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Whole genome analysis reveals aneuploidies in early pregnancy loss in the horse

Shilton, Charlotte A.; Kahler, Anne; Davis, Brian W.; Crabtree, James R.; Crowhurst, James; McGladdery, Andrew J.; Wathes, D. Claire; Raudsepp, Terje; de Mestre, Amanda M.


Charlotte A. Shilton

Anne Kahler

Brian W. Davis

James R. Crabtree

James Crowhurst

Andrew J. McGladdery

D. Claire Wathes

Terje Raudsepp

Amanda M. de Mestre


The first 8 weeks of pregnancy is a critical time, with the majority of pregnancy losses occurring during this period. Abnormal chromosome number (aneuploidy) is a common finding in human miscarriage, yet is rarely reported in domestic animals. Equine early pregnancy loss (EPL) has no diagnosis in over 80% of cases. The aim of this study was to characterise aneuploidies associated with equine EPL. Genomic DNA from clinical cases of spontaneous miscarriage (EPLs; 14–65 days of gestation) and healthy control placentae (various gestational ages) were assessed using a high density genotyping array. Aneuploidy was detected in 12/55 EPLs (21.8%), and 0/15 healthy control placentae. Whole genome sequencing (30X) and digital droplet PCR (ddPCR) validated results. The majority of these aneuploidies have never been reported in live born equines, supporting their embryonic/fetal lethality. Aneuploidies were detected in both placental and fetal compartments. Rodents are currently used to study how maternal ageing impacts aneuploidy risk, however the differences in reproductive biology is a limitation of this model. We present the first evidence of aneuploidy in naturally occurring equine EPLs at a similar rate to human miscarriage. We therefore suggest the horse as an alternative to rodent models to study mechanisms resulting in aneuploid pregnancies.


Shilton, C. A., Kahler, A., Davis, B. W., Crabtree, J. R., Crowhurst, J., McGladdery, A. J., …de Mestre, A. M. (2020). Whole genome analysis reveals aneuploidies in early pregnancy loss in the horse. Scientific Reports, 10(1),

Journal Article Type Article
Acceptance Date Jul 20, 2020
Publication Date Aug 7, 2020
Deposit Date Aug 12, 2020
Publicly Available Date Aug 12, 2020
Journal Scientific Reports
Publisher Nature Research
Peer Reviewed Peer Reviewed
Volume 10
Issue 1
Public URL
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Related Public URLs


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