Haploseek: a 24-hour all-in-one method for preimplantation genetic diagnosis (PGD) of monogenic disease and aneuploidy

Daniel Backenroth, Fouad Zahdeh, Yehuda Kling, Aharon Peretz, Tzvia Rosen, Dina Kort, Sharon Zeligson, Tal Dror, Sophie Kirshberg, Efrat Burak, Reeval Segel, Ephrat Levy-Lahad, David Zangen, Gheona Altarescu, Shai Carmi*, David A. Zeevi

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


Purpose: To develop an economical, user-friendly, and accurate all-in-one next-generation sequencing (NGS)-based workflow for single-cell gene variant detection combined with comprehensive chromosome screening in a 24-hour workflow protocol. Methods: We subjected single lymphoblast cells or blastomere/blastocyst biopsies from four different families to low coverage (0.3×–1.4×) genome sequencing. We combined copy-number variant (CNV) detection and whole-genome haplotype phase prediction via Haploseek, a novel, user-friendly analysis pipeline. We validated haplotype predictions for each sample by comparing with clinical preimplantation genetic diagnosis (PGD) case results or by single-nucleotide polymorphism (SNP) microarray analysis of bulk DNA from each respective lymphoblast culture donor. CNV predictions were validated by established commercial kits for single-cell CNV prediction. Results: Haplotype phasing of the single lymphoblast/embryo biopsy sequencing data was highly concordant with relevant ground truth haplotypes in all samples/biopsies from all four families. In addition, whole-genome copy-number assessments were concordant with the results of a commercial kit. Conclusion: Our results demonstrate the establishment of a reliable method for all-in-one molecular and chromosomal diagnosis of single cells. Important features of the Haploseek pipeline include rapid sample processing, rapid sequencing, streamlined analysis, and user-friendly reporting, so as to expedite clinical PGD implementation.

Original languageAmerican English
Pages (from-to)1390-1399
Number of pages10
JournalGenetics in Medicine
Issue number6
StatePublished - 1 Jun 2019

Bibliographical note

Funding Information:
The authors acknowledge the Shaare Zedek Mirsky intramural grant and thank Rabbi David Fuld for funding this research. S. C. thanks the Israel Science Foundation grant 407/17.

Publisher Copyright:
© 2018, American College of Medical Genetics and Genomics.


  • PGT
  • combined molecular PGD and comprehensive chromosome screening
  • low coverage sequencing
  • rapid diagnostic method


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