Need clarity on the concept of germline mutations

Question

[inayat45shaikh]

Hello everyone

I am analyzing some cancer samples wherein I have mutations have been detected from normal blood sample and tumor tissue sample of the same patient. Now I am getting mutation that are present in normal but not in tumor sample. What kind of mutation is this?? As far as i know germline mutation should be present in both normal as well as tumor sample as it is from birth and somatic is the one that is present only in tumor sample. How can we have unique mutations in normal sample. Ideally there should not be any unique mutations in normal sample. Am i thinking wrong??

[poisonAlien]

If the mutation in normal sample is heterozygous probably you're looking at LOH.

Answer 1

[trausch]

There are multiple possible reasons for "pseudo-somatic" mutations in the normal sample:

1. Tumor's harbor somatic structural rearrangements and if, for instance, a deletion "deletes" the ALT germline SNP allele then you get a "pseudo-somatic" call in the normal sample.
2. False positive variant calls in the normal sample that are absent in the tumor due to the random sequencing process, e.g., lack of tumor coverage.
3. Sample processing or library preparation artifacts that weren't removed in the data processing, e.g., missed adapter sequences, failures to detect PCR artifacts or FFPE-induced mutations.
4. Human errors (sample swaps, sample cross-contamination, etc.)

Answer 2

[michael.d.mclellan]

If you are mostly seeing mutations in DNMT3A, TET2, JAK1, ASXL1, in older individuals - these are typical markers of clonal hematopoiesis that increase with age.

• http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313872/figure/F1/
• http://www.nejm.org/doi/full/10.1056/NEJMoa1409405
• http://www.nejm.org/doi/full/10.1056/NEJMoa1408617

If you see odd shifts in the mutations spectrum...read this

• http://nar.oxfordjournals.org/content/early/2013/01/08/nar.gks1443.full
• D-ToxoG is a tool for removing the OxoG artifact from a set of SNV calls.
  • https://www.broadinstitute.org/cancer/cga/dtoxog

If you see that the somatic variants that mostly overlap germline dbSNPs (Check http://exac.broadinstitute.org/) you have cross contamination from other individuals.