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.


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.


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.


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.

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Equal contributing authors: Gheona Altarescu, Shai Carmi, and David A. Zeevi


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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.

Author information


  1. Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel

    • Daniel Backenroth PhD
    •  & Shai Carmi PhD
  2. Translational Genomics Lab, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel

    • Fouad Zahdeh PhD
    • , Yehuda Kling MSc
    • , Tzvia Rosen BSc
    • , Dina Kort BSc
    •  & David A. Zeevi PhD
  3. IVF Unit, Division of Obstetrics and Gynecology, Shaare Zedek Medical Center, Jerusalem, Israel

    • Aharon Peretz BSc
  4. Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel

    • Sharon Zeligson MSc
    • , Tal Dror BSc
    • , Sophie Kirshberg MSc
    • , Efrat Burak MSc
    • , Reeval Segel MD
    • , Ephrat Levy-Lahad MD
    •  & Gheona Altarescu MD
  5. Hebrew University Faculty of Medicine, Jerusalem, Israel

    • Reeval Segel MD
    • , Ephrat Levy-Lahad MD
    •  & Gheona Altarescu MD
  6. Division of Pediatric Endocrinology and Diabetes, Hadassah Hebrew University Medical Center, Jerusalem, Israel

    • David Zangen MD


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The authors declare no conflicts of interest.

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Correspondence to Shai Carmi PhD or David A. Zeevi PhD.

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