Frequency and spectrum of mutations in human sperm measured using duplex sequencing correlate with trio-based de novo mutation analyses
Axelsson, J.; LeBlanc, D.; Shojaeisaadi, H.; Meier, M. J.; Fitzgerald, D. M.; Nachmanson, D.; Carlson, J.; Golubeva, A.; Higgins, J.; Smith, T.; Lo, F. Y.; Pilsner, R.; Williams, A.; Salk, J.; Marchetti, F.; Yauk, C.
Show abstract
De novo mutations (DNMs) are drivers of genetic disorders. However, the study of DNMs is hampered by technological limitations preventing accurate quantification of ultra-rare mutations. Duplex Sequencing (DS) theoretically has < 1 error/billion base-pairs (bp). To determine the utility of DS to quantify and characterize DNMs, we analyzed DNA from blood and spermatozoa from six healthy, 18-year-old Swedish men using the TwinStrand DS mutagenesis panel (48 kb spanning 20 genic and intergenic loci). The mean single nucleotide variant mutation frequency (MF) was 1.2 x 10-7 per bp in blood and 2.5 x 10-8 per bp in sperm, with the most common base substitution being C>T. Blood MF and substitution spectrum were similar to those reported in blood cells with an orthogonal method. The sperm MF was in the same order of magnitude and had a strikingly similar spectrum to DNMs from publicly available whole genome sequencing data from human pedigrees (1.2 x 10-8 per bp). DS revealed much larger numbers of insertions and deletions in sperm over blood, driven by an abundance of putative extra-chromosomal circular DNAs. The study indicates the strong potential of DS to characterize human DNMs to inform factors that contribute to disease susceptibility and heritable genetic risks.
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