Question: Which specimen type for normal paired sample in blood cancer?
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gravatar for jrkim9607
10 months ago by
jrkim96070
jrkim96070 wrote:

Hello. When sequencing cancer sample, it is recommended to sequence normal paired sample to exclude germline variants. For solid cancer, blood is normally used as norrmal paired sample. But for blood cancer like leukemia, blood cannot be used as normal paired sample, so other solid tissue like skin fibroblast should be used, which needs biopsy. However, in clinical context, it is hard to implement painful biopsy procedure for every patients.

Because body fluids including urine and saliva are all originated from blood, I think they may contain cfDNA from blood or lekocytes itself. And buccal swap sample also contains lekucytes along with epithelial cell.

When I only sequenced blood cancer sample without normal paired sample, I sometimes encountered situations that identifed genes or variants are known to be both germline and somatic, which is very confusing especially when the variant allele frequency is around 50%.

Are there any good ways to easily obtain a normal paired sample in blood cancer patients?

ADD COMMENTlink modified 10 months ago by pbpanigrahi180 • written 10 months ago by jrkim96070

Hello,

Please use appropriate tags. When you add appropriate tags, users that follow the tag (usually experts interested in helping others in that subject matter) get notified of your question, and this means you stand a better chance at getting a relevant, useful response faster.

You can edit your question and add a few more relevant tags.

ADD REPLYlink modified 10 months ago • written 10 months ago by RamRS21k
0
gravatar for pbpanigrahi
10 months ago by
pbpanigrahi180
pbpanigrahi180 wrote:

Probably you can check TCGA, how they have done for AML. TCGA says "Each AML genome was compared to the normal genome derived from a skin sample of the same patient.". You can read more in published paper of TCGA.

Hope this gives some hint.

ADD COMMENTlink written 10 months ago by pbpanigrahi180
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