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 advanced technologies that are not available in commercial service.

Female scientists, young scientists, and researchers who have newly started genome science research are encouraged to apply the PAGS support. 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.

Applications for PAGS Support must be based on KAKENHI projects. Eligible KAKENHI projects for the 2nd Call for applications must be determined to be funded in FY2021.

3.1 Technologies:

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

3.2 Devices:

1. DNA sequencer (short reads): Illumina Novaseq6000, HiSeq3000/2500/1500, MiSeq, IonPGM etc.
2. DNA sequencer (long reads): PacBio Sequel/Sequel2, Nanopore MinION/GridION/PromethION etc.
3. Single cell analysis: 10X Genomics Chromium, Fluidigm C1 system
4. Spatial transcriptome analysis: 10X Genomics VISIUM

Note:

1. Human GWAS analysis is NOT accepted.
2. Applications for only Sanger sequencing and/or clone 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 provided 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. Since FY2021 is the final year of PAGS, it may be limited to provide support for bioinformatic analysis. See the section 6 for details.

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 need 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 fit their application. The Review Committee selects candidate applications in each pair of categories, and after examining the technical survey of the candidate applications with respect to feasibility and costs that will be performed by PAGS members, finally selects the applications, called hereafter "selected applications", for the PAGS support.

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, Single cell analysis, Bioinformatic analysis

Note:

1. As to novelty, application for simple cell clustering only does not meet the criteria for the PAGS support: plans to obtain novel findings through single cell analysis are needed.
2. The selection may be conducted in multiple pairs of the categories, depending on the number of applications.
3. 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.
4. Analysis of materials derived from countries other than Japan must abide by the countries' regulations based on the Convention on Biological Diversity and the Nagoya Protocol. The PAGS support could not be provided if the analyses are not in compliance with these regulations. (For details of ABS, http://abs.env.go.jp/english.html)
5. Be sure to use the application form for the 2021 2nd call for application but not for previous ones.
6. The selected applicant's name, affiliation, and title of the KAKENHI project will be posted on the PAGS web site.
7. Information obtained during the selection process is used only for selection purposes.
8. The name of the Review Committee member will be disclosed in the following fiscal year.

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 using the data is published or at the time determined by the applicants and the PAGS, in principle, 1 year after the finishing 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.

6.1 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.
3. Since single cell analysis takes much labor and cost, application for simple cell clustering only does not meet the criteria for the PAGS support: plans to obtain novel findings through single cell analysis are needed.

6.2 Bioinformatic analysis

1. Conventional bioinformatic analysis for just after sequencing, peak call, mapping, visualization by IGV, SNP/Indel call, analysis by Cell Ranger, etc. will be provided by the sequencing team, but, further bioinformatic analysis may not be available due to the shortage of the analysis period in the final year of PAGS. For the same reason, de novo genome analysis can be provided only when the target genome size is about 1 Gb or shorter.
2. For the same reason, applications for the category of “bioinformatic analysis only” may not be supported if the analysis will take long time.

6.3 Samples for analysis

1. According to the budget rule, the PAGS support must finish by the end of the fiscal year, thus the samples for the 2nd Call should be sent to the PAGS team by the end of October, 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.

6.4 The way 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 are welcome and, in this case, since it requires a collaboration between the applicants and the PAGS team, joint authorship will be required.
3. One important mission of the PAGS is to train bioinformaticists. The PAGS support provided 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.

6.5 Publication

1. When a paper is published based on or containing the results of the PAGS support, the information of the paper should be provided 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 at least by describing its grant number: JSPS KAKENHI Grant Number 16H06279(PAGS).
3. The selected applicants will be required to submit a progress report every fiscal year.

6.6 Disclaimer

1. Success of analysis is not guaranteed. It should be understood that data or results of the expected quality 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 should be covered by the applicant, unless the re-analysis is needed because of a PAGS-associated defect.

Application period of the call for applications:
From May 7 (Friday) to May 27 (Thursday) Noon.

The start of the PAGS support: Around early-August 2021.

Schedule of the selection process:

After the application is closed, the Review Committee will perform a paper review and then selects 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 early August. After this decision, the PAGS team will start to discuss the details of the support with the selected applicants.

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