Dinh/Dinh 2013/NOTES/2014-4-7: Difference between revisions
Jump to navigation
Jump to search
>Dinh mNo edit summary |
>Dinh |
||
Line 1: | Line 1: | ||
= Cancer detection project meeting notes = | = Cancer detection project meeting notes = | ||
* We need to look into each cancer individually on the list | * We need to look into each cancer individually on the list, maybe rank the cancer samples from most preferable to least preferable. Once we get optimistic results, we can further ask for samples from other centers. We cannot realistically ask specifically for each stage of cancer, although having samples from multiple stages might be better. | ||
** prevalence | ** prevalence | ||
** treatment options for early detection (stage 1) | ** treatment options for early detection (stage 1) | ||
Line 8: | Line 8: | ||
** check Blueprint data to see how successful we were at capturing DNA purified from FFPE samples | ** check Blueprint data to see how successful we were at capturing DNA purified from FFPE samples | ||
** look into the kit for fixing degraded DNA | ** look into the kit for fixing degraded DNA | ||
* Noi said we successfully captured with 50 ng converted DNA before, and it is possible to obtain this much from 2 tubes of serum samples, however, we can also look into the amplified DNA from Illumina (can we perform capture on these samples?) | |||
=== RRBS option === | === RRBS option === | ||
* Dinh need to check the bayes classification algorithm | * Dinh need to check the bayes classification algorithm | ||
** Can it be used on RRBS data? We can downsample high coverage data to lower the effect of clonal reads on the analysis. | ** Can it be used on RRBS data? We can downsample high coverage data to lower the effect of clonal reads on the analysis. | ||
* Noi to check the input requirement for performing RRBS, can we perform RRBS in parallel on the test samples. | * Noi to check the input requirement for performing RRBS, can we perform RRBS in parallel on the test samples. |
Latest revision as of 00:20, 11 April 2014
Cancer detection project meeting notes[edit]
- We need to look into each cancer individually on the list, maybe rank the cancer samples from most preferable to least preferable. Once we get optimistic results, we can further ask for samples from other centers. We cannot realistically ask specifically for each stage of cancer, although having samples from multiple stages might be better.
- prevalence
- treatment options for early detection (stage 1)
- current diagnostic methods
- We need to ask for buffy coat (1 tube) and matched serum samples (2 tubes) per patient
- We need to ask for primary tumor samples, they might be Formalin-fixed, paraffin-embedded (FFPE) samples
- check Blueprint data to see how successful we were at capturing DNA purified from FFPE samples
- look into the kit for fixing degraded DNA
- Noi said we successfully captured with 50 ng converted DNA before, and it is possible to obtain this much from 2 tubes of serum samples, however, we can also look into the amplified DNA from Illumina (can we perform capture on these samples?)
RRBS option[edit]
- Dinh need to check the bayes classification algorithm
- Can it be used on RRBS data? We can downsample high coverage data to lower the effect of clonal reads on the analysis.
- Noi to check the input requirement for performing RRBS, can we perform RRBS in parallel on the test samples.