Question

Germline mutations occur in sperm or egg and are heritable, whereas somatic mutations occur in non-germ cells and are not heritable. Imagine that you are working in a laboratory which is studying on tissue/cell specific mutation pattern. You have all the tools (such as cell culture, imaging, sequencing etc.) and materials (such as genomic DNA, tissue and primary fibroblast cells from a human individuals). By using a NGS analysis please set up experiments/pipeline, including which method/algorithm would you use to map your data and call the somatic and germline mutations. You should focus on the question “How can you distinguish between germline and somatic mutations ?” (Please indicate the steps/methods/algorithms only, No need to indicate the details).

Answer 1

Answer :)

Germline mutations are analyzed by performing single-nucleotide variants (SNVs) in DNA from progeny not present in parental DNA, though somatic mutations are recognized as those present in solitary amplified fibroblasts or unamplified fibroblast replicas, but not exist in bulk DNA from the identical cell populations.

The following procedure is required for germline mutations:

• Take 10 male and female mice.
• Establish 20 breeding pairs.
• Take out tissue samples of kidney, spleen, and tail from pups and from the parents whichever when one of the deceased or became ill or after no pregnancies resulted from mattings over a period of 3 months.
• When all pairs stop breeding, chose the pair from all crosses with the longest breeding time and the most progenies for the initial WGS experiment.
• Then, 4 additional pedigrees, 2 from each of the reciprocal mattings, have to choose to undertake sequencing in an additional sequencing experiment.
• Tissues are stored at −80 °C directly after harvest. DNA is prepared using Qiagen DNeasy kits.
• Sequence the extracted DNA.
• Analyze the result to find out the germline mutations.

On the other hand, somatic mutations can simply be induced in organisms like drosophila. These are observable mutations and cannot transmit to offspring. Therefore, these mutations once induced are analyzed after showing phenotypes or death of the organism.