announced on the website in advance, and will take effect after a certain time period.

 

(Enforcement Date: Dec 1, 2009)

Members of Preparatory Committee for the Data Sharing Review Board
(Integrated Database Project - Disease Analysis DB Group)

Ryuichi IDA (Chairperson, Graduate School of Law, Kyoto Univ.)
Yoshimitsu FUKUSHIMA (School of Medicine, Shinshu Univ.)
Ituro INOUE (School of Medicine, Tokai Univ.)
Kazuto KATO (Inst. for Research in Humanities, Kyoto Univ.)
Kaori MUTO (Inst. of Medical Science, Univ. of Tokyo)
Katsushi TOKUNAGA (Graduate School of Medicine, Univ. of Tokyo)
Shoji TSUJI (Graduate School of Medicine, Univ. of Tokyo)
Shohei YONEMOTO (Research Center for Advanced Science and Technology, Univ. of Tokyo)

End of list