Shallow whole genome sequencing is well suited for the detection of chromosomal aberrations in human blastocysts

A validation study on 47 embryonic trophectoderm samples demonstrates that shallow whole genome sequencing is a preferable alternative for array comparative genomic hybridization in detecting structural and numerical chromosomal rearrangements in preimplantation genetic diagnosis.


Lieselot Deleye, M.Sc., Annelies Dheedene, M.Sc., Dieter De Coninck, Ph.D., Tom Sante, M.Sc., Christodoulos Christodoulou, M.Sc., Björn Heindryckx, Ph.D., Etienne Van den Abbeel, Ph.D., Petra De Sutter, Ph.D., Dieter Deforce, Ph.D., Björn Menten, Ph.D., Filip Van Nieuwerburgh, Ph.D.

Volume 104, Issue 5, Pages 1276-1285



To add evidence that massive parallel sequencing (MPS) is a valuable substitute for array comparative genomic hybridization with a resolution that is more appropriate for preimplantation genetic diagnosis in translocation carriers.


Study of diagnostic accuracy.


University hospital setting.


Fifteen patients with a balanced structural rearrangement were included in the study: eight reciprocal translocations, four Robertsonian translocations, two inversions, and one insertional translocation.


Trophectoderm biopsy was performed on 47 blastocysts.

Main Outcome Measure(s):

In the current study, shallow whole genome MPS on a NextSeq500 (Illumina) and Ion Proton (Life Technologies) instrument was performed in parallel on 47 WGA amplified trophectoderm samples. Data analyses were performed using the QDNAseq algorithm implemented in Vivar.


In total, 5 normal and 42 abnormal embryos were analyzed. All aberrations previously detected with array comparative genomic hybridization could be readily detected in the MPS data using both technologies and were correctly identified. The smallest detected abnormality was a ∼4.5 Mb deletion/duplication.


This study demonstrates that shallow whole genome sequencing can be applied efficiently for the detection of numerical and structural chromosomal aberrations in embryos, equaling or even exceeding the resolution of the routinely used microarrays.

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