Question: NA12878 vs RM 8398 Reference DNA
1
gravatar for bruceracey
11 weeks ago by
bruceracey10
bruceracey10 wrote:

Does anyone know what the difference is between the Coriell sample NA12878 and the NIST sample RM 8398? As far as I can tell, RM 8398 and NA12878 are extracted from the exact same cell lines, except the Coriell sample is $84 and the NIST sample is $453. Links are below:

NA12878: https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=NA12878&Product=DNA

RM 8398: https://www-s.nist.gov/srmors/view_detail.cfm?srm=8398

Any help would be great! Thank you.

validation ngs • 198 views
ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by bruceracey10

Oh wow, I thought I read that but apparently I glossed over the part where they wrote "DNA is currently available from this same cell line from Coriell with the number NA12878, but it may contain small differences in the DNA sequence due to different mutations occurring in different batches of the cells.".

Thanks for the response!

ADD REPLYlink written 11 weeks ago by bruceracey10
4
gravatar for Garan
11 weeks ago by
Garan540
United Kingdom
Garan540 wrote:

The NIST source preparation material discusses how RM8398 was extracted from the NA12878 cell. It notes that the cell lines are subject to mutation and so the sequence can start to vary over time. NIST controls for this by producing a large batch of NA12878 and mixing the extracted DNA to reduce the variation between the pooled DNA sequences (at least that's what I understand from the notes):

SOURCE PREPARATION ( 1)Coriell Institute for Medical Research(Camden, NJ) grew a large growth of their cell line GM12878 in multiple stages, produced approximately 83 mg of extracted DNA, and then mixed the DNA and aliquoted it into vials, with the DNA divided approximately equally into vials. Specifically, the pool of cells was split into three separate volumes for DNA extraction, and the extracted DNA was re-pooled and gently mixed at 4 °C for greater than 48 h before the material was aliquoted automatically into vials of 10 μg of DNA. Note: This RM is isolated DNA rather than live cells because cells are less stable and can mutate with each cell division, so that the sequence of live cells may not be stable over time. Extracting DNA from a large batch of cells helps ensure that all vials contain essentially the same sequences of DNA. DNA is currently available from this same cell line from Coriell with the number NA12878, but it may contain small differences in the DNA sequence due to different mutations occurring in different batches of the cells.

Stability: Stability was assessed by measuring the size distribution of DNA with pulsed field gel
electrophoresis (PFGE). Using PFGE, no change in the size distribution was detected after storage at 4 °C for eight weeks, but the size distribution decreased significantly when stored at 37 °C for 8 weeks. In addition, no change was detected after five freeze-thaw cycles, pipetting vigorously, or vortexing. However, because we only measure size distribution, we still recommend storing at –20 °C for long periods of time and limiting freeze-thaw cycles, particularly if the measurement method requires long, undamaged DNA fragments.

Homogeneity: NIST sequenced multiple vials in an experiment designed to assess homogeneity of the samples. No significant differences were detected in terms of proportion of variant or copy number, except for a few in regions known to be susceptible to systematic errors. These results, along with the mixing of DNA before aliquoting, provide confidence that no large differences in small variants or copy number are likely to exist between different vials

I guess the extra QC steps and the fact that it's this sample that was used for GIAB variant calls would make RM9398 the gold standard if you were looking to validate your pipeline etc.

https://www-s.nist.gov/srmors/certificates/8398.pdf

ADD COMMENTlink written 11 weeks ago by Garan540
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