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Xiao Y, Cheng D, Luo K, Li M, Tan Y, Lin G, Hu L. Evaluation of genetic risk of apparently balanced chromosomal rearrangement carriers by breakpoint characterization. J Assist Reprod Genet 2024; 41:147-159. [PMID: 37993578 PMCID: PMC10789712 DOI: 10.1007/s10815-023-02986-7] [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: 08/03/2023] [Accepted: 10/31/2023] [Indexed: 11/24/2023] Open
Abstract
PURPOSE To report genetic characteristics and associated risk of chromosomal breaks due to chromosomal rearrangements in large samples. METHODS MicroSeq, a technique that combines chromosome microdissection and next-generation sequencing, was used to identify chromosomal breakpoints. Long-range PCR and Sanger sequencing were used to precisely characterize 100 breakpoints in 50 ABCR carriers. RESULTS In addition to the recurrent regions of balanced rearrangement breaks in 8q24.13, 11q11.23, and 22q11.21 that had been documented, we have discovered a 10-Mb region of 12q24.13-q24.3 that could potentially be a sparse region of balanced rearrangement breaks. We found that 898 breakpoints caused gene disruption and a total of 188 breakpoints interrupted genes recorded in OMIM. The percentage of breakpoints that disrupted autosomal dominant genes recorded in OMIM was 25.53% (48/188). Fifty-four of the precisely characterized breakpoints had 1-8-bp microhomologous sequences. CONCLUSION Our findings provide a reference for the evaluation of the pathogenicity of mutations in related genes that cause protein truncation in clinical practice. According to the characteristics of breakpoints, non-homologous end joining and microhomology-mediated break-induced replication may be the main mechanism for ABCRs formation.
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Affiliation(s)
- Yanqin Xiao
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - Dehua Cheng
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410023, Hunan, China
| | - Keli Luo
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410023, Hunan, China
| | - Mengge Li
- National Engineering and Research Center of Human Stem Cells, Changsha, 410023, Hunan, China
- Hunan Guangxiu Hospital, Changsha, 410023, Hunan, China
| | - Yueqiu Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410023, Hunan, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410023, Hunan, China
- National Engineering and Research Center of Human Stem Cells, Changsha, 410023, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, 410008, Hunan, China
| | - Liang Hu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China.
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410023, Hunan, China.
- National Engineering and Research Center of Human Stem Cells, Changsha, 410023, Hunan, China.
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, 410008, Hunan, China.
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Li S, Li H, Gao Y, Zou Y, Yin X, Chen ZJ, Choy KW, Dong Z, Yan J. Identification of cryptic balanced translocations in couples with unexplained recurrent pregnancy loss based upon embryonic PGT-A results. J Assist Reprod Genet 2024; 41:171-184. [PMID: 38102500 PMCID: PMC10789697 DOI: 10.1007/s10815-023-02999-2] [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: 09/11/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023] Open
Abstract
PURPOSE The goal of this study is to determine whether any balanced translocation (BT) had been missed by previous karyotyping in patients with unexplained recurrent pregnancy loss (uRPL). METHODS This case series included 48 uRPL-affected couples with normal karyotypes. The embryos from these couples have all undergone preimplantation testing for aneuploidies (PGT-A). Based on the PGT-A's results, 48 couples could be categorized into two groups: 17 couples whose multiple embryos were detected with similar structural variations (SVs, segmental/complete) and 31 couples without such findings but who did not develop any euploid embryo despite at least three high-quality blastocysts being tested. The peripheral blood sample of each partner was then collected for mate-pair sequencing (MPseq) to determine whether any of them were BT carriers. RESULTS MPseq analyses identified 13 BTs in the 17 couples whose multiple embryos had similar SVs detected (13/17, 76.47%) and three BTs in the 31 couples without euploid embryo obtained (3/31, 9.7%). Among the 16 MPseq-identified BTs, six were missed due to the limited resolution of G-banding karyotyping analysis, and the rest were mostly owing to the similar banding patterns and/or comparable sizes shared by the two segments exchanged. CONCLUSION A normal karyotype does not eliminate the possibility of carrying BT for couples with uRPL. The use of PGT-A allows us to perceive the "carrier couples" missed by karyotyping analysis, providing an increased risk of finding cryptic BTs if similar SVs are always detected on two chromosomes among multiple embryos. Nonetheless, certain carriers with translocated segments of sub-resolution may still go unnoticed.
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Affiliation(s)
- Shuo Li
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Shandong University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Hongchang Li
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Shandong University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Yuan Gao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Shandong University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Yang Zou
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Shandong University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Xunqiang Yin
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Shandong University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Shandong University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai Jiao Tong University, Shanghai, China
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kwong Wai Choy
- Department of Obstetrics & Gynecology, The Chinese University of Hong Kong, Hong Kong, China.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China.
- Hong Kong Branches of Chinese National Engineering Research Centers-Center for Assisted Reproductive Technology and Reproductive Genetics, Hong Kong, China.
| | - Zirui Dong
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.
- Department of Obstetrics & Gynecology, The Chinese University of Hong Kong, Hong Kong, China.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
| | - Junhao Yan
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China.
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Shandong University, Jinan, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China.
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Li K, Zhao Y, Chau MHK, Cao Y, Leung TY, Kwok YK, Choy KW, Dong Z. Low-Pass Genome Sequencing-Based Detection of Paternity: Validation in Clinical Cytogenetics. Genes (Basel) 2023; 14:1357. [PMID: 37510263 PMCID: PMC10379141 DOI: 10.3390/genes14071357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Submission of a non-biological parent together with a proband for genetic diagnosis would cause a misattributed parentage (MP), possibly leading to misinterpretation of the pathogenicity of genomic variants. Therefore, a rapid and cost-effective paternity/maternity test is warranted before genetic testing. Although low-pass genome sequencing (GS) has been widely used for the clinical diagnosis of germline structural variants, it is limited in paternity/maternity tests due to the inadequate read coverage for genotyping. Herein, we developed rapid paternity/maternity testing based on low-pass GS with trio-based and duo-based analytical modes provided. The optimal read-depth was determined as 1-fold per case regardless of sequencing read lengths, modes, and library construction methods by using 10 trios with confirmed genetic relationships. In addition, low-pass GS with different library construction methods and 1-fold read-depths were performed for 120 prenatal trios prospectively collected, and 1 trio was identified as non-maternity, providing a rate of MP of 0.83% (1/120). All results were further confirmed via quantitative florescent PCR. Overall, we developed a rapid, cost-effective, and sequencing platform-neutral paternity/maternity test based on low-pass GS and demonstrated the feasibility of its clinical use in confirming the parentage for genetic diagnosis.
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Affiliation(s)
- Keying Li
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yilin Zhao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew Hoi Kin Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
- Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, Hong Kong, China
| | - Ye Cao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
- The Fertility Preservation Research Center, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
- Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, Hong Kong, China
- The Fertility Preservation Research Center, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yvonne K Kwok
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
- Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, Hong Kong, China
- The Fertility Preservation Research Center, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Zirui Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
- The Fertility Preservation Research Center, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
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Fang C, Sun X, Fan F, Zhang X, Wang O, Zheng H, Peng Z, Luo X, Chen A, Zhang W, Drmanac R, Peters BA, Song Z, Kristiansen K. High-resolution single-molecule long-fragment rRNA gene amplicon sequencing of bacterial and eukaryotic microbial communities. CELL REPORTS METHODS 2023; 3:100437. [PMID: 37056375 PMCID: PMC10088238 DOI: 10.1016/j.crmeth.2023.100437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 01/28/2023] [Accepted: 03/01/2023] [Indexed: 03/29/2023]
Abstract
Sequencing of hypervariable regions as well as internal transcribed spacer regions of ribosomal RNA genes (rDNA) is broadly used to identify bacteria and fungi, but taxonomic and phylogenetic resolution is hampered by insufficient sequencing length using high throughput, cost-efficient second-generation sequencing. We developed a method to obtain nearly full-length rDNA by assembling single DNA molecules combining DNA co-barcoding with single-tube long fragment read technology and second-generation sequencing. Benchmarking was performed using mock bacterial and fungal communities as well as two forest soil samples. All mock species rDNA were successfully recovered with identities above 99.5% compared to the reference sequences. From the soil samples we obtained good coverage with identification of more than 20,000 unknown species, as well as high abundance correlation between replicates. This approach provides a cost-effective method for obtaining extensive and accurate information on complex environmental microbial communities.
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Affiliation(s)
- Chao Fang
- BGI-Shenzhen, Shenzhen 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Fei Fan
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaowei Zhang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Ou Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Haotian Zheng
- BGI-Shenzhen, Shenzhen 518083, China
- Section of Microbiology, University of Copenhagen, 2100 Copenhagen, Denmark
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Zhuobing Peng
- BGI-Shenzhen, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Xiaoqing Luo
- BGI-Shenzhen, Shenzhen 518083, China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ao Chen
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Radoje Drmanac
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Brock A. Peters
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
- PREDICT, Center for Molecular Prediction of Inflammatory Bowel Disease, Faculty of Medicine, Aalborg University, 2450 Copenhagen, Denmark
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Dong Z, Qian J, Law TSM, Chau MHK, Cao Y, Xue S, Tong S, Zhao Y, Kwok YK, Ng K, Chan DYL, Chiu PKF, Ng CF, Chung CHS, Mak JSM, Leung TY, Chung JPW, Morton CC, Choy KW. Mate-pair genome sequencing reveals structural variants for idiopathic male infertility. Hum Genet 2023; 142:363-377. [PMID: 36526900 DOI: 10.1007/s00439-022-02510-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022]
Abstract
Currently, routine genetic investigation for male infertility includes karyotyping analysis and PCR for Y chromosomal microdeletions to provide prognostic information such as sperm retrieval success rate. However, over 85% of male infertility remain idiopathic. We assessed 101 male patients with primary infertility in a retrospective cohort analysis who have previously received negative results from standard-of-care tests. Mate-pair genome sequencing (large-insert size library), an alternative long-DNA sequencing method, was performed to detect clinically significant structural variants (SVs) and copy-number neutral absence of heterozygosity (AOH). Candidate SVs were filtered against our in-house cohort of 1077 fertile men. Genes disrupted by potentially clinically significant variants were correlated with single-cell gene expression profiles of human fetal and postnatal testicular developmental lineages and adult germ cells. Follow-up studies were conducted for each patient with clinically relevant finding(s). Molecular diagnoses were made in 11.1% (7/63) of patients with non-obstructive azoospermia and 13.2% (5/38) of patients with severe oligozoospermia. Among them, 12 clinically significant SVs were identified in 12 cases, including five known syndromes, one inversion, and six SVs with direct disruption of genes by intragenic rearrangements or complex insertions. Importantly, a genetic defect related to intracytoplasmic sperm injection (ICSI) failure was identified in a patient with non-obstructive azoospermia, illustrating the additional value of an etiologic diagnosis in addition to determining sperm retrieval rate. Our study reveals a landscape of various genomic variants in 101 males with idiopathic infertility, not only advancing understanding of the underlying mechanisms of male infertility, but also impacting clinical management.
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Affiliation(s)
- Zirui Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China. .,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China. .,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China. .,The Fertility Preservation Research Center, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Jicheng Qian
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China
| | - Tracy Sze Man Law
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China
| | - Matthew Hoi Kin Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Ye Cao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China.,The Fertility Preservation Research Center, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Shuwen Xue
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China
| | - Steve Tong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yilin Zhao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yvonne K Kwok
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Karen Ng
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - David Yiu Leung Chan
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Peter K-F Chiu
- SH Ho Urology Centre, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi-Fai Ng
- SH Ho Urology Centre, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Cathy Hoi Sze Chung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Jennifer Sze Man Mak
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China.,The Fertility Preservation Research Center, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Jacqueline Pui Wah Chung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China.,The Fertility Preservation Research Center, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Cynthia C Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Manchester Centre for Audiology and Deafness, School of Health Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China. .,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China. .,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China. .,The Fertility Preservation Research Center, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China. .,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China.
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6
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Cao Y, Luk HM, Zhang Y, Chau MHK, Xue S, Cheng SSW, Li AM, Chong JSC, Leung TY, Dong Z, Choy KW, Lo IFM. Investigation of Chromosomal Structural Abnormalities in Patients With Undiagnosed Neurodevelopmental Disorders. Front Genet 2022; 13:803088. [PMID: 35495136 PMCID: PMC9046776 DOI: 10.3389/fgene.2022.803088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Structural variations (SVs) are various types of the genomic rearrangements encompassing at least 50 nucleotides. These include unbalanced gains or losses of DNA segments (copy number changes, CNVs), balanced rearrangements (such as inversion or translocations), and complex combinations of several distinct rearrangements. SVs are known to play a significant role in contributing to human genomic disorders by disrupting the protein-coding genes or the interaction(s) with cis-regulatory elements. Recently, different types of genome sequencing-based tests have been introduced in detecting various types of SVs other than CNVs and regions with absence of heterozygosity (AOH) with clinical significance.Method: In this study, we applied the mate-pair low pass (∼4X) genome sequencing with large DNA-insert (∼5 kb) in a cohort of 100 patients with neurodevelopmental disorders who did not receive informative results from a routine CNV investigation. Read-depth-based CNV analysis and chimeric-read-pairs analysis were used for CNV and SV analyses. The region of AOH was indicated by a simultaneous decrease in the rate of heterozygous SNVs and increase in the rate of homozygous SNVs.Results: First, we reexamined the 25 previously reported CNVs among 24 cases in this cohort. The boundaries of these twenty-five CNVs including 15 duplications and 10 deletions detected were consistent with the ones indicated by the chimeric-read-pairs analysis, while the location and orientation were determined in 80% of duplications (12/15). Particularly, one duplication was involved in complex rearrangements. In addition, among all the 100 cases, 10% of them were detected with rare or complex SVs (>10 Kb), and 3% were with multiple AOH (≥5 Mb) locating in imprinting chromosomes identified. In particular, one patient with an overall value of 214.5 Mb of AOH identified on 13 autosomal chromosomes suspected parental consanguinity.Conclusion: In this study, mate-pair low-pass GS resolved a significant proportion of CNVs with inconclusive significance, and detected additional SVs and regions of AOH in patients with undiagnostic neurodevelopmental disorders. This approach complements the first-tier CNV analysis for NDDs, not only by increasing the resolution of CNV detection but also by enhancing the characterization of SVs and the discovery of potential causative regions (or genes) contributory to could be complex in composition NDDs.
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Affiliation(s)
- Ye Cao
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ho Ming Luk
- Clinical Genetic Service, Department of Health, Hong Kong SAR, China
| | - Yanyan Zhang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Matthew Hoi Kin Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shuwen Xue
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | | | - Albert Martin Li
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Josephine S. C. Chong
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zirui Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- *Correspondence: Kwong Wai Choy, ; Ivan Fai Man Lo,
| | - Ivan Fai Man Lo
- Clinical Genetic Service, Department of Health, Hong Kong SAR, China
- *Correspondence: Kwong Wai Choy, ; Ivan Fai Man Lo,
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7
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Dong Z, Chau MHK, Zhang Y, Yang Z, Shi M, Wah YM, Kwok YK, Leung TY, Morton CC, Choy KW. Low-pass genome sequencing-based detection of absence of heterozygosity: validation in clinical cytogenetics. Genet Med 2021; 23:1225-1233. [PMID: 33772221 PMCID: PMC8522200 DOI: 10.1038/s41436-021-01128-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/11/2021] [Indexed: 11/21/2022] Open
Abstract
PURPOSE Absence of heterozygosity (AOH) is a genetic characteristic known to cause human genetic disorders through autosomal recessive or imprinting mechanisms. However, the analysis of AOH via low-pass genome sequencing (GS) is not yet clinically available. METHODS Low-pass GS (fourfold) with different types of libraries was performed on 17 clinical samples with previously ascertained AOH by chromosomal microarray analysis (CMA). In addition, AOH detection was performed with low-pass GS data in 1,639 cases that had both GS and high-probe density CMA data available from the 1000 Genomes Project. Cases with multiple AOHs (coefficient of inbreeding F ≥ 1/32) or terminal AOHs ≥5 Mb (suspected uniparental disomy [UPD]) were reported based on the guidelines of the American College of Medical Genetics and Genomics. RESULTS Low-pass GS revealed suspected segmental UPD and multiple AOHs (F ≥ 1/32) in nine and eight clinical cases, respectively, consistent with CMA. Among the 1,639 samples, low-pass GS not only consistently detected multiple AOHs (F ≥ 1/32) in 18 cases, but also reported 60 terminal AOHs in 44 cases including four mosaic AOHs at a level ranging from 50% to 75%. CONCLUSION Overall, our study demonstrates the feasibility of AOH analysis (≥5 Mb) with low-pass GS data and shows high concordance compared with CMA.
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Affiliation(s)
- Zirui Dong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew Hoi Kin Chau
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Yanyan Zhang
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhenjun Yang
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Mengmeng Shi
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yi Man Wah
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yvonne K Kwok
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Tak Yeung Leung
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China
| | - Cynthia C Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Manchester Centre for Audiology and Deafness, School of Health Sciences, University of Manchester, Manchester, UK.
| | - Kwong Wai Choy
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China.
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China.
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8
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Deciphering the complexity of simple chromosomal insertions by genome sequencing. Hum Genet 2020; 140:361-380. [PMID: 32728808 DOI: 10.1007/s00439-020-02210-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
Abstract
Chromosomal insertions are thought to be rare structural rearrangements. The current understanding of the underlying mechanisms of their origin is still limited. In this study, we sequenced 16 cases with apparent simple insertions previously identified by karyotyping and/or chromosomal microarray analysis. Using mate-pair genome sequencing (GS), we identified all 16 insertions and revised previously designated karyotypes in 75.0% (12/16) of the cases. Additional cryptic rearrangements were identified in 68.8% of the cases (11/16). The incidence of additional cryptic rearrangements in chromosomal insertions was significantly higher compared to balanced translocations and inversions reported in other studies by GS. We characterized and classified the cryptic insertion rearrangements into four groups, which were not mutually exclusive: (1) insertion segments were fragmented and their subsegments rearranged and clustered at the insertion site (10/16, 62.5%); (2) one or more cryptic subsegments were not inserted into the insertion site (5/16, 31.3%); (3) segments of the acceptor chromosome were scattered and rejoined with the insertion segments (2/16, 12.5%); and (4) copy number gains were identified in the flanking regions of the insertion site (2/16, 12.5%). In addition to the observation of these chromothripsis- or chromoanasynthesis-like events, breakpoint sequence analysis revealed microhomology to be the predominant feature. However, no significant correlation was found between the number of cryptic rearrangements and the size of the insertion. Overall, our study provide molecular characterization of karyotypically apparent simple insertions, demonstrate previously underappreciated complexities, and evidence that chromosomal insertions are likely formed by nonhomologous end joining and/or microhomology-mediated replication-based DNA repair.
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9
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Low-pass genome sequencing: a validated method in clinical cytogenetics. Hum Genet 2020; 139:1403-1415. [PMID: 32451733 DOI: 10.1007/s00439-020-02185-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022]
Abstract
Clinically significant copy-number variants (CNVs) known to cause human diseases are routinely detected by chromosomal microarray analysis (CMA). Recently, genome sequencing (GS) has been introduced for CNV analysis; however, sequencing depth (determined by sequencing read-length and read-amount) is a variable parameter across different laboratories. Variating sequencing depths affect the CNV detection resolution and also make it difficult for cross-laboratory referencing or comparison. In this study, by using data from 50 samples with high read-depth GS (30×) and the reported clinically significant CNVs, we first demonstrated the optimal read-amount and the most cost-effective read-length for CNV analysis to be 15 million reads and single-end 50 bp (equivalent to a read-depth of 0.25-fold), respectively. In addition, we showed that CNVs at mosaic levels as low as 30% are readily detected, furthermore, CNVs larger than 2.5 Mb are also detectable at mosaic levels as low as 20%. Herein, by conducting a retrospective back-to-back comparison study of low-pass GS versus routine CMA for 532 prenatal, miscarriage, and postnatal cases, the overall diagnostic yield was 22.4% (119/532) for CMA and 23.1% (123/532) for low-pass GS. Thus, the overall relative improvement of the diagnostic yield by low-pass GS versus CMA was ~ 3.4% (4/119). Identification of cryptic and clinically significant CNVs among prenatal, miscarriage, and postnatal cases demonstrated that CNV detection at higher resolutions is warranted for clinical diagnosis regardless of referral indications. Overall, our study supports low-pass GS as the first-tier genetic test for molecular cytogenetic testing.
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10
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Wang H, Dong Z, Zhang R, Chau MHK, Yang Z, Tsang KYC, Wong HK, Gui B, Meng Z, Xiao K, Zhu X, Wang Y, Chen S, Leung TY, Cheung SW, Kwok YK, Morton CC, Zhu Y, Choy KW. Low-pass genome sequencing versus chromosomal microarray analysis: implementation in prenatal diagnosis. Genet Med 2020; 22:500-510. [PMID: 31447483 PMCID: PMC7042067 DOI: 10.1038/s41436-019-0634-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/26/2019] [Indexed: 11/12/2022] Open
Abstract
PURPOSE Emerging studies suggest that low-pass genome sequencing (GS) provides additional diagnostic yield of clinically significant copy-number variants (CNVs) compared with chromosomal microarray analysis (CMA). However, a prospective back-to-back comparison evaluating accuracy, efficacy, and incremental yield of low-pass GS compared with CMA is warranted. METHODS A total of 1023 women undergoing prenatal diagnosis were enrolled. Each sample was subjected to low-pass GS and CMA for CNV analysis in parallel. CNVs were classified according to guidelines of the American College of Medical Genetics and Genomics. RESULTS Low-pass GS not only identified all 124 numerical disorders or pathogenic or likely pathogenic (P/LP) CNVs detected by CMA in 121 cases (11.8%, 121/1023), but also defined 17 additional and clinically relevant P/LP CNVs in 17 cases (1.7%, 17/1023). In addition, low-pass GS significantly reduced the technical repeat rate from 4.6% (47/1023) for CMA to 0.5% (5/1023) and required less DNA (50 ng) as input. CONCLUSION In the context of prenatal diagnosis, low-pass GS identified additional and clinically significant information with enhanced resolution and increased sensitivity of detecting mosaicism as compared with the CMA platform used. This study provides strong evidence for applying low-pass GS as an alternative prenatal diagnostic test.
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Affiliation(s)
- Huilin Wang
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Zirui Dong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Rui Zhang
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Matthew Hoi Kin Chau
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Zhenjun Yang
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kathy Yin Ching Tsang
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Hoi Kin Wong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Baoheng Gui
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Zhuo Meng
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Kelin Xiao
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Xiaofan Zhu
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yanfang Wang
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Shaoyun Chen
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Tak Yeung Leung
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China
| | - Sau Wai Cheung
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yvonne K Kwok
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Cynthia C Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- Manchester Center for Audiology and Deafness, University of Manchester, Manchester Academic Health Science Center, Manchester, UK.
| | - Yuanfang Zhu
- Maternal-Fetal Medicine Institute, Bao'an Maternity and Child Health Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China.
| | - Kwong Wai Choy
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China.
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11
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Choy KW, Wang H, Shi M, Chen J, Yang Z, Zhang R, Yan H, Wang Y, Chen S, Chau MHK, Cao Y, Chan OYM, Kwok YK, Zhu Y, Chen M, Leung TY, Dong Z. Prenatal Diagnosis of Fetuses With Increased Nuchal Translucency by Genome Sequencing Analysis. Front Genet 2019; 10:761. [PMID: 31475041 PMCID: PMC6706460 DOI: 10.3389/fgene.2019.00761] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/17/2019] [Indexed: 11/13/2022] Open
Abstract
Background: Increased nuchal translucency (NT) is an important biomarker associated with increased risk of fetal structural anomalies. It is known to be contributed by a wide range of genetic etiologies from single-nucleotide variants to those affecting millions of base pairs. Currently, prenatal diagnosis is routinely performed by karyotyping and chromosomal microarray analysis (CMA); however, both of them have limited resolution. The diversity of the genetic etiologies warrants an integrated assay such as genome sequencing (GS) for comprehensive detection of genomic variants. Herein, we aim to evaluate the feasibility of applying GS in prenatal diagnosis for the fetuses with increased NT. Methods: We retrospectively applied GS (> 30-fold) for fetuses with increased NT (≥3.5 mm) who underwent routine prenatal diagnosis. Detection of single-nucleotide variants, copy number variants, and structural rearrangements was performed simultaneously, and the results were integrated for interpretation in accordance with the guidelines of the American College of Medical Genetics and Genomics. Pathogenic or likely pathogenic (P/LP) variants were selected for validation and parental confirmation, when available. Results: Overall, 50 fetuses were enrolled, including 34 cases with isolated increased NT and 16 cases with other fetal structural malformations. Routine CMA and karyotyping reported eight P/LP CNVs, yielding a diagnostic rate of 16.0% (8/50). In comparison, GS provided a twofold increase in diagnostic yield (32.0%, 16/50), including one mosaic turner syndrome, eight cases with microdeletions/microduplications, and seven cases with P/LP point mutations. Moreover, GS identified two cryptic insertions and two inversions. Follow-up study further demonstrated the potential pathogenicity of an apparently balanced insertion that disrupted an OMIM autosomal dominant disease-causing gene at the insertion site. Conclusions: Our study demonstrates that applying GS in fetuses with increased NT can comprehensively detect and delineate the various genomic variants that are causative to the diseases. Importantly, prenatal diagnosis by GS doubled the diagnostic yield compared with routine protocols. Given a comparable turnaround time and less DNA required, our study provides strong evidence to facilitate GS in prenatal diagnosis, particularly in fetuses with increased NT.
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Affiliation(s)
- Kwong Wai Choy
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Huilin Wang
- Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Mengmeng Shi
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Jingsi Chen
- Department of Obstetrics and Gynecology, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhenjun Yang
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Rui Zhang
- Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Huanchen Yan
- Department of Obstetrics and Gynecology, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yanfang Wang
- Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Shaoyun Chen
- Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Matthew Hoi Kin Chau
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ye Cao
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Olivia Y M Chan
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yvonne K Kwok
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuanfang Zhu
- Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital Affiliated to Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Min Chen
- Department of Obstetrics and Gynecology, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Tak Yeung Leung
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Zirui Dong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Department of Obstetrics and Gynecology, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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