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Militaru MS, Babliuc IM, Bloaje-Florică VL, Danci VA, Filip-Deac I, Kutasi E, Simon V, Militaru M, Cătană A. The Impact of Chromosomal Mosaicisms on Prenatal Diagnosis and Genetic Counseling-A Narrative Review. J Pers Med 2024; 14:774. [PMID: 39064028 PMCID: PMC11277968 DOI: 10.3390/jpm14070774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/13/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Genetic disorders represent a high-impact diagnosis for both patients and their families. Prenatal screening methods and, when recommended, genetic testing allow parents to make informed decisions about the course a pregnancy is going to take. Although offering certainty about the potential evolution and prognosis of the pregnancy, and then the newborn, is usually not possible, genetic counseling can offer valuable insights into genetic disorders. Chromosomal mosaicisms are genetic anomalies that affect only some cell lines in either the fetus or the placenta or both. They can affect autosomal or heterosomal chromosomes, and they can be either numerical or structural. The prognosis seems to be more severe if the genetic alterations are accompanied by malformations visible in ultrasounds. Several genetic techniques can be used to diagnose certain mosaicisms, depending on their nature. A novel approach in prenatal care is non-invasive prenatal screening (NIPS), also known as non-invasive prenatal testing (NIPT), which, although it does not always have diagnostic value, can provide valuable information about potential genetic anomalies, especially numerical, with high sensitivity (Se).
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Affiliation(s)
- Mariela Sanda Militaru
- Department of Molecular Sciences, Faculty of Medicine, University of Medicine and Pharmacy “Iuliu Hatieganu”, 400012 Cluj-Napoca, Romania; (M.S.M.); (A.C.)
- Regional Laboratory Cluj-Napoca, Department of Medical Genetics, Regina Maria Health Network, 400363 Cluj-Napoca, Romania
| | - Ioana-Mădălina Babliuc
- Department for Mother and Child Health, Pediatric 1, Emergency County Hospital, No. 68 Motilor Street, 400394 Cluj-Napoca, Romania; (I.-M.B.); (V.-A.D.); (V.S.)
| | | | - Valentin-Adrian Danci
- Department for Mother and Child Health, Pediatric 1, Emergency County Hospital, No. 68 Motilor Street, 400394 Cluj-Napoca, Romania; (I.-M.B.); (V.-A.D.); (V.S.)
| | - Iulia Filip-Deac
- County Emergency Clinical Hospital, 50 Dr. Gheorghe Marinescu Street, 540136 Târgu Mureș, Romania;
| | - Enikő Kutasi
- Department of Molecular Sciences, Faculty of Medicine, University of Medicine and Pharmacy “Iuliu Hatieganu”, 400012 Cluj-Napoca, Romania; (M.S.M.); (A.C.)
- Department for Mother and Child Health, Pediatric 1, Emergency County Hospital, No. 68 Motilor Street, 400394 Cluj-Napoca, Romania; (I.-M.B.); (V.-A.D.); (V.S.)
| | - Vasile Simon
- Department for Mother and Child Health, Pediatric 1, Emergency County Hospital, No. 68 Motilor Street, 400394 Cluj-Napoca, Romania; (I.-M.B.); (V.-A.D.); (V.S.)
- Department of Urology, University of Medicine and Pharmacy “Iuliu Hatieganu”, 11 Tăbăcarilor Street, 400139 Cluj-Napoca, Romania
| | - Mihai Militaru
- Pediatric 2 Discipline, University of Medicine and Pharmacy “Iuliu Hatieganu”, Emergency County Hospital, No. 3-5 Clinicilor Street, 400535 Cluj-Napoca, Romania;
| | - Andreea Cătană
- Department of Molecular Sciences, Faculty of Medicine, University of Medicine and Pharmacy “Iuliu Hatieganu”, 400012 Cluj-Napoca, Romania; (M.S.M.); (A.C.)
- Regional Laboratory Cluj-Napoca, Department of Medical Genetics, Regina Maria Health Network, 400363 Cluj-Napoca, Romania
- Department of Oncogenetics, Institute of Oncology, “Prof. Dr. I. Chiricuță”, 400015 Cluj-Napoca, Romania
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Qian Y, Zhu J, Tang Z, Sun Y, Wang Z, Tang F, Yang Y, Fan L, Sun Y, Liu B, Chen M, Luo Y, Hu J, Yan K, Man J, Wang L, Jia C, Tang P, Zhu X, Wang C, Tang J, Xia Y, Guo X, Zhang K, Wang X, Li S, Song L, Zhu J, Dong M. Validation and depth evaluation of recurrent neural network-based ultra low-pass genome sequencing for the detection of absence of heterozygosity: A multi-centre study of 409 cases. Clin Transl Med 2024; 14:e1752. [PMID: 38965452 PMCID: PMC11223989 DOI: 10.1002/ctm2.1752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 07/06/2024] Open
Affiliation(s)
- Yeqing Qian
- Department of Reproductive Genetics, Women's Hospital, Zhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of MedicineZhejiang UniversityHangzhouChina
| | - Jianjun Zhu
- Department of Fetal Medical CenterJiaxing Maternity and Children Health Care Hospital, Jiaxing UniversityJiaxingChina
| | - Zhiguo Tang
- Andrological Medicine, Maternity and Child Health Hospital of Anhui ProvinceAffiliated Maternity and Child Health Hospital of Anhui Medical UniversityHefeiChina
| | | | | | - Fei Tang
- Clin Lab, BGI GenomicsTianjinChina
| | - Yun Yang
- Clin Lab, BGI GenomicsWuhanChina
| | | | - Yixi Sun
- Department of Reproductive Genetics, Women's Hospital, Zhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of MedicineZhejiang UniversityHangzhouChina
| | - Bei Liu
- Department of Reproductive Genetics, Women's Hospital, Zhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of MedicineZhejiang UniversityHangzhouChina
| | - Min Chen
- Department of Reproductive Genetics, Women's Hospital, Zhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of MedicineZhejiang UniversityHangzhouChina
| | - Yuqin Luo
- Department of Reproductive Genetics, Women's Hospital, Zhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of MedicineZhejiang UniversityHangzhouChina
| | - Junjie Hu
- Department of Reproductive Genetics, Women's Hospital, Zhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of MedicineZhejiang UniversityHangzhouChina
| | - Kai Yan
- Department of Reproductive Genetics, Women's Hospital, Zhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of MedicineZhejiang UniversityHangzhouChina
| | | | | | | | - Ping Tang
- Department of Fetal Medical CenterJiaxing Maternity and Children Health Care Hospital, Jiaxing UniversityJiaxingChina
| | - Xinyi Zhu
- Department of Fetal Medical CenterJiaxing Maternity and Children Health Care Hospital, Jiaxing UniversityJiaxingChina
| | - Chaohong Wang
- Medical Genetics Center, Maternity and Child Health Hospital of Anhui ProvinceAffiliated Maternity and Child Health Hospital of Anhui Medical UniversityHefeiChina
| | - Junxiang Tang
- Medical Genetics Center, Maternity and Child Health Hospital of Anhui ProvinceAffiliated Maternity and Child Health Hospital of Anhui Medical UniversityHefeiChina
| | - Yuanyuan Xia
- Medical Genetics Center, Maternity and Child Health Hospital of Anhui ProvinceAffiliated Maternity and Child Health Hospital of Anhui Medical UniversityHefeiChina
| | | | | | | | - Suping Li
- Department of Fetal Medical CenterJiaxing Maternity and Children Health Care Hospital, Jiaxing UniversityJiaxingChina
| | - Lijie Song
- Clin Lab, BGI GenomicsTianjinChina
- DTU Bioengineering, Technical University of Denmark2800 Kongens LyngbyDenmark
| | - Jiansheng Zhu
- Medical Genetics Center, Maternity and Child Health Hospital of Anhui ProvinceAffiliated Maternity and Child Health Hospital of Anhui Medical UniversityHefeiChina
| | - Minyue Dong
- Department of Reproductive Genetics, Women's Hospital, Zhejiang University School of MedicineHangzhouChina
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of MedicineZhejiang UniversityHangzhouChina
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Marchionni E, Guadagnolo D, Mastromoro G, Pizzuti A. Prenatal Genome-Wide Sequencing analysis (Exome or Genome) in detecting pathogenic Single Nucleotide Variants in fetal Central Nervous System Anomalies: systematic review and meta-analysis. Eur J Hum Genet 2024; 32:759-769. [PMID: 38486024 PMCID: PMC11219734 DOI: 10.1038/s41431-024-01590-2] [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: 09/16/2023] [Revised: 02/04/2024] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Prenatal Exome (pES) or Genome (pGS) Sequencing analysis showed a significant incremental diagnostic yield over karyotype and chromosomal microarray analysis (CMA) in fetal structural anomalies. Optimized indications and detection rates in different fetal anomalies are still under investigation. The aim of this study was to assess the incremental diagnostic yield in prenatally diagnosed Central Nervous System (CNS) anomalies. A systematic review on antenatal CNS anomalies was performed according to PRISMA guidelines, including n = 12 paper, accounting for 428 fetuses. Results were pooled in a meta-analysis fitting a logistic random mixed-effect model. The effect of interest was the incremental diagnostic rate of pES over karyotype/CMA in detecting likely pathogenic/pathogenic Single Nucleotide Variants (SNVs). A further meta-analysis adding the available pGS studies (including diagnostic coding SNVs only) and submeta-analysis on three CNS subcategories were also performed. The pooled incremental diagnostic yield estimate of pES studies was 38% (95% C.I.: [29%;47%]) and 36% (95% C.I.: [28%;45%]) when including diagnostic SNVs of pGS studies. The point estimate of the effect resulted 22% (95% C.I.: [15%;31%]) in apparently isolated anomalies, 33% (95% C.I.: [22%;46%]) in CNS-only related anomalies (≥1) and 46% (95% C.I.: [38%;55%]) in non-isolated anomalies (either ≥ 2 anomalies in CNS, or CNS and extra-CNS). Meta-analysis showed a substantial diagnostic improvement in performing Prenatal Genome-Wide Sequencing analysis (Exome or Genome) over karyotype and CMA in CNS anomalies.
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Affiliation(s)
- Enrica Marchionni
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.
| | - Daniele Guadagnolo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Gioia Mastromoro
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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Tang F, Wang Z, Sun Y, Fan L, Yang Y, Guo X, Wang Y, Yan S, Qiao Z, Li Y, Jiang T, Wang X, Man J, Wang L, Wang S, Peng H, Peng Z, Xie X, Song L. Recurrent neural network for predicting absence of heterozygosity from low pass WGS with ultra-low depth. BMC Genomics 2024; 25:470. [PMID: 38745141 PMCID: PMC11092001 DOI: 10.1186/s12864-024-10400-4] [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: 11/17/2023] [Accepted: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND The absence of heterozygosity (AOH) is a kind of genomic change characterized by a long contiguous region of homozygous alleles in a chromosome, which may cause human genetic disorders. However, no method of low-pass whole genome sequencing (LP-WGS) has been reported for the detection of AOH in a low-pass setting of less than onefold. We developed a method, termed CNVseq-AOH, for predicting the absence of heterozygosity using LP-WGS with ultra-low sequencing data, which overcomes the sparse nature of typical LP-WGS data by combing population-based haplotype information, adjustable sliding windows, and recurrent neural network (RNN). We tested the feasibility of CNVseq-AOH for the detection of AOH in 409 cases (11 AOH regions for model training and 863 AOH regions for validation) from the 1000 Genomes Project (1KGP). AOH detection using CNVseq-AOH was also performed on 6 clinical cases with previously ascertained AOHs by whole exome sequencing (WES). RESULTS Using SNP-based microarray results as reference (AOHs detected by CNVseq-AOH with at least a 50% overlap with the AOHs detected by chromosomal microarray analysis), 409 samples (863 AOH regions) in the 1KGP were used for concordant analysis. For 784 AOHs on autosomes and 79 AOHs on the X chromosome, CNVseq-AOH can predict AOHs with a concordant rate of 96.23% and 59.49% respectively based on the analysis of 0.1-fold LP-WGS data, which is far lower than the current standard in the field. Using 0.1-fold LP-WGS data, CNVseq-AOH revealed 5 additional AOHs (larger than 10 Mb in size) in the 409 samples. We further analyzed AOHs larger than 10 Mb, which is recommended for reporting the possibility of UPD. For the 291 AOH regions larger than 10 Mb, CNVseq-AOH can predict AOHs with a concordant rate of 99.66% with only 0.1-fold LP-WGS data. In the 6 clinical cases, CNVseq-AOH revealed all 15 known AOH regions. CONCLUSIONS Here we reported a method for analyzing LP-WGS data to accurately identify regions of AOH, which possesses great potential to improve genetic testing of AOH.
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Affiliation(s)
- Fei Tang
- Clin Lab, BGI Genomics, Tianjin, 300308, China
| | | | - Yan Sun
- BGI Genomics, Shenzhen, 518083, China
| | - Linlin Fan
- Clin Lab, BGI Genomics, Tianjin, 300308, China
| | - Yun Yang
- Clin Lab, BGI Genomics, Wuhan, 430074, China
| | - Xueqin Guo
- Clin Lab, BGI Genomics, Wuhan, 430074, China
| | | | - Saiying Yan
- Clin Lab, BGI Genomics, Tianjin, 300308, China
| | | | - Yun Li
- Clin Lab, BGI Genomics, Shenzhen, 518083, China
| | - Ting Jiang
- Clin Lab, BGI Genomics, Shenzhen, 518083, China
| | - Xiaoli Wang
- Clin Lab, BGI Genomics, Shenzhen, 518083, China
| | - Jianfen Man
- Clin Lab, BGI Genomics, Wuhan, 430074, China
| | - Lina Wang
- Clin Lab, BGI Genomics, Wuhan, 430074, China
| | | | | | | | - Xiaoyuan Xie
- Tianjin Women's and Children's Health Center, Tianjin, 300070, China.
| | - Lijie Song
- Clin Lab, BGI Genomics, Tianjin, 300308, China.
- DTU Bioengineering, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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He X, Tian P, Zhong L, Peng S, Chen S, Pan L, Du Y, Zhang R. A Novel 165 Kb Duplication Involving the α-Globin Gene Cluster Is Identified by Low-Pass Whole Genome Sequencing in a Chinese Thalassemia Intermedia Patient. Hemoglobin 2024:1-6. [PMID: 38693050 DOI: 10.1080/03630269.2024.2346143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/08/2024] [Indexed: 05/03/2024]
Abstract
Copy number variations (CNVs) involving the α-globin gene cluster can lead to an imbalance in the proportion of α- and β-globin chains and consequently cause clinical symptoms of β-thalassemia. In our case, a 6-year-old boy, clinically diagnosed with β thalassemia intermedia, was admitted for further genetic diagnosis with his family. Targeted sequencing and third generation sequencing (TGS) were used to detect the possible variants of the thalassemia genes. Low-pass whole genome sequencing (lpWGS) was conducted to specify the exact location of relevant CNVs across the genome, which was then validated by multiplex ligation-dependent probe amplification.The results revealed that the patient had a heterozygous β0 mutation of Codon17 (A > T) and a full duplication of the α-globin gene cluster, inherited from his mother and father, respectively. Besides, a novel point mutation within the 5' untranslated region of β-Globin (HBB: c. -175 (G > A) was only detected in the patient. This study suggests that lpWGS seems a powerful alternative to detect large CNVs related to thalassemia with second intention for more information of the breakpoints and a simultaneous genome-scale detection of other pathogenic CNVs.
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Affiliation(s)
- Xiaohong He
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | | | - Lijuan Zhong
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | - Shanshan Peng
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | | | - Lei Pan
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | - Yutao Du
- BGI-Shenzhen, Shenzhen, China
- Hebei Medical University, Shijiazhuang, China
| | - Rui Zhang
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
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Yan X, Hu Y, Zhang X, Gao X, Zhao Y, Peng H, Ouyang L, Zhang C. Identification of a novel intronic mutation of MAGED2 gene in a Chinese family with antenatal Bartter syndrome. BMC Med Genomics 2024; 17:23. [PMID: 38238844 PMCID: PMC10795325 DOI: 10.1186/s12920-024-01797-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Antenatal Bartter syndrome is a life-threatening disease caused by a mutation in the MAGED2 gene located on chromosome Xp11. It is characterized by severe polyhydramnios and extreme prematurity. While most reported mutations are located in the exon region, variations in the intron region are rarely reported. METHODS In our study, we employed whole exome sequencing and Sanger sequencing to genotype members of this family. Additionally, a minigene assay was conducted to evaluate the impact of genetic variants on splicing. RESULTS Our findings reveal a novel intronic variant (NM_177433.3:c.1271 + 4_1271 + 7delAGTA) in intron 10 of the MAGED2 gene. Further analysis using the minigene assay demonstrated that this variant activated an intronic cryptic splice site, resulting in a 96 bp insertion in mature mRNA. CONCLUSIONS Our results indicate that the novel intronic variant (c.1271 + 4_1271 + 7delAGTA) in intron 10 of the MAGED2 gene is pathogenic. This expands the mutation spectrum of MAGED2 and highlights the significance of intronic sequence analysis.
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Affiliation(s)
- Xu Yan
- Reproductive Medicine Center, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China
- Biomedical Engineering College, Hubei University of Medicine, Shiyan, 442000, China
- Hubei Clinical Research Center for Reproductive Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Yueyue Hu
- Reproductive Medicine Center, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Xin Zhang
- Reproductive Medicine Center, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Xia Gao
- Obstetrics, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Yang Zhao
- Neonatal Intensive Care, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Haiying Peng
- Reproductive Medicine Center, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China
- Biomedical Engineering College, Hubei University of Medicine, Shiyan, 442000, China
| | - Liu Ouyang
- Obstetrics, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China
| | - Changjun Zhang
- Reproductive Medicine Center, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, China.
- Biomedical Engineering College, Hubei University of Medicine, Shiyan, 442000, China.
- Hubei Clinical Research Center for Reproductive Medicine, Shiyan, China.
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China.
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Dai YF, Wu XQ, Huang HL, He SQ, Guo DH, Li Y, Lin N, Xu LP. Experience of copy number variation sequencing applied in spontaneous abortion. BMC Med Genomics 2024; 17:15. [PMID: 38191380 PMCID: PMC10775620 DOI: 10.1186/s12920-023-01699-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 10/13/2023] [Indexed: 01/10/2024] Open
Abstract
PURPOSE We evaluated the value of copy number variation sequencing (CNV-seq) and quantitative fluorescence (QF)-PCR for analyzing chromosomal abnormalities (CA) in spontaneous abortion specimens. METHODS A total of 650 products of conception (POCs) were collected from spontaneous abortion between April 2018 and May 2020. CNV-seq and QF-PCR were performed to determine the characteristics and frequencies of copy number variants (CNVs) with clinical significance. The clinical features of the patients were recorded. RESULTS Clinically significant chromosomal abnormalities were identified in 355 (54.6%) POCs, of which 217 (33.4%) were autosomal trisomies, 42(6.5%) were chromosomal monosomies and 40 (6.2%) were pathogenic CNVs (pCNVs). Chromosomal trisomy occurs mainly on chromosomes 15, 16, 18, 21and 22. Monosomy X was not associated with the maternal or gestational age. The frequency of chromosomal abnormalities in miscarriages from women with a normal live birth history was 55.3%; it was 54.4% from women without a normal live birth history (P > 0.05). There were no significant differences among women without, with 1, and with ≥ 2 previous miscarriages regarding the rate of chromosomal abnormalities (P > 0.05); CNVs were less frequently detected in women with advanced maternal age than in women aged ≤ 29 and 30-34 years (P < 0.05). CONCLUSION Chromosomal abnormalities are the most common cause of pregnancy loss, and maternal and gestational ages are strongly associated with fetal autosomal trisomy aberrations. Embryo chromosomal examination is recommended regardless of the gestational age, modes of conception or previous abortion status.
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Affiliation(s)
- Yi-Fang Dai
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Xiao-Qing Wu
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Hai-Long Huang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Shu-Qiong He
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Dan-Hua Guo
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China.
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China.
| | - Liang-Pu Xu
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China.
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China.
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8
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Xue S, Wang L, Wei J, Liu Y, Ding G, Dai P. Clinical application of single nucleotide polymorphism microarray analysis in pregnancy loss in Northwest China. Front Genet 2023; 14:1319624. [PMID: 38155718 PMCID: PMC10754489 DOI: 10.3389/fgene.2023.1319624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023] Open
Abstract
Background: Spontaneous abortion is the most common complication of early pregnancy. In this study, we aim to investigate the clinical application value of genetic diagnosis using single nucleotide polymorphism (SNP) microarray analysis on the products of conception and to characterize the types of genetic abnormalities and their prevalence in pregnancy loss in Northwest China. Methods: Over 48 months, we selected 652 products of conception, which included chorionic villi, fetal tissues, germ cell samples, amniotic fluid samples, cord blood samples, and a cardiac blood sample. We analyzed the distribution of chromosomal abnormalities leading to fetal arrest or abortion using SNP array. The patients were then categorized divided into groups based on maternal age, gestational age, number of miscarriages, and maternal ethnic background. The incidences of various chromosomal abnormalities in each group were compared. Results: Of the 652 cases, 314 (48.16%) exhibited chromosomal abnormalities. These included 286 cases with numerical chromosomal abnormalities, 24 cases with copy number variation, and four cases with loss of heterozygosity. Among them, there were 203 trisomy cases, 55 monosomy cases, and 28 polyploidy cases. In the subgroup analysis, significant differences were found in the frequency of numerical chromosomal abnormalities and copy number variation between the advanced and younger maternal age group as well as between the early and late abortion groups. Furthermore, we identified significant differences in the frequency of numerical chromosomal abnormalities between the first spontaneous abortion and recurrent miscarriage groups. However, there were no significant differences in the frequency of numerical chromosomal abnormalities between the Han and Uighur groups. Conclusion: Our research highlights chromosomal abnormalities as the primary cause of spontaneous abortion, with a higher incidence in early pregnancy and among women of advanced age. The use of SNP array analysis emerges as an effective and reliable technique for chromosome analysis in aborted fetuses. This method offers a comprehensive and dependable genetic investigation into the etiology of miscarriage, establishing itself as a valuable routine selection for genetic analysis in cases of natural abortions.
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Affiliation(s)
- ShuYuan Xue
- The College of Life Sciences, Northwest University, Xi’an, Shanxi, China
- Prenatal Diagnosis Center, Urumqi Maternal and Child Healthcare Hospital, Urumqi, Xinjiang, China
| | - LiXia Wang
- Prenatal Diagnosis Center, Urumqi Maternal and Child Healthcare Hospital, Urumqi, Xinjiang, China
| | - Jie Wei
- Prenatal Diagnosis Center, Urumqi Maternal and Child Healthcare Hospital, Urumqi, Xinjiang, China
| | - YuTong Liu
- College of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, China
| | - GuiFeng Ding
- Department of Obstetrics, Urumqi Maternal and Child Healthcare Hospital, Urumqi, Xinjiang, China
| | - PengGao Dai
- The College of Life Sciences, Northwest University, Xi’an, Shanxi, China
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9
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Liu Y, Hao S, Guo X, Fan L, Qiao Z, Wang Y, Wang X, Man J, Wang L, Wei X, Peng H, Peng Z, Sun Y, Song L. Accuracy and depth evaluation of clinical low pass genome sequencing in the detection of mosaic aneuploidies and CNVs. BMC Med Genomics 2023; 16:294. [PMID: 37978521 PMCID: PMC10656965 DOI: 10.1186/s12920-023-01703-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/14/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Low-pass genome sequencing (LP GS) has shown distinct advantages over traditional methods for the detection of mosaicism. However, no study has systematically evaluated the accuracy of LP GS in the detection of mosaic aneuploidies and copy number variants (CNVs) in prenatal diagnosis. Moreover, the influence of sequencing depth on mosaicism detection of LP GS has not been fully evaluated. METHODS To evaluate the accuracy of LP GS in the detection of mosaic aneuploidies and mosaic CNVs, 27 samples with known aneuploidies and CNVs and 1 negative female sample were used to generate 6 simulated samples and 21 virtual samples, each sample contained 9 different mosaic levels. Mosaic levels were simulated by pooling reads or DNA from each positive sample and the negative sample according to a series of percentages (ranging from 3 to 40%). Then, the influence of sequencing depth on LP GS in the detection of mosaic aneuploidies and CNVs was evaluated by downsampling. RESULTS To evaluate the accuracy of LP GS in the detection of mosaic aneuploidies and CNVs, a comparative analysis of mosaic levels was performed using 6 simulated samples and 21 virtual samples with 35 M million (M) uniquely aligned high-quality reads (UAHRs). For mosaic levels > 30%, the average difference (detected mosaic levels vs. theoretical mosaic levels) of 6 mosaic CNVs in simulated samples was 4.0%, and the average difference (detected mosaic levels vs. mosaic levels of Y chromosome) of 6 mosaic aneuploidies and 15 mosaic CNVs in virtual samples was 2.7%. Furthermore, LP GS had a higher detection rate and accuracy for the detection of mosaic aneuploidies and CNVs of larger sizes, especially mosaic aneuploidies. For depth evaluation, the results of LP GS in downsampling samples were compared with those of LP GS using 35 M UAHRs. The detection sensitivity of LP GS for 6 mosaic aneuploidies and 15 mosaic CNVs in virtual samples increased with UAHR. For mosaic levels > 30%, the total detection sensitivity reached a plateau at 30 M UAHRs. With 30 M UAHRs, the total detection sensitivity was 99.2% for virtual samples. CONCLUSIONS We demonstrated the accuracy of LP GS in mosaicism detection using simulated data and virtual samples, respectively. Thirty M UAHRs (single-end 35 bp) were optimal for LP GS in the detection of mosaic aneuploidies and most mosaic CNVs larger than 1.48 Mb (Megabases) with mosaic levels > 30%. These results could provide a reference for laboratories that perform clinical LP GS in the detection of mosaic aneuploidies and CNVs.
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Affiliation(s)
- Yanqiu Liu
- Jiangxi Maternal and Child Health Hospital Affiliated to Nanchang Medical College, Nanchang, 33000, Jiangxi, China
| | - Shengju Hao
- Medical Genetics Center, Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Gansu Provincial Maternity and Child-care Hospital, Lanzhou, 730050, China
| | - Xueqin Guo
- Clin Lab, BGI Genomics, Wuhan, 430074, China
| | - Linlin Fan
- Clin Lab, BGI Genomics, Tianjin, 300308, China
| | | | | | - Xiaoli Wang
- Clin Lab, BGI Genomics, Shenzhen, 518083, China
| | - Jianfen Man
- Clin Lab, BGI Genomics, Wuhan, 430074, China
| | - Lina Wang
- Clin Lab, BGI Genomics, Wuhan, 430074, China
| | | | | | | | - Yan Sun
- BGI Genomics, Shenzhen, 518083, China.
| | - Lijie Song
- Clin Lab, BGI Genomics, Tianjin, 300308, China.
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, 2800, Denmark.
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10
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Liu Z, Jing C. Two- and three-dimensional sonographic findings of harlequin ichthyosis: case report and literature review. An Bras Dermatol 2023; 98:806-813. [PMID: 37355352 PMCID: PMC10589490 DOI: 10.1016/j.abd.2022.09.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/24/2022] [Accepted: 09/30/2022] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND Harlequin ichthyosis (HI) is a rare skin disorder with extremely high lethality due to a mutation of the ABCA12 gene. Because of its rarity and the often-late onset, prenatal screening for HI is extremely difficult, and most pregnant women might easily miss the period for optimal examinations. OBJECTIVE To summarize the sonographic features of HI for prenatal diagnostic purposes. METHODS The authors describe a case of HI with no family history who was diagnosed by using prenatal ultrasound scanning. The sonographic features of HI and the clinical characteristics of pregnant women were summarized by searching relevant literature over nearly two decades. RESULTS The unique sonographic presentations including peeling skin, clenched hands and clubfeet, ectropion, flat nose, fetal growth impairment, polyhydramnios and echogenic amniotic fluid may be primarily related to skin disorders in HI fetuses. The authors also identified a novel pathogenic ABCA12 gene mutation and explained the possible pathogenic mechanisms. STUDY LIMITATIONS Caution should be exercised in summarizing disease characteristics because of the small number of cases, and the authors are faced with the possibility of incomplete case searching. CONCLUSIONS HI has relatively unique sonographic features. Therefore, 2D-ultrasound combined with 3D-ultrasound may be an effective method for the prenatal diagnosis of HI. Moreover, a novel pathogenic ABCA12 gene mutation may provide important clues for future research on the etiology of HI. However, the authors consider that additional studies are needed to provide more evidence for prenatal diagnosis.
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Affiliation(s)
- Zesi Liu
- Department of Gynecology and Obstetrics, The First Affiliated Hospital Dalian Medical University, Dalian, China
| | - Chunli Jing
- Department of Ultrasound of Gynecology and Obstetrics, The Second Affiliated Hospital Dalian Medical University, Dalian, China.
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11
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Pan L, Liang H, Meng Z, Wang J, Zhang R, Wu Y. Assessing the value of second-trimester nasal bone hypoplasia in predicting chromosomal abnormalities: a retrospective chromosomal microarray analysis of 351 fetuses. Arch Gynecol Obstet 2023; 308:1263-1270. [PMID: 36269386 DOI: 10.1007/s00404-022-06808-6] [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: 07/02/2022] [Accepted: 09/27/2022] [Indexed: 11/02/2022]
Abstract
PURPOSE To evaluate the value of fetal nasal bone hypoplasia and other prenatal risk factors in predicting chromosomal abnormalities. METHODS In this retrospective cohort study, we collected data on singleton pregnancies diagnosed with fetal nasal bone hypoplasia during second-trimester ultrasound. Fetal karyotyping and chromosomal microarray analysis (CMA) were performed, and pregnancy outcomes were assessed. The association between fetal nasal bone hypoplasia and chromosomal abnormalities was evaluated according to whether other prenatal risk factors were observed. RESULTS Our final analysis included 351 pregnancies, of which 62 (17.7%) fetuses had chromosomal abnormalities, including 36 cases of trisomy-21, six cases of trisomy-18, one case each of trisomy-13, and 47, XYY syndrome, and 18 cases of copy number variations (CNVs). Among the 243 cases of isolated nasal bone hypoplasia, 28 (11.5%) cases of chromosomal aberrations were identified. The incidence was significantly higher if other soft markers or structural abnormalities were simultaneously detected. Pregnancy was terminated in 43 aneuploid fetuses and nine fetuses detected with CNVs. The parents of the fetuses diagnosed with 47, XYY syndrome and the other nine CNVs chose to continue the pregnancy, and no abnormalities were detected in the newborns. Furthermore, we found that other prenatal risk factors should be considered in evaluating the likelihood of chromosomal abnormalities in fetuses with nasal bone hypoplasia. CONCLUSIONS Nasal bone hypoplasia is a highly specific soft marker that is associated with multiple chromosomal abnormalities. The risk of chromosomal abnormalities increases when combined with structural abnormalities or increased nuchal translucency (NT). Chromosomal microarray analysis is a powerful prenatal test for chromosomal abnormalities, which may be warranted in fetuses with nasal bone hypoplasia.
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Affiliation(s)
- Lei Pan
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, 518102, China
| | - Hui Liang
- Central Laboratory, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, 518102, China
| | - Zhuo Meng
- Department of Medical Image Center, Medical Research Institute, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, 518102, China
| | - Jun Wang
- Medical Research Institute, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, 518102, China
| | - Rui Zhang
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, 518102, China.
| | - Yong Wu
- Medical Research Institute, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, 518102, China.
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12
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Qian Y, Sun Y, Guo X, Song L, Sun Y, Gao X, Liu B, Xu Y, Chen N, Chen M, Luo Y, Qiao Z, Fan L, Man J, Zhang K, Wang X, Rong T, Wang Z, Liu F, Zhao J, Wei X, Chen M, Peng Z, Peng H, Sun J, Dong M. Validation and depth evaluation of low-pass genome sequencing in prenatal diagnosis using 387 amniotic fluid samples. J Med Genet 2023; 60:933-938. [PMID: 37012053 DOI: 10.1136/jmg-2022-109112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/16/2023] [Indexed: 04/05/2023]
Abstract
BACKGROUND Low-pass genome sequencing (LP GS) is an alternative to chromosomal microarray analysis (CMA). However, validations of LP GS as a prenatal diagnostic test for amniotic fluid are rare. Moreover, sequencing depth of LP GS in prenatal diagnosis has not been evaluated. OBJECTIVE The diagnostic performance of LP GS was compared with CMA using 375 amniotic fluid samples. Then, sequencing depth was evaluated by downsampling. RESULTS CMA and LP GS had the same diagnostic yield (8.3%, 31/375). LP GS showed all copy number variations (CNVs) detected by CMA and six additional variant of uncertain significance CNVs (>100 kb) in samples with negative CMA results; CNV size influenced LP GS detection sensitivity. CNV detection was greatly influenced by sequencing depth when the CNV size was small or the CNV was located in the azoospermia factor c (AZFc) region of the Y chromosome. Large CNVs were less affected by sequencing depth and more stably detected. There were 155 CNVs detected by LP GS with at least a 50% reciprocal overlap with CNVs detected by CMA. With 25 M uniquely aligned high-quality reads (UAHRs), the detection sensitivity for the 155 CNVs was 99.14%. LP GS using samples with 25 M UAHRs showed the same performance as LP GS using total UAHRs. Considering the detection sensitivity, cost and interpretation workload, 25 M UAHRs are optimal for detecting most aneuploidies and microdeletions/microduplications. CONCLUSION LP GS is a promising, robust alternative to CMA in clinical settings. A total of 25 M UAHRs are sufficient for detecting aneuploidies and most microdeletions/microduplications.
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Affiliation(s)
- Yeqing Qian
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xueqin Guo
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 430074, China
| | - Lijie Song
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
- DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Yixi Sun
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoyang Gao
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bei Liu
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuqing Xu
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Na Chen
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Min Chen
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuqin Luo
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhihong Qiao
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Linlin Fan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Jianfen Man
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 430074, China
| | - Kang Zhang
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 430074, China
| | - Xiaoli Wang
- Clinical laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Tingting Rong
- Clinical laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhonghua Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Fengxia Liu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Jing Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xiaoming Wei
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 430074, China
| | - Minfeng Chen
- Clinical laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huanhuan Peng
- Clinical laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Minyue Dong
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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Pan L, Wu J, Liang D, Yuan J, Wang J, Shen Y, Lu J, Xia A, Li J, Wu L. Association analysis between chromosomal abnormalities and fetal ultrasonographic soft markers based on 15,263 fetuses. Am J Obstet Gynecol MFM 2023; 5:101072. [PMID: 37393030 DOI: 10.1016/j.ajogmf.2023.101072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/03/2023]
Abstract
BACKGROUND Soft markers are common prenatal ultrasonographic findings that indicate an increased risk for fetal aneuploidy. However, the association between soft markers and pathogenic or likely pathogenic copy number variations is still unclear, and clinicians lack clarity on which soft markers warrant a recommendation for invasive prenatal genetic testing of the fetus. OBJECTIVE This study aimed to provide guidance on ordering prenatal genetic testing for fetuses with different soft markers and to elucidate the association between specific types of chromosomal abnormalities and specific ultrasonographic soft markers. STUDY DESIGN Low-pass genome sequencing was performed for 15,263 fetuses, including 9123 with ultrasonographic soft markers and 6140 with normal ultrasonographic findings. The detection rate of pathogenic or likely pathogenic copy number variants among fetuses with various ultrasonographic soft markers were compared with that of fetuses with normal ultrasonography. The association of soft markers with aneuploidy and pathogenic or likely pathogenic copy number variants were investigated using Fisher exact tests with Bonferroni correction. RESULTS The detection rate of aneuploidy and pathogenic or likely pathogenic copy number variants was 3.04% (277/9123) and 3.40% (310/9123), respectively, in fetuses with ultrasonographic soft markers. An absent or a hypoplastic nasal bone was the soft marker in the second trimester with the highest diagnostic rate for aneuploidy of 5.22% (83/1591) among all isolated groups. Four types of isolated ultrasonographic soft markers, namely a thickened nuchal fold, single umbilical artery, mild ventriculomegaly, and absent or hypoplastic nasal bone, had higher diagnostic rates for pathogenic or likely pathogenic copy number variants (P<.05; odds ratio, 1.69-3.31). Furthermore, this study found that the 22q11.2 deletion was associated with an aberrant right subclavian artery, whereas the 16p13.11 deletion, 10q26.13-q26.3 deletion, and 8p23.3-p23.1 deletion were associated with a thickened nuchal fold, and the 16p11.2 deletion and 17p11.2 deletion were associated with mild ventriculomegaly (P<.05). CONCLUSION Ultrasonographic phenotype-based genetic testing should be considered in clinical consultations. Copy number variant analysis is recommended for fetuses with an isolated thickened nuchal fold, a single umbilical artery, mild ventriculomegaly, and an absent or a hypoplastic nasal bone. A comprehensive definition of genotype-phenotype correlations in aneuploidy and pathogenic or likely pathogenic copy number variants could provide better information for genetic counseling.
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Affiliation(s)
- Lijuan Pan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China (Drs Pan, J Wu, Liang, and L Wu); Department of Obstetrics, Xiangya Hospital, Central South University, Changsha, Hunan, China (Dr Pan)
| | - Jiayu Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China (Drs Pan, J Wu, Liang, and L Wu)
| | - Desheng Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China (Drs Pan, J Wu, Liang, and L Wu)
| | - Jing Yuan
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China (Dr Yuan)
| | - Jue Wang
- Department of Obstetrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China (Dr Wang)
| | - Yinchen Shen
- Department of Maternity Care, Nanning Maternity and Child Health Hospital, Nanning, Guangxi, China (Dr Shen)
| | - Junjie Lu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital, Army Military Medical University, Chongqing, China (Dr Lu)
| | - Aihua Xia
- Department of Obstetrics, Beihai People's Hospital, Beihai, Guangxi, China (Dr Xia)
| | - Jinchen Li
- Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China (Dr Li).
| | - Lingqian Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China (Drs Pan, J Wu, Liang, and L Wu).
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14
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Tian W, Yuan Y, Yuan E, Zhang L, Liu L, Li Y, Guo J, Cui X, Li P, Cui S. Evaluation of the clinical utility of extended non-invasive prenatal testing in the detection of chromosomal aneuploidy and microdeletion/microduplication. Eur J Med Res 2023; 28:304. [PMID: 37644576 PMCID: PMC10466692 DOI: 10.1186/s40001-023-01285-2] [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: 01/30/2023] [Accepted: 08/12/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND With the development of whole-genome sequencing technology, non-invasive prenatal testing (NIPT) has been applied gradually to screen chromosomal microdeletions and microduplications that cannot be detected by traditional karyotyping. However, in NIPT, some false positives and false negatives occur. This study aimed to investigate the applicability of extended NIPT (NIPT-PLUS) in the detection of chromosomal aneuploidy and microdeletion/microduplication syndrome (MMS). METHODS A total of 452 pregnancies that underwent prenatal diagnostic testing (amniocentesis or chorionic villus sampling) by chromosomal microarray analysis (CMA), were screened by NIPT-PLUS from the peripheral blood sample of the pregnant women. The results of the two tested items were compared and analysed. RESULTS Of the 452 cases, 335 (74.12%) had positive CMA results, and 117 (25.88%) had no abnormal results. A total of 86 cases of trisomy 21, 18 and 13 and sex chromosome aneuploidy (SCA) were detected by CMA and NIPT-PLUS, with a detection rate of 96.51% (83/86). Among them, the detection rates of T18, T13; 47, XXY; 47, XXX and 47 XYY were 100%, and the detection rates of T21 and 45 XO were 96.55% and 90%, respectively. The detection sensitivity of rare chromosomal trisomy (RAT) was 80% (4/5). The positive predictive values of NIPT-PLUS for chromosome aneuploidy T21, T18 and T13 and for SCA and RAT were 90.32%, 87.50%, 25.00%, 88.89% and 50%, respectively. A total of 249 cases (74.32%) of chromosomal MMS were detected by CMA. The detection rate of NIPT-PLUS was 63.86% (159/249), and 90 cases (36.14%) were missed. The larger the MMS fragment, the higher the NIPT-PLUS detection sensitivity. In addition, most small fragments were of maternal origin. CONCLUSION The comparison between the CMA and NIPT-PLUS techniques shows that NIPT-PLUS has high sensitivity for detecting chromosomal aneuploidy and chromosomal copy number variations (CNVs) with fragments > 5 M. However, the sensitivity of CNV for fragments < 5 M is low, and the missed detection rate is high. Additionally, confined placental mosaicism and foetal mosaicism are the key factors causing false negatives in NIPT-PLUS, while maternal chromosomal abnormalities and confined placental mosaicism are key contributors to false positives, so appropriate genetic counselling is especially important for pregnant women before and after NIPT-PLUS testing.
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Affiliation(s)
- Weifang Tian
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Yangyang Yuan
- Department of Medical Research Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, Zhengzhou, 450052, China
| | - Erfeng Yuan
- Department of Clinical Laboratory Science, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, Zhengzhou, 450052, China
| | - Linlin Zhang
- Department of Clinical Laboratory Science, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, Zhengzhou, 450052, China
| | - Ling Liu
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
- Perinatal Disease and Prevention of Birth Defects, Advanced Medical Center, Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Clinical Research Center for Perinatal Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Ying Li
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Jing Guo
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Xueyin Cui
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Pengyun Li
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Shihong Cui
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China.
- Perinatal Disease and Prevention of Birth Defects, Advanced Medical Center, Zhengzhou University, Zhengzhou, 450052, China.
- Henan Provincial Clinical Research Center for Perinatal Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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15
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Bonini KE, Thomas-Wilson A, Marathe PN, Sebastin M, Odgis JA, Biase MD, Kelly NR, Ramos MA, Insel BJ, Scarimbolo L, Rehman AU, Guha S, Okur V, Abhyankar A, Phadke S, Nava C, Gallagher KM, Elkhoury L, Edelmann L, Zinberg RE, Abul-Husn NS, Diaz GA, Greally JM, Suckiel SA, Horowitz CR, Kenny EE, Wasserstein M, Gelb BD, Jobanputra V. Identification of copy number variants with genome sequencing: Clinical experiences from the NYCKidSeq program. Clin Genet 2023; 104:210-225. [PMID: 37334874 PMCID: PMC10505482 DOI: 10.1111/cge.14365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/28/2023] [Accepted: 05/15/2023] [Indexed: 06/21/2023]
Abstract
Copy number variations (CNVs) play a significant role in human disease. While chromosomal microarray has traditionally been the first-tier test for CNV detection, use of genome sequencing (GS) is increasing. We report the frequency of CNVs detected with GS in a diverse pediatric cohort from the NYCKidSeq program and highlight specific examples of its clinical impact. A total of 1052 children (0-21 years) with neurodevelopmental, cardiac, and/or immunodeficiency phenotypes received GS. Phenotype-driven analysis was used, resulting in 183 (17.4%) participants with a diagnostic result. CNVs accounted for 20.2% of participants with a diagnostic result (37/183) and ranged from 0.5 kb to 16 Mb. Of participants with a diagnostic result (n = 183) and phenotypes in more than one category, 5/17 (29.4%) were solved by a CNV finding, suggesting a high prevalence of diagnostic CNVs in participants with complex phenotypes. Thirteen participants with a diagnostic CNV (35.1%) had previously uninformative genetic testing, of which nine included a chromosomal microarray. This study demonstrates the benefits of GS for reliable detection of CNVs in a pediatric cohort with variable phenotypes.
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Affiliation(s)
- Katherine E. Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Priya N. Marathe
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Jacqueline A. Odgis
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Nicole R. Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Michelle A. Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Beverly J. Insel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Laura Scarimbolo
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Saurav Guha
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Volkan Okur
- Molecular Diagnostics, New York Genome Center, New York, NY
| | | | - Shruti Phadke
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Caroline Nava
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Katie M. Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | | | | | - Randi E. Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Noura S. Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - George A. Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - John M. Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Sabrina A. Suckiel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Carol R. Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Melissa Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Bruce D. Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
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16
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Li Y, Chau MHK, Zhang YX, Zhao Y, Xue S, Li TC, Cao Y, Dong Z, Choy KW, Chung JPW. A pilot investigation of low-pass genome sequencing identifying site-specific variation in chromosomal mosaicisms by a multiple site sampling approach in first-trimester miscarriages. Hum Reprod 2023; 38:1628-1642. [PMID: 37218343 DOI: 10.1093/humrep/dead090] [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: 02/02/2023] [Revised: 04/06/2023] [Indexed: 05/24/2023] Open
Abstract
STUDY QUESTION Can multiple-site low-pass genome sequencing (GS) of products of conception (POCs) improve the detection of genetic abnormalities, especially heterogeneously distributed mosaicism and homogeneously distributed mosaicism in first-trimester miscarriage? SUMMARY ANSWER Multiple-site sampling combined with low-pass GS significantly increased genetic diagnostic yield (77.0%, 127/165) of first-trimester miscarriages, with mosaicisms accounting for 17.0% (28/165), especially heterogeneously distributed mosaicisms (75%, 21/28) that are currently underappreciated. WHAT IS KNOWN ALREADY Aneuploidies are well known to cause first-trimester miscarriage, which are detectable by conventional karyotyping and next-generation sequencing (NGS) on a single-site sampling basis. However, there are limited studies demonstrating the implications of mosaic genetic abnormalities in first-trimester miscarriages, especially when genetic heterogeneity is present in POCs. STUDY DESIGN, SIZE, DURATION This is a cross-sectional cohort study carried out at a university-affiliated public hospital. One hundred seventy-four patients diagnosed with first-trimester miscarriage from December 2018 to November 2021 were offered ultrasound-guided manual vacuum aspiration (USG-MVA) treatment. Products of conception were subjected to multiple-site low-pass GS for the detection of chromosomal imbalances. PARTICIPANTS/MATERIALS, SETTING, METHODS For each POC, multiple sites of villi (three sites on average) were biopsied for low-pass GS. Samples with maternal cell contamination (MCC) and polyploidy were excluded based on the quantitative fluorescence polymerase chain reaction (QF-PCR) results. The spectrum of chromosomal abnormalities, including mosaicism (heterogeneously distributed and homogeneously distributed) and constitutional abnormalities was investigated. Chromosomal microarray analysis and additional DNA fingerprinting were used for validation and MCC exclusion. A cross-platform comparison between conventional karyotyping and our multiple-site approach was also performed. MAIN RESULTS AND THE ROLE OF CHANCE One hundred sixty-five POCs (corresponding to 490 DNA samples) were subjected to low-pass GS. Genetic abnormalities were detected in 77.0% (127/165) of POCs by our novel approach. Specifically, 17.0% (28/165) of cases had either heterogeneously distributed mosaicism (12.7%, 21/165) or homogeneously distributed mosaicism (6.1%, 10/165) (three cases had both types of mosaicism). The remaining 60.0% (99/165) of cases had constitutional abnormalities. In addition, in the 71 cases with karyotyping performed in parallel, 26.8% (19/71) of the results could be revised by our approach. LIMITATIONS, REASONS FOR CAUTION Lack of a normal gestational week-matched cohort might hinder the establishment of a causative link between mosaicisms and first-trimester miscarriage. WIDER IMPLICATIONS OF THE FINDINGS Low-pass GS with multiple-site sampling increased the detection of chromosomal mosaicisms in first-trimester miscarriage POCs. This innovative multiple-site low-pass GS approach enabled the novel discovery of heterogeneously distributed mosaicism, which was prevalent in first-trimester miscarriage POCs and frequently observed in preimplantation embryos, but is currently unappreciated by conventional single-site cytogenetic investigations. STUDY FUNDING/COMPETING INTEREST(S) This work was supported partly by Research Grant Council Collaborative Research Fund (C4062-21GF to K.W.C), Science and Technology Projects in Guangzhou (202102010005 to K.W.C), Guangdong-Hong Kong Technology Cooperation Funding Scheme (TCFS), Innovation and Technology Fund (GHP/117/19GD to K.W.C), HKOG Direct Grant (2019.050 to J.P.W.C), and Hong Kong Health and Medical Research Fund (05160406 to J.P.W.C). The authors have no competing interests to declare. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Ying Li
- Department of Obstetrics and 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
- Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, 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
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ying Xin Zhang
- Department of Obstetrics and 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
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
- Center of Prenatal Diagnosis, Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yilin Zhao
- Department of Obstetrics and 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
| | - Shuwen Xue
- Department of Obstetrics and 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
| | - Tin Chiu Li
- Department of Obstetrics and Gynaecology, 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
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Fertility Preservation Research Centre, 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
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Fertility Preservation Research Centre, 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
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Fertility Preservation Research Centre, 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
- Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, 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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18
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Points to consider in the detection of germline structural variants using next-generation sequencing: A statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100316. [PMID: 36507974 DOI: 10.1016/j.gim.2022.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
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Abstract
The options for prenatal genetic testing have evolved rapidly in the past decade, and advances in sequencing technology now allow genetic diagnoses to be made down to the single-base-pair level, even before the birth of the child. This offers women the opportunity to obtain information regarding the foetus, thereby empowering them to make informed decisions about their pregnancy. As genetic testing becomes increasingly available to women, clinician knowledge and awareness of the options available to women is of great importance. Additionally, comprehensive pretest and posttest genetic counselling about the advantages, pitfalls and limitations of genetic testing should be provided to all women. This review article aims to cover the range of genetic tests currently available in prenatal screening and diagnosis, their current applications and limitations in clinical practice as well as what the future holds for prenatal genetics.
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Affiliation(s)
- Karen Mei Xian Lim
- Department of Obstetrics and Gynaecology, National University Health System, Singapore
| | - Aniza Puteri Mahyuddin
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, National University Health System, Singapore,Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Correspondence: A/Prof Mahesh Choolani, Head and Senior Consultant, Department of Obstetrics and Gynaecology, National University Health System, NUHS Tower Block, Level 12, 1E Kent Ridge Road, 119228, Singapore. E-mail:
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Lázaro-Guevara JM, Flores-Robles BJ, Garrido-Lopez KM, McKeown RJ, Flores-Morán AE, Labrador-Sánchez E, Pinillos-Aransay V, Trasahedo EA, López-Martín JA, Soberanis LSR, Melgar MY, Téllez-Arreola JL, Thébault SC. Identification of RP1 as the genetic cause of retinitis pigmentosa in a multi-generational pedigree using Extremely Low-Coverage Whole Genome Sequencing (XLC-WGS). Gene X 2023; 851:146956. [DOI: 10.1016/j.gene.2022.146956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 09/25/2022] [Accepted: 10/03/2022] [Indexed: 11/04/2022] Open
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21
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Zhang S, Xu Y, Lu D, Fu D, Zhao Y. Combined use of karyotyping and copy number variation sequencing technology in prenatal diagnosis. PeerJ 2022; 10:e14400. [PMID: 36523456 PMCID: PMC9745786 DOI: 10.7717/peerj.14400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 10/25/2022] [Indexed: 12/12/2022] Open
Abstract
Background Karyotyping and genome copy number variation sequencing (CNV-seq) are two techniques frequently used in prenatal diagnosis. This study aimed to explore the diagnostic potential of using a combination of these two methods in order to provide a more accurate clinical basis for prenatal diagnosis. Methods We selected 822 pregnant women undergoing amniocentesis and separated them into six groups according to different risk indicators. Karyotyping and CNV-seq were performed simultaneously to compare the diagnostic performance of the two methods. Results Among the different amniocentesis indicators, abnormal fetal ultrasounds accounted for 39.29% of the total number of examinees and made up the largest group. The abnormal detection rate of non-invasive prenatal testing (NIPT) high risk was 37.93% and significantly higher than the other five groups (P < 0.05). The abnormal detection rate of mixed indicators was significantly higher than the history of the adverse reproductive outcomes group (P = 0.0151). The two methods combined found a total of 119 abnormal cases (14.48%). Karyotyping detected 57 cases (6.93%) of abnormal karyotypes, 30 numerical aberrations, and 27 structural aberrations. CNV-seq identified 99 cases (12.04%) with altered CNVs, 30 cases of chromosome aneuploidies, and 69 structural aberrations (28 pathogenic, eight that were likely pathogenic, and 33 microdeletion/duplication variants of uncertain significance (VUS)). Thirty-seven cases were found abnormal by both methods, 20 cases were detected abnormally by karyotyping (mainly mutual translocation and mostly balanced), and 62 cases of microdeletion/duplication were detected by CNV-seq. Steroid sulfatase gene (STS) deletion was identified at chromosome Xp22.31 in three cases. Postnatal follow-up confirmed that babies manifested skin abnormalities one week after birth. Six fetuses had Xp22.31 duplications ranging from 1.5 Kb to 1.7 Mb that were detected by CNV-seq. Follow-up showed that five babies presented no abnormalities during follow-up, except for one terminated pregnancy due to a history of adverse reproductive outcomes. Conclusion The combination of using CNV-seq and karyotyping significantly improved the detection rate of fetal pathogenic chromosomal abnormalities. CNV-seq is an effective complement to karyotyping and improves the accuracy of prenatal diagnosis.
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Affiliation(s)
- Suhua Zhang
- Department of Gynaecology and Obstetrics, Clinical Medical College of Yangzhou University, Northern Jiangsu People’s Hospital, Yang Zhou, Jiangsu Province, China
| | - Yuexin Xu
- Department of Gynaecology and Obstetrics, Clinical Medical College of Yangzhou University, Northern Jiangsu People’s Hospital, Yang Zhou, Jiangsu Province, China
| | - Dan Lu
- Department of Gynaecology and Obstetrics, Clinical Medical College of Yangzhou University, Northern Jiangsu People’s Hospital, Yang Zhou, Jiangsu Province, China
| | - Dan Fu
- Department of Gynaecology and Obstetrics, Clinical Medical College of Yangzhou University, Northern Jiangsu People’s Hospital, Yang Zhou, Jiangsu Province, China
| | - Yan Zhao
- Medical Research Center, Clinical Medical College of Yangzhou University, Northern Jiangsu People’s Hospital, Yang Zhou, Jiangsu Province, China
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22
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Xiang J, Peng Z. Applications of Noninvasive Prenatal Testing for Subchromosomal Copy Number Variations Using Cell-Free DNA. Clin Lab Med 2022; 42:613-625. [PMID: 36368786 DOI: 10.1016/j.cll.2022.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jiale Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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23
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Segmental aneuploidies with 1 Mb resolution in human preimplantation blastocysts. Genet Med 2022; 24:2285-2295. [PMID: 36107168 DOI: 10.1016/j.gim.2022.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/22/2022] Open
Abstract
PURPOSE This study aimed to investigate the spectrum and characteristics of segmental aneuploidies (SAs) of <10 megabase (Mb) length in human preimplantation blastocysts. METHODS Preimplantation genetic testing for aneuploidy was performed in 15,411 blastocysts from 5171 patients using a validated 1 Mb resolution platform. The characteristics and spectrum of SAs, including the incidence, sizes, type, inheritance pattern, clinical significance, and embryo distribution, were studied. RESULTS In total, 6.4% of the 15,411 blastocysts carried SAs of >10 Mb, 4.9% of embryos had SAs ranging between 1 to 10 Mb, and 84.3% of 1 to 10 Mb SAs were <5 Mb in size. Inheritance pattern analysis indicated that approximately 63.8% of 1 to 10 Mb SAs were inherited and were predominantly 1 to 3 Mb in size. Furthermore, 18.4% of inherited SAs and 51.9% de novo 1 to 10 Mb SAs were pathogenic or likely pathogenic (P/LP). Different from whole-chromosome aneuploidies, reanalysis indicated that 50% of the de novo 1 to 10 Mb SAs and 70% of the >10 Mb SAs arose from mitotic errors. CONCLUSION Based on the established platform, 1 to 10 Mb SAs are common in blastocysts and include a subset of P/LP SAs. Inheritance pattern analysis and clinical interpretation based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines contributed to determine the P/LP SAs.
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24
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Liu X, Liu S, Wang H, Hu T. Potentials and challenges of chromosomal microarray analysis in prenatal diagnosis. Front Genet 2022; 13:938183. [PMID: 35957681 PMCID: PMC9360565 DOI: 10.3389/fgene.2022.938183] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/11/2022] [Indexed: 11/19/2022] Open
Abstract
Introduction: For decades, conventional karyotyping analysis has been the gold standard for detecting chromosomal abnormalities during prenatal diagnosis. With the development of molecular cytogenetic methods, this situation has dramatically changed. Chromosomal microarray analysis (CMA), a method of genome-wide detection with high resolution, has been recommended as a first-tier test for prenatal diagnosis, especially for fetuses with structural abnormalities. Methods: Based on the primary literature, this review provides an updated summary of the application of CMA for prenatal diagnosis. In addition, this review addresses the challenges that CMA faces with the emergence of genome sequencing techniques, such as copy number variation sequencing, genome-wide cell-free DNA testing, and whole exome sequencing. Conclusion: The CMA platform is still suggested as priority testing methodology in the prenatal setting currently. However, pregnant women may benefit from genome sequencing, which enables the simultaneous detection of copy number variations, regions of homozygosity and single-nucleotide variations, in near future.
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Affiliation(s)
- Xijing Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Shanling Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - He Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- *Correspondence: Ting Hu,
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25
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Chu G, Li P, Wen J, Zheng G, Zhao Y, He R. Copy Number Variation Analysis of 5p Deletion Provides Accurate Prenatal Diagnosis and Reveals Candidate Pathogenic Genes. Front Med (Lausanne) 2022; 9:883565. [PMID: 35911393 PMCID: PMC9329539 DOI: 10.3389/fmed.2022.883565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/21/2022] [Indexed: 11/19/2022] Open
Abstract
Objective 5p deletion syndrome, that characterized by cat-like cry and peculiar timbre of voice, is believed to be one of the most common pathogenic copy number variations (CNVs). Variable critical regions on 5p involving a variety of genes contribute to the phenotypic heterogeneity without specific correlation. The objective of this study was to examine the genotype–phenotype correlation of 5p deletion syndrome, and to redefine 5p deletion syndrome relevant regions. In addition, we demonstrate the potential use of whole genome sequencing (WGS) to identify chromosomal breakpoints in prenatal diagnosis. Methods Three families with women undergoing prenatal diagnosis and two children were recruited. Karyotyping, CNV-seq, fluorescence in situ hybridization, WGS, and Sanger sequencing were performed to identify the chromosomal disorder. Results We reported three families and two children with CNVs of 5p deletion or combined 6p duplication. Five different sizes of 5p deletion were detected and their pathogenicity was determined, including 5p15.33-p15.31 [1–7,700,000, family1-variant of uncertain significance (VUS)], 5p15.33 (1–3,220,000, family 2-VUS), 5p15.33-p15.31 (1–7,040,000, family 3-VUS), 5p15.33-p15.31 (1–8,740,000, child 1-pathogenic) and 5p15.31-p15.1 (8,520,001–18,080,000, child 2-pathogenic). One duplication at 6p25.3-p24.3 (1–10,420,000) was detected and determined as likely pathogenic. The chromosomal breakpoints in family 3 were successfully identified by WGS. Conclusion Some critical genes that were supposed to be causative of the symptoms were identified. Relevant region in 5p deletion syndrome was redefined, and the chr5:7,700,000–8,740,000 region was supposed to be responsible for the cat-like cry. The great potential of WGS in detecting chromosomal translocations was demonstrated. Our findings may pave the way for further research on the prevention, diagnosis, and treatment of related diseases.
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Affiliation(s)
- Guoming Chu
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Pingping Li
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Juan Wen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Gaoyan Zheng
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yanyan Zhao
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Rong He
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Rong He,
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46,XY disorders of sex development: the use of NGS for prevalent variants. Hum Genet 2022; 141:1863-1873. [PMID: 35729303 DOI: 10.1007/s00439-022-02465-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/05/2022] [Indexed: 11/04/2022]
Abstract
46,XY disorders of sex development (DSD) present with diverse phenotypes and complicated genetic causes. Precise genetic diagnosis contributes to accurate management, and targeted next-generation sequencing (NGS) and whole-exome sequencing are powerful tools for investigating DSD. However, the prevalent variants resulting in 46,XY DSD remain unclear, especially those associated with mild forms, such as isolated hypospadias, inguinal cryptorchidism, and micropenis. From 2019 to 2021, 74 patients with 46,XY DSD (48 typical and 26 mild) from the First Affiliated Hospital of Sun Yat-sen University were enrolled in our cohort study for targeted NGS or whole-exome sequencing. Our targeted 46,XY DSD panel included 108 genes involved in disorders of gonadal development and differentiation, steroid hormone synthesis and activation, persistent Müllerian duct syndrome, idiopathic hypogonadotropic hypogonadism, syndromic disorder, and others. Variants were classified as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign following the American College of Medical Genetics guidelines. As a result, 28 of 74 (37.8%) patients with pathogenic and/or likely pathogenic variants acquired genetic diagnoses. The Mild DSD patients acquired a diagnosis rate of 30.7%. We detected 44 variants in 28 DSD genes from 31 patients, including 33 novel and 11 reported variants. Heterozygous (65%) and missense (70.5%) variants were the most common. Variants associated with steroid hormone synthesis and activation were the main genetic causes of 46,XY DSD. In conclusion, 46,XY DSD manifests as a series of complicated polygenetic diseases. NGS reveals prevalent variants and improves the genetic diagnoses of 46,XY DSD, regardless of severity.
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The Burden and Benefits of Knowledge: Ethical Considerations Surrounding Population-Based Newborn Genome Screening for Hearing. Int J Neonatal Screen 2022; 8:ijns8020036. [PMID: 35735787 PMCID: PMC9224714 DOI: 10.3390/ijns8020036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 12/04/2022] Open
Abstract
Recent advances in genomic sequencing technologies have expanded practitioners' utilization of genetic information in a timely and efficient manner for an accurate diagnosis. With an ever-increasing resource of genomic data from progress in the interpretation of genome sequences, clinicians face decisions about how and when genomic information should be presented to families, and at what potential expense. Presently, there is limited knowledge or experience in establishing the value of implementing genome sequencing into newborn screening. Herein we provide insight into the complexities and the burden and benefits of knowledge resulting from genome sequencing of newborns.
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Zheng Y, Zhu B, Tan J, Guan Y, Morton CC, Lu G. Experience of Low-Pass Whole-Genome Sequencing-Based Copy Number Variant Analysis: A Survey of Chinese Tertiary Hospitals. Diagnostics (Basel) 2022; 12:diagnostics12051098. [PMID: 35626254 PMCID: PMC9139561 DOI: 10.3390/diagnostics12051098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/14/2022] [Accepted: 04/23/2022] [Indexed: 11/16/2022] Open
Abstract
In China, low-pass whole-genome sequencing (low-pass WGS) is emerging as an alternative diagnostic test to detect copy number variants (CNVs). This survey aimed to study the laboratory practice, service quality, and case volumes of low-pass WGS-based CNV analysis among national accredited Chinese tertiary hospitals that have routinely applied low-pass WGS for more than a year and that have been certified in next-generation sequencing (NGS) clinical applications for more than three years. The questionnaire focused on (1) the composition of patients’ referral indications for testing and annual case volumes; (2) the capacity of conducting laboratory assays, bioinformatic analyses, and reporting; (3) the sequencing platforms and parameters utilized; and (4) CNV nomenclature in reports. Participants were required to respond based on their routine laboratory practices and data audited in a 12-month period from February 2019 to January 2020. Overall, 24 participants representing 24 tertiary referral hospitals from 21 provincial administrative regions in China returned the questionnaires. Excluding three hospitals routinely applying low-pass WGS for non-invasive prenatal testing (NIPT) only, the analysis only focused on the data submitted by the rest 21 hospitals. These hospitals applied low-pass WGS-based CNV analysis for four primary applications: high-risk pregnancies, spontaneous abortions, couples with adverse pregnancy history, and children with congenital birth defects. The overall estimated annual sample volume was over 36,000 cases. The survey results showed that the most commonly reported detection limit for CNV size (resolution) was 100 kb; however, the sequencing methods utilized by the participants were variable (single-end: 61.90%, 13/21; paired-end: 28.57%, 6/21; both: 9.52%, 2/21). The diversity was also reflected in the sequencing parameters: the mean read count was 13.75 million reads/case (95% CI, 9.91–17.60) and the read-length median was 65 bp (95% CI, 75.17–104.83). To assess further the compliance of the CNV reporting nomenclature according to the 2016 edition of International System for Human Cytogenomics Nomenclature (ISCN 2016), a scoring metric was applied and yielded responses from 19 hospitals; the mean compliance score was 7.79 out of 10 points (95% CI, 6.78–8.80). Our results indicated that the low-pass WGS-based CNV analysis service is in great demand in China. From a quality control perspective, challenges remain regarding the establishment of standard criteria for low-pass WGS-based CNV analysis and data reporting formats. In summary, the low-pass WGS-based method is becoming a common diagnostic approach, transforming the possibilities for genetic diagnoses for patients in China.
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Affiliation(s)
- Yu Zheng
- Prenatal Genetic Diagnosis Centre, Department of Obstetrics & Gynecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China;
| | - Baosheng Zhu
- Department of Genetics Medicine, First People’s Hospital of Yunnan Province, Kunming 650021, China;
| | - Jichun Tan
- Reproductive Medicine Centre, Shengjing Hospital of China Medical University, Shenyang 110055, China;
| | - Yichun Guan
- Reproductive Medicine Centre, Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China;
| | | | - Cynthia C. Morton
- Department of Obstetrics and Gynecology and Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Manchester Centre for Audiology and Deafness (ManCAD), School of Health Sciences, University of
Manchester, Manchester M13 9PL, UK
- Correspondence: (C.C.M.); (G.L.)
| | - Guangxiu Lu
- Genetics Centre, Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha 410008, China
- Correspondence: (C.C.M.); (G.L.)
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Cao Y, Chau M, Zheng Y, Zhao YL, Kwan A, Hui A, Lam YH, Tan T, Tse WT, Wong L, Leung TY, Dong Z, Choy KW. Exploring the diagnostic utility of genome sequencing for fetal congenital heart defects. Prenat Diagn 2022; 42:862-872. [PMID: 35441720 DOI: 10.1002/pd.6151] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 11/09/2022]
Abstract
OBJECTIVE The diagnostic yield for congenital heart defects (CHD) with routine genetic testing is around 10-20% when considering the pathogenic CNVs or aneuploidies as positive findings. This is a pilot study to investigate the utility of genome sequencing (GS) for prenatal diagnosis of CHD. METHODS Genome sequencing (GS, 30X) was performed on 13 trios with CHD for which karyotyping and/or chromosomal microarray results were non-diagnostic. RESULTS Trio GS provided a diagnosis for 4/13 (30.8%) fetuses with complex CHDs and other structural anomalies. Findings included pathogenic or likely pathogenic variants in DNAH5, COL4A1, PTPN11, and KRAS. Of nine cases without a possibly genetic etiology by GS, we had follow-up on eight. For five of them (60%), the parents chose to keep the pregnancy. A balanced translocation [46,XX,t(14;22)(q32.33;q13.31)mat] was detected in a trio with biallelic DNAH5 mutations, which together explained the recurrent fetal situs inversus and dextrocardia that was presumably due to de novo Phelan-McDermid syndrome. A secondary finding of a BRCA2 variant and carrier status of HBB, USH2A, HBA1/HBA2 were detected in the trio. CONCLUSIONS GS expands the diagnostic scope of mutation types over conventional testing, revealing the genetic etiology for fetal heart anomalies. Patients without a known genetic abnormality indicated by GS likely opted to keep pregnancy especially if the heart issue could be repaired. We provide evidence to support the application of GS for fetuses with CHD. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Y Cao
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Laboratory Genetics and Genomics, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mhk Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Laboratory Genetics and Genomics, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Y Zheng
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Y L Zhao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ahw Kwan
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Asy Hui
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Y H Lam
- OB GYN ULTRASOUND, Henley Building, 5 Queen's Road C, Central, Hong Kong SAR, China
| | - Tyt Tan
- Tony Tan Women and Fetal Clinic, Mount Alvernia Hospital, Singapore
| | - W T Tse
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - L Wong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - T Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Laboratory Genetics and Genomics, 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 SAR, China
| | - Z Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Laboratory Genetics and Genomics, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - K W Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Laboratory Genetics and Genomics, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Fertility Preservation Research Centre, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong SAR, China
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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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Mastromoro G, Guadagnolo D, Khaleghi Hashemian N, Marchionni E, Traversa A, Pizzuti A. Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis. Diagnostics (Basel) 2022; 12:575. [PMID: 35328129 PMCID: PMC8947110 DOI: 10.3390/diagnostics12030575] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.
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Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (N.K.H.); (E.M.); (A.T.); (A.P.)
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Jing X, Liu H, Zhu Q, Liu S, Liu J, Bai T, Deng C, Xia T, Liu Y, Cheng J, Wei X, Xing L, Luo Y, Zhou Q, Chen L, Li L, Wang J. Clinical Selection of Prenatal Diagnostic Techniques Following Positive Noninvasive Prenatal Screening Results in Southwest China. Front Genet 2022; 12:811414. [PMID: 35154255 PMCID: PMC8834880 DOI: 10.3389/fgene.2021.811414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Background: This study aims to evaluate prenatal diagnosis methods following positive noninvasive prenatal screening (NIPS) results. Methods: According to the positive noninvasive prenatal screening results, 926 pregnant women were divided into three groups: main target disease group (high risk for trisomy 21, trisomy 18, or trisomy 13), sex chromosome aneuploidy (SCA) group, and other chromosomal abnormalities group [abnormal Z-scores for chromosomes other than trisomy (T)21/T18/T13 or SCAs]. The verification methods and results were then retrospectively analysed. Results: In the main target disease group, the positive rate of chromosomal abnormalities confirmed by quantitative fluorescence polymerase chain reaction (QF-PCR) was 75.18% (212/282), which was not significantly different from that by karyotyping (79.36%, 173/218) and copy number variation (CNV) detection methods (71.43%, 65/91). The positive rate of additional findings confirmed by karyotyping and copy number variation detection methods in main target disease group was 0.46% (1/218) and 8.79% (8/91), respectively. The positive rate of chromosomal abnormalities confirmed by karyotyping and CNV detection methods were 27.11% (45/166) and 38.46% (95/247) in the SCA group and 4.17% (1/24) and 20% (36/180) in the other chromosomal abnormalities group, respectively. Fetal sex chromosome mosaicism was detected in 16.13% (20/124) of the confirmed SCA cases. There were no significant differences in the detection rates of chromosomal microarray analysis (CMA) and CNV sequencing (CNVseq) among the three groups (p > 0.05). Conclusion: QF-PCR can quickly and accurately identify aneuploidies following NIPS-positive results for common aneuploidy, and in combination with karyotyping and CNV detection techniques can provide more comprehensive results. With the NIPS-positive results for SCA or other abnormalities, CMA and CNVseq may have the same effect on increasing the detection rate. The addition of fluorescence in situ hybridization assay may help to identify true fetal mosaicism.
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Affiliation(s)
- Xiaosha Jing
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Hongqian Liu
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- *Correspondence: Hongqian Liu, ; Qian Zhu,
| | - Qian Zhu
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- *Correspondence: Hongqian Liu, ; Qian Zhu,
| | - Sha Liu
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Jianlong Liu
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Ting Bai
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Cechuan Deng
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Tianyu Xia
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Yunyun Liu
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Jing Cheng
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Xiang Wei
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Lingling Xing
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Yuan Luo
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Quanfang Zhou
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Lin Chen
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Lingping Li
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Jiamin Wang
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
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Meng X, Jiang L. Prenatal detection of chromosomal abnormalities and copy number variants in fetuses with congenital gastrointestinal obstruction. BMC Pregnancy Childbirth 2022; 22:50. [PMID: 35045821 PMCID: PMC8772214 DOI: 10.1186/s12884-022-04401-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/12/2022] [Indexed: 12/13/2022] Open
Abstract
Background Congenital gastrointestinal obstruction (CGIO) mainly refers to the stenosis or atresia of any part from the esophagus to the anus and is one of the most common surgical causes in the neonatal period. The concept of genetic factors as an etiology of CGIO has been accepted, but investigations about CGIO have mainly focused on aneuploidy, and the focus has been on duodenal obstruction. The objective of this study was to evaluate the risk of chromosome aberrations (including numeric and structural aberrations) in different types of CGIO. A second objective was to assess the risk of abnormal CNVs detected by copy number variation sequencing (CNV-seq) in fetuses with different types of CGIO. Methods Data from pregnancies referred for invasive testing and CNV-seq due to sonographic diagnosis of fetal CGIO from 2015 to 2020 were obtained retrospectively from the computerized database. The rates of chromosome aberrations and abnormal CNV-seq findings for isolated CGIOs and complicated CGIOs and different types of CGIOs were calculated. Results Of the 240 fetuses with CGIO that underwent karyotyping, the detection rate of karyotype abnormalities in complicated CGIO was significantly higher than that of the isolated group (33.8% vs. 10.8%, p < 0.01). Ninety-three cases with normal karyotypes further underwent CNV-seq, and CNV-seq revealed an incremental diagnostic value of 9.7% over conventional karyotyping. In addition, the incremental diagnostic yield of CNV-seq analysis in complicated CGIOs (20%) was higher than that in isolated CGIOs (4.8%), and the highest prevalence of pathogenic CNVs/likely pathogenic CNVs was found in the duodenal stenosis/atresia group (17.5%), followed by the anorectal malformation group (15.4%). The 13q deletion, 10q26 deletion, 4q24 deletion, and 2p24 might be additional genetic etiologies of duodenal stenosis/atresia. Conclusions The risk of pathogenic chromosomal abnormalities and CNVs increased in the complicated CGIO group compared to that in the isolated CGIO group, especially when fetuses presented duodenal obstruction (DO) and anorectal malformation. CNV-seq was recommended to detect submicroscopic chromosomal aberrations for DO and anorectal malformation when the karyotype was normal. The relationship between genotypes and phenotypes needs to be explored in the future to facilitate prenatal diagnosis of fetal CGIO and yield new clues into their etiologies.
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Jiang Y, Wu L, Ge Y, Zhang J, Huang Y, Wu Q, Zhang Y, Zhou Y. Clinical Utility of the Prenatal BACs-on-Beads™ Assay in Invasive Prenatal Diagnosis. Front Genet 2022; 12:789625. [PMID: 35096007 PMCID: PMC8795869 DOI: 10.3389/fgene.2021.789625] [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: 10/05/2021] [Accepted: 12/28/2021] [Indexed: 11/13/2022] Open
Abstract
Background: The prenatal BACs-on-Beads™ (PNBoBs™) assay has been applied worldwide for prenatal diagnosis. However, there are neither guidelines nor consensus on choosing patients, sample types, or clinical pathways for using this technique. Moreover, different perspectives have emerged regarding its clinical value. This study aimed to evaluate its clinical utility in the context of clinical practice located in a prenatal diagnostic center in Xiamen, a city in southeast China. Methods: We tested 2,368 prenatal samples with multiple referral indications using both conventional karyotyping and PNBoBs™. Positive results from PNBoBs™ were verified using current gold-standard approaches. Results: The overall rates for the detection of pathogenic copy number variation (pCNV) by karyotyping and PNBoBs™ were 1.9% (46/2,368) and 2.0% (48/2,368), respectively. The overall detection rate of karyotyping combined with PNBoBs™ for pCNV was 2.3% (54/2,368). A total of 13 cases of copy number variation (CNV)with a normal karyotype were detected by PNBoBs™. Another case with a normal karyotype that was detected as a CNV of sex chromosomes by PNBoBs™ was validated to be maternal cell contamination by short tandem repeat analysis. Conclusion: Karyotyping combined with PNBoBs™ can improve both the yield and efficiency of prenatal diagnosis and is appropriate in the second trimester in all patients without fetal ultrasound anomalies who undergo invasive prenatal diagnosis.
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Affiliation(s)
- Yu Jiang
- United Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital, School of Medicine and School of Public Health, Xiamen University, Xiamen, China
- *Correspondence: Yu Jiang, ; Yulin Zhou,
| | - Lili Wu
- Department of Obstetrics and Gynecology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Yunshen Ge
- United Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital, School of Medicine and School of Public Health, Xiamen University, Xiamen, China
| | - Jian Zhang
- United Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital, School of Medicine and School of Public Health, Xiamen University, Xiamen, China
| | - Yanru Huang
- United Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital, School of Medicine and School of Public Health, Xiamen University, Xiamen, China
| | - Qichang Wu
- Department of Obstetrics and Gynecology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Yanhong Zhang
- Department of Medical Ultrasonics, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Yulin Zhou
- United Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital, School of Medicine and School of Public Health, Xiamen University, Xiamen, China
- *Correspondence: Yu Jiang, ; Yulin Zhou,
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Mokveld T, Al-Ars Z, Sistermans EA, Reinders M. WisecondorFF: Improved Fetal Aneuploidy Detection from Shallow WGS through Fragment Length Analysis. Diagnostics (Basel) 2021; 12:59. [PMID: 35054227 PMCID: PMC8774687 DOI: 10.3390/diagnostics12010059] [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: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/18/2022] Open
Abstract
In prenatal diagnostics, NIPT screening utilizing read coverage-based profiles obtained from shallow WGS data is routinely used to detect fetal CNVs. From this same data, fragment size distributions of fetal and maternal DNA fragments can be derived, which are known to be different, and often used to infer fetal fractions. We argue that the fragment size has the potential to aid in the detection of CNVs. By integrating, in parallel, fragment size and read coverage in a within-sample normalization approach, it is possible to construct a reference set encompassing both data types. This reference then allows the detection of CNVs within queried samples, utilizing both data sources. We present a new methodology, WisecondorFF, which improves sensitivity, while maintaining specificity, relative to existing approaches. WisecondorFF increases robustness of detected CNVs, and can reliably detect even at lower fetal fractions (<2%).
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Affiliation(s)
- Tom Mokveld
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, 2628 XE Delft, The Netherlands;
| | - Zaid Al-Ars
- Computer Engineering, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands;
| | - Erik A. Sistermans
- Department of Human Genetics and Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands;
| | - Marcel Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, 2628 XE Delft, The Netherlands;
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Shi M, Leng X, Li Y, Chen Z, Cao Y, Chung T, Ip BY, Ip VH, Soo YO, Fan FS, Ma SH, Ma K, Chan AYY, Au LW, Leung H, Lau AY, Mok VC, Choy KW, Dong Z, Leung TW. Genome sequencing reveals the role of rare genomic variants in Chinese patients with symptomatic intracranial atherosclerotic disease. Stroke Vasc Neurol 2021; 7:182-189. [PMID: 34880113 PMCID: PMC9240611 DOI: 10.1136/svn-2021-001157] [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: 06/04/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
Objectives The predisposition of intracranial atherosclerotic disease (ICAD) to East Asians over Caucasians infers a genetic basis which, however, remains largely unknown. Higher prevalence of vascular risk factors (VRFs) in Chinese over Caucasian patients who had a stroke, and shared risk factors of ICAD with other stroke subtypes indicate genes related to VRFs and/or other stroke subtypes may also contribute to ICAD. Methods Unrelated symptomatic patients with ICAD were recruited for genome sequencing (GS, 60-fold). Rare and potentially deleterious single-nucleotide variants (SNVs) and small insertions/deletions (InDels) were detected in genome-wide and correlated to genes related to VRFs and/or other stroke subtypes. Rare aneuploidies, copy number variants (CNVs) and chromosomal structural rearrangements were also investigated. Lastly, candidate genes were used for pathway and gene ontology enrichment analysis. Results Among 92 patients (mean age at stroke onset 61.0±9.3 years), GS identified likely ICAD-associated rare genomic variants in 54.3% (50/92) of patients. Forty-eight patients (52.2%, 48/92) had 59 rare SNVs/InDels reported or predicted to be deleterious in genes related to VRFs and/or other stroke subtypes. None of the 59 rare variants were identified in local subjects without ICAD (n=126). 31 SNVs/InDels were related to conventional VRFs, and 28 were discovered in genes related to other stroke subtypes. Our study also showed that rare CNVs (n=7) and structural rearrangement (a balanced translocation) were potentially related to ICAD in 8.7% (8/92) of patients. Lastly, candidate genes were significantly enriched in pathways related to lipoprotein metabolism and cellular lipid catabolic process. Conclusions Our GS study suggests a role of rare genomic variants with various variant types contributing to the development of ICAD in Chinese patients.
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Affiliation(s)
- Mengmeng Shi
- Department of Obstetrics and 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
| | - Xinyi Leng
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Ying Li
- Department of Obstetrics and 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
| | - Zihan Chen
- Department of Obstetrics and 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
| | - Ye Cao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Tiffany Chung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Bonaventure Ym Ip
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Vincent Hl Ip
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Yannie Oy Soo
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Florence Sy Fan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Sze Ho Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Karen Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Anne Y Y Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Lisa Wc Au
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Howan Leung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Alexander Y Lau
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Vincent Ct Mok
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Kwong Wai Choy
- Department of Obstetrics and 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, 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 .,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
| | - Thomas W Leung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
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Shamseldin HE, AlAbdi L, Maddirevula S, Alsaif HS, Alzahrani F, Ewida N, Hashem M, Abdulwahab F, Abuyousef O, Kuwahara H, Gao X, Alkuraya FS. Lethal variants in humans: lessons learned from a large molecular autopsy cohort. Genome Med 2021; 13:161. [PMID: 34645488 PMCID: PMC8511862 DOI: 10.1186/s13073-021-00973-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Molecular autopsy refers to DNA-based identification of the cause of death. Despite recent attempts to broaden its scope, the term remains typically reserved to sudden unexplained death in young adults. In this study, we aim to showcase the utility of molecular autopsy in defining lethal variants in humans. METHODS We describe our experience with a cohort of 481 cases in whom the cause of premature death was investigated using DNA from the index or relatives (molecular autopsy by proxy). Molecular autopsy tool was typically exome sequencing although some were investigated using targeted approaches in the earlier stages of the study; these include positional mapping, targeted gene sequencing, chromosomal microarray, and gene panels. RESULTS The study includes 449 cases from consanguineous families and 141 lacked family history (simplex). The age range was embryos to 18 years. A likely causal variant (pathogenic/likely pathogenic) was identified in 63.8% (307/481), a much higher yield compared to the general diagnostic yield (43%) from the same population. The predominance of recessive lethal alleles allowed us to implement molecular autopsy by proxy in 55 couples, and the yield was similarly high (63.6%). We also note the occurrence of biallelic lethal forms of typically non-lethal dominant disorders, sometimes representing a novel bona fide biallelic recessive disease trait. Forty-six disease genes with no OMIM phenotype were identified in the course of this study. The presented data support the candidacy of two other previously reported novel disease genes (FAAH2 and MSN). The focus on lethal phenotypes revealed many examples of interesting phenotypic expansion as well as remarkable variability in clinical presentation. Furthermore, important insights into population genetics and variant interpretation are highlighted based on the results. CONCLUSIONS Molecular autopsy, broadly defined, proved to be a helpful clinical approach that provides unique insights into lethal variants and the clinical annotation of the human genome.
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Affiliation(s)
- Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hessa S Alsaif
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Center of Excellence for Biomedicine, King Abdulaziz City for Science and Technology, Riyadh, 12354, Saudi Arabia
| | - Fatema Alzahrani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nour Ewida
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abuyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hiroyuki Kuwahara
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
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38
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Chau MHK, Qian J, Chen Z, Li Y, Zheng Y, Tse WT, Kwok YK, Leung TY, Dong Z, Choy KW. Trio-Based Low-Pass Genome Sequencing Reveals Characteristics and Significance of Rare Copy Number Variants in Prenatal Diagnosis. Front Genet 2021; 12:742325. [PMID: 34616436 PMCID: PMC8488434 DOI: 10.3389/fgene.2021.742325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/25/2021] [Indexed: 01/22/2023] Open
Abstract
Background: Low-pass genome sequencing (GS) detects clinically significant copy number variants (CNVs) in prenatal diagnosis. However, detection at improved resolutions leads to an increase in the number of CNVs identified, increasing the difficulty of clinical interpretation and management. Methods: Trio-based low-pass GS was performed in 315 pregnancies undergoing invasive testing. Rare CNVs detected in the fetuses were investigated. The characteristics of rare CNVs were described and compared to curated CNVs in other studies. Results: A total of 603 rare CNVs, namely, 597 constitutional and 6 mosaic CNVs, were detected in 272 fetuses (272/315, 86.3%), providing 1.9 rare CNVs per fetus (603/315). Most CNVs were smaller than 1 Mb (562/603, 93.2%), while 1% (6/603) were mosaic. Forty-six de novo (7.6%, 46/603) CNVs were detected in 11.4% (36/315) of the cases. Eighty-four CNVs (74 fetuses, 23.5%) involved disease-causing genes of which the mode of inheritance was crucial for interpretation and assessment of recurrence risk. Overall, 31 pathogenic/likely pathogenic CNVs were detected, among which 25.8% (8/31) were small (<100 kb; n = 3) or mosaic CNVs (n = 5). Conclusion: We examined the landscape of rare CNVs with parental inheritance assignment and demonstrated that they occur frequently in prenatal diagnosis. This information has clinical implications regarding genetic counseling and consideration for trio-based CNV analysis.
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Affiliation(s)
- Matthew Hoi Kin Chau
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China.,Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China
| | - Jicheng Qian
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China
| | - Zihan Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China
| | - Ying Li
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China.,Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China
| | - Yu Zheng
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China
| | - Wing Ting Tse
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China
| | - Yvonne K Kwok
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Shatin, Hong Kong, SAR China
| | - Zirui Dong
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China.,Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China.,Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Shatin, Hong Kong, SAR China
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Han G, Jin T, Zhang L, Guo C, Gui H, Na R, Wang X, Bai H. Application of Combined Ultrasound and Maternal Serum Biochemical Indexes in the Detection of Fetal Structural Abnormalities and Chromosomal Abnormalities. JOURNAL OF MEDICAL IMAGING AND HEALTH INFORMATICS 2021. [DOI: 10.1166/jmihi.2021.3551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
By exploring different prenatal diagnosis indications of fetal chromosomal abnormalities, it can provide a theoretical basis and reference value for clinical consultation of pregnant women with similar high-risk factors. In this paper, 1800 pregnant women undergoing amniotic fluid aspiration
chromosomal examination in the prenatal diagnosis center were selected as the object of this study. Amniocentesis, fetal cell culture, and karyotype analysis were performed on pregnant women who were 14-20 weeks pregnant and had signed an informed consent. After amniocentesis fetal chromosome
analysis, the type of fetal chromosomal abnormality was determined, and the detection rate of chromosomal abnormality was statistically described. Chi-square test was used for comparison between groups, P < 0.05. This study shows that the use of ultrasound screening combined with
maternal serum indicators is effective in screening fetal structural abnormalities and chromosomal abnormalities in early pregnancy, and significantly improves the detection rate of chromosomal abnormalities. The detection of fetal structural malformations is also very high, but it should
be combined with ultrasound screening of mid-to-late pregnancy. The tricuspid regurgitation and umbilical vein a-wave reversal in the soft ultrasound index can be used as predictors of fetal congenital heart disease in early pregnancy.
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Affiliation(s)
- Guowei Han
- Affiliated Hospital of Inner Mongolia University for Nationalities Tongliao City, 028000, Inner Mongolia
| | - Tianliang Jin
- Affiliated Hospital of Inner Mongolia University for Nationalities Tongliao City, 028000, Inner Mongolia
| | - Li Zhang
- Affiliated Hospital of Inner Mongolia University for Nationalities Tongliao City, 028000, Inner Mongolia
| | - Chen Guo
- Affiliated Hospital of Inner Mongolia University for Nationalities Tongliao City, 028000, Inner Mongolia
| | - Hua Gui
- Affiliated Hospital of Inner Mongolia University for Nationalities Tongliao City, 028000, Inner Mongolia
| | - Risu Na
- Affiliated Hospital of Inner Mongolia University for Nationalities Tongliao City, 028000, Inner Mongolia
| | - Xuesong Wang
- Affiliated Hospital of Inner Mongolia University for Nationalities Tongliao City, 028000, Inner Mongolia
| | - Haihua Bai
- Inner Mongolia Engineering and Technical Research Center for Personalized Medicine, Tongliao City, Inner Mongolia, 028000, China
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Chen L, Wang L, Tang F, Zeng Y, Yin D, Zhou C, Zhu H, Li L, Zhang L, Wang J. Copy number variation sequencing combined with quantitative fluorescence polymerase chain reaction in clinical application of pregnancy loss. J Assist Reprod Genet 2021; 38:2397-2404. [PMID: 34052955 DOI: 10.1007/s10815-021-02243-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 05/23/2021] [Indexed: 12/24/2022] Open
Abstract
PURPOSE In this study, we evaluated the feasibility of the combining CNV-seq and quantitative fluorescence polymerase chain reaction (QF-PCR) for miscarriage analysis in clinical practice. METHODS Over a 35-month period, a total of 389 fetal specimens including 356 chorionic villi and 33 fetal muscle tissues were analyzed by CNV-seq and QF-PCR. Relationships between the risk factors (e.g., advanced maternal age, abnormal pregnancy history, and gestational age) and incidence of these chromosomal abnormalities were further analyzed by subgroup. RESULTS Clinically significant chromosomal abnormalities were identified in 58.95% cases. Aneuploidy was the most common abnormality (46.84%), followed by polyploidy (8.16%) and structural chromosome anomalies (3.95%). In sub-group analysis, significant differences were found in the total frequency of chromosomal abnormalities between the early abortion and the late abortion group, as well as in the distribution of chromosomal abnormalities between the advanced and the younger maternal age group. Meanwhile, the results of the logistic regression analysis identified a trend suggesting that the percentage of fetal chromosomal abnormalities is significantly higher in advanced maternal age, lesser gestational age, and lesser number of prior miscarriages. CONCLUSION Our study suggests that CNV-seq and QF-PCR are efficient and reliable technologies in the fetal chromosome analysis of miscarriages and could be used as a routine selection method for the genetic analysis of spontaneous abortion.
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Affiliation(s)
- Lin Chen
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Li Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Feng Tang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Yang Zeng
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Daishu Yin
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Cong Zhou
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Hongmei Zhu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Linping Li
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Lili Zhang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Jing Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China. .,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China.
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The role of chromosomal microarray and exome sequencing in prenatal diagnosis. Curr Opin Obstet Gynecol 2021; 33:148-155. [PMID: 33620893 DOI: 10.1097/gco.0000000000000692] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE OF REVIEW Advancements in technologies have revolutionized prenatal diagnosis. Chromosomal microarray analysis (CMA) became a proven method and was implemented to detect gains and losses of DNA and absence of heterozygosity across the genome. Next-generation sequencing technologies have brought opportunities and challenges to genetic testing. Exome sequencing detects single-nucleotide variants (SNVs) across the exome and its prenatal application is an emerging field. We reviewed the literature to define the role of CMA and exome sequencing in prenatal diagnosis. RECENT FINDING The application of exome sequencing in genetic diagnosis shows increased diagnostic yield and could be potentially implemented for prenatal diagnosis of fetuses with one or more ultrasound structural abnormalities or suspected monogenetic conditions. Although CMA is a gold standard for copy number variant (CNV) detection, large clinical cohort studies emphasized integrated CNV and SNV analyses for precise molecular diagnosis. Recent studies also suggest low-pass genome sequencing-based CNV detection can identify genome-wide imbalances at higher resolutions. SUMMARY Data suggest exome sequencing for SNVs and CMA for CNV detection are the most effective approach for prenatal genetic diagnosis. Emerging evidences show genome sequencing has the potential to replace CMA and even exome sequencing to become a comprehensive genetic test in the clinical diagnostic laboratory.
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Yan X, Peng H, Zhang C. Prenatal diagnosis of a de novo trisomy 20p detected by noninvasive prenatal testing. Clin Case Rep 2021; 9:1845-1848. [PMID: 33936600 PMCID: PMC8077397 DOI: 10.1002/ccr3.3587] [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: 07/12/2020] [Revised: 09/02/2020] [Accepted: 09/19/2020] [Indexed: 11/07/2022] Open
Abstract
Prenatal diagnosis of trisomy 20p seems to be difficult, considering the capacity of ultrasound to detect mild dysmorphic. NIPT has good performance in detecting fetal trisomy 20p combined with low coverage WGS and karyotype analysis.
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Affiliation(s)
- Xu Yan
- Reproductive Medicine CenterRenmin HospitalHubei University of MedicineShiyanChina
- Biomedical Engineering CollegeHubei University of MedicineShiyanChina
| | - Haiying Peng
- Reproductive Medicine CenterRenmin HospitalHubei University of MedicineShiyanChina
| | - Changjun Zhang
- Reproductive Medicine CenterRenmin HospitalHubei University of MedicineShiyanChina
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Lai Y, Zhu X, He S, Dong Z, Tang Y, Xu F, Chen Y, Meng L, Tao Y, Yi S, Su J, Huang H, Luo J, Leung TY, Wei H. Performance of Cell-Free DNA Screening for Fetal Common Aneuploidies and Sex Chromosomal Abnormalities: A Prospective Study from a Less Developed Autonomous Region in Mainland China. Genes (Basel) 2021; 12:478. [PMID: 33806256 PMCID: PMC8067030 DOI: 10.3390/genes12040478] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/01/2021] [Accepted: 03/19/2021] [Indexed: 12/24/2022] Open
Abstract
To evaluate the performance of noninvasive prenatal screening (NIPS) in the detection of common aneuploidies in a population-based study, a total of 86,262 single pregnancies referred for NIPS were prospectively recruited. Among 86,193 pregnancies with reportable results, follow-up was successfully conducted in 1160 fetuses reported with a high-risk result by NIPS and 82,511 cases (95.7%) with a low-risk result. The screen-positive rate (SPR) of common aneuploidies and sex chromosome abnormalities (SCAs) provided by NIPS were 0.7% (586/83,671) and 0.6% (505/83,671), respectively. The positive predictive values (PPVs) for Trisomy 21, Trisomy 18, Trisomy 13 and SCAs were calculated as 89.7%, 84.0%, 52.6% and 38.0%, respectively. In addition, less rare chromosomal abnormalities, including copy number variants (CNVs), were detected, compared with those reported by NIPS with higher read-depth. Among these rare abnormalities, only 23.2% (13/56) were confirmed by prenatal diagnosis. In total, four common trisomy cases were found to be false negative, resulting in a rate of 0.48/10,000 (4/83,671). In summary, this study conducted in an underdeveloped region with limited support for the new technology development and lack of cost-effective prenatal testing demonstrates the importance of implementing routine aneuploidy screening in the public sector for providing early detection and precise prognostic information.
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Affiliation(s)
- Yunli Lai
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
- Guangxi Clinical Research Center for Fetal Diseases, Nanning 530000, China
| | - Xiaofan Zhu
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; (X.Z.); (Z.D.); (T.Y.L.)
- Genetics and Prenatal Diagnosis Center, The First Affiliation Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Sheng He
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Zirui Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; (X.Z.); (Z.D.); (T.Y.L.)
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518000, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Yanqing Tang
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Fuben Xu
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Yun Chen
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Lintao Meng
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Yuli Tao
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Shang Yi
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Jiasun Su
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Hongqian Huang
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Jingsi Luo
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; (X.Z.); (Z.D.); (T.Y.L.)
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518000, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Hongwei Wei
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Guangxi Clinical Research Center for Fetal Diseases, Nanning 530000, China
- Department of Obstetrics and Gynaecology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
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Ma N, Xi H, Chen J, Peng Y, Jia Z, Yang S, Hu J, Pang J, Zhang Y, Hu R, Wang H, Liu J. Integrated CNV-seq, karyotyping and SNP-array analyses for effective prenatal diagnosis of chromosomal mosaicism. BMC Med Genomics 2021; 14:56. [PMID: 33632221 PMCID: PMC7905897 DOI: 10.1186/s12920-021-00899-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/09/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Emerging studies suggest that low-coverage massively parallel copy number variation sequencing (CNV-seq) more sensitive than chromosomal microarray analysis (CMA) for detecting low-level mosaicism. However, a retrospective back-to-back comparison evaluating accuracy, efficacy, and incremental yield of CNV-seq compared with CMA is warranted. METHODS A total of 72 mosaicism cases identified by karyotyping or CMA were recruited to the study. There were 67 mosaic samples co-analysed by CMA and CNV-seq, comprising 40 with sex chromosome aneuploidy, 22 with autosomal aneuploidy and 5 with large cryptic genomic rearrangements. RESULTS Of the 67 positive mosaic cases, the levels of mosaicism defined by CNV-seq ranged from 6 to 92% compared to the ratio from 3 to 90% by karyotyping and 20% to 72% by CMA. CNV-seq not only identified all 43 chromosomal aneuploidies or large cryptic genomic rearrangements detected by CMA, but also provided a 34.88% (15/43) increased yield compared with CMA. The improved yield of mosaicism detection by CNV-seq was largely due to the ability to detect low level mosaicism below 20%. CONCLUSION In the context of prenatal diagnosis, CNV-seq identified additional and clinically significant mosaicism with enhanced resolution and increased sensitivity. This study provides strong evidence for applying CNV-seq as an alternative to CMA for detection of aneuploidy and mosaic variants.
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Affiliation(s)
- Na Ma
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Hui Xi
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Jing Chen
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Ying Peng
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Zhengjun Jia
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Shuting Yang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Jiancheng Hu
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Jialun Pang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Yanan Zhang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Rong Hu
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Hua Wang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China.
- National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, 410008, Hunan, China.
| | - Jing Liu
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China.
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A Rapid PCR-Free Next-Generation Sequencing Method for the Detection of Copy Number Variations in Prenatal Samples. Life (Basel) 2021; 11:life11020098. [PMID: 33525582 PMCID: PMC7911416 DOI: 10.3390/life11020098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/15/2021] [Accepted: 01/25/2021] [Indexed: 11/17/2022] Open
Abstract
Next-generation sequencing (NGS) is emerging as a new method for the detection of clinically significant copy number variants (CNVs). In this study, we developed and validated rapid CNV-sequencing (rCNV-seq) for clinical application in prenatal diagnosis. Low-pass whole-genome sequencing was performed on PCR libraries prepared from amniocyte genomic DNA. From 10-40 ng of input DNA, PCR-free libraries consistently produced sequencing data with high unique read mapping ratios, low read redundancy, low coefficient of variation for all chromosomes and high genomic coverage. In validation studies, reliable and accurate CNV detection using PCR-free-based rCNV-seq was demonstrated for a range of common trisomies and sex chromosome aneuploidies as well as microdeletion and duplication syndromes. In reproducibility studies, CNV copy number and genomic intervals closely matched those defined by chromosome microarray analysis. Clinical testing of genomic DNA samples from 217 women referred for prenatal diagnosis identified eight samples (3.7%) with known chromosome disorders. We conclude that PCR-free-based rCNV-seq is a sensitive, specific, reproducible and efficient method that can be used in any NGS-based diagnostic laboratory for detection of clinically significant CNVs.
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Chitty LS, Ghidini A, Deprest J, Van Mieghem T, Levy B, Hui L, Bianchi DW. Right or wrong? Looking through the retrospectoscope to analyse predictions made a decade ago in prenatal diagnosis and fetal surgery. Prenat Diagn 2020; 40:1627-1635. [PMID: 33231306 DOI: 10.1002/pd.5870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK.,UCL Great Ormond Street Institute of Child Health, London, UK
| | - Alessandro Ghidini
- Department of Obstetrics and Gynecology, Georgetown University Hospital, Washington, DC.,Antenatal Testing Center, Inova Alexandria Hospital, Alexandria, VA
| | - Jan Deprest
- Department of Obstetrics and Gynaecology, University of Leuven, Leuven, Belgium and the Institute for Women's Health, UCL, London
| | - Tim Van Mieghem
- Fetal Medicine Unit and Ontario Fetal Centre, Department of Obstetrics and Gynaecology, Mount Sinai Hospital and University of Toronto, Toronto, Ontario, Canada
| | - Brynn Levy
- Division of Personalized Genomic Medicine, Columbia University Medical Center & the New York Presbyterian Hospital, New York, New York, USA
| | - Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Victoria, Australia.,Mercy Hospital for Women, Heidelberg, Victoria, Australia.,Murdoch Children's Research Institute, Parkville, Victoria, Australia.,The Northern Hospital, Epping, Victoria, Australia
| | - Diana W Bianchi
- Division of Prenatal Genomics and Fetal Therapy, Medical Genomics and Metabolic Genetics Branch, National Human Genome Institute, National Human Genome Institute, National Institutes of Health, Bethesda, Maryland, USA
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Clinical Significance of Non-Invasive Prenatal Screening for Trisomy 7: Cohort Study and Literature Review. Genes (Basel) 2020; 12:genes12010011. [PMID: 33374124 PMCID: PMC7824243 DOI: 10.3390/genes12010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/09/2020] [Accepted: 12/21/2020] [Indexed: 12/24/2022] Open
Abstract
Trisomy 7 is the most frequently observed type of rare autosomal trisomies in genome-wide non-invasive prenatal screening (NIPS). Currently, the clinical significance of trisomy 7 NIPS-positive results is still unknown. We reviewed two independent cohorts from two laboratories where similar NIPS metrics were applied. A total of 70,441 singleton cases who underwent genome-wide NIPS were analyzed, among which 39 pregnancies were positive for trisomy 7, yielding a screen-positive rate of 0.055% (39/70,441). There were 28 cases with invasive testing results available; the positive predictive value (PPV) was 3.6% (1/28). We then searched the published NIPS studies to generate a large cohort of 437,873 pregnancies and identified 247 cases (0.056%) that were screened positive for trisomy 7. The overall PPV was 3.4% (4/118) in the combined data. The presence of uniparental disomy 7 was not detected in the NIPS trisomy 7-positive pregnancies with normal fetal karyotype. Among the 85 cases with pregnancy outcome available in combined data, 88.2% were normal live births, 14.1% had intrauterine growth restriction, preterm birth or low birth weight, 3.5% presented with ultrasound abnormality, and no fetal loss was observed. Our data provide valuable information for counseling and management of trisomy 7-positive NIPS pregnancies.
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Lomov N, Zerkalenkova E, Lebedeva S, Viushkov V, Rubtsov MA. Cytogenetic and molecular genetic methods for chromosomal translocations detection with reference to the KMT2A/MLL gene. Crit Rev Clin Lab Sci 2020; 58:180-206. [PMID: 33205680 DOI: 10.1080/10408363.2020.1844135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Acute leukemias (ALs) are often associated with chromosomal translocations, in particular, KMT2A/MLL gene rearrangements. Identification or confirmation of these translocations is carried out by a number of genetic and molecular methods, some of which are routinely used in clinical practice, while others are primarily used for research purposes. In the clinic, these methods serve to clarify diagnoses and monitor the course of disease and therapy. On the other hand, the identification of new translocations and the confirmation of known translocations are of key importance in the study of disease mechanisms and further molecular classification. There are multiple methods for the detection of rearrangements that differ in their principle of operation, the type of problem being solved, and the cost-result ratio. This review is intended to help researchers and clinicians studying AL and related chromosomal translocations to navigate this variety of methods. All methods considered in the review are grouped by their principle of action and include karyotyping, fluorescence in situ hybridization (FISH) with probes for whole chromosomes or individual loci, PCR and reverse transcription-based methods, and high-throughput sequencing. Another characteristic of the described methods is the type of problem being solved. This can be the discovery of new rearrangements, the determination of unknown partner genes participating in the rearrangement, or the confirmation of the proposed rearrangement between the two genes. We consider the specifics of the application, the basic principle of each method, and its pros and cons. To illustrate the application, examples of studying the rearrangements of the KMT2A/MLL gene, one of the genes that are often rearranged in AL, are mentioned.
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Affiliation(s)
- Nikolai Lomov
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Elena Zerkalenkova
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Svetlana Lebedeva
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Vladimir Viushkov
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail A Rubtsov
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,Department of Biochemistry, Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
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Xu L, Zhang M, Huang H, Wang Y, Chen L, Chen M, Wang J, Chen C, Li B, Li Z. The Comprehensive Comparison of Bacterial Artificial Chromosomes (BACs)-on-Beads Assay and Copy Number Variation Sequencing in Prenatal Diagnosis of Southern Chinese Women. J Mol Diagn 2020; 22:1324-1332. [PMID: 32858251 DOI: 10.1016/j.jmoldx.2020.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 07/15/2020] [Accepted: 07/28/2020] [Indexed: 11/30/2022] Open
Abstract
Bacterial artificial chromosomes (BACs)-on-Beads (BoBs) assay and copy number variation sequencing (CNV-seq) are two frequently used methods in today's prenatal diagnosis. Several studies were conducted to investigate the performance of each approach, but they were never compared side by side. In this article, a comprehensive comparison of BoBs and CNV-seq was conducted using 1876 amniotic fluid and umbilical cord blood samples collected from Fujian Maternity and Child Health Hospital between 2015 and 2019. Karyotyping was used as the gold standard for chromosome structure variation, and chromosomal microarray analysis was performed to validate inconsistent results. Overall, 174 cases of confirmed chromosome anomalies were detected, including 73 chromosomal aneuploidies, 10 mosaics, 30 pathogenic CNVs, and 61 other structural anomalies. BoBs and CNV-seq achieved a 100% concordance in all 55 pathogenic euchromosome aneuploidies, but CNV-seq had a higher detection rate in sex chromosome aneuploidy and mosaic identification. For CNV detection, all of the 20 pathogenic CNVs discovered by the BoBs assay also were identified by CNV-seq and 10 additional pathogenic CNVs were observed by CNV-seq. The results of this study showed that CNV-seq was a reliable and more favorable method in terms of detection rate, costs, and disease range. In combination with karyotyping, CNV-seq could improve the efficiency and accuracy of a prenatal diagnosis to alleviate maternal emotional anxiety and deduce birth defects.
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Affiliation(s)
- LiangPu Xu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, China.
| | - Min Zhang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, China
| | - HaiLong Huang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, China
| | - Yan Wang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, China
| | - LingJi Chen
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, China
| | - MeiHuan Chen
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, China
| | - Juan Wang
- Annoroad Gene Technology (Beijing) Co., Ltd., Beijing, China
| | - Chen Chen
- Zhejiang Annoroad Biotechnology Co., Ltd., Zhejiang, China
| | - Bo Li
- Annoroad Life Sciences Research Institute, Zhejiang, China
| | - ZhiMin Li
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, China; Annoroad Gene Technology (Beijing) Co., Ltd., Beijing, China.
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50
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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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