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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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Ling J, Deng Y, Long X, Liu J, Du H, Cao B, Xu K. Single-nucleotide polymorphism array coupled with multiple displacement amplification: accuracy and spatial resolution for analysis of chromosome copy numbers in few cells. Biotechnol Appl Biochem 2012; 59:35-44. [PMID: 22332743 DOI: 10.1002/bab.64] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 10/07/2011] [Indexed: 12/17/2022]
Abstract
When coupled with multiple displacement amplification (MDA), microarray-based comparative genomic intensity allows detection of chromosome copy number aberrations even in single or few cells, but the actual performance of the system and their influencing factors have not been well defined. Here, using single-nucleotide polymorphism (SNP) array, we analyzed copy number profiles from DNA amplified by MDA in 1-10 cells and estimated the accuracy and spatial resolution of the analysis. Based on the concordance of SNP copy numbers for DNA with and without MDA, the accuracy of the system can be significantly enhanced by using MDA-amplified DNA as reference and also by increasing the cell numbers. Analyses under different smoothing treatments revealed a practical resolution of 2 Mb for 10 cells and 10 Mb for a single cell. When both cells with known chromosomal duplication and deletion were analyzed, this platform detected a copy number "loss" more accurately than a "gain" (P < 0.01), particularly in single-cell MDA products. Together, we demonstrated that SNP array coupled with MDA is reliable and efficient for detection of copy number aberrations in a small number of cells, and its accuracy and resolution can both be significantly enhanced with increasing the number of cells as MDA template.
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Affiliation(s)
- Jiawei Ling
- Center for Reproductive Medicine, Guangzhou Institute of Obstetrics and Gynecology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
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Ling J, Zhuang G, Tazon-Vega B, Zhang C, Cao B, Rosenwaks Z, Xu K. Evaluation of genome coverage and fidelity of multiple displacement amplification from single cells by SNP array. Mol Hum Reprod 2009; 15:739-47. [PMID: 19671595 PMCID: PMC2762374 DOI: 10.1093/molehr/gap066] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The scarce amount of DNA contained in a singe cell is a limiting factor for clinical application of preimplantation genetic diagnosis mainly due to the risk of misdiagnosis caused by allele dropout and the difficulty in obtaining copy number variations in all 23 pairs of chromosomes. Multiple displacement amplification (MDA) has been reported to generate large quantity of products from small amount of templates. Here, we evaluated the fidelity of whole-genome amplification MDA from single or a few cells and determined the accuracy of chromosome copy number assessment on these MDA products using an Affymetrix 10K 2.0 SNP Mapping Array. An average coverage rate (86.2%) from single cells was obtained and the rates increased significantly when five or more cells were used as templates. Higher concordance for chromosome copy number from single cells could be achieved when the MDA amplified product was used as reference (93.1%) than when gDNA used as reference (82.8%). The present study indicates that satisfactory genome coverage can be obtained from single-cell MDA which may be used for studies where only a minute amount of genetic materials is available. Clinically, MDA coupled with SNP mapping array may provide a reliable and accurate method for chromosome copy number analysis and most likely for the detection of single-gene disorders as well.
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Affiliation(s)
- Jiawei Ling
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine and Infertility, Weill Cornell Medical College of Cornell University, 1305 York Avenue, New York, NY 10021, USA
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Abstract
Preimplantation genetic diagnosis (PGD) for monogenic diseases has known a considerable evolution since its first application in the early 1990s. Especially the technical aspects of the genetic diagnosis itself, the single-cell genetic analysis, has constantly evolved to reach levels of accuracy and efficiency nearing those of genetic diagnosis on regular DNA samples. In this review, we will focus on the molecular biological techniques that are currently in use in the most advanced centers for PGD for monogenic disorders, including multiplex polymerase chain reaction (PCR) and post-PCR diagnostic methods, whole genome amplification (WGA) and multiple displacement amplification (MDA). As it becomes more and more clear that when it comes to ethically difficult indications, PGD goes further than prenatal diagnosis (PND), we will also briefly discuss ethical issues.
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Affiliation(s)
- Claudia Spits
- Department of Embryology and Genetics of the Vrije Universiteit Brussel and the Centre for Medical Genetics of the UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium.
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Guignot F, Baril G, Dupont F, Cognie Y, Folch J, Alabart JL, Poulin N, Beckers JF, Bed'hom B, Babilliot JM, Mermillod P. Determination of sex and scrapie resistance genotype in preimplantation ovine embryos. Mol Reprod Dev 2009; 76:183-90. [PMID: 18543282 DOI: 10.1002/mrd.20940] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The aim of this study was to test the accuracy of genotype diagnosis after pre-amplification of DNA extracted from biopsies obtained by microblade cutting of ovine embryos and to evaluate the viability of biopsied embryos after vitrification/warming and transfer to recipients. Sex and PrP genotypes were determined. Sex diagnosis was done by PCR amplification of ZFX/ZFY and SRY sequences after PEP-PCR while PrP genotype determination was performed after specific pre-amplification of specific target including codons 136, 154 and 171. Embryos were collected at Day 7 after oestrus. Blastocysts and expanded blastocysts were biopsied immediately after collection whereas compacted morulae were biopsied after 24 hr of in vitro culture. Eighty-nine biopsied embryos were frozen by vitrification. Fresh and vitrified whole embryos were kept as control. DNA of biopsies was extracted and pre-amplified. Sex diagnosis was efficient for 96.6% of biopsies and PrP genotyping was determined in 95.8% of codons. After embryo transfer, no significant difference was observed in lambing rate between biopsied, vitrified control and fresh embryos (54.5%, 60% and 66.6%, respectively). Embryo survival rate was not different between biopsied and whole vitrified embryos (P = 0.38). At birth, 96.7% of diagnosed sex and 95.4% of predetermined codons were correct. Lamb PrP profiles were in agreement with parental genotype. PEP-PCR coupled with sex diagnosis and nested PCR coupled with PrP genotype predetermination are very accurate techniques to genotype ovine embryo before transfer. These original results allow planning of selection of resistant genotype to scrapie and sex of offspring before transfer of cryopreserved embryo.
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Affiliation(s)
- Florence Guignot
- UMR INRA-CNRS-Université de Tours-Haras Nationaux, Physiologie de la Reproduction et des Comportements, Nouzilly, France.
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Honaramooz A, Megee S, Zeng W, Destrempes MM, Overton SA, Luo J, Galantino-Homer H, Modelski M, Chen F, Blash S, Melican DT, Gavin WG, Ayres S, Yang F, Wang PJ, Echelard Y, Dobrinski I. Adeno‐associated virus (AAV)‐mediated transduction of male germ line stem cells results in transgene transmission after germ cell transplantation. FASEB J 2007; 22:374-82. [PMID: 17873102 DOI: 10.1096/fj.07-8935com] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We explored whether exposure of mammalian germ line stem cells to adeno-associated virus (AAV), a gene therapy vector, would lead to stable transduction and transgene transmission. Mouse germ cells harvested from experimentally induced cryptorchid donor testes were exposed in vitro to AAV vectors carrying a GFP transgene and transplanted to germ cell-depleted syngeneic recipient testes, resulting in colonization of the recipient testes by transgenic donor cells. Mating of recipient males to wild-type females yielded 10% transgenic offspring. To broaden the approach to nonrodent species, AAV-transduced germ cells from goats were transplanted to recipient males in which endogenous germ cells had been depleted by fractionated testicular irradiation. Transgenic germ cells colonized recipient testes and produced transgenic sperm. When semen was used for in vitro fertilization (IVF), 10% of embryos were transgenic. Here, we report for the first time that AAV-mediated transduction of mammalian germ cells leads to transmission of the transgene through the male germ line. Equally important, this is also the first report of transgenesis via germ cell transplantation in a nonrodent species, a promising approach to generate transgenic large animal models for biomedical research.
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Affiliation(s)
- Ali Honaramooz
- Center for Animal Transgenesis and Germ Cell Research, University of Pennsylvania, 382 W. State Road, Kennett Square, PA 19348, USA
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Coskun S, Alsmadi O. Whole genome amplification from a single cell: a new era for preimplantation genetic diagnosis. Prenat Diagn 2007; 27:297-302. [PMID: 17278176 DOI: 10.1002/pd.1667] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Preimplantation genetic diagnosis (PGD) is a technique used for determining the genetic status of a single cell biopsied from embryos or oocytes. Genetic analysis from a single cell is both rewarding and challenging, especially in PGD. The starting material is very limited and not replaceable, and the diagnosis has to be made in a very short time. Different whole genome amplification (WGA) techniques have been developed to specifically increase the DNA quantities originating from clinical samples with limited DNA contents. In this review, currently available WGA techniques are introduced and, among them, multiple displacement amplification (MDA) is discussed in detail. MDA generates abundant assay-ready DNA to perform broad panels of genetic assays through its ability to rapidly amplify genomes from single cells. The utilization of MDA for single-cell molecular analysis is expanding at a high rate, and MDA is expected to soon become an integral part of PGD.
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Affiliation(s)
- Serdar Coskun
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
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Liu D, Liu C, DeVries S, Waldman F, Cote RJ, Datar RH. LM-PCR permits highly representative whole genome amplification of DNA isolated from small number of cells and paraffin-embedded tumor tissue sections. ACTA ACUST UNITED AC 2004; 13:105-15. [PMID: 15167012 DOI: 10.1097/00019606-200406000-00007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Analysis of genetic changes is often hampered by insufficient starting DNA from limited clinical tissue specimens. We employed ligation-mediated PCR (LM-PCR) for global amplification of the genome to overcome this limitation, generating up to 5 microg of representative amplicons of genomic DNA from as little as one cell. We demonstrate successful global genome amplification in high-quality starting DNA source like laser-captured cultured cells, as well as partially degraded starting DNA from old formalin-fixed paraffin-embedded tissue sections. This process generates adaptor-tailed templates that can be repeatedly amplified almost ad infinitum. We have further modified this technique such that, instead of a single endonuclease digest, we can achieve higher amplicon coverage by combining 3 endonuclease digests prior to LM-PCR. As tested by examining amplification of STS sequences scattered genome-wide, the coverage was improved from the published 70% to 96%. The faithful representation of global losses and gains in the amplified genomic DNA was confirmed by array-comparative genomic hybridization. Further, we exemplify the utility of this technique for finer p53 point mutation analysis by PCR-SSCP. This technique is thus a clinically useful tool for globally amplifying and archiving DNA from finite sources like paraffin tissue sections, providing a potentially unlimited resource for genetic analyses.
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Affiliation(s)
- Dongxin Liu
- Department of Pathology, University of Southern California, Keck School of Medicine, Los Angeles, 90033, USA
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Wang T, Chen H, Ma T. Noninvasive prenatal diagnosis of fetal sex by single-cell PEP-PCR method. Curr Med Sci 2004; 24:66-7, 78. [PMID: 15165119 DOI: 10.1007/bf02830709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2002] [Indexed: 11/28/2022]
Abstract
A new method for noninvasive prenatal diagnosis of fetal sex was developed by using single-cell PEP-PCR techniques. Micromamipulation techniques were used to obtain single fetal cells from 273 maternal blood samples. The genome of single cells was preamplified by PEP and SRY genes were analyzed by PCR method. The SRY genes of 149 samples were detected by the new method among 153 samples carrying male fetus, while 119 out of 120 samples carrying female fetus were proved negative for SRY genes. The sensitivity and specificity of the new method were 97.39% and 99.17% respectively and the correct rate was 98.17%. The new method has the advantage of high sensitivity and specificity in noninvasive prenatal diagnosis of fetal sex and provides the basis of other researches such as sex-linked inherited diseases.
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Affiliation(s)
- Taoran Wang
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030
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Jiao Z, Zhou C, Li J, Shu Y, Liang X, Zhang M, Zhuang G. Birth of healthy children after preimplantation diagnosis of beta-thalassemia by whole-genome amplification. Prenat Diagn 2003; 23:646-51. [PMID: 12913871 DOI: 10.1002/pd.659] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Preimplantation genetic diagnosis (PGD) offers couples at risk for transmitting an inherited disorder the possibility to avoid the need to terminate affected pregnancies. PGD for monogenic diseases is most commonly accomplished by blastomere biopsy from cleavage-stage embryos, followed by PCR-based DNA analysis. However, the molecular heterogeneity of many monogenic diseases requires a diagnostic strategy capable of detecting a range of mutations and compound genotypes. With the above considerations, we developed an accurate and reliable strategy for analysis of beta-globin gene mutations, applicable for PGD for the wide spectrum of beta-thalassemia major mutations in the Chinese population. The strategy involves primer-extension preamplification (PEP), followed by nested PCR and reverse dot blot (RDB) for mutation detection since it facilitates simultaneous analysis of more than one mutation in a single cell. This report describes the application of the strategy in two clinical IVF/PGD cycles at risk for transmitting beta-thalassemia major, which resulted in the first thalassemia-free children born after PGD in China.
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Affiliation(s)
- Zexu Jiao
- Reproductive Medical Center, First Affiliated Hospital of Sun Yet-Sen University, Guangzhou, China.
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Stoecklein NH, Erbersdobler A, Schmidt-Kittler O, Diebold J, Schardt JA, Izbicki JR, Klein CA. SCOMP is superior to degenerated oligonucleotide primed-polymerase chain reaction for global amplification of minute amounts of DNA from microdissected archival tissue samples. THE AMERICAN JOURNAL OF PATHOLOGY 2002; 161:43-51. [PMID: 12107088 PMCID: PMC1850686 DOI: 10.1016/s0002-9440(10)64155-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Global genome amplification from formalin-fixed tissues is still problematic when performed with low cell numbers. Here, we tested a recently developed method for whole genome amplification termed "SCOMP" (single cell comparative genomic hybridization) on archival tissues of different ages. We show that the method is very well suited for formalin-fixed paraffin-embedded samples obtained by nuclei extraction or laser microdissection. The polymerase chain reaction (PCR) products can be used for subsequent comparative genomic hybridization, loss of heterozygosity studies, and DNA sequencing. To control for PCR-induced artifacts we amplified genomic DNA isolated from 20 nuclei of archival formalin-fixed, paraffin-embedded nonpathological lymph nodes. Subsequent comparative genomic hybridization revealed the expected balanced profiles. For loss of heterozygosity analysis by microsatellite PCR 60 to 160 cells were sufficient. In comparative experiments the approach turned out to be superior to published degenerated oligonucleotide-primed-PCR protocols. The method provides a robust and valuable tool to study very small cell samples, such as the genomes of dysplastic cells or the clonal evolution within heterogeneous tumors.
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Affiliation(s)
- Nikolas H Stoecklein
- Institut für Immunologie, Ludwig-Maximilians-Universität München, München, Germany
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Affiliation(s)
- Alan R Thornhill
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.
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Behboodi E, Groen W, Destrempes MM, Williams JL, Ohlrichs C, Gavin WG, Broek DM, Ziomek CA, Faber DC, Meade HM, Echelard Y. Transgenic production from in vivo-derived embryos: effect on calf birth weight and sex ratio. Mol Reprod Dev 2001; 60:27-37. [PMID: 11550265 DOI: 10.1002/mrd.1058] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We examined transgenic-cattle production by DNA microinjection into 1-, 2-, and 4-cell embryos, analyzing the impact on calf size and subsequent viability. Embryos were either collected at an abattoir by flushing oviducts from superovulated and artificially inseminated cows (in vivo-derived) or obtained by in vitro maturation and in vitro fertilization of oocytes aspirated from excised ovaries (in vitro-derived). A human serum albumin (hSA) milk-expression DNA construct was microinjected, either in one of the visible pronuclei of in vitro- and in vivo-derived 1-cell embryos or in the nuclei of two blastomeres of 2- and 4-cell in vivo-derived embryos. Microinjection-induced mortality (lysis and developmental block) was equivalent ( approximately 40%) for all microinjected embryos. Embryos were co-cultured with BRL cells in B-2 medium containing 10% fetal calf serum (FSC). Overall, embryo development to morulae/blastocysts was significantly greater for in vivo-derived ova (15.5%) than for in vitro-derived oocytes (9.3%). All morulae and blastocysts were transferred to synchronized recipient females on Days 6-8 post-fertilization. A total of 189 calves were delivered. Birth weights were significantly greater for calves generated from in vitro-derived oocytes compared with those generated from in vivo-derived oocytes. One transgenic bull calf was obtained from the microinjection of a 2-cell embryo. Fluorescence in situ hybridization (FISH) analysis of lymphocytes detected one transgenic integration site in all cells. Transmission frequency of the hSA transgene in embryos obtained through IVM/IVF/IVC utilizing the semen of the transgenic calf confirmed that it was not mosaic.
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Affiliation(s)
- E Behboodi
- Genzyme Transgenics Corporation, Framingham, Massachusetts 01701-9322, USA
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Park JH, Lee JH, Choi KM, Joung SY, Kim JY, Chung GM, Jin DI, Im KS. Rapid sexing of preimplantation bovine embryo using consecutive and multiplex polymerase chain reaction (PCR) with biopsied single blastomere. Theriogenology 2001; 55:1843-53. [PMID: 11414489 DOI: 10.1016/s0093-691x(01)00526-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The objective of this study was to establish a rapid and reliable PCR method for the sexing of 8- to 16-cell stage bovine embryos. The BOV97M and bovine 1.715 satellite DNA sequences were selected for amplification of male- and bovine-specific DNA, respectively. But the unequal number of copies of these two repetitive sequences required some modification of the multiplex PCR method. In consecutive and multiplex PCR, the first 10 PCR cycles were done with male-specific primer followed by an additional 23 cycles with bovine-specific primer. In this PCR method, the appearance of male- and bovine-specific bands was independent of the DNA concentration. This PCR method was applied successfully using groups of 8, 4, 2, and 1 blastomeres dissociated from the embryos, and the sexing efficiency was 100.0, 96.3, 94.3 and 92.1%, respectively. The coincident rate of sex determination between biopsied single blastomere and matched blastocyst was 90.0%. Therefore the developmental potential from 8- to 16-cell stage embryos to the blastocyst stage was not significantly different (P>0.2) for intact embryo (42.3%) than for demi-embryos (53.8%), suggesting that trauma to the demi-embryo caused by single-blastomere aspiration using a bevelled micropipette was very small. In conclusion, we developed a rapid (within 2 hours) and effective PCR method for the sexing of 8- to 16-cell stage bovine embryos using a single blastomere.
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Affiliation(s)
- J H Park
- Institute of Animal Science and Technology, College of Agriculture and Life Sciences, Seoul National University, Suweon, Korea
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Abstract
The advent of the polymerase chain reaction (PCR) and the development of fluorescence in situ hybridization (FISH) have had a tremendous impact on preimplantation genetic diagnosis (PGD). While PCR is a powerful tool in detecting genetic diseases or molecular markers affecting quantitative trait loci, the main use of FISH is screening for chromosomal aberrations. This presentation reviews the recent progress in preimplantation genetic diagnosis with an emphasis on bovine embryos. In particular the importance of biopsy size and strategies to avoid PCR contamination are discussed. Alternative DNA amplification and detection methods as well as methods to meet the challenge of multiple locus detection for marker assisted selection are presented.
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Coombes MM, Mao L, Steck KD, Luna MA, El-Naggar AK. Genotypic analysis of flow-sorted and microdissected head and neck squamous lesions by whole-genome amplification. DIAGNOSTIC MOLECULAR PATHOLOGY : THE AMERICAN JOURNAL OF SURGICAL PATHOLOGY, PART B 1998; 7:197-201. [PMID: 9917129 DOI: 10.1097/00019606-199808000-00003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
To investigate the utility of primer extension preamplification (PEP) in the genetic analysis of head and neck squamous tumorigenesis, microsatellite analysis was performed on matched deoxyribonucleic acid (DNA) samples extracted from 32 flow-sorted and microdissected specimens before and after PEP. Eighteen fresh and nine archival specimens were taken from invasive carcinomas, and five specimens were obtained from microdissected archival premalignant squamous epithelial lesions. Identical microsatellite patterns were observed in 276 (87%) of the 319 paired PEP and non-PEP genotypes with sufficient DNA. Overall, 13 (4%) of the PEP and 28 (8.8%) of the non-PEP fresh tissue samples failed specific microsatellite amplification. All 14 PEP-archival specimens were successfully amplified. Sorted cells showed a higher incidence (42.8%) of loss of heterozygosity (LOH) in both PEP and non-PEP samples compared with their unsorted counterparts. The results of this study indicate that (a) PEP is a simple and reliable technique for enhancing the DNA yield from small specimens; (b) flow sorting, in certain cases, improves the interpretation of genetic results; and (c) PEP may be used to compensate for PCR failure of unamplified DNA specimens in these lesions.
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Affiliation(s)
- M M Coombes
- Department of Pathology, University of Texas, M. D. Anderson Cancer Center, Houston 77030, USA
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Lucito R, Nakimura M, West JA, Han Y, Chin K, Jensen K, McCombie R, Gray JW, Wigler M. Genetic analysis using genomic representations. Proc Natl Acad Sci U S A 1998; 95:4487-92. [PMID: 9539764 PMCID: PMC22516 DOI: 10.1073/pnas.95.8.4487] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Analysis of the genetic changes in human tumors is often problematical because of the presence of normal stroma and the limited availability of pure tumor DNA. However, large amounts of highly reproducible "representations" of tumor and normal genomes can be made by PCR from nanogram amounts of restriction endonuclease cleaved DNA that has been ligated to oligonucleotide adaptors. We show here that representations are useful for many types of genetic analyses, including measuring relative gene copy number, loss of heterozygosity, and comparative genomic hybridization. Representations may be prepared even from sorted nuclei from fixed and archived tumor biopsies.
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Affiliation(s)
- R Lucito
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
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18
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Tasca RJ, McClure ME. The emerging technology and application of preimplantation genetic diagnosis. THE JOURNAL OF LAW, MEDICINE & ETHICS : A JOURNAL OF THE AMERICAN SOCIETY OF LAW, MEDICINE & ETHICS 1998; 26:7-3. [PMID: 11067588 DOI: 10.1111/j.1748-720x.1998.tb01901.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Authors argue that although preimplantation genetic diagnosis is a promising new reproductive technology that can prevent birth defects and other devastating inherited diseases, PGD poses the risk of misdiagnosis and misuse.
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Affiliation(s)
- R J Tasca
- Reproductive Sciences Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
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Grifo JA, Tang YX, Krey L. Update in preimplantation genetic diagnosis. Age, genetics, and infertility. Ann N Y Acad Sci 1997; 828:162-5. [PMID: 9329835 DOI: 10.1111/j.1749-6632.1997.tb48535.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
PGD has been successfully used for several years. Over 40 babies have been born worldwide by use of these techniques. Unfortunately, a number of misdiagnoses have been made, a distressing consequence of a new frontier. Significant advances have been made to improve the efficiency and accuracy of PCR and FISH. The widespread use of this technology awaits further documentation of safety and accuracy. Other issues must also be addressed. First, the cost-effectiveness of the techniques relative to the traditional alternatives must be evaluated. A number of ethical issues regarding embryo screening must be addressed including what diseases are serious enough to warrant the procedure. Another concern is the use of this technology for nongenetic disorders such as gender selection. Finally, the experimental nature of these procedures must continually be discussed with patients, and long-term follow-up studies must be undertaken. Development of more accurate and less expensive assays coupled with improved IVF success rates may make PGD a more widely used clinical tool. The future awaits these developments.
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Affiliation(s)
- J A Grifo
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York 10016, USA
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Liu HC, He ZY, Tang YX, Mele CA, Veeck LL, Davis O, Rosenwaks Z. Simultaneous detection of multiple gene expression in mouse and human individual preimplantation embryos. Fertil Steril 1997; 67:733-41. [PMID: 9093203 DOI: 10.1016/s0015-0282(97)81375-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE To detect simultaneously multiple gene expression in mouse and human individual embryos by reverse transcriptase-polymerase chain reaction. DESIGN Transcripts involved in the insulin-like growth factor (IGF) system were detected in mouse and human preimplantation embryos. SETTING An academic teaching hospital. MAIN OUTCOME MEASURE(S) Transcripts of the IGF family genes. RESULT(S) In the mouse, genes are expressed differentially and messenger RNA transcripts of maternal origin in nonfertilized ova decline gradually until the initiation of the embryonic genome transcription. Insulin-like growth factor-binding protein-2 (IGFBP)-2, -3, -4, and beta-actin transcripts appear to be initiated at the two- to four-cell stage, whereas IGFBP-1, -5, and -6 transcripts are initiated at later stages. Transcription, once initiated, appears to continue through to the blastocyst stage. In humans, almost all genes of the IGF system were expressed in preimplantation embryos. This is the first report of the assessment of IGF family transcripts in individual embryos, and introduces a novel method for research and clinical diagnosis of preimplantation embryos.
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Affiliation(s)
- H C Liu
- Center for Reproductive Medicine and Infertility, Cornell University Medical College, New York, New York 10021, USA
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Lissens W, Sermon K, Staessen C, Assche EV, Janssenswillen C, Joris H, Van Steirteghem A, Liebaers I. Review: preimplantation diagnosis of inherited disease. J Inherit Metab Dis 1996; 19:709-23. [PMID: 8982942 DOI: 10.1007/bf01799159] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Preimplantation diagnosis of inherited diseases has become possible with the techniques of in vitro fertilization, blastomere biopsy of the 6- to 10-cell embryo and DNA analysis of the single blastomeres. Disease-free embryos are selected for transfer to the uterus, thereby avoiding the need for termination of a fetus diagnosed as affected in prenatal diagnosis in the first or early-second trimester of pregnancy. The genetic indications for preimplantation diagnosis are theoretically the same as for prenatal diagnosis, but the defects must be detectable by the polymerase chain reaction. For X-linked recessive diseases, fluorescence in situ hybridization can be used as an alternative for the selection of female embryos. So far almost 40 healthy children have been born worldwide after preimplantation diagnosis for genetic disease. The possibilities and limitations of preimplantation diagnosis, especially in prevention of inherited disease, are discussed in this review.
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Affiliation(s)
- W Lissens
- Centre for Medical Genetics, University Hospital of the Dutch-speaking Brussels Free University (Vrije Universiteit Brussel, Belgium
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Rojas FJ, Garner C, Schiewe M, Asch RH, Balmaceda JP, Moretti-Rojas I. Enzymatic amplification of specific deoxyribonucleic acid sequences from single cells: evaluation of a simplified and rapid method for use in preimplantation genetic diagnosis. Fertil Steril 1995; 64:255-60. [PMID: 7615099 DOI: 10.1016/s0015-0282(16)57719-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
OBJECTIVE To develop a simplified polymerase chain reaction (PCR) protocol on single cells for the purpose of preimplantation genetic diagnosis. Also to evaluate a new thermal cycler, RoboCycler 40 (Stratagene, La Jolla, CA), for reducing the time to complete PCR amplification. DESIGN PCR amplification without DNA purification or reamplification of a 149 base pair (bp) segment of the human Y chromosome was used as a model. The assay was tested in human fetal cells, single lymphocytes and single human blastomeres. RESULTS Amplification of the 149 bp segment using fetal cells was 100% correct. Results on single lymphocytes were concordant in all but one of the 15 male cases. However, 2 of the 25 female cases were identified as male suggesting the occurrence of DNA contamination. Analysis of 61 blastomeres were concordant in 57 cases (93%); results for male blastomeres showed 12% of false negatives. No false positives were detected for female cells. Amplification using the simplified PCR protocol in combination with the RoboCycler was completed in 2 hours. CONCLUSION These data show that this PCR assay performed directly, without DNA extraction or purification and without re-amplification is a practical and effective approach for amplification of specific DNA sequences in single cells. Furthermore, the simplified PCR protocol significantly reduced the time to complete DNA amplification. The reduced time is expected to facilitate the management of a routine program for preimplantation genetic diagnosis.
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Affiliation(s)
- F J Rojas
- Department of Obstetrics and Gynecology, University of California, Irvine, Orange, USA
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Gibbons WE, Gitlin SA, Lanzendorf SE. Strategies to respond to polymerase chain reaction deoxyribonucleic acid amplification failure in a preimplantation genetic diagnosis program. Am J Obstet Gynecol 1995; 172:1088-95; discussion 1095-6. [PMID: 7726246 DOI: 10.1016/0002-9378(95)91468-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
OBJECTIVES Our purpose was to identify and evaluate practical methods within a preimplantation genetic diagnosis program that will increase the percentage of embryos for which a genetic diagnosis can be obtained, including clinical responses after failure of deoxyribonucleic acid amplification has occurred. STUDY DESIGN Known human lymphoblast cell lines and human embryo blastomeres were evaluated in a single-cell, nested primer polymerase chain reaction system with primer sequences for the specific locus surrounding the four base pair insertion mutation on exon 11 of beta-hexosaminidase A-Tay-Sachs disease, the delta F508 mutation of cystic fibrosis, and the sex-determining region on the Y chromosome. Reamplification polymerase chain reaction with standard polymerase chain reaction and primer extension preamplification was performed in deoxyribonucleic acid preparations after previous polymerase chain reaction amplification attempts had resulted in failure of amplification. RESULTS The amplification efficiency of Tay-Sachs disease, 51% (97/187), was significantly lower than that for cystic fibrosis, 85% (87/107), and for the sex-determining region on the Y chromosome, 85% (77/90). Tay-Sachs disease polymerase chain reaction amplification occurred in 51% of one-cell lymphoblasts, 89% of two-cell lymphoblasts, and 94% of samples when more than two cells were processed together. When previous amplification failure had occurred, standard Tay-Sachs disease polymerase chain reaction resulted in an amplification efficiency of 16% (three of 19), whereas primer extension preamplification polymerase chain reaction for Tay-Sachs disease resulted in amplification of 52% (31/59) lymphoblasts and 54% (13/24) of polyspermic human blastomeres. Four of six human blastomeres in which amplification failure occurred in a Tay-Sachs disease preimplantation genetic diagnosis cycle amplified by primer extension preamplification polymerase chain reaction, which increased the diagnostic information obtained from four to six of the seven embryos on which biopsy was performed. CONCLUSIONS We suggest that practical approaches for consideration within a clinical preimplantation genetic diagnosis program to limit the net effect of amplification failure (i.e., reduced embryo transfer number) include increasing the deoxyribonucleic acid content in the polymerase chain reaction tube by using more than one blastomere and by using primer extension preamplification when the initial attempt at amplification fails.
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Affiliation(s)
- W E Gibbons
- Jones Institute for Reproductive Medicine, Department of Obstetrics and Gynecology, Eastern Virginia Medical School, Norfolk 23507-1912, USA
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Abstract
We know today that classical eugenics, of an essentially negative nature, was not only an aggressive and brutal practice but, like its positive counterpart, inefficient as well. In fact, numerous biological, sociological, and psychological events beyond our control arise to prevent the realisation of any eugenic plan. Thus, like all human beings, individuals whose procreation is encouraged by positive eugenics suffer unexpected mutations that are transmitted to their offspring by their gametes. Gene distribution among the gametes at meiosis is the result of an uncontrollable, natural lottery. As an effect of this lottery, positive eugenics could allow the birth of defective babies whereas negative eugenics precludes the birth of normal babies.
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Affiliation(s)
- J Testart
- L'UNITE INSERM, Maturation gametique et fecondation, Clamart, France
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