Preferred TechDev Samples
From GSA
This priority list of hapmap samples will help to improve the selection of samples for technology development and pilot sequencing and analysis projects. The idea is to create a ranked list of hapmap samples in order of our current knowledge of their genetics, make sure that these samples have readily available DNA here at the Broad, and then press the sequencing platform, GAP, BSP and others to use these samples as much as possible for development work. This would ensure that development sequencing, genotyping, etc gets the maximum value from the samples by enabling comparisons with extensive validated genotypes, CNVs, and previous sequencing data. This is especially relevant now that the 1000 Genomes project has vastly expanded our genetic knowledge of a subset of the 1115 hapmap3 samples.
Following this scheme will make we can learn as much as possible from our exploratory tech dev work here.
The current ranking order is:
- Tier 1 -- 1000 genomes pilot 2 trios daughters (CEU + YRI)
- Tier 2 -- 1000 genomes pilot 2 trios parents (CEU + YRI)
- Tier 3 -- 1000 genomes pilot 1 samples also in pilot 3 with hapmap3 genotypes from CEU
- Tier 4 -- 1000 genomes pilot 1 samples also in pilot 3 with hapmap3 genotypes from YRI
- Tier 5 -- 1000 genomes pilot 1 samples also in pilot 3 with hapmap3 genotypes from JPT+CHB
Using the list
When selecting samples for technology development or pilot studies, please choose samples from this list in top to bottom. This will ensure that downstream analysis will be able to use the most detailed genotypes, CNV, indels in assessing the value of your dev. work or pilot
