Haploseek: a 24-hour all-in-one method for preimplantation genetic diagnosis (PGD) of monogenic disease and aneuploidy
| Autor: | David A. Zeevi, Sophie Kirshberg, Dina Kort, Sharon Zeligson, Aharon Peretz, Ephrat Levy-Lahad, Tal Dror, Gheona Altarescu, Yehuda Kling, Fouad Zahdeh, Tzvia Rosen, Reeval Segel, Daniel Backenroth, Efrat Burak, David Zangen, Shai Carmi |
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| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
DNA Copy Number Variations Biopsy Aneuploidy Fertilization in Vitro Computational biology 030105 genetics & heredity Biology Preimplantation genetic diagnosis Chromosomes DNA sequencing 03 medical and health sciences Pregnancy medicine Humans SNP Genetic Testing Preimplantation Diagnosis Genetics (clinical) Microarray analysis techniques Lymphoblast Haplotype Genetic Diseases Inborn High-Throughput Nucleotide Sequencing Chromosome medicine.disease Blastocyst 030104 developmental biology Haplotypes Female |
| Zdroj: | Genetics in Medicine. 21:1390-1399 |
| ISSN: | 1098-3600 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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