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

doi:10.1038/s41436-018-0351-7

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 journal › Article › peer-review

40 Scopus citations

Abstract

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 language	English
Pages (from-to)	1390-1399
Number of pages	10
Journal	Genetics in Medicine
Volume	21
Issue number	6
DOIs	https://doi.org/10.1038/s41436-018-0351-7
State	Published - 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.

Keywords

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

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10.1038/s41436-018-0351-7

Cite this

Backenroth, D., Zahdeh, F., Kling, Y., Peretz, A., Rosen, T., Kort, D., Zeligson, S., Dror, T., Kirshberg, S., Burak, E., Segel, R., Levy-Lahad, E., Zangen, D., Altarescu, G., Carmi, S., & Zeevi, D. A. (2019). Haploseek: a 24-hour all-in-one method for preimplantation genetic diagnosis (PGD) of monogenic disease and aneuploidy. Genetics in Medicine, 21(6), 1390-1399. https://doi.org/10.1038/s41436-018-0351-7

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

abstract = "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.",

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

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doi = "10.1038/s41436-018-0351-7",

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Backenroth, D, Zahdeh, F, Kling, Y, Peretz, A, Rosen, T, Kort, D, Zeligson, S, Dror, T, Kirshberg, S, Burak, E, Segel, R, Levy-Lahad, E, Zangen, D, Altarescu, G, Carmi, S & Zeevi, DA 2019, 'Haploseek: a 24-hour all-in-one method for preimplantation genetic diagnosis (PGD) of monogenic disease and aneuploidy', Genetics in Medicine, vol. 21, no. 6, pp. 1390-1399. https://doi.org/10.1038/s41436-018-0351-7

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T2 - a 24-hour all-in-one method for preimplantation genetic diagnosis (PGD) of monogenic disease and aneuploidy

AU - Backenroth, Daniel

AU - Zahdeh, Fouad

AU - Kling, Yehuda

AU - Peretz, Aharon

AU - Rosen, Tzvia

AU - Kort, Dina

AU - Zeligson, Sharon

AU - Dror, Tal

AU - Kirshberg, Sophie

AU - Burak, Efrat

AU - Segel, Reeval

AU - Levy-Lahad, Ephrat

AU - Zangen, David

AU - Altarescu, Gheona

AU - Carmi, Shai

AU - Zeevi, David A.

PY - 2019/6/1

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N2 - 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.

AB - 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.

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

Abstract

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Keywords

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