1
|
Wang X, Liu Y, Liu H, Pan W, Ren J, Zheng X, Tan Y, Chen Z, Deng Y, He N, Chen H, Li S. Recent advances and application of whole genome amplification in molecular diagnosis and medicine. MedComm (Beijing) 2022; 3:e116. [PMID: 35281794 PMCID: PMC8906466 DOI: 10.1002/mco2.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/30/2022] Open
Abstract
Whole genome amplification (WGA) is a technology for non-selective amplification of the whole genome sequence, first appearing in 1992. Its primary purpose is to amplify and reflect the whole genome of trace tissues and single cells without sequence bias and to provide sufficient DNA template for subsequent multigene and multilocus analysis, along with comprehensive genome research. WGA provides a method to obtain a large amount of genetic information from a small amount of DNA and provides a valuable tool for preserving limited samples in molecular biology. WGA technology is especially suitable for forensic identification and genetic disease research, along with new technologies such as next-generation sequencing (NGS). In addition, WGA is also widely used in single-cell sequencing. Due to the small amount of DNA in a single cell, it is often unable to meet the amount of samples needed for sequencing, so WGA is generally used to achieve the amplification of trace samples. This paper reviews WGA methods based on different principles, summarizes both amplification principle and amplification quality, and discusses the application prospects and challenges of WGA technology in molecular diagnosis and medicine.
Collapse
Affiliation(s)
- Xiaoyu Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yapeng Liu
- School of Early‐Childhood Education, Nanjing Xiaozhuang UniversityNanjingChina
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Xiangming Zheng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yimin Tan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
- State Key Laboratory of BioelectronicsSoutheast UniversityNanjingChina
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| |
Collapse
|
2
|
Gieldon L, Jauch A, Obeid K, Kaufmann L, Hinderhofer K, Haug U, Moog U. Germ cell mosaicism for AUTS2 exon 6 deletion. Am J Med Genet A 2021; 185:1261-1265. [PMID: 33577136 DOI: 10.1002/ajmg.a.62091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/07/2021] [Accepted: 01/09/2021] [Indexed: 11/11/2022]
Abstract
Haploinsufficiency of AUTS2 has been associated with neurodevelopmental disorders and dysmorphic features (MIM # 615834). More than 50 patients have been described, mostly carrying de novo deletions of one or more exons, including eight patients with exon 6 deletions. We report on two siblings, a girl and a boy aged 11 and 13 years, in whom the same pathogenic 85 kb deletion on 7q11.22 encompassing exon 6 of AUTS2 by SNP array analysis was identified. Both children had typical symptoms of AUTS2 syndrome such as intellectual impairment and behavioral problems, but with markedly different expression. SNP array analysis excluded the deletion in blood samples of both parents and a healthy brother. Conventional karyotyping of both parents and additional FISH analyses, marking the flanking regions of the deletion, did not show any structural rearrangements involving 7q11.22. A germ cell mosaicism was suggested as the most probable explanation for occurrence of the same deletion in these two siblings. To our knowledge this is the first report of germ cell mosaicism for AUTS2 syndrome. It additionally provides further evidence of intrafamilial phenotypic variability in AUTS2 syndrome and adds clinical information to the phenotypic spectrum of patients with AUTS2 exon 6 deletions.
Collapse
Affiliation(s)
- Laura Gieldon
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Anna Jauch
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Katharina Obeid
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Lilian Kaufmann
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Ulrich Haug
- Center for Child Neurology and Social Pediatrics Maulbronn, Maulbronn, Germany
| | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| |
Collapse
|
3
|
Nguyen HT, Nghia NT, Lien NTH, Dang-Nguyen TQ, Men NT, Viet Linh N, Xuan Nguyen B, Noguchi J, Kaneko H, Kikuchi K. Pluripotency-associated genes reposition during early embryonic developmental stages in pigs. Anim Sci J 2020; 91:e13408. [PMID: 32578338 PMCID: PMC7378944 DOI: 10.1111/asj.13408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/13/2020] [Accepted: 05/22/2020] [Indexed: 02/06/2023]
Abstract
We examined the allelic expression and positioning of two pluripotency‐associated genes, OCT4 and SOX2, and two housekeeping genes, ACTB and TUBA, in 4‐ and 8‐cell porcine embryos utilizing RNA and DNA fluorescence in situ hybridization (FISH) in single blastomeres. The proportion of blastomeres expressing SOX2 bi‐allelically increased from 45% at the 4‐cell stage to 60% at the 8‐cell stage. Moreover, in 8‐cell embryos, SOX2 was expressed bi‐allelically in significantly more blastomeres than was the case for OCT4, and this was associated with a tendency for SOX2 alleles to move toward the nuclear interior during 4‐ to 8‐cell transition. However, the radial location of OCT4 alleles did not change significantly during this transition. The locations of active and inactive alleles based on DNA and RNA FISH signals were also calculated. Inactive OCT4 alleles were located in very close proximity to the nuclear membrane, whereas active OCT4 alleles were more centrally disposed in the nucleus. Nevertheless, the nuclear location of active and inactive SOX2 alleles did not change in either 4‐ or 8‐cell blastomeres. Our RNA and DNA FISH data provide novel information on the allelic expression patterns and positioning of pluripotency‐associated genes, OCT4 and SOX2, during embryonic genome activation in pigs.
Collapse
Affiliation(s)
- Hiep Thi Nguyen
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan.,The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan.,Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nguyen Trong Nghia
- Institute of Physics, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nghiem Thi Ha Lien
- Institute of Physics, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thanh Quang Dang-Nguyen
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Nguyen Thi Men
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Nguyen Viet Linh
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Bui Xuan Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Junko Noguchi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Hiroyuki Kaneko
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Kazuhiro Kikuchi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan.,The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| |
Collapse
|
4
|
Evers C, Mitter D, Strobl-Wildemann G, Haug U, Hackmann K, Maas B, Janssen JWG, Jauch A, Hinderhofer K, Moog U. Duplication Xp11.22-p14 in females: does X-inactivation help in assessing their significance? Am J Med Genet A 2016; 167A:553-62. [PMID: 25691408 DOI: 10.1002/ajmg.a.36897] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 10/31/2014] [Indexed: 11/08/2022]
Abstract
In females, large duplications in Xp often lead to preferential inactivation of the aberrant X chromosome and a normal phenotype. Recently, a recurrent ∼4.5 Mb microduplication of Xp11.22-p11.23 was found in females with developmental delay/intellectual disability and other neurodevelopmental disorders (speech development disorder, epilepsy or EEG anomalies, autism spectrum disorder, or behavioral disorder). Unexpectedly, most of them showed preferential inactivation of the normal X chromosome. We describe five female patients carrying de novo Xp duplications encompassing p11.23. Patient 1 carried the recurrent microduplication Xp11.22-p11.23, her phenotype and X-chromosome inactivation (XI) pattern was consistent with previous reports. The other four patients had novel Xp duplications. Two were monozygotic twins with a similar phenotype to Patient 1 and unfavorable XI skewing carrying an overlapping ∼5 Mb duplication of Xp11.23-p11.3. Patient 4 showed a duplication of ∼5.5 Mb comparable to the twins but had a more severe phenotype and unskewed XI. Patient 5 had a ∼8.5 Mb duplication Xp11.23-p11.4 and presented with mild ID, epilepsy, behavioral problems, and inconsistent results of XI analysis. A comparison of phenotype, size and location of the duplications and XI patterns in Patients 1-5 and previously reported females with overlapping duplications provides further evidence that microduplications encompassing Xp11.23 are associated with ID and other neurodevelopmental disorders in females. To further assess the implication of XI for female carriers, we recommend systematic analysis of XI pattern in any female with X imbalances that are known or suspected to be pathogenic.
Collapse
Affiliation(s)
- Christina Evers
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Masset H, Hestand MS, Van Esch H, Kleinfinger P, Plaisancié J, Afenjar A, Molignier R, Schluth-Bolard C, Sanlaville D, Vermeesch JR. A Distinct Class of Chromoanagenesis Events Characterized by Focal Copy Number Gains. Hum Mutat 2016; 37:661-8. [DOI: 10.1002/humu.22984] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 02/24/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Heleen Masset
- Department of Human Genetics; KU Leuven; Leuven Belgium
| | | | | | - Pascale Kleinfinger
- Laboratoire Cerba; Département de Génétique Humaine; Saint-Ouen l'Aumône France
| | - Julie Plaisancié
- Service de Génétique Médicale; Hôpital Purpan; CHU Toulouse France
| | - Alexandra Afenjar
- APHP; Hôpital Armand-Trousseau; Service de Génétique Clinique; Paris France
- APHP; Hôpital Armand-Trousseau; Service de Neuropédiatrie; Paris France
| | - Romain Molignier
- Laboratoire de Biologie Clinique; Clinique Saint Jean Languedoc; Toulouse France
| | - Caroline Schluth-Bolard
- Laboratoire de Cytogénétique Constitutionnelle; Hospices Civils de Lyon; France
- Lyon Neuroscience Research Center; CNRS UMR5292, INSERM U1028, UCBL Lyon France
| | - Damien Sanlaville
- Laboratoire de Cytogénétique Constitutionnelle; Hospices Civils de Lyon; France
- Lyon Neuroscience Research Center; CNRS UMR5292, INSERM U1028, UCBL Lyon France
| | | |
Collapse
|
6
|
Lumaka A, Van Hole C, Casteels I, Ortibus E, De Wolf V, Vermeesch JR, Lukusa T, Devriendt K. Variability in expression of a familial 2.79 Mb microdeletion in chromosome14q22.1-22.2. Am J Med Genet A 2012; 158A:1381-7. [DOI: 10.1002/ajmg.a.35353] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 01/29/2012] [Indexed: 01/09/2023]
|
7
|
Darouich S, Popovici C, Missirian C, Moncla A. Use of DOP-PCR for amplification and labeling of BAC DNA for FISH. Biotech Histochem 2011; 87:117-21. [PMID: 21314248 DOI: 10.3109/10520295.2011.559175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a powerful molecular cytogenetic method that permits rapid detection of specific chromosomal rearrangements. It is based on the hybridization of fluorescent labeled probes to metaphase chromosomes or interphase nuclei. The DNA probes commonly are generated from cloned sources such as bacterial artificial chromosomes (BACs). The major disadvantage of this approach is that it requires laborious and time-consuming work. We used a degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR) for both amplification and labeling of very small amounts of purified BAC DNA for FISH. The DOP-PCR reaction was processed in two steps: pre-amplification followed by simultaneous amplification and labeling of BAC DNA. The DOP-PCR probes obtained provided good hybridization signals and low background. Thus, DOP-PCR can be used to produce unlimited quantities of FISH probes with decreased cost and labor.
Collapse
Affiliation(s)
- S Darouich
- Electron Microscopy Laboratory, Faculty of Medicine of Tunis, Tunisia
| | | | | | | |
Collapse
|