GIAB Sep2016 Lightning rosenfeld dna from blood

1. The need for expanded sample
types from the GIAB samples
Jeffrey Rosenfeld
Rutgers Cancer Institute of New Jersey

2. Clinical Samples and Cell Lines
❖ Clinical sequencing is generally performed on fresh
blood
❖ Exception is cancer samples which are FFPE
preserved and have their own set of concerns
❖ The GIAB data are all being collected on DNA from cell
lines

3. Cell Lines
❖ Lymphoblastoid Cell Lines are created by infecting
PMBCs from a donor with Epstein-Barr Virus (EBV)
❖ Cell Lines are immortal and therefore can provide a
continuos collection of DNA from the sample

4. Cell Lines of children are not directly related to the parents
❖ Each cell line will have its own set of mutations
generated during the transformation
Mother
Son
Father

5. Cell Line Variation
❖ The Cell Line transformation is known to introduce changes into the genome
❖ Conrad et. al (2011)
❖ 20X increase in SNPs
❖ Could be caused by the number of passages of the cell lines
❖ The few papers that have looked at Structural Variations between cell lines and blood don’t
show many changes
❖ But, the SV callers that were used were not necessarily optimal and the data was not
nearly the quality we have for GIAB.
Yoruban NA12878
Blood
de novo mutations
35 49
Cell-Line
de novo mutations
643 952

6. Genomes of the Netherlands
❖ Sequenced 250 families with DNA from Blood (trios and
quads)
❖ Mean of 43 de novo mutations per child (range of 18-74)

7. RTG Calls on the AJ child
❖ Real Time Genomics has a method for calling de novo
mutations
❖ Prepared with the help of Francisco Da La Vega and Len
Trigg
❖ 4109 De Novo Loci
❖ 2214 SNPs
❖ Available on the ftp site

8. DNA from Blood
❖ A large amount of DNA could be derived from a single 1
pint unit of blood
❖ ~190 mg of DNA
❖ Can be frozen and distributed to different centers for
sequencing
❖ This blood DNA does not have any of the problems
related to a cell line

9. Results
1.A good picture of the variation in a genome produced
from cell-line transformation
2.A reference of variation for blood-derived DNA