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  • Technical artefacts create supposed fake mosaics

    Dear community,

    In recent months, we have observed an increase in incidents in which we find de novo variants in the index in a trio (exome and genome) analysis and the variant is present in 1-2% of the reads in the parents.
    Due to the accumulation, we rather assume a technical artefact of Illumina sequencing (NovaSeq6000) where we cannot explain where it comes from.
    Do you also see something like this in your data or do you have an idea where it could come from?

    For the following reasons we assume a technical artefact and not a real parental mosaic:

    1. exclusion of cotamination of the parental samples by the child's DNA, because the samples were processed in different batches at different times.
    2. we see this in both exomes and genomes (PCR free) and conclude that it is not due to the lib prep.
    3. there are cases where both parents carry the same supposedly heterozygous de novo variant (in child) in the mosaic. This is extremely unlikely.

    Thank you very much for your input
    Best regards
    EliG

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