Pedigree-based estimation of human mobile element retrotransposition rates

• DOI: 10.1101/gr.247965.118
• Publication Date: 2019-10-01T18:49:19Z
• Authors: Julie Feusier; W. Scott Watkins; Jainy Thomas; Andrew Farrell; David J. Witherspoon; Lisa Baird; Hongseok Ha; Jinchuan Xing; Lynn B. Jorde
• Keywords: Retrotransposon; Pedigree chart; Alu element; Transposition (logic)

Germline mutation rates in humans have been estimated for a variety of types, including single-nucleotide and large structural variants. Here, we directly measure the germline retrotransposition rate three active retrotransposon elements: L1, Alu , SVA. We used tools calling mobile element insertions (MEIs) (MELT, RUFUS, TranSurVeyor) on blood-derived whole-genome sequence (WGS) data from 599 CEPH individuals, comprising 33 three-generation pedigrees. identified 26 de novo MEIs 437 births. The estimates elements, one 40 births, is roughly half using phylogenetic analyses, difference magnitude similar to that observed L1 63 births within range previous (1:20–1:200 births). SVA rate, much higher than estimate 900 Our large, pedigrees allowed us assess parent-of-origin effects timing insertion events either gametogenesis or early embryonic development. find statistically significant paternal bias retrotransposition. study represents first in-depth analysis dynamics human WGS