Platform for Advanced Genome Science (PAGS)

Genome-related technologies are being developed very rapidly and are essential for the field of life sciences. The mission of the project "Platform for Advanced Genome Science" (PAGS) is to advance technologies in genomics and bioinformatics and to provide them for a wide range of research projects that are supported by the Grants-in-Aid for Scientific Research (KAKENHI). This provision of the state-of-the-art technologies, hereafter called the "PAGS support", is expected to lead to the creation of cutting-edge research and the advancement of life sciences. Appropriate KAKENHI projects will be selected for the PAGS support 2018, for which many applications are welcome.

PAGS Support 2018: Call for applications

  1. Basic policy of PAGS support
  2. Eligible projects for application
  3. Technologies and devices provided by the PAGS support
  4. Selection of applications
  5. Publication and sharing of data
  6. Points of attention for the application
  7. Application period
  8. Schedule
  9. Contact

1. Basic policy of PAGS support

Projects for the PAGS support are selected from the applications which are based on KAKENHI projects. The major criteria for successful applications are as follows:

  1. Applications that are expected to produce outcome exceeding the initial plan of the applicant's KAKENHI project by receiving the PAGS support.
  2. Applications that contain challenging tasks that require advanced technologies.
  3. Applications that contain request for advanced technologies that are not available in commercial service.

The PAGS encourages female scientists, young scientists, and researchers who have newly started genome science research to apply. These applications, along with first-time applications, will be given a preference among the applications that are evaluated at the same level by the review committee.

The cost of the PAGS support will be covered by the PAGS' budget, but in order to provide the PAGS support for more applicants, the applicants might be required to bear a part of the cost.

2. Eligible projects for application

Applications for PGAS support 2018 must be based on the KAKENHI projects that are newly adopted or ongoing in Fiscal Year 2018.

3. Technologies and devices provided by the PAGS support

3.1 Technologies:

  1. de novo genome analysis, SNP/SNV analysis, Modification/Epigenome analysis, RNA analysis, Metagenome/Environment/Hologenome analysis, Ultrasensitive analysis, Bioinformatic analysis.

3.2 Devices:

  1. DNA sequencer (short reads): Illumina HiSeq3000/2500/1500, MiSeq, IonPGM etc.
  2. DNA sequencer (long reads): PacBio RSII/Sequel, NanoPore
  3. Single cell analysis: 10X genomics Chromium/GemCode, Fluidigm C1 system
  4. Optical genome mapping: BioNano Genomics Irys system

Note:

  1. Human GWAS analysis is NOT accepted.
  2. Only Sanger sequencing and/or genome library construction are NOT accepted except when they are judged to be necessary for whole genome analysis.
  3. For the analysis of recombinant organisms, the samples to be analyzed should be in the form of DNA or RNA. Applications that require the transfer of recombinant organisms from applicants to the PAGS are, in principle, NOT accepted.

4. Selection of applications

Selection for PAGS support is carried out by a Review Committee, which is composed of experts outside the PAGS. The major criteria for successful applications are as follows:

  1. Applications that are closely related to the initial plan of the applicant's KAKENHI project.
  2. Applications that are expected to produce outcome exceeding the initial plan of the applicant's KAKENHI project by providing the PAGS support.
  3. Applications that contain advanced technologies that are available in the PAGS support but not in commercial service.
  4. Applications that contain novelty with regards to the field of genome sciences.
  5. Applications that are feasible in terms of technology and costs.

4.1 Process of selection

Each applicant is asked to indicate the pair of the material and technology categories that best fits their application. The Review Committee evaluates applications in each pair of categories, and after examining the survey of candidate applications, finally selects the applications for the PAGS support (called hereafter "selected application").

4.2 Material categories

Human, Animal #1 (mouse, rat), Animal #2 (other than mouse), Plant, Microbe, and Data analysis only

4.3 Technology categories

De novo genome analysis, SNP/SNV analysis, Modification/Epigenome analysis, RNA analysis, Metagenome/Environment/Hologenome analysis, Ultrasensitive analysis, Bioinformatic analysis

Note:

  1. The selection may be conducted in multiple pairs of the categories, depending on the number of applications.
  2. Applications containing the analyses of human-derived materials are evaluated considering ethical regulations. In the case that the ethical procedure is due, applications to the PAGS support can be made by attaching the document submitted, or to be submitted, to the IRB of the applicant's institution.
  3. Analysis of some materials derived from foreign countries must abide by the countries' regulations based on the Convention on Biological Diversity and the Nagoya Protocol. The PAGS support cannot be provided if the analyses are not in compliance with these regulations.
  4. The selected applicant's name, affiliation, and title of the KAKENHI project will be posted on the PAGS web site.
  5. Information obtained during the selection process is used only for selection purposes.
  6. The name of the Review Committee member will be disclosed in the following fiscal year.

5. Publication and sharing of data

  1. The data and results obtained by the PAGS support should be published or shared by the research community in a timely and appropriate manner, such as a scientific paper and/or database.
  2. Nucleotide sequence data not including human individual genome information will be deposited in DDBJ (DNA Databank of Japan, http://www.ddbj.nig.ac.jp/) or DRA (DDBJ Sequence Read Archive; http://trace.ddbj.nig.ac.jp/dra/index.html) at the same time when the data are sent to the applicant. The data will be made open when a paper on the data is published or at the time determined by the applicants and the PAGS, in principle, 1 year after the end of the PAGS support.
  3. Human personal genome data will be deposited in NBDC JGA (http://humandbs.biosciencedbc.jp/) at the same time when the data are sent to the applicant. The data will not be made open, but after it is published in a scientific journal or at the previously determined time point, the data will be shared by the research community in a "restricted access" manner, in which the data can be accessed only by the researchers approved by the NBDC review committee. Information that does not lead to personal identification, such as statistical data, will be made open.

6. Points of attention for the application

6.1 Amount of analysis and costs

  1. Applicants should avoid unnecessarily excessive requests. In order to provide the PAGS support for as many applicants as possible, the selected applicants might be required to change the plan to reduce the project costs or to bear a part of the cost.
  2. When additional analysis is required, its cost will be, in principle, covered by the applicant.

6.2 Samples for analysis

  1. According to the budget rule, the PAGS support must finish by the end of the fiscal year; from April 2018 to March 2019. Samples for analysis should be sent to the PAGS team by the end of December, otherwise the PAGS support cannot be provided. If the approval from IRB is necessary, it is recommended that the approval process be completed by the end of October.
  2. Metadata for database submission must be attached to the sample sent to the PAGS team. Without the metadata, the PAGS support cannot be provided.
  3. In principle, DNA preparation must be performed by the applicants. Since both DNA quantity and quality are critical for any type of genome analysis, consultation with the PAGS team is recommended. If the sample is not suitable for analysis with respect to quantity and/or quality, subsequent analyses will not be performed and the countermeasures, i.e. re-preparation of sample, will be discussed between the applicants and PAGS team.
  4. In principle, RNA preparation for RNA-seq analysis must be performed by the applicants. Subsequent preprocessing will be performed based on discussions between the applicant and the PAGS team. It is critical that the expected target transcripts are included in the sample; thus, the applicant might be asked to perform some basic analyses, such as real time RT-PCR.

6.3 Form of the PAGS support

  1. The PAGS support is a kind of collaboration between the applicant researchers and the PAGS team researchers. Thus, the proper credit, authorship, or acknowledgement should be given to the PAGS researchers, depending on their contribution.
  2. Challenging subjects for the PAGS support are welcome and, in this case, since it requires an organized collaboration among the applicants, the research community, and the PAGS team, joint authorship will be required.
  3. One mission of the PAGS is to train bioinformaticists. The PAGS support offered by the bioinformatics team usually takes time and great effort. Thus, the PAGS would like to request that appropriate authorship to the bioinformatics team be given in the resulting paper.
  4. In order to develop advanced bioinformatics algorithms and/or software, real data obtained by the PAGS support are invaluable, and thus, the selected applicants will be required to allow the PAGS bioinformatics team members to share the data.
  5. Assistance for the IRB application will be provided to the selected applicants, if necessary.

6.4 Publication

  1. When a paper is published based on or containing the results of the PAGS support, you are requested to inform the PAGS secretariat. The PAGS secretariat will survey the relevant publication regularly, for which cooperation would be appreciated.
  2. Any publication resulting from the PAGS support must include the acknowledgement to the PAGS by describing its grant number: JSPS KAKENHI Grant Number 16H06279.
  3. The selected applicants will be required to submit a progress report every fiscal year.

6.5 Disclaimer

  1. Success of analysis is not guaranteed. It should be understood that the expected data or results may not be obtained due to various reasons, including unexpected accidents.
  2. The PAGS team will do their best in producing and providing data, but the data might have errors. Thus, it is recommended that the selected applicants check the data carefully before use.
  3. When re-analysis is needed, its cost will be covered by the applicant, unless the re-analysis is needed because of a PAGS-associated defect.

7. Application period

Application period for FY2018:
From May 7th (Monday) to June 1st (Friday) Noon.

Application form in English is available at "here"
Note that the Web application system is currently available in Japanese only.

8. Schedule

The start of the PAGS support: Around September 2018.

Schedule of the selection process:

After the application deadline, the Review Committee will perform a paper review and then select candidates for the PAGS support. The details of the analysis requested by the candidates will be interviewed by the PAGS members (called "hearing"). The results of the hearing are submitted to the Review Committee, and the committee will finally select the applicants for the PAGS support by the middle of August. After this decision, the PAGS team will start to discuss the details of the support with the selected applicants.

9. Contact

Secretariat, Platform for Advanced Genome Science (PAGS)
Advanced Genomics Center, National Institute of Genetics
E-mail : genome-sec@genome-sci.jp

Application form for PAGS support