Somatic mutation detection: a critical evaluation through simulations and reanalyses in oaks

Abstract

Mutation, the source of genetic diversity, is the raw material of evolution; however, it remains an understudied process in plants. Using simulations, we demonstrate that generic variant callers, commonly used to detect mutations in plants, are outperformed by methods developed for cancer research. Reanalysis of published data identified up to 7x more somatic mutations than initially reported, advocating the use of cancer research callers to boost mutation research in plants.

Causes of Mutation Rate Variability in Plant Genomes

“…The mutation rate of somatic tissues arising in cells that have already transitioned from the meristem toward differentiated tissues may be much higher but also considerably more difficult to measure because only a subset of sampled cells (as few as one) will contain each mutation (110,118). The trade-off between sensitivity and precision challenges somatic mutation calling at this scale: Mutation rates may increase late in tissue development [given elevated DNA repair observed in meristems (21,55,115,136,138)], yet true positives may be more difficult to distinguish since late-occurring mutations will be shared by fewer cells and thus supported by fewer sequencing reads.…”

How to best call the somatic mosaic tree?

“…In order to tackle these issues, Schmitt et al (2022) conducted an extensive simulation analysis to compare different variant callers. Then, they reanalyzed two large published datasets on pedunculate oak, Quercus robur.…”

“…I recommend the study of Schmitt et al (2022) first because it shows the benefit of using cancer callers in the study of somatic mutations, whatever the allelic fraction you are interested in at the end. You can select fixed heterozygotes if this is your ultimate target, but cancer callers allow you to have in addition a valuable overview of the allelic fractions of somatic mutations in your sample, and most do as well as SNP callers for fixed heterozygous mutations.…”

“…You can select fixed heterozygotes if this is your ultimate target, but cancer callers allow you to have in addition a valuable overview of the allelic fractions of somatic mutations in your sample, and most do as well as SNP callers for fixed heterozygous mutations. In addition, Schmitt et al (2022) provide the pipelines that allow investigating in silico data that should correspond to a given study design, encouraging to compare different variant callers rather than arbitrarily going with only one. We can anticipate that the study of somatic mutations in non-model species will increasingly attract attention now that multiple tissues of the same individual can be sequenced at low cost, and the study of Schmitt et al (2022) paves the way for questioning and choosing the best variant caller for the question one wants to address.…”

“…In addition, Schmitt et al (2022) provide the pipelines that allow investigating in silico data that should correspond to a given study design, encouraging to compare different variant callers rather than arbitrarily going with only one. We can anticipate that the study of somatic mutations in non-model species will increasingly attract attention now that multiple tissues of the same individual can be sequenced at low cost, and the study of Schmitt et al (2022) paves the way for questioning and choosing the best variant caller for the question one wants to address. Basically both referees think that you interpreted as performance differences between callers what are indeed different purposes.…”