Examples of Acceptable Project Milestones from Past Genomics Projects
Examples of appropriate milestones submitted for NIH grants that are active are below. These milestones provide an example of the detail that will be needed for first year milestones for the H3Africa applications. H3Africa applicants are asked to provide yearly milestones. The milestones for subsequent years do not need to be as detailed as seen in the examples below.
Example 1: Production Milestones: Detailed Plan for Years 01-04
- Project Coordinators hired and trained
- Clinical Subjects Coordinator hired and trained
- Literature printed
- Pamphlet about project
- Consent Forms
- Health History
- Faculty and/or residents trained in sample collection
- Initial database established
- Collection begins at clinics
- Sample processing, testing and validation completed
- DNA samples tested and validated, rNA amplified from samples
- rNA spacer DNA from samples amplified and sequenced using Applied Biosystems Analyzer
- Test sequence analysis begins on subject samples (3 – 6 months)
- DNA amplified and sequenced from rRNA locus with Titanium technology
˜ 80 samples processed (sequenced: 4 runs of 20 samples per run)
- DNA amplified from clones sequenced with Titanium technology
˜ 4 samples processed and analyzed
- DNA amplified from clones sequenced with Illumina technology
˜ 16 samples processed and analyzed
- Database completed and all personnel trained
- Web GUI interface completed
- Remote access established, tested, security measures validated
- Patient visitors now routinely processed by Clinical Coordinators
- Completed initial visits to the clinic by twins for genetic twin studies
- Initial twin samples collected
- 10 twin pairs processed
- Sequencing of samples of amplified rRNA using Titanium technology should now be routine
- 160 samples processed with Titanium technology
- Initial statistical comparisons of conditions
- Metagenome sequencing with Titanium technology
- 4 samples completed &analyzed
- Sequencing of samples by Illumina Technology
- 32 clones processed
- Mechanism for sequence data release
- Data deposited on web for public access (ftp)
- All patients at clinic are requested to join protocol
- Database with web interface in full operation
- Initial 40 twin pairs visits to clinic complete
- 240 initial samples (40 twin pairs, 160 patient samples) sequenced on Titanium technology
- 64 clones sequenced with Illumina Technology
- 8 samples sequenced with Titanium Technology
- Analysis pipeline in full operation
- Statistical comparison of samples begins
- New Titanium Technology instrument/ancillary equipment purchased and installed
- 400 additional samples subjected to rRNA sequencing with the Titanium Technology (cumulative total 640)
- 30 twin pairs (cumulative total 70 pairs)
- 340 clinical samples (cumulative total 500)
- 80 additional clones sequenced with Illumina Technology (total 144)
- selected samples
- 16 samples selected for sequencing (total 28)
- 800 additional samples processed (1440 total)
- 30 more twin pairs (total 100)
- 740 more clinical samples (total 1240)
- 120 additional clones sequenced (264 total)
- 20 additional sequences (48 total)
Aim 1: Longitudinal Study of Disease Patients
1.1. Recruit and collect clinical samples from 15 subjects, as follows:
- Full Internal Review Board (IRB) approval has already been obtained for this study. Consents are specifically tailored for sampling, sequencing, and data deposition.
- Clinical and molecular data already being tracked with SOFTWARE, which assigns unique barcodes to clinical samples and resulting biomaterials, records accurate storage location of all clinical materials, and maintains detailed records in a HIPAA-compliant manner.
- Recruit 10 pediatric patients with moderate to severe DISEASE. This will involve 20 patient visits: 10 patients at baseline with 5 returning for longitudinal survey, both during active DISEASE and post-DISEASE [20 patient visits = 10 (baseline) + 5 (flare) + 5 (post-DISEASE)].
- Recruit 5 pediatric age-matched healthy controls for 5 patient visits.
- Collect 175 clinical samples for sequencing. Each of the 7 clinical sites receive 25 subjects (20 DISEASED + 5 controls) and collect clinical samples from the subjects [175 clinical samples = 7 sites x 25 patient visits]. DNA from these 175 clinical samples will be prepared as follows:
- In the first 6 months:
Collect a total of 75 clinical samples from 5 of the 7 sites. Each of the 7 sites will provide 10 baseline samples and 5 controls.
- In the first 12 months:
Collect a total of 50 samples from5 of the 7 sites. Each site will provide 5 samples from 5 DISEASED and 5 post-DISEASE subjects. Samples will be stored for future analysis.
- Obtain 50 isolate libraries. To derive isolates, swab and culture samples from 25 subjects at 2 clinical sites. This process will create a 50 isolate library [50 Isolates = 2 sites x 25 subjects]. From each library, select 100 morphologically distinct bacterial colonies for analysis.
- In the first 6 months:
Process DNA from colonies from 30 libraries. Composition of the libraries is as follows: 10 baseline samples from the DISEASE pool from 2 sites (total 20) and 5 control sample
- In the first 12 months:
Process DNA from colonies from the remaining 20 libraries
1.2. 16S rRNA Sanger-based sequencing of clinical samples and isolates.
- Generate full-length 16S rRNA gene sequences from 75 (of the 175 total) clinical samples: 86,400 Sanger-based sequence reads = 75 clinical samples x 384 clones x 3 primers.
- Generate full-length 16S rRNA gene sequences from 30 (of 50 total) libraries. From each library, 100 morphologically distinct colonies are sequenced: 9,000 Sanger-based sequence reads = 30 libraries x 100 colonies/library x 3 primers/16S rRNA gene.
1.3. Sequence analysis
- Assemble a comprehensive database of high-quality, aligned, and checked sequences.
- Analyze community membership and structure of skin samples from DISEASE patients compared to age-matched controls using the SOFTWARE package.
- Analyze tree of sequences using the SOFTWARE package to determine existence of lineages unique or over/under-represented among samples from DISEASE patients.
- Integrate 16S rRNA sequences from isolates with sequence surveys from clinical sample information, assigning taxonomy. Identify novel isolates for subjecting to whole-genome shotgun sequencing.