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 2023 must be based on KAKENHI projects that are newly adopted or ongoing in Fiscal Year 2023.

3.1 Technologies:

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

3.2 Devices:

1. DNA sequencer (short reads): Illumina Novaseq6000, HiSeq2500, MiSeq, iSeq etc.
2. DNA sequencer (long reads): PacBio Sequel2/Sequel2e, Nanopore MinION/GridION/PromethION, MGI T7/400 etc.
3. Single cell analysis: 10X Genomics Chromium, Standard BioTools (Fluidigm) C1 system etc.
4. Spatial multiomics analysis: 10X Genomics Visium, Xenium, PhenoCycler (CODEX)

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. WGS analysis of HeLa cells or PIGI analysis (Personally Identifying Genetic Information analysis. e.g. WGS, WES, whole-genome SNP array) using samples from the "1000 Genomes Project" are not accepted because that obtained sequence data must be registered in dbGAP but not in JGA. (See section 5. Publication and sharing of data)

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, Spatial multiomics 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. If you already have your own sequence data and only request to have support for bioinformatics analysis, please select "Data analysis only" in the material category. Applications requiring technologies or devices not available in the PAGS Support may be decline to support.
3. For RNAseq analysis, single cell analysis, and spatial multi-omics analysis, a detailed information on the availability or quality of the reference genome sequence is required.
4. Xenium is a new technology. It will operate on a limited trial support for a relatively small number of applicants.
5. 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.
6. 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)
7. The selection may be conducted in multiple pairs of the categories, depending on the number of applications.
8. Be sure to use the application form for the 2023 for application but not for previous ones.
9. The selected applicant's name, affiliation, and title of the KAKENHI project will be posted on the PAGS web site.
10. 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, https://www.ddbj.nig.ac.jp/index-e.html) or DRA (DDBJ Sequence Read Archive;https://www.ddbj.nig.ac.jp/dra/index-e.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 (https://humandbs.biosciencedbc.jp/en/) 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.
4. In principle, sequence data will be provided to the applicants by accessing DDBJ or other sources and downloading the data themselves. However, if the file size is large, the number of samples is huge, or the data is from human-derived samples, the data can be sent on a HDD/SSD, etc. In such cases, please consult with the PAGS team.
5. If the applicants does not publish a paper on the data obtained through the PAGS Support, we may consider releasing the sequence data in the public interest. In the case of de novo genome analysis, if there is no prospect of publication of the results of the analysis after approximately 3 years have from the final provision of the results, the genome data will be considered for release by the DDBJ or other sources.

Disclaimer

1. After providing the sequence data to the applicants, the PAGS Support will, in principle, keep the raw data for a period of three years, after which the raw data will be discarded.
2. Applicants are responsible for dealing with various inquiries from DDBJ, such as data release and postpone the hold-date after data submission. Therefore, please be sure to notify DDBJ of any change in contact information due to transfer or other reasons. The PAGS Support cannot be held responsible for unintentional release of data due to failure to receive notification from DDBJ.

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.
4. The PAGS Support does not allocate reagent costs or the reagents themselves to the applicants.

6.2 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 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. In this support, data is provided to the applicants via DDBJ (see section 5. Publication and sharing of data). 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.
5. The cost of any analysis performed by the applicants will be at the applicant's expense.

6.3 The way of the PAGS Support

1. The PAGS Support is a kind of collaboration between the applicant researchers and the PAGS team researchers.
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.

6.4 Publication

1. The results of the PAGS Support must be published in a paper as soon as possible.
2. 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.
3. 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 22H04925 (PAGS).
4. Similarly, if you issue a press release, please mention in the release that you have received the PAGS Support.
5. Thus, the proper credit, authorship or acknowledgement, should be given to the PAGS researchers, depending on their contribution.
6. The results obtained through the PAGS Support must be reported annually to the Ministry of Education, Culture, Sports, Science and Technology (MEXT). The selected applicants will be required to submit a progress report twice a year, even after the support has been completed. We would appreciate your cooperation in this regard.

6.5 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:
April 11 (Tuesday) to May 9 (Tuesday) Noon.

The start of the PAGS Support: Around early-September 2023.

Schedule of the selection process:

1. 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 late August. After this decision, the PAGS team will start to discuss the details of the support with the selected applicants.
2. An orientation will be held at the start of the PAGS Support. Attendance by the applicant and/or a person in charge is mandatory.

1. The information obtained during the selection process will be used for selection purposes (including after technical consultation).
2. Registered contacts may be notified of events such as information analysis workshops in support of genome advancement and information about the next open call for applications.
3. If you do not need such information, you can stop providing it by submitting an application to the secretariat.

Secretariat, Platform for Advanced Genome Science (PAGS)
Advanced Genomics Center, National Institute of Genetics Contact