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Janssen AEJ, Koeck RM, Essers R, Cao P, van Dijk W, Drüsedau M, Meekels J, Yaldiz B, van de Vorst M, de Koning B, Hellebrekers DMEI, Stevens SJC, Sun SM, Heijligers M, de Munnik SA, van Uum CMJ, Achten J, Hamers L, Naghdi M, Vissers LELM, van Golde RJT, de Wert G, Dreesen JCFM, de Die-Smulders C, Coonen E, Brunner HG, van den Wijngaard A, Paulussen ADC, Zamani Esteki M. Clinical-grade whole genome sequencing-based haplarithmisis enables all forms of preimplantation genetic testing. Nat Commun 2024; 15:7164. [PMID: 39223156 PMCID: PMC11369272 DOI: 10.1038/s41467-024-51508-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 08/08/2024] [Indexed: 09/04/2024] Open
Abstract
High-throughput sequencing technologies have increasingly led to discovery of disease-causing genetic variants, primarily in postnatal multi-cell DNA samples. However, applying these technologies to preimplantation genetic testing (PGT) in nuclear or mitochondrial DNA from single or few-cells biopsied from in vitro fertilised (IVF) embryos is challenging. PGT aims to select IVF embryos without genetic abnormalities. Although genotyping-by-sequencing (GBS)-based haplotyping methods enabled PGT for monogenic disorders (PGT-M), structural rearrangements (PGT-SR), and aneuploidies (PGT-A), they are labour intensive, only partially cover the genome and are troublesome for difficult loci and consanguineous couples. Here, we devise a simple, scalable and universal whole genome sequencing haplarithmisis-based approach enabling all forms of PGT in a single assay. In a comparison to state-of-the-art GBS-based PGT for nuclear DNA, shallow sequencing-based PGT, and PCR-based PGT for mitochondrial DNA, our approach alleviates technical limitations by decreasing whole genome amplification artifacts by 68.4%, increasing breadth of coverage by at least 4-fold, and reducing wet-lab turn-around-time by ~2.5-fold. Importantly, this method enables trio-based PGT-A for aneuploidy origin, an approach we coin PGT-AO, detects translocation breakpoints, and nuclear and mitochondrial single nucleotide variants and indels in base-resolution.
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Affiliation(s)
- Anouk E J Janssen
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW Research Institute Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Rebekka M Koeck
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW Research Institute Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Rick Essers
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW Research Institute Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Ping Cao
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW Research Institute Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Wanwisa van Dijk
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Marion Drüsedau
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Jeroen Meekels
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Burcu Yaldiz
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Maartje van de Vorst
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Bart de Koning
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Debby M E I Hellebrekers
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Su Ming Sun
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Malou Heijligers
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Sonja A de Munnik
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Chris M J van Uum
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Jelle Achten
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Lars Hamers
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Marjan Naghdi
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW Research Institute Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Faculty of Psychology and Neuroscience, Section Applied Social Psychology, Maastricht University, Maastricht, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ron J T van Golde
- Department of Obstetrics and Gynaecology, GROW Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Guido de Wert
- Department of Health, Ethics and Society, GROW Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- CAPHRI Research Institute for Public Health and Primary Care, Maastricht University, Maastricht, The Netherlands
| | - Jos C F M Dreesen
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Christine de Die-Smulders
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW Research Institute Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Edith Coonen
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
- Department of Obstetrics and Gynaecology, GROW Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW Research Institute Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Aimee D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
- Department of Genetics and Cell Biology, GROW Research Institute Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Masoud Zamani Esteki
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands.
- Department of Genetics and Cell Biology, GROW Research Institute Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands.
- Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden.
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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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Xie P, Hu X, Kong L, Mao Y, Cheng D, Kang K, Dai J, Zhao D, Zhang Y, Lu N, Wan Z, Du R, Xiong B, Zhang J, Tan Y, Lu G, Gong F, Lin G, Liang B, Du J, Hu L. A novel multifunctional haplotyping-based preimplantation genetic testing for different genetic conditions. Hum Reprod 2022; 37:2546-2559. [PMID: 36066440 DOI: 10.1093/humrep/deac190] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 07/24/2022] [Indexed: 11/13/2022] Open
Abstract
STUDY QUESTION Is there an efficient and cost-effective detection platform for different genetic conditions about embryos? SUMMARY ANSWER A multifunctional haplotyping-based preimplantation genetic testing platform was provided for detecting different genetic conditions. WHAT IS KNOWN ALREADY Genetic disease and chromosomal rearrangement have been known to significantly impact fertility and development. Therefore, preimplantation genetic testing for aneuploidy (PGT-A), monogenic disorders (PGT-M) and structural rearrangements (PGT-SR), a part of ART, has been presented together to minimize the fetal genetic risk and increase pregnancy rate. For patients or their families who are suffering from chromosome abnormality, monogenic disease, unexplained repeated spontaneous abortion or implantation failure, after accepting genetic counseling, they may be suggested to accept detection from more than one PGT platforms about the embryos to avoid some genetic diseases. However, PGT platforms work through different workflows. The high costliness, lack of material and long-time operation of combined PGT platforms limit their application. STUDY DESIGN, SIZE, DURATION All 188 embryonic samples from 43 families were tested with HaploPGT platform, and most of their genetic abnormalities had been determined by different conventional PGT methods beforehand. Among them, there were 12 families only carrying structural rearrangements (115 embryos) in which 9 families accepted implantation and 5 families had normal labor ART outcomes, 7 families only carrying monogenic diseases (26 embryos) and 3 families carrying both structural rearrangements and monogenic diseases (26 embryos). Twelve monopronucleated zygotes (1PN) samples and 9 suspected triploid samples were collected from 21 families. PARTICIPANTS/MATERIALS, SETTINGS, METHODS Here, we raised a comprehensive PGT method called HaploPGT, combining reduced representation genome sequencing, read-count analysis, B allele frequency and haplotyping analysis, to simultaneously detect different genetic disorders in one single test. MAIN RESULTS AND THE ROLE OF CHANCE With 80 million reads (80M) genomic data, the proportion of windows (1 million base pairs (Mb)) containing two or more informative single nucleotide polymorphism (SNP) sites was 97.81%, meanwhile the genotyping error rate stabilized at a low level (2.19%). Furthermore, the informative SNPs were equally distributed across the genome, and whole-genomic haplotyping was established. Therefore, 80M was chosen to balance the cost and accuracy in HaploPGT. HaploPGT was able to identify abnormal embryos with triploid, global and partial loss of heterozygosity, and even to distinguish parental origin of copy number variation in mosaic and non-mosaic embryos. Besides, by retrospectively analyzing 188 embryonic samples from 43 families, HaploPGT revealed 100% concordance with the available results obtained from reference methods, including PGT-A, PGT-M, PGT-SR and PGT-HLA. LIMITATIONS, REASON FOR CAUTION Despite the numerous benefits HaploPGT could bring, it still required additional family members to deduce the parental haplotype for identifying balanced translocation and monogenic mutation in tested embryos. In terms of PGT-SR, the additional family member could be a reference embryo with unbalanced translocation. For PGT-M, a proband was normally required. In both cases, genomic information from grandparents or parental siblings might help for haplotyping theoretically. Another restriction was that haploid, and diploid resulting from the duplication of a haploid, could not be told apart by HaploPGT, but it was able to recognize partial loss of heterozygosity in the embryonic genome. In addition, it should be noted that the location of rearrangement breakpoints and the situation of mutation sites were complicated, which meant that partial genetic disorders might not be completely detected. WIDER IMPLICATIONS OF THE FINDINGS HaploPGT is an efficient and cost-effective detection platform with high clinical value for detecting genetic status. This platform could promote the application of PGT in ART, to increase pregnancy rate and decrease the birth of children with genetic diseases. STUDY FUNDING/COMPETING INTEREST(S) This study was supported by grants from the National Natural Science Foundation of China (81873478, to L.H.), National Key R&D Program of China (2018YFC1003100, to L.H.), the Natural Science Foundation of Hunan Province (Grant 2022JJ30414, to P.X.), Hunan Provincial Grant for Innovative Province Construction (2019SK4012) and the Scientific Research Foundation of Reproductive and Genetic Hospital of China International Trust & Investment Corporation (CITIC)-Xiangya (YNXM-201910). Haplotyping analysis has been licensed to Basecare Co., Ltd. L.K., Y.M., K.K., D.Z., N.L., J.Z. and R.D. are Basecare Co., Ltd employees. The other authors declare no competing interests. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Pingyuan Xie
- Genetic Department, Hunan Normal University School of Medicine, Changsha, Hunan, China.,Genetic Department, National Engineering and Research Center of Human Stem Cells, Changsha, China.,Genetic Department, Hunan International Scientific and Technological Cooperation Base of Development and carcinogenesis, Changsha, Hunan, China
| | - Xiao Hu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
| | | | - Yan Mao
- Basecare Medical Device Co., Ltd, Suzhou, China
| | - Dehua Cheng
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
| | - Kai Kang
- Basecare Medical Device Co., Ltd, Suzhou, China
| | - Jing Dai
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
| | | | - Yi Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
| | - Naru Lu
- Basecare Medical Device Co., Ltd, Suzhou, China
| | - Zhenxing Wan
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
| | - Renqian Du
- Basecare Medical Device Co., Ltd, Suzhou, China
| | - Bo Xiong
- Genetic Department, National Engineering and Research Center of Human Stem Cells, Changsha, China
| | - Jun Zhang
- Basecare Medical Device Co., Ltd, Suzhou, China
| | - Yueqiu Tan
- Genetic Department, National Engineering and Research Center of Human Stem Cells, Changsha, China.,Genetic Department, Hunan International Scientific and Technological Cooperation Base of Development and carcinogenesis, Changsha, Hunan, China.,Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China.,Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Guangxiu Lu
- Genetic Department, National Engineering and Research Center of Human Stem Cells, Changsha, China.,Genetic Department, Hunan International Scientific and Technological Cooperation Base of Development and carcinogenesis, Changsha, Hunan, China.,Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China.,Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Fei Gong
- Genetic Department, National Engineering and Research Center of Human Stem Cells, Changsha, China.,Genetic Department, Hunan International Scientific and Technological Cooperation Base of Development and carcinogenesis, Changsha, Hunan, China.,Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China.,Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Ge Lin
- Genetic Department, National Engineering and Research Center of Human Stem Cells, Changsha, China.,Genetic Department, Hunan International Scientific and Technological Cooperation Base of Development and carcinogenesis, Changsha, Hunan, China.,Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China.,Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Bo Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Juan Du
- Genetic Department, National Engineering and Research Center of Human Stem Cells, Changsha, China.,Genetic Department, Hunan International Scientific and Technological Cooperation Base of Development and carcinogenesis, Changsha, Hunan, China.,Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China.,Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Liang Hu
- Genetic Department, National Engineering and Research Center of Human Stem Cells, Changsha, China.,Genetic Department, Hunan International Scientific and Technological Cooperation Base of Development and carcinogenesis, Changsha, Hunan, China.,Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China.,Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
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Volozonoka L, Miskova A, Gailite L. Whole Genome Amplification in Preimplantation Genetic Testing in the Era of Massively Parallel Sequencing. Int J Mol Sci 2022; 23:4819. [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] [MESH Headings] [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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Affiliation(s)
- Ludmila Volozonoka
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, LV-1007 Riga, Latvia;
| | - Anna Miskova
- Department of Obstetrics and Gynaecology, Riga Stradins University, LV-1007 Riga, Latvia;
| | - Linda Gailite
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, LV-1007 Riga, Latvia;
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Masset H, Ding J, Dimitriadou E, Debrock S, Tšuiko O, Smits K, Peeraer K, Voet T, Zamani Esteki M, Vermeesch JR. Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing. Nucleic Acids Res 2022; 50:e63. [PMID: 35212381 PMCID: PMC9226495 DOI: 10.1093/nar/gkac134] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 01/10/2022] [Accepted: 02/11/2022] [Indexed: 02/07/2023] Open
Abstract
Single-cell whole-genome haplotyping allows simultaneous detection of haplotypes associated with monogenic diseases, chromosome copy-numbering and subsequently, has revealed mosaicism in embryos and embryonic stem cells. Methods, such as karyomapping and haplarithmisis, were deployed as a generic and genome-wide approach for preimplantation genetic testing (PGT) and are replacing traditional PGT methods. While current methods primarily rely on single-nucleotide polymorphism (SNP) array, we envision sequencing-based methods to become more accessible and cost-efficient. Here, we developed a novel sequencing-based methodology to haplotype and copy-number profile single cells. Following DNA amplification, genomic size and complexity is reduced through restriction enzyme digestion and DNA is genotyped through sequencing. This single-cell genotyping-by-sequencing (scGBS) is the input for haplarithmisis, an algorithm we previously developed for SNP array-based single-cell haplotyping. We established technical parameters and developed an analysis pipeline enabling accurate concurrent haplotyping and copy-number profiling of single cells. We demonstrate its value in human blastomere and trophectoderm samples as application for PGT for monogenic disorders. Furthermore, we demonstrate the method to work in other species through analyzing blastomeres of bovine embryos. Our scGBS method opens up the path for single-cell haplotyping of any species with diploid genomes and could make its way into the clinic as a PGT application.
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Affiliation(s)
- Heleen Masset
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Jia Ding
- Center of Human Genetics, University Hospitals of Leuven, Leuven, 3000, Belgium
| | | | - Sophie Debrock
- Leuven University Fertility Center, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Olga Tšuiko
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium.,Center of Human Genetics, University Hospitals of Leuven, Leuven, 3000, Belgium
| | - Katrien Smits
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, 9820, Belgium
| | - Karen Peeraer
- Leuven University Fertility Center, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Masoud Zamani Esteki
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, 6202 AZ, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, 6229 ER, The Netherlands
| | - Joris R Vermeesch
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium.,Center of Human Genetics, University Hospitals of Leuven, Leuven, 3000, Belgium
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7
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Verdyck P, Berckmoes V, Van Laere S, Keymolen K, Olsen C, De Rycke M. Analysis of parental contribution for aneuploidy detection (APCAD): a novel method to detect aneuploidy and mosaicism in preimplantation embryos. Reprod Biomed Online 2021; 44:459-468. [PMID: 34930679 DOI: 10.1016/j.rbmo.2021.10.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/03/2021] [Accepted: 10/29/2021] [Indexed: 12/27/2022]
Abstract
RESEARCH QUESTION Can (mosaic) aneuploidy be reliably detected in preimplantation embryos after multiple displacement amplification and single nucleotide polymorphism detection, independent of haplotyping and copy number detection, with a new method 'analysis of parental contribution for aneuploidy detection' or 'APCAD'? DESIGN This method is based on the maternal contribution, a parameter that reflects the proportion of DNA that is of maternal origin for a given chromosome or chromosome segment. A maternal contribution deviating from 50% for autosomes is strongly indicative of a (mosaic) chromosomal anomaly. The method was optimized using cell mixtures with varying ratios of euploid and aneuploid (47,XY,+21) lymphocytes. Next, the maternal contribution was retrospectively measured for all chromosomes from 349 Karyomapping samples. RESULTS Retrospective analysis showed a skewed maternal contribution (<36.4 or >63.6%) in 57 out of 59 autosome meiotic trisomies and all autosome monosomies (n = 57), with values close to theoretical expectation. Thirty-two out of 7436 chromosomes, for which no anomalies had been observed with Karyomapping, showed a similarly skewed maternal contribution. CONCLUSIONS APCAD was used to measure the maternal contribution, which is an intuitive parameter independent of copy number detection. This method is useful for detecting copy number neutral anomalies and can confirm diagnosis of (mosaic) aneuploidy detected based on copy number. Mosaic and complete aneuploidy can be distinguished and the parent of origin for (mosaic) chromosome anomalies can be determined. Because of these benefits, the APCAD method has the potential to improve aneuploidy detection carried out by comprehensive preimplantation genetic testing methods.
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Affiliation(s)
- Pieter Verdyck
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Centrum Medische Genetica, Laarbeeklaan 101, Brussels 1090, Belgium.
| | - Veerle Berckmoes
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Centrum Medische Genetica, Laarbeeklaan 101, Brussels 1090, Belgium
| | - Sven Van Laere
- Vrije Universiteit Brussel (VUB), Interfaculty Center Data Processing and Statistics, Laarbeeklaan 103, Brussels 1090, Belgium
| | - Kathelijn Keymolen
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Centrum Medische Genetica, Laarbeeklaan 101, Brussels 1090, Belgium
| | - Catharina Olsen
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Centrum Medische Genetica, Laarbeeklaan 101, Brussels 1090, Belgium; Brussels Interuniversity Genomics High Throughput core (BRIGHTcore), VUB-ULB, Laarbeeklaan 101, Brussels 1090, Belgium
| | - Martine De Rycke
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Centrum Medische Genetica, Laarbeeklaan 101, Brussels 1090, Belgium
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