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PGRN PacBio® Twist Long Read Sequencing Grant

The PGRN is seeking proposals for a long-read sequencing project funded by PGRN, PacBio, and Twist. Applicants should make a proposal that takes advantage of free long-read sequencing of 49 pharmacogenes for up to 288 patient samples. Proposals must include a scientific question(s) that leverages the rich genetic information generated from long-read sequencing from at least one target on the 49-gene panel (Table 1) to improve prediction or understanding of a drug-related phenotype. Proposals must include samples from individuals of non-European ancestry.

Table 1. Gene Targets


















































* Full-gene coverage

+ Inclusion in a CPIC Level A guideline

Target regions for this panel is available at https://www.twistbioscience.com/resources/data-files/twist-alliance-long-read-pgx-panel-bed-file

PacBio systems are powered by Single Molecule, Real-Time (SMRT®) sequencing, a technology proven to produce highly accurate long reads, known as HiFi reads. HiFi reads allow for comprehensive variant calling of SNPs, Structural Variants, and Indels on a single platform. This results in reliable, high confidence variant calling for reportable pharmacogenomic variants, as well as the ability to identify novel and rare variants. Additionally, with direct haplotyping across pharmacogenes, HiFi sequencing offers direct phasing to enable unambiguous star (*) allele assignment and accurate phenotype predictions. HiFi sequencing can comprehensively capture important variation that may be missed with biased methods for genotyping, such as arrays or short-read sequencing, that may have gaps in coverage or rely on computational imputation for phasing. This grant will utilize the Twist Bioscience’s Alliance Long-Read PGx panel, a hybrid capture panel designed to cover 49 genes, including those with CPIC guidance, FDA recommendations, and genes of PGx research interest (see Table 1).

PacBio will provide four Revio™ SMRT® Cells for targeted sequencing of up to 288 samples, as well as cover sequencing costs and third-party reagents. Twist will provide probes free of charge for the Twist Alliance PGx panel. If needed, PacBio will also provide bioinformatic support free of charge, i.e., calling single nucleotide variants and structural variants from long-read sequencing dataset, but their intellectual contribution should be recognized properly (if any). There is no direct financial support associated with this award.

Proposals must include sequencing of a population that includes samples from at least 200 participants of non-European ancestry. Projects that include samples from ancestrally understudied groups, in whom clinical implementation could be advanced and/or novel alleles and haplotypes could be discovered, will be prioritized. Awardees are encouraged to also conduct analyses or variant frequency determination for genes that are not the focus of their scientific proposal. It is understandable that investigators may elect to focus on a subset of pharmacogenes on this panel that are most relevant to their drug of interest. However, for those genes they will not explore and publish on, they are strongly encouraged to make the sequencing data available via a public repository, such as NCBI’s Sequence Read Archive, assuming they have appropriate consent for such sharing.  The goal is to encourage the broadest scientific use of the data generated to benefit the pharmacogenomics research community.   

Proposals will be reviewed based on scientific merit and significance, the degree to which the proposal helps advance pharmacogenomics knowledge in understudied populations, and qualifications of the investigator team. It is anticipated that one PGRN-PacBio-Twist grant will be awarded this year.


Applicants must be PGRN members. Trainee members are eligible with faculty sponsorship documented in a letter of support.  An individual can be listed as a principal investigator (PI) or co-principal investigator (co-PI) on only one proposal to the PGRN Research Grant opportunities in each funding cycle.

  • Sample requirements: Applicants must have samples in their possession at the time application is submitted. Awardees will need to send extracted DNA (QC’d according to Qubit), minimum of 1000 ng of high-quality input genomic DNA per sample (50% ≥ 30 kb & 90% ≥ 10 kb). If awardee is US-based, tissue and/or blood may be sent (no saliva or buccal samples as high molecular weight DNA is needed).

Proposal (no more than 4 pages, excluding references, budget justification, biographical sketches, and letters of support)

The following sections should be included in your proposal. Applicants have flexibility in the organization, but all the following sections are required.

  1. Aims - no more than 1 page Background and significance
  2. Statement of diversity and inclusion of understudied populations - including description of the study population and knowledge gap to be filled with the research

3.       Research strategy and approach – Include statistical analysis. Studies focused on diverse and understudied populations are encouraged.

4.    Sample attestation  - attestation that samples are in hand and of sufficient quantity and quality to qualify for this funding mechanism

5.    Consnet attestation - attestation that the appropriate consent/permissions are in place for data sharing. This is not a requirement for funding but is strongly encouraged. If data sharing is prohibited due to individual or community consent processes and policies, please explicitly state this in your proposal  

6.    Timeline

Investigator(s) Biographical Sketch/CV

A brief (max 5 pages) NIH or equivalent biographical sketch is required for all investigators with funded effort on the grant. NIH biographical sketch format, instructions, and examples can be found here: https://grants.nih.gov/grants/forms/biosketch.htm.  If a biosketch is not available a CV (5 pages max) can be provided.

Budget and justification (half page)

Provide an overview budget justification that describes how the project will be funded/supported beyond the sequencing provided by this award. Budgets should be realistic and any additional funds available to support the project should be discussed at a high level. A detailed budget for items that are part of the infrastructure that support the project, but are outside of the scope of the grant, are not required.

Indirect fees are not allowed for this grant as the sponsor will provide in-kind support for sequencing only

Letters of Support

Your application should include letters of support from collaborators and other significant contributors.

Criteria for Review

Proposals will be reviewed by an Expert Review Panel organized by the PGRN Scientific Committee. Scorable criteria include significance, study design and analysis, diversity of the study population, and feasibility of completion during funding period. Investigators will be assessed as acceptable or not, consistent with new NIH criteria.  Each proposal will be reviewed by at least two reviewers and applicants with competitive scores will be reviewed for prioritization for funding by the entire review panel. Reviewer comments will be summarized and shared with all applicants after the final funding decision. The final selection for funding will be made by the PGRN Executive Council.

Application Due Date, Project Period, and Deliverables:

The grant is due by midnight, Pacific Time February 15, 2024. The project period for this grant is 1 year from the time of fund distribution.


  • A one-page final progress report will be due at the end of the 1-year grant or 6 months after receipt of data from PacBio, whichever is later.
  •  Presentation of data is required within 24 months after award notification and will include:
  • A PGRN Research in Progress seminar or abstract at the PGRN Annual Meeting.
  • A presentation selected in consultation with PacBio that may include a PacBio Webinar, speaking at local events/seminars, or scientific conferences (e.g., ASHG). Travel costs (if any) incurred by awardee will be covered by PacBio.  

·   Pre-print or manuscript within 30 months of award. Writing or analysis support from PacBio is available upon request. All published work supported by this grant must include the following acknowledgement: “This project was supported (or supported in part) by the PGRN PacBio Twist Long Read Sequencing Grant”

  • PacBio blog or vlog post (usually in promotion of a pre-print or manuscript but may ask for quotes about grant experience).
  • Data sharing: We encourage sequencing data of selected reference or consented samples to be released as a public data resource on pacb.com. These data may also be used for benchmarking PacBio’s variant calling algorithm. Investigators are strongly encouraged (but not required) to make all sequencing data publicly available within 12 months of manuscript acceptance via a public repository, such as NCBI’s Sequence Read Archive, assuming they have appropriate consent for such sharing. Investigators are also strongly encouraged (but not required) to submit novel haplotypes to PharmVar for designation. If data sharing is prohibited due to individual or community consent processes and policies, please explicitly state this in your proposal.


Combine the materials mentioned above into a single .pdf

Send as an attachment to: grants@pgrn.org

Deadline: Midnight (PST) February 15th, 2024

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