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Backenroth D, Altarescu G, Zahdeh F, Mann T, Murik O, Renbaum P, Segel R, Zeligson S, Hakam-Spector E, Carmi S, Zeevi DA. SHaploseek is a sequencing-only, high-resolution method for comprehensive preimplantation genetic testing. Sci Rep 2023; 13:18036. [PMID: 37865712 PMCID: PMC10590366 DOI: 10.1038/s41598-023-45292-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023] Open
Abstract
Recent advances in genomic technologies expand the scope and efficiency of preimplantation genetic testing (PGT). We previously developed Haploseek, a clinically-validated, variant-agnostic comprehensive PGT solution. Haploseek is based on microarray genotyping of the embryo's parents and relatives, combined with low-pass sequencing of the embryos. Here, to increase throughput and versatility, we aimed to develop a sequencing-only implementation of Haploseek. Accordingly, we developed SHaploseek, a universal PGT method to determine genome-wide haplotypes of each embryo based on low-pass (≤ 5x) sequencing of the parents and relative(s) along with ultra-low-pass (0.2-0.4x) sequencing of the embryos. We used SHaploseek to analyze five single lymphoblast cells and 31 embryos. We validated the genome-wide haplotype predictions against either bulk DNA, Haploseek, or, at focal genomic sites, PCR-based PGT results. SHaploseek achieved > 99% concordance with bulk DNA in two families from which single cells were derived from grown-up children. In embryos from 12 PGT families, all of SHaploseek's focal site haplotype predictions were concordant with clinical PCR-based PGT results. Genome-wide, there was > 99% median concordance between Haploseek and SHaploseek's haplotype predictions. Concordance remained high at all assayed sequencing depths ≥ 2x, as well as with only 1ng of parental DNA input. In subtelomeric regions, significantly more haplotype predictions were high-confidence in SHaploseek compared to Haploseek. In summary, SHaploseek constitutes a single-platform, accurate, and cost-effective comprehensive PGT solution.
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Affiliation(s)
- Daniel Backenroth
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gheona Altarescu
- PGT Unit, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Fouad Zahdeh
- Translational Genomics Lab, Medical Genetics Institute, Shaare Zedek Medical Center, Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel
| | - Tzvia Mann
- Translational Genomics Lab, Medical Genetics Institute, Shaare Zedek Medical Center, Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel
| | - Omer Murik
- Translational Genomics Lab, Medical Genetics Institute, Shaare Zedek Medical Center, Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel
| | - Paul Renbaum
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Reeval Segel
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Sharon Zeligson
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | | | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David A Zeevi
- Translational Genomics Lab, Medical Genetics Institute, Shaare Zedek Medical Center, Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel.
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Zhao H, Du C, Yang G, Wang Y. Diagnosis, treatment, and research status of rare diseases related to birth defects. Intractable Rare Dis Res 2023; 12:148-160. [PMID: 37662624 PMCID: PMC10468410 DOI: 10.5582/irdr.2023.01052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023] Open
Abstract
Rare diseases are diseases that occur at low prevalence, and most of them are chronic and serious diseases that are often life-threatening. Currently, there is no unified definition for rare diseases. The diagnosis, treatment, and research of rare diseases have become the focus of medicine and biopharmacology, as well as the breakthrough point of clinical and basic research. Birth defects are the hard-hit area of rare diseases and the frontiers of its research. Since most of these defects have a genetic basis, early screening and diagnosis have important scientific value and social significance for the prevention and control of such diseases. At present, there is no effective treatment for most rare diseases, but progress in prenatal diagnosis and screening can prevent the occurrence of diseases and help prevent and treat rare diseases. This article discusses the progress in genetic-related birth defects and rare diseases.
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Affiliation(s)
- Hongjuan Zhao
- Department of Gynecology and Obstetrics, Shandong Provincial Third Hospital, Shandong University, Ji'nan, China
| | - Chen Du
- Department of Gynecology and Obstetrics, Inner Mongolia Medical University Affiliated Hospital, Hohhot, China
| | - Guang Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Wang
- Department of Gynecology and Obstetrics, Inner Mongolia Medical University Affiliated Hospital, Hohhot, China
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Whole Genome Amplification in Preimplantation Genetic Testing in the Era of Massively Parallel Sequencing. Int J Mol Sci 2022; 23:ijms23094819. [PMID: 35563216 PMCID: PMC9102663 DOI: 10.3390/ijms23094819] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 12/16/2022] Open
Abstract
Successful whole genome amplification (WGA) is a cornerstone of contemporary preimplantation genetic testing (PGT). Choosing the most suitable WGA technique for PGT can be particularly challenging because each WGA technique performs differently in combination with different downstream processing and detection methods. The aim of this review is to provide insight into the performance and drawbacks of DOP-PCR, MDA and MALBAC, as well as the hybrid WGA techniques most widely used in PGT. As the field of PGT is moving towards a wide adaptation of comprehensive massively parallel sequencing (MPS)-based approaches, we especially focus our review on MPS parameters and detection opportunities of WGA-amplified material, i.e., mappability of reads, uniformity of coverage and its influence on copy number variation analysis, and genomic coverage and its influence on single nucleotide variation calling. The ability of MDA-based WGA solutions to better cover the targeted genome and the ability of PCR-based solutions to provide better uniformity of coverage are highlighted. While numerous comprehensive PGT solutions exploiting different WGA types and adjusted bioinformatic pipelines to detect copy number and single nucleotide changes are available, the ones exploiting MDA appear more advantageous. The opportunity to fully analyse the targeted genome is influenced by the MPS parameters themselves rather than the solely chosen WGA.
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Selektion zum Wohl des zukünftigen Kindes? Ethik Med 2021. [DOI: 10.1007/s00481-021-00665-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
ZusammenfassungDer Beitrag setzt sich kritisch mit dem Prinzip des prokreativen Wohltuns (principle of procreative beneficence, PB) von Julian Savulescu und seinen Implikationen für den Umgang mit der Präimplantationsdiagnostik (PID) auseinander. PB fordert angehende Eltern dazu auf, aus mehreren möglichen zukünftigen Kindern dasjenige auszuwählen, dessen Leben voraussichtlich am besten verlaufen wird. Paare mit Kinderwunsch sind danach zumindest unter bestimmten Umständen (z. B. wenn im Rahmen einer unabhängig indizierten IVF mehr Embryonen entstehen, als übertragen werden können) moralisch verpflichtet, eine PID in Anspruch zu nehmen, um die Weitergabe genetisch bedingter Krankheiten zu verhindern. Die Auswahl von Embryonen im Rahmen einer PID kann jedoch nur dann mit dem Wohlergehen des zukünftigen Kindes begründet werden, wenn man die entsprechende Wohltunspflicht mit Savulescu und Kahane als „unpersönliche“ moralische Pflicht versteht. PB wirft daher die Frage nach der Relevanz unpersönlicher Erwägungen für Entscheidungen über Fortpflanzung und Familiengründung auf. Gegen Savulescu und Kahane argumentiere ich dafür, reproduktive Verantwortung als einen integralen Aspekt elterlicher Verantwortung und damit als personenbezogene Verantwortung zu deuten, und verteidige diese Konzeption reproduktiver Verantwortung gegen Einwände, die sich aus einem von Savulescu und Kahane konstruierten hypothetischen Szenario – dem Röteln-Beispiel – ergeben.
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Grosso V, Marcolungo L, Maestri S, Alfano M, Lavezzari D, Iadarola B, Salviati A, Mariotti B, Botta A, D’Apice MR, Novelli G, Delledonne M, Rossato M. Characterization of FMR1 Repeat Expansion and Intragenic Variants by Indirect Sequence Capture. Front Genet 2021; 12:743230. [PMID: 34646309 PMCID: PMC8504923 DOI: 10.3389/fgene.2021.743230] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/26/2021] [Indexed: 11/30/2022] Open
Abstract
Traditional methods for the analysis of repeat expansions, which underlie genetic disorders, such as fragile X syndrome (FXS), lack single-nucleotide resolution in repeat analysis and the ability to characterize causative variants outside the repeat array. These drawbacks can be overcome by long-read and short-read sequencing, respectively. However, the routine application of next-generation sequencing in the clinic requires target enrichment, and none of the available methods allows parallel analysis of long-DNA fragments using both sequencing technologies. In this study, we investigated the use of indirect sequence capture (Xdrop technology) coupled to Nanopore and Illumina sequencing to characterize FMR1, the gene responsible of FXS. We achieved the efficient enrichment (> 200×) of large target DNA fragments (~60-80 kbp) encompassing the entire FMR1 gene. The analysis of Xdrop-enriched samples by Nanopore long-read sequencing allowed the complete characterization of repeat lengths in samples with normal, pre-mutation, and full mutation status (> 1 kbp), and correctly identified repeat interruptions relevant for disease prognosis and transmission. Single-nucleotide variants (SNVs) and small insertions/deletions (indels) could be detected in the same samples by Illumina short-read sequencing, completing the mutational testing through the identification of pathogenic variants within the FMR1 gene, when no typical CGG repeat expansion is detected. The study successfully demonstrated the parallel analysis of repeat expansions and SNVs/indels in the FMR1 gene at single-nucleotide resolution by combining Xdrop enrichment with two next-generation sequencing approaches. With the appropriate optimization necessary for the clinical settings, the system could facilitate both the study of genotype-phenotype correlation in FXS and enable a more efficient diagnosis and genetic counseling for patients and their relatives.
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Affiliation(s)
- Valentina Grosso
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Luca Marcolungo
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Simone Maestri
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Denise Lavezzari
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Barbara Iadarola
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Alessandro Salviati
- Department of Biotechnology, University of Verona, Verona, Italy
- GENARTIS srl, Verona, Italy
| | - Barbara Mariotti
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | - Annalisa Botta
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome "Tor Vergata", Rome, Italy
| | | | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Medical Genetics Section, University of Rome "Tor Vergata", Rome, Italy
- IRCCS Neuromed Mediterranean Neurological Institute, Pozzilli, Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV, United States
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Verona, Italy
- GENARTIS srl, Verona, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Verona, Italy
- GENARTIS srl, Verona, Italy
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