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Zhao M, Lian M, Cheah FSH, Tan ASC, Agarwal A, Chong SS. Identification of Novel Microsatellite Markers Flanking the SMN1 and SMN2 Duplicated Region and Inclusion Into a Single-Tube Tridecaplex Panel for Haplotype-Based Preimplantation Genetic Testing of Spinal Muscular Atrophy. Front Genet 2019; 10:1105. [PMID: 31781167 PMCID: PMC6851269 DOI: 10.3389/fgene.2019.01105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
Preimplantation genetic testing for the monogenic disorder (PGT-M) spinal muscular atrophy (SMA) is significantly improved by supplementation of SMN1 deletion detection with marker-based linkage analysis. To expand the availability of informative markers for PGT-M of SMA, we identified novel non-duplicated and highly polymorphic microsatellite markers closely flanking the SMN1 and SMN2 duplicated region. Six of the novel markers within 0.5 Mb of the 1.7 Mb duplicated region containing SMN1 and SMN2 (SMA6863, SMA6873, SMA6877, SMA7093, SMA7115, and SMA7120) and seven established markers (D5S1417, D5S1413, D5S1370, D5S1408, D5S610, D5S1999, and D5S637), all with predicted high heterozygosity values, were selected and optimized in a tridecaplex PCR panel, and their polymorphism indices were determined in two populations. Observed marker heterozygosities in the Chinese and Caucasian populations ranged from 0.54 to 0.86, and 98.4% of genotyped individuals (185 of 188) were heterozygous for ≥2 markers on either side of SMN1. The marker panel was evaluated for disease haplotype phasing using single cells from two parent–child trios after whole-genome amplification, and applied to a clinical IVF (in vitro fertilization) PGT-M cycle in an at-risk couple, in parallel with SMN1 deletion detection. Both direct and indirect test methods determined that none of five tested embryos were at risk for SMA, with haplotype analysis further identifying one embryo as unaffected and four as carriers. Fresh transfer of the unaffected embryo did not lead to implantation, but subsequent frozen-thaw transfer of a carrier embryo produced a pregnancy, with fetal genotype confirmed by amniocentesis, and a live birth at term.
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Affiliation(s)
- Mingjue Zhao
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mulias Lian
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Felicia S H Cheah
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Arnold S C Tan
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Preimplantation Genetic Diagnosis Center, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Anupriya Agarwal
- Clinic for Human Reproduction, Department of Obstetrics and Gynecology, National University Hospital, Singapore, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Preimplantation Genetic Diagnosis Center, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore.,Molecular Diagnosis Center and Clinical Cytogenetics Service, Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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Chen M, Chang SP, Ma GC, Lin WH, Chen HF, Chen SU, Tsai HD, Tsai FP, Shen MC. Preimplantation genetic diagnosis of hemophilia A. Thromb J 2016; 14:33. [PMID: 27766059 PMCID: PMC5056473 DOI: 10.1186/s12959-016-0098-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Preimplantation genetic diagnosis (PGD) is a powerful tool to tackle the transmission of monogenic inherited disorders in families carrying the diseases from generation to generation. It currently remains a challenging task, despite PGD having been developed over 25 years ago. The major difficulty is it does not have an easy and general formula for all mutations. Different gene locus needs individualized, customized design to make the diagnosis accurate enough to be applied on PGD, in which the quantity of DNA is scanty, whereas timely laboratory diagnosis is mandatory if fresh embryo transfer is desired occasionally. Indicators for outcome assessment of a successful PGD program include the successful diagnosis rate on blastomeres (Day 3 cleavage-stage embryo biopsy) or trophectoderm cells (Day 5/6 blastocyst biopsy), the implantation rate per embryo transferred, and the livebirth rate per oocyte retrieval cycle. Hemophilia A (HA) is an X-linked recessive bleeding disorder caused by various types of pathological defects in the factor VIII gene (F8). The mutation spectrum of the F8 is complex, according to our previous report, including large segmental intra-gene inversions, large segmental deletions spanning a few exons, point mutations, and total deletion caused by chromosomal structural rearrangements. In this review, the molecular methodologies used to tackle different mutants of the F8 in the PGD of HA are to be explained, and the experiences of successful use of amplification refractory mutation system-quantitative polymerase chain reaction (ARMS-qPCR) and linkage analysis for PGD of HA in our laboratory are also provided.
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Affiliation(s)
- Ming Chen
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan.,Department of Genomic Science and Technology, Changhua Christian Hospital Healthcare System, Changhua, Taiwan.,Department of Obstetrics and Gynecology, College of Medicine and Hospital, National Taiwan University, Taipei, Taiwan.,Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Department of Life Science, Tunghai University, Taichung, Taiwan.,Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua, Taiwan
| | - Shun-Ping Chang
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan.,Department of Genomic Science and Technology, Changhua Christian Hospital Healthcare System, Changhua, Taiwan
| | - Gwo-Chin Ma
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan.,Department of Genomic Science and Technology, Changhua Christian Hospital Healthcare System, Changhua, Taiwan.,Institute of Biochemistry, Microbiology and Immunology, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan
| | - Wen-Hsian Lin
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan.,Department of Genomic Science and Technology, Changhua Christian Hospital Healthcare System, Changhua, Taiwan
| | - Hsin-Fu Chen
- Department of Obstetrics and Gynecology, College of Medicine and Hospital, National Taiwan University, Taipei, Taiwan
| | - Shee-Uan Chen
- Department of Obstetrics and Gynecology, College of Medicine and Hospital, National Taiwan University, Taipei, Taiwan
| | - Horng-Der Tsai
- Institute of Biochemistry, Microbiology and Immunology, Chung Shan Medical University, Taichung, Taiwan
| | - Feng-Po Tsai
- Po-Yuan Women's Clinic and IVF Center, Changhua, Taiwan
| | - Ming-Ching Shen
- Department of Internal Medicine, and Thrombosis and Hemostasis Center, Changhua Christian Hospital, Changhua, Taiwan
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Clinical applications of MARSALA for preimplantation genetic diagnosis of spinal muscular atrophy. J Genet Genomics 2016; 43:541-547. [PMID: 27599922 DOI: 10.1016/j.jgg.2016.03.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 11/22/2022]
Abstract
Conventional PCR methods combined with linkage analysis based on short tandem repeats (STRs) or Karyomapping with single nucleotide polymorphism (SNP) arrays, have been applied to preimplantation genetic diagnosis (PGD) for spinal muscular atrophy (SMA), an autosome recessive disorder. However, it has limitations in SMA diagnosis by Karyomapping, and these methods are unable to distinguish wild-type embryos with carriers effectively. Mutated allele revealed by sequencing with aneuploidy and linkage analyses (MARSALA) is a new method allowing embryo selection by a one-step next-generation sequencing (NGS) procedure, which has been applied in PGD for both autosome dominant and X-linked diseases in our group previously. In this study, we carried out PGD based on MARSALA for two carrier families with SMA affected children. As a result, one of the couples has given birth to a healthy baby free of mutations in SMA-causing gene. It is the first time that MARSALA was applied to PGD for SMA, and we can distinguish the embryos with heterozygous deletion (carriers) from the wild-type (normal) ones accurately through this NGS-based method. In addition, direct mutation detection allows us to identify the affected embryos (homozygous deletion), which can be regarded as probands for linkage analysis, in case that the affected family member is absent. In the future, the NGS-based MARSALA method is expected to be used in PGD for all monogenetic disorders with known pathogenic gene mutation.
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Watanabe M, Kusano J, Ohtaki S, Ishikura T, Katayama J, Koguchi A, Paumen M, Hayashi Y. Simultaneous genomic identification and profiling of a single cell using semiconductor-based next generation sequencing. Appl Transl Genom 2014; 3:70-7. [PMID: 27294018 PMCID: PMC4887956 DOI: 10.1016/j.atg.2014.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 05/19/2014] [Accepted: 05/29/2014] [Indexed: 12/02/2022]
Abstract
Combining single-cell methods and next-generation sequencing should provide a powerful means to understand single-cell biology and obviate the effects of sample heterogeneity. Here we report a single-cell identification method and seamless cancer gene profiling using semiconductor-based massively parallel sequencing. A549 cells (adenocarcinomic human alveolar basal epithelial cell line) were used as a model. Single-cell capture was performed using laser capture microdissection (LCM) with an Arcturus® XT system, and a captured single cell and a bulk population of A549 cells (≈ 106 cells) were subjected to whole genome amplification (WGA). For cell identification, a multiplex PCR method (AmpliSeq™ SNP HID panel) was used to enrich 136 highly discriminatory SNPs with a genotype concordance probability of 1031–35. For cancer gene profiling, we used mutation profiling that was performed in parallel using a hotspot panel for 50 cancer-related genes. Sequencing was performed using a semiconductor-based bench top sequencer. The distribution of sequence reads for both HID and Cancer panel amplicons was consistent across these samples. For the bulk population of cells, the percentages of sequence covered at coverage of more than 100 × were 99.04% for the HID panel and 98.83% for the Cancer panel, while for the single cell percentages of sequence covered at coverage of more than 100 × were 55.93% for the HID panel and 65.96% for the Cancer panel. Partial amplification failure or randomly distributed non-amplified regions across samples from single cells during the WGA procedures or random allele drop out probably caused these differences. However, comparative analyses showed that this method successfully discriminated a single A549 cancer cell from a bulk population of A549 cells. Thus, our approach provides a powerful means to overcome tumor sample heterogeneity when searching for somatic mutations.
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Affiliation(s)
- Manabu Watanabe
- Life Technologies Japan Ltd., a part of Thermo Fisher Scientific. 4-2-8 Shibaura, Minato-ku Tokyo 108-0023, Japan
| | - Junko Kusano
- Life Technologies Japan Ltd., a part of Thermo Fisher Scientific. 4-2-8 Shibaura, Minato-ku Tokyo 108-0023, Japan
| | - Shinsaku Ohtaki
- Life Technologies Japan Ltd., a part of Thermo Fisher Scientific. 4-2-8 Shibaura, Minato-ku Tokyo 108-0023, Japan
| | - Takashi Ishikura
- Life Technologies Japan Ltd., a part of Thermo Fisher Scientific. 4-2-8 Shibaura, Minato-ku Tokyo 108-0023, Japan
| | - Jin Katayama
- Life Technologies Japan Ltd., a part of Thermo Fisher Scientific. 4-2-8 Shibaura, Minato-ku Tokyo 108-0023, Japan
| | - Akira Koguchi
- Life Technologies Japan Ltd., a part of Thermo Fisher Scientific. 4-2-8 Shibaura, Minato-ku Tokyo 108-0023, Japan
| | - Michael Paumen
- Life Technologies Japan Ltd., a part of Thermo Fisher Scientific. 4-2-8 Shibaura, Minato-ku Tokyo 108-0023, Japan
| | - Yoshiharu Hayashi
- Life Technologies Japan Ltd., a part of Thermo Fisher Scientific. 4-2-8 Shibaura, Minato-ku Tokyo 108-0023, Japan
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Chen HF, Chang SP, Wu SH, Lin WH, Lee YC, Ni YH, Chen CA, Ma GC, Ginsberg NA, You EM, Tsai FP, Chen M. Validating a rapid, real-time, PCR-based direct mutation detection assay for preimplantation genetic diagnosis. Gene 2014; 548:299-305. [PMID: 25034658 DOI: 10.1016/j.gene.2014.07.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 07/08/2014] [Accepted: 07/12/2014] [Indexed: 01/24/2023]
Abstract
Although co-amplification of polymorphic microsatellite markers is the current gold standard for preimplantation genetic diagnosis (PGD) of single-gene disorders (SGD), this approach can be hampered by the lack of availability of informative markers. We recently (2011) devised a novel in-house assay for PGD of aromatic L-amino acid decarboxylase deficiency, based on an amplification refractory mutation system and quantitative PCR (ARMS-qPCR). The objective of the present study was to verify ARMS-qPCR in a cohort of 20 PGD cycles with a diverse group of SGDs (15 couples at risk for 10 SGDs). Day-3 cleavage-stage embryos were subjected to biopsy and genotyping, followed by fresh embryo transfer (FET). The diagnostic rate was 82.9%; unaffected live births were achieved in 9 of 20 FET cycles (45%), with only one false negative (among 54 transferred embryos). Overall, the ARMS-qPCR had frequent allele-dropout (ADO), rendering it inappropriate as the sole diagnostic method (despite a favorable live-birth rate). Regardless, it has the potential to complement the current gold-standard methodology, especially when trophectoderm biopsy becomes a preferred option and genotyping needs to be timely enough to enable FET.
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Affiliation(s)
- Hsin-Fu Chen
- Department of Obstetrics and Gynecology, College of Medicine, and Hospital, National Taiwan University, Taipei, Taiwan; Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shun-Ping Chang
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua, Taiwan; Department of Life Science, National Chung-Hsing University, Taichung, Taiwan
| | - Sheng-Hai Wu
- Department of Life Science, National Chung-Hsing University, Taichung, Taiwan
| | - Wen-Hsiang Lin
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Yi-Chung Lee
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yen-Hsuan Ni
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Chi-An Chen
- Department of Obstetrics and Gynecology, College of Medicine, and Hospital, National Taiwan University, Taipei, Taiwan
| | - Gwo-Chin Ma
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua, Taiwan; Institute of Biochemistry and Biotechnology, Chung Shan Medical University, Taichung, Taiwan
| | - Norman A Ginsberg
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - En-Min You
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | | | - Ming Chen
- Department of Obstetrics and Gynecology, College of Medicine, and Hospital, National Taiwan University, Taipei, Taiwan; Department of Genomic Medicine, Changhua Christian Hospital, Changhua, Taiwan; Department of Life Science, National Chung-Hsing University, Taichung, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan; Department of Life Science, Tunghai University, Taichung, Taiwan.
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