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Ma L, Li Y, Li L, Wu H, Liu Y, Yang X, Lin A. A high Z-score might increase the positive predictive value of cell-free noninvasive prenatal testing for singleton-pregnant women. J Matern Fetal Neonatal Med 2023; 36:2233662. [PMID: 37433666 DOI: 10.1080/14767058.2023.2233662] [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: 03/09/2023] [Revised: 05/19/2023] [Accepted: 07/01/2023] [Indexed: 07/13/2023]
Abstract
OBJECTIVE To explore the positive predictive value (PPV) in noninvasive prenatal testing (NIPT)-positive cases and analyze the effect of the Z-score intervals on PPV performance. METHODS In this retrospective study, 26,667 pregnant women underwent NIPT from November 2014 to August 2022, of which 169 were NIPT-positive cases. NIPT-positive cases were divided into three groups according to the Z-score: 3 ≤ Z < 6, 6 ≤ Z < 10, and Z ≥ 10. RESULTS The PPVs of NIPT were 91.26% (94/103) for trisomy (T) 21, 80.65% (25/31) for T18, and 36.84% (7/19) for T13. The PPVs for the 3 ≤ Z < 6, 6 ≤ Z < 10, and Z ≥ 10 groups were 50%, 84.62%, and 87.95%, respectively. A higher PPV was found in the NIPT results when the Z-score was larger, with significant differences. The PPVs for T21/T18/T13 were 71.43%/42.86%/25% for 3 ≤ Z < 6, 90.32%/85.71%/57.14% for 6 ≤ Z < 10, and 93.85%/100%/25% for Z ≥ 10. For T21, T18, and T13, the correlations between the Z-score and fetal fraction concentration in true positives were r = 0.85, r = 0.59, and r = 0.71 (all p < .001), respectively. CONCLUSION Z-score is associated with the PPV performance of NIPT in fetal T13, T18, and T21. The possibility of false positives caused by placental chimerism should be considered when determining whether high Z-values lead to high PPVs.
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Affiliation(s)
- Li Ma
- Center for Laboratory Diagnosis, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Yulan Li
- Center for Laboratory Diagnosis, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Lei Li
- Department of Obstetrics, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Hong Wu
- Center for Laboratory Diagnosis, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Yongming Liu
- Center for Laboratory Diagnosis, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Xin Yang
- Center for Laboratory Diagnosis, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
| | - Aimin Lin
- Department of Gynaecology, Yantai Yuhuangding Hospital Affiliated to Medical College of Qingdao University, Yantai, Shandong, P.R. China
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Wang Z, Tang X, Yang S, Zhao Y, Yin T, Chen M, Zhang Y, Wang Y, Zhang F, Wang L. Noninvasive prenatal screening with conventional sequencing depth to screen fetal copy number variants: A retrospective study of 19 144 pregnant women. J Obstet Gynaecol Res 2023; 49:2825-2835. [PMID: 37806662 DOI: 10.1111/jog.15805] [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: 06/05/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023]
Abstract
AIM To investigate the detectability of noninvasive prenatal screening (NIPS) with conventional sequencing depth to detect fetal copy number variants. METHODS We performed a retrospective study in a total of 19 144 pregnant women. Their cell-free plasma DNA were assessed for trisomy 21, trisomy 18, trisomy 13, sex chromosome aneuploidies, and genome-wide copy number variants by NIPS at conventional sequencing depth. RESULTS Three hundred seventy-four cases (2.0%, 374/19 144) with abnormal results were detected, which including 84 cases (0.4%, 84/19 144) with high risk of trisomy 21, 18, and 13, 90 cases (0.5%, 90/19 144) with high risk of sex chromosome abnormalities (SCA), and 44 cases (0.2%, 44/19 144) with high risk of other chromosome aneuploidies. One hundred fifty-six cases (0.8%, 156/19 144) with high risk of copy number variations (CNVs) were also detected. In following prenatal diagnosis, composite positive predictive value (PPV) of trisomy 21, 18, and 13 was 69.6% (48/69). The PPV of SCAs was 37.3% (19/51). And the PPVs for CNVs was detected as 51.0% (<5 Mb), 71.4% (5 Mb ≤ CNV ≤10 Mb), 56.5% (>10 Mb). Finally, a follow-up about the pregnancy outcomes were conducted for all available cases. CONCLUSIONS NIPS yielded high PPVs for trisomy 21, 18, and 13 aneuploidies and moderate PPVs for SCAs and CNVs. The screening effectiveness was closely related to the size of CNV fragments. Larger CNVs, especially larger than 5 Mb, could be detected more accurately by NIPS in our analytic technique. Meanwhile, diagnostic confirmation by microarray analysis was highly recommended.
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Affiliation(s)
- Zhiwei Wang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Xinxin Tang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Shuting Yang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Yali Zhao
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Ting Yin
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Min Chen
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Yue Zhang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Yongan Wang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Fang Zhang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Leilei Wang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
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Combined fetal fraction to analyze the Z-score accuracy of noninvasive prenatal testing for fetal trisomies 13, 18, and 21. J Assist Reprod Genet 2023; 40:803-810. [PMID: 36763299 DOI: 10.1007/s10815-022-02694-8] [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: 09/14/2022] [Accepted: 12/12/2022] [Indexed: 02/11/2023] Open
Abstract
OBJECTIVE This study aims to evaluate the correlation combined fetal fraction and Z-score for fetal trisomies 13, 18, and 21 of NIPT by the semiconductor sequencing platform and further analyze the differences of different sequencing depths. METHODS A cohort of 61,581 pregnancies were recruited for NIPT. Invasive prenatal diagnostic confirmation is recommended in all high-risk NIPT cases. Logistic regression and rank correlation analysis were applied to analyze the relationship between different parameters. ROC curve analysis was adopted to analyze the cutoff values of Z-score and fetal fraction. RESULTS A total of 278 common trisomy pregnancies were verified in 377 NIPT-positive results. The fitted logistic regression models revealed that Z-scores of NIPT-positive results were significantly associated with PPVs (p < 0.05). The ROC curve analysis showed that the optimal cutoff value of Z-scores for T21, T18, and T13 was 7.597, 4.944, and 9.135 for NIPT and 9.489, 8.004, and 12.4 for NIPT-plus. If combing fetal fraction as another evaluation factor, the PPV of trisomy 21 gradually improved. We analyzed the correlation between the fetal fraction and the PPV, which revealed that the fetal fraction was significantly correlated with PPV. By analyzing the PPV of different groups divided by the associated criteria obtained from ROC curve, the PPV of high Z-score and high fetal fraction is higher in groups of Z-score > the optimal cutoff value. CONCLUSION The results of this study show that the fetal fraction is significantly correlated with the PPV. Combining fetal fraction with Z-score is significantly better than in groups of Z-score-associated criteria; clinicians can give more accurate and efficient prenatal genetic counseling.
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Tian M, Feng L, Li J, Zhang R. Focus on the frontier issue: progress in noninvasive prenatal screening for fetal trisomy from clinical perspectives. Crit Rev Clin Lab Sci 2023; 60:248-269. [PMID: 36647189 DOI: 10.1080/10408363.2022.2162843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The discovery of cell-free fetal DNA (cffDNA) in maternal blood and the rapid development of massively parallel sequencing have revolutionized prenatal testing from invasive to noninvasive. Noninvasive prenatal screening (NIPS) based on cffDNA enables the detection of fetal trisomy through sequencing, comparison, and bioassays. Its accuracy is better than that of traditional screening methods, and it is the most advanced clinical application of high-throughput sequencing technologies. However, the existing sequencing methods are limited by high costs and complex sequencing procedures. These limitations restrict the availability of NIPS for pregnant women. Many amplification methods have been developed to overcome the limitations of sequencing methods. The rapid development of non-sequencing methods has not been accompanied by reviews to summarize them. In this review, we initially describe the detection principles for sequencing-based NIPS. We summarize the rapidly evolving amplification technologies, focusing on the need to reduce costs and simplify the procedures. To ensure that the testing systems are feasible and that the testing processes are reliable, we expand our vision to the clinic. We evaluate the clinical validity of NIPS in terms of sensitivity, specificity, and positive predictive value. Finally, we summarize the application guidelines and discuss the corresponding quality control methods for NIPS. In addition to cffDNA, extracellular vesicle DNA, RNA, protein/peptide, and fetal cells can also be detected as biomarkers of NIPS. With the development of prenatal testing, NIPS has become increasingly important. Notably, NIPS is a screening test instead of a diagnostic test. The testing methods and procedures used in the NIPS process require standardization.
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Affiliation(s)
- Meng Tian
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Peking University Fifth School of Clinical Medicine, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Lei Feng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Peking University Fifth School of Clinical Medicine, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Peking University Fifth School of Clinical Medicine, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
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5
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Huang Q, Liu Y, Lei W, Liang J, Wang Y, Zheng M, Huang X, Liu Y, Huang K, Huang M. Detecting mitochondrial mutations associated with aminoglycoside ototoxicity by noninvasive prenatal testing. J Clin Lab Anal 2022; 37:e24827. [PMID: 36579624 PMCID: PMC9833975 DOI: 10.1002/jcla.24827] [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: 09/09/2022] [Revised: 12/11/2022] [Accepted: 12/18/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Numerous diseases and disorders are associated with mitochondrial DNA (mtDNA) mutations, among which m.1555A > G and m.1494C > T mutations in the 12 S ribosomal RNA gene contribute to aminoglycoside-induced and nonsyndromic hearing loss worldwide. METHODS A total of 76,842 qualified non-invasive prenatal (NIPT) samples were subjected to mtDNA mutation and haplogroup analysis. RESULTS We detected 181 m.1555A > G and m.1494C > T mutations, 151 of which were subsequently sequenced for full-length mitochondrial genome verification. The positive predictive values for the m.1555A > G and m.1494C > T mutations were 90.78% and 90.00%, respectively, a performance comparable to that attained with newborn hearing screening. Furthermore, mitochondrial haplogroup analysis revealed that the 12 S rRNA 1555A > G mutation was enriched in sub-haplotype D5[p = 0, OR = 4.6706(2.81-7.78)]. CONCLUSIONS Our findings indicate that the non-invasive prenatal testing of cell-free DNA obtained from maternal plasma can successfully detect m.1555A > G and m.1494C > T mutations.
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Affiliation(s)
- Quanfei Huang
- Institute of Clinical Pharmacology, School of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Yanhui Liu
- Dongguan Maternal and Child Health HospitalDongguanChina,Dongguan maternal and Child Health Hospital Affiliated to Southern Medical UniversityDongguanChina
| | - Wei Lei
- CapitalBio Genomics Co., Ltd.DongguanChina,CapitalBio Technology Co., Ltd.BeijingChina
| | - Jiajie Liang
- Dongguan Maternal and Child Health HospitalDongguanChina,Dongguan maternal and Child Health Hospital Affiliated to Southern Medical UniversityDongguanChina
| | - Yang Wang
- CapitalBio Genomics Co., Ltd.DongguanChina,CapitalBio Technology Co., Ltd.BeijingChina
| | - Minhua Zheng
- Dongguan Maternal and Child Health HospitalDongguanChina,Dongguan maternal and Child Health Hospital Affiliated to Southern Medical UniversityDongguanChina
| | - Xiaoyan Huang
- CapitalBio Genomics Co., Ltd.DongguanChina,CapitalBio Technology Co., Ltd.BeijingChina
| | - Yuanru Liu
- CapitalBio Technology Co., Ltd.BeijingChina,Guangdong CapitalBio Medical LaboratoryDongguanChina
| | - Kaisheng Huang
- CapitalBio Technology Co., Ltd.BeijingChina,Guangdong CapitalBio Medical LaboratoryDongguanChina
| | - Min Huang
- Institute of Clinical Pharmacology, School of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouChina
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6
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Jiang Y, Zhang Y, Yang Q, Zeng D, Zhao K, Ma X, Yin W. The association between fetal fraction and pregnancy-related complications among Chinese population. PLoS One 2022; 17:e0271219. [PMID: 35819933 PMCID: PMC9275705 DOI: 10.1371/journal.pone.0271219] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 06/25/2022] [Indexed: 11/18/2022] Open
Abstract
To examine the association of fetal fraction with a wide spectrum of pregnancy-related complications among Chinese population, we carried out a single-institution retrospective cohort study of women with negative Noninvasive prenatal testing (NIPT) results and singleton pregnancies between May 2018 and May 2020. Indicators of pregnancy-related complications were examined individually, including preterm birth, low birth weight, hypertensive disorders of pregnancy, gestational diabetes, oligohydramnios and intrahepatic cholestasis. We evaluated disease odds ratios (ORs) and 95% confidence intervals (CIs), after controlling for potential confounders including body mass index (BMI), maternal age and gestational week at NIPT. A total of 3534 women were included in our analyses. Women with fetal fraction<15.15% had increased risk of gestational hypertension (OR 4.41, CI [1.65, 12.45]) and oligohydramnios (OR 2.26, CI [1.33, 3.80]) compared to women with fetal fraction≥15.15%. No significant associations with fetal fraction were found for preterm birth, low birth weight, gestational diabetes, and intrahepatic cholestasis. In Summary, fetal fraction is inversely associated with the risk of gestational hypertension and oligohydramnios.
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Affiliation(s)
- Yan Jiang
- Department of Obstetrics, Mianyang People’s Hospital, Mianyang, Sichuan, China
| | | | - Qin Yang
- Department of Clinical Laboratory, Mianyang People’s Hospital, Mianyang, Sichuan, China
| | - Dan Zeng
- Chengdu CapitalBio Technology Co., Ltd., Chengdu, Sichuan, China
| | | | - Xin Ma
- GenomCan Inc., Chengdu, Sichuan, China
- Department of Statistics, Stanford University, Stanford, CA, United States of America
- * E-mail: (XM); (WY)
| | - Wei Yin
- Department of Obstetrics, Mianyang People’s Hospital, Mianyang, Sichuan, China
- * E-mail: (XM); (WY)
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7
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Li X, Wang L, Yao Z, Ruan F, Hu Z, Song W. Clinical evaluation of non-invasive prenatal screening in 32,394 pregnancies from Changzhi Maternal and Child Health Care Hospital of Shanxi China. J Med Biochem 2021; 41:341-346. [PMID: 36042897 PMCID: PMC9375529 DOI: 10.5937/jomb0-33513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/01/2021] [Indexed: 11/02/2022] Open
Abstract
Non-invasive prenatal screening (NIPS)was performed in 32,394 pregnancies, out of which results were available in 32,361 (99.9%) of them.Among the 32,361confirmed samples, 164 cases had positive results and 32197 cases had negative results. Of these positive cases, 116 cases were trisomy 21, 34 cases were trisomy 18 and 14 cases were trisomy 13. No false negative results were found in this cohort. The overall sensitivity and specificity were 100% and 99.91%, respectively. There was no significant difference in test performance between the 7,316 high-risk and 25,045 low-risk pregnancies,(sensitivity, 100% vs 100% (P >0.05); specificity, 99.96% vs 99.95% (P > 0.05)). Factors contributing to false-positive results included fetal CNVs, fetal mosaicism and typically producing Z scores between 3 and 4. Moreover, we analyze NIPT whole-genome sequencing to investigate the Single Nucleotide Polymorphisms (SNPs) associations with drug response or risk of disease. As compare to the 1000g East Asian genome data, the results reveal a significant difference in 7,285,418 SNPs variants of Shanxi pregnant women including 19,293 clinvar recorded variants and 7,266,125 non- clinvar recorded. Our findings showed that NIPS was an effective assay that may be applied as routine screening for fetal trisomies in the prenatal setting. In addition, this study also provides an accurate assessment of significant differencein 7,285,418 SNPs variants in Shanxi pregnant women that were previously unavailable to clinicians in Shanxi population.
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Affiliation(s)
- XiaoZe Li
- Changzhi Maternal and Child Health Care Hospital Affiliated Hospital of Changzhi Medical College, Department of Medical Genetic, Changzhi City, Shanxi Province, China
| | - LiHong Wang
- Changzhi Maternal and Child Health Care Hospital Affiliated Hospital of Changzhi Medical College, Department of Medical Genetic, Changzhi City, Shanxi Province, China
| | - ZeRong Yao
- Changzhi Maternal and Child Health Care Hospital Affiliated Hospital of Changzhi Medical College, Department of Medical Genetic, Changzhi City, Shanxi Province, China
| | - FangYing Ruan
- Changzhi Maternal and Child Health Care Hospital Affiliated Hospital of Changzhi Medical College, Department of Medical Genetic, Changzhi City, Shanxi Province, China
| | - ZhiPeng Hu
- Changzhi Maternal and Child Health Care Hospital Affiliated Hospital of Changzhi Medical College, Department of Medical Genetic, Changzhi City, Shanxi Province, China
| | - WenXia Song
- Changzhi Maternal and Child Health Care Hospital Affiliated Hospital of Changzhi Medical College, Department of Medical Genetic, Changzhi City, Shanxi Province, China
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Yeganeh Kazemi N, Fedyshyn B, Sutor S, Fedyshyn Y, Markovic S, Enninga EAL. Maternal Monocytes Respond to Cell-Free Fetal DNA and Initiate Key Processes of Human Parturition. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:2433-2444. [PMID: 34663619 PMCID: PMC8578468 DOI: 10.4049/jimmunol.2100649] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/12/2021] [Indexed: 12/14/2022]
Abstract
Throughout gestation, the maternal immune system is tightly modulated to allow growth of a semiallogeneic fetus. During the third trimester, the maternal immune system shifts to a proinflammatory phenotype in preparation for labor. What induces this shift remains unclear. Cell-free fetal DNA (cffDNA) is shed by the placenta and enters maternal circulation throughout pregnancy. Levels of cffDNA are increased as gestation progresses and peak before labor, coinciding with a shift to proinflammatory maternal immunity. Furthermore, cffDNA is abnormally elevated in plasma from women with complications of pregnancy, including preterm labor. Given the changes in maternal immunity at the end of pregnancy and the role of sterile inflammation in the pathophysiology of spontaneous preterm birth, we hypothesized that cffDNA can act as a damage-associated molecular pattern inducing an inflammatory cytokine response that promotes hallmarks of parturition. To test this hypothesis, we stimulated human maternal leukocytes with cffDNA from primary term cytotrophoblasts or maternal plasma and observed significant IL-1β and CXCL10 secretion, which coincides with phosphorylation of IFN regulatory factor 3 and caspase-1 cleavage. We then show that human maternal monocytes are crucial for the immune response to cffDNA and can activate bystander T cells to secrete proinflammatory IFN-γ and granzyme B. Lastly, we find that the monocyte response to cffDNA leads to vascular endothelium activation, induction of myometrial contractility, and PGE2 release in vitro. Our results suggest that the immune response to cffDNA can promote key features of the parturition cascade, which has physiologic consequences relevant to the timing of labor.
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Affiliation(s)
| | - Bohdana Fedyshyn
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN
| | - Shari Sutor
- Department of Immunology, Mayo Clinic, Rochester, MN
| | - Yaroslav Fedyshyn
- Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN; and
| | - Svetomir Markovic
- Department of Immunology, Mayo Clinic, Rochester, MN;,Department of Oncology, Mayo Clinic, Rochester, MN
| | - Elizabeth Ann L. Enninga
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN;,Department of Immunology, Mayo Clinic, Rochester, MN
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Peng H, Yang J, Wang D, Guo F, Hou Y, Yin A. Outcomes of pregnancies with trisomy 16 mosaicism detected by NIPT: a series of case reports. Mol Cytogenet 2021; 14:44. [PMID: 34544454 PMCID: PMC8454120 DOI: 10.1186/s13039-021-00559-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/13/2021] [Indexed: 11/12/2022] Open
Abstract
Background Trisomy 16 (T16) is thought to be the most frequent chromosome abnormality at conception, which is often associated with a high risk of abnormal outcomes. Methods A retrospective analysis of 14 cases with high risk of T16 by noninvasive prenatal testing (NIPT) was conducted. All cases in the analysis involved prenatal diagnosis, karyotyping and chromosomal microarray analysis. Case reports NIPT detected 12 cases of T16 and 2 cases of T16 mosaicism. Prenatal diagnosis confirmed 5 true positive cases and 9 false positive cases. Among the 5 true positive cases, 3 cases had ultrasound abnormalities. All of the 9 false positive cases continued their pregnancies. The newborns who were from these 9 false positive cases except 1 case (case 7) had low birth weights (< 2.5 kg) and there were also 2 premature deliveries. Conclusion NIPT serves as a fast and early prenatal screening method, giving clues to chromosome abnormalities and providing guidance for managing pregnancy. Confined placental mosaicism in 16 pregnancies may be at higher risk for preterm delivery.
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Affiliation(s)
- Haishan Peng
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China
| | - Jiexia Yang
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China
| | - Dongmei Wang
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China
| | - Fangfang Guo
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China
| | - Yaping Hou
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China
| | - Aihua Yin
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China.
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10
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Yang J, Wu J, Peng H, Hou Y, Guo F, Wang D, Ouyang H, Wang Y, Yin A. Performances of NIPT for copy number variations at different sequencing depths using the semiconductor sequencing platform. Hum Genomics 2021; 15:41. [PMID: 34215332 PMCID: PMC8252301 DOI: 10.1186/s40246-021-00332-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/13/2021] [Indexed: 12/03/2022] Open
Abstract
Objective To evaluate the performance of noninvasive prenatal testing (NIPT) and NIPT-PLUS for the detection of genome-wide microdeletion and microduplication syndromes (MMSs) at different sequencing depths. The NIPT sequencing depth was 0.15X, and the data volume was 3 million reads; the NIPT-PLUS sequencing depth was 0.4X, and the data volume was 8 million reads. Methods A cohort of 50,679 pregnancies was recruited. A total of 42,969 patients opted for NIPT, and 7710 patients opted for NIPT-PLUS. All high-risk cases were advised to undergo invasive prenatal diagnosis and were followed up. Results A total of 373 cases had a high risk of a copy number variation (CNV) as predicted by NIPT and NIPT-PLUS: NIPT predicted 250 high-risk CNVs and NIPT-PLUS predicted 123. NIPT-PLUS increased the detection rate by 1.02% (0.58% vs 1.60%, p < 0.001). A total of 291 cases accepted noninvasive prenatal diagnosis, with 197 cases of NIPT and 94 cases of NIPT-PLUS. The PPV of CNV > 10 Mb for NIPT-PLUS was significantly higher than that for NIPT (p = 0.02). The total PPV of NIPT-PLUS was 12.56% higher than that of NIPT (43.61% vs 30.96%, p = 0.03). Conclusion NIPT-PLUS had a better performance in detecting CNVs in terms of the total detection rate and total PPV. However, great care must be taken in presenting results and providing appropriate counseling to patients when deeper sequencing is performed in clinical practice.
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Affiliation(s)
- Jiexia Yang
- Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China
| | - Jing Wu
- Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China
| | - Haishan Peng
- Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China
| | - Yaping Hou
- Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China
| | - Fangfang Guo
- Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China
| | - Dongmei Wang
- Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China
| | - Haoxin Ouyang
- Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China
| | - Yixia Wang
- Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China
| | - Aihua Yin
- Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China. .,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400, Guangdong, China. .,Department of Prenatal Diagnosis Center, Guangdong Women and Children Hospital, No. 521 Xingnan Road, Panyu District, Guangzhou, 511400, China.
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11
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Yang J, Hou Y, Guo F, Peng H, Wang D, Li Y, Oy H, Wang Y, Lu J, Yin A. Noninvasive prenatal detection of fetal sex chromosome abnormalities using the semiconductor sequencing platform (SSP) in Southern China. J Assist Reprod Genet 2021; 38:727-734. [PMID: 33564935 PMCID: PMC7910337 DOI: 10.1007/s10815-020-02056-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 12/28/2020] [Indexed: 11/25/2022] Open
Abstract
Background Noninvasive prenatal testing (NIPT) has been widely used to screen for fetal aneuploidies, including fetal sex chromosome aneuploidies (SCAs). However, there is less information on the performance of NIPT in detecting SCAs. Methods A cohort of 47,800 pregnancies was recruited to review the high-risk NIPT results for SCAs. Cell-free fetal DNA (cffDNA) was extracted and sequenced. All NIPT high-risk cases were recommended to undergo invasive prenatal diagnosis for karyotyping analysis and chromosome microarray analysis (CMA). Results A total of 238 high-risk cases were detected by NIPT, including 137 cases of 45,X, 27 cases of 47,XXX, and 74 cases of 47,XYY/47,XXY. Prenatal diagnosis, including karyotyping analysis and CMA, was available in 170 cases. The positive predictive value (PPV) was 30.00% for 45,X, 70.58% for 47,XXX, and 81.13% for 47,XYY/47,XXY. In addition, 13 cases of sex chromosome mosaicism and 9 cases of sex chromosome CNVs were incidentally found in this study. Conclusion Our study showed that NIPT was reliable for screening SCAs based on a large sample, and it performed better in predicting sex chromosome trisomies than monosomy X. Our study will provide an important reference for clinical genetic counseling and further processing of the results.
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Affiliation(s)
- Jiexia Yang
- Department of Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, China.,Department of Prenatal Diagnosis Center, Guangdong Women and Children Hospital, No. 521 Xingnan Road, Panyu District, Guangzhou, 511400, China
| | - Yaping Hou
- Department of Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, China.,Department of Prenatal Diagnosis Center, Guangdong Women and Children Hospital, No. 521 Xingnan Road, Panyu District, Guangzhou, 511400, China
| | - Fangfang Guo
- Department of Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, China.,Department of Prenatal Diagnosis Center, Guangdong Women and Children Hospital, No. 521 Xingnan Road, Panyu District, Guangzhou, 511400, China
| | - Haishan Peng
- Department of Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, China.,Department of Prenatal Diagnosis Center, Guangdong Women and Children Hospital, No. 521 Xingnan Road, Panyu District, Guangzhou, 511400, China
| | - Dongmei Wang
- Department of Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, China.,Department of Prenatal Diagnosis Center, Guangdong Women and Children Hospital, No. 521 Xingnan Road, Panyu District, Guangzhou, 511400, China
| | - Yi Li
- Department of Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, China.,Department of Prenatal Diagnosis Center, Guangdong Women and Children Hospital, No. 521 Xingnan Road, Panyu District, Guangzhou, 511400, China
| | - Haoxin Oy
- Department of Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, China.,Department of Prenatal Diagnosis Center, Guangdong Women and Children Hospital, No. 521 Xingnan Road, Panyu District, Guangzhou, 511400, China
| | - Yixia Wang
- Department of Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, China.,Department of Prenatal Diagnosis Center, Guangdong Women and Children Hospital, No. 521 Xingnan Road, Panyu District, Guangzhou, 511400, China
| | - Jian Lu
- Department of Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, China.,Department of Prenatal Diagnosis Center, Guangdong Women and Children Hospital, No. 521 Xingnan Road, Panyu District, Guangzhou, 511400, China
| | - Aihua Yin
- Department of Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, China. .,Department of Prenatal Diagnosis Center, Guangdong Women and Children Hospital, No. 521 Xingnan Road, Panyu District, Guangzhou, 511400, China.
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12
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Lu W, Huang T, Wang XR, Zhou JH, Yuan HZ, Yang Y, Huang TT, Liu DP, Liu YQ. Next-generation sequencing: a follow-up of 36,913 singleton pregnancies with noninvasive prenatal testing in central China. J Assist Reprod Genet 2020; 37:3143-3150. [PMID: 33094428 PMCID: PMC7714822 DOI: 10.1007/s10815-020-01977-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/12/2020] [Indexed: 12/18/2022] Open
Abstract
PURPOSE To evaluate the noninvasive prenatal testing (NIPT) results of 36,913 cases in Jiangxi province of central China and explore its application value in prenatal screening and diagnosis. METHODS This retrospective analysis included 36,913 singleton pregnant women who underwent NIPT because of moderate-/high-risk pregnancy or voluntary requirements between January 2017 and December 2019 in our hospital. Chromosomal abnormalities such as trisomies 21, 18, and 13 (T21, T18, T13) and sex chromosome aneuploidies (SCAs) were judged by standard Z-score analysis. Positive NIPT results were confirmed by amniocentesis and karyotyping. Pregnancy outcomes were followed up via telephone interview. RESULTS A total of 1.01% (371/36,913) positive cases were detected by NIPT, comprising 137, 46, 31, and 157 cases of T21, T18, T13, and SCAs, respectively. A total of 116 of T21, 27 of T18, 13 of T13, and 51 of SCAs were confirmed to be true positive; all normal cases that had been followed up were verified to be true negative. The NIPT sensitivity in T21, T18, T13, and SCAs was 100.00% individually, whereas the specificity was 99.94% (36,488/36,509), 99.95% (36,579/36,598), 99.95% (36,594/36,612), and 99.72% (36,472/36,574), respectively. Furthermore, the negative predictive values of T21, T18, T13, and SCAs were all 100%, while the positive predictive values were 84.67%, 58.70%, 41.94%, and 33.33%, respectively. CONCLUSION NIPT is highly sensitive and has a low false positive rate in testing clinically significant fetal aneuploidies of general reproductive women. However, this technique cannot substitute for amniocentesis and karyotyping, and detailed genetic counseling is also essential for the high-risk group of NIPT.
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Affiliation(s)
- Wan Lu
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Ting Huang
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Xin-Rong Wang
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Ji-Hui Zhou
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Hui-Zhen Yuan
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Yan Yang
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Ting-Ting Huang
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Dan-Ping Liu
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Yan-Qiu Liu
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China.
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13
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Wu X, Li Y, Xie X, Su L, Cai M, Lin N, Du S, Xu L, Huang H. Clinical Review of Noninvasive Prenatal Testing: Experience from 551 Pregnancies with Noninvasive Prenatal Testing-Positive Results in a Tertiary Referral Center. J Mol Diagn 2020; 22:1469-1475. [PMID: 33069877 DOI: 10.1016/j.jmoldx.2020.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/15/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
A total of 551 pregnancies with positive results for noninvasive prenatal testing (NIPT) using traditional karyotyping and chromosomal microarray analysis were analyzed. Confirmatory results, positive predictive values, etiology exploration of false-positive results, and pregnancy outcomes were recorded. The study demonstrated that NIPT performed better in predicting trisomy 21 and trisomy 18 for pregnancies with advanced maternal age than for pregnancies with young maternal age; as for trisomy 13 and sex chromosomal aneuploidy (SCA) prediction, there was no significant difference between the two groups. The positive predictive values for trisomy 21, trisomy 18, trisomy 13, and SCA showed no significant upward trend when compared based on specific age categories (an interval of 5 years), which suggested that NIPT-positive result deserves equal attention from both providers and patients regardless of maternal age. In addition, the termination rates of 45,X, 47,XXY, 47,XXX, and 47,XYY were 100% (2/2), 92.9% (26/28), 33.3% (5/15), and 9.5% (2/21), respectively, which demonstrated that the decision-making regarding pregnancies varied greatly according to the types of SCAs, and further reinforce the importance of confirmatory prenatal diagnosis. The current study also supported the viewpoint that confined placental mosaicism and maternal mosaicism were the important etiology of false-positive results.
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Affiliation(s)
- Xiaoqing Wu
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China
| | - Ying Li
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China
| | - Xiaorui Xie
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China
| | - Linjuan Su
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China
| | - Meiying Cai
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China
| | - Na Lin
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China
| | - Shengrong Du
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China
| | - Liangpu Xu
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China.
| | - Hailong Huang
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China.
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14
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Zhao L, Yang H, Liu G. Relationship between age at menarche and chromosome numerical abnormalities in chorionic villus among missed abortions: A cross-sectional study of 459 women in China. J Obstet Gynaecol Res 2020; 46:2582-2589. [PMID: 33006206 DOI: 10.1111/jog.14499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/16/2020] [Accepted: 09/07/2020] [Indexed: 11/30/2022]
Abstract
AIMS To assess the relationship between age at menarche and the numerical abnormalities of chorionic villi chromosomes in patients with missed abortion. METHODS Unexplained miscarriage patients were admitted to an outpatient clinic in Tianjin Central Hospital of Gynecology Obstetrics, China. Embryonic villi tissues were collected aseptically after curettage. Chromosome analysis was performed subsequently using multiplex ligation-dependent probe amplification method. RESULTS Among 459 cases of missed abortion, chromosome numerical abnormalities were found in 231 cases (50.33%). Autosomal trisomy occurs most frequently, with 16-trisomy being most common. Patients (age more than 35 years old) had more frequent miscarriages compared with those who were less than 35 years old. However, there was no statistically significant difference in chromosome numerical abnormalities. In addition, compared with patients less than 30 years old, women with age ≥ 30 years old had higher abortions frequency (P = 0.002), and the proportion of chromosome numeric abnormalities increased (P = 0.000). The number of patients with abnormal chromosomes is higher among patients whose age of menarche are less than 12 years old than that of patients whose age of menarche was over 12 years old (P = 0.003). CONCLUSION Chromosome numerical abnormalities are important cause of missed abortion. The incidence of chromosome numeric abnormalities increases among patients ≥30 years old. Besides, age of menarche is an important risk factor for chromosome numerical abnormalities.
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Affiliation(s)
- Lu Zhao
- Obstetrics and Gynecology Department, Tianjin Medical University General Hospital, Tianjin, China
- Obstetrics and Gynecology Department, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Hua Yang
- Obstetrics and Gynecology Department, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Guoyan Liu
- Obstetrics and Gynecology Department, Tianjin Medical University General Hospital, Tianjin, China
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15
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Shokrof M, Abouelhoda M. IonCRAM: a reference-based compression tool for ion torrent sequence files. BMC Bioinformatics 2020; 21:397. [PMID: 32907531 PMCID: PMC7487613 DOI: 10.1186/s12859-020-03726-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/31/2020] [Indexed: 12/29/2022] Open
Abstract
Background Ion Torrent is one of the major next generation sequencing (NGS) technologies and it is frequently used in medical research and diagnosis. The built-in software for the Ion Torrent sequencing machines delivers the sequencing results in the BAM format. In addition to the usual SAM/BAM fields, the Ion Torrent BAM file includes technology-specific flow signal data. The flow signals occupy a big portion of the BAM file (about 75% for the human genome). Compressing SAM/BAM into CRAM format significantly reduces the space needed to store the NGS results. However, the tools for generating the CRAM formats are not designed to handle the flow signals. This missing feature has motivated us to develop a new program to improve the compression of the Ion Torrent files for long term archiving. Results In this paper, we present IonCRAM, the first reference-based compression tool to compress Ion Torrent BAM files for long term archiving. For the BAM files, IonCRAM could achieve a space saving of about 43%. This space saving is superior to what achieved with the CRAM format by about 8–9%. Conclusions Reducing the space consumption of NGS data reduces the cost of storage and data transfer. Therefore, developing efficient compression software for clinical NGS data goes beyond the computational interest; as it ultimately contributes to the overall cost reduction of the clinical test. The space saving achieved by our tool is a practical step in this direction. The tool is open source and available at Code Ocean, github, and http://ioncram.saudigenomeproject.com.
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Affiliation(s)
- Moustafa Shokrof
- Faculty of Computer Science, University of California at Davis, Davis, CA, USA
| | - Mohamed Abouelhoda
- King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,Saudi Human Genome Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia. .,Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, University Square, Giza, Egypt.
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16
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Qi Y, Yang J, Hou Y, Hu R, Wang D, Peng H, Yin A. Potential influence of parental copy number variations on noninvasive prenatal testing (NIPT): two case reports. Mol Cytogenet 2020; 13:18. [PMID: 32508984 PMCID: PMC7249382 DOI: 10.1186/s13039-020-00485-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/15/2020] [Indexed: 11/10/2022] Open
Abstract
Background Small subchromosomal deletions and duplications caused by copy number variants (CNVs) can now be detected with noninvasive prenatal testing (NIPT) technology. However, the clinical utility and validity of this screening for CNVs are still unknown. Here, we discuss some special conditions in which both cases simultaneously exhibited false positives caused by maternal CNVs and false negatives due to limitations of the technology. Case presentation In case 1, NIPT indicated a 1.1 Mb deletion at 21q21.1, but the umbilical cord for array CGH (aCGH) revealed a 422 kb deletion at 15q13.3. Peripheral blood of the parents for aCGH showed a 1.1 Mb deletion at 21q21.1 in the mother’s sample, and the same deletion at 15q13.3 was detected in the father’s blood. In case 2, NIPT showed a 1.5 Mb deletion at 22q11.21, but aCGH of amniocytes revealed a 1.377 Mb duplication rather than a 1.5 Mb deletion at 22q11.21. Furthermore, aCGH analysis of the parental blood revealed a 647 kb deletion at 22q11.21 in the mother and a 2.8 Mb duplication of 22q11.21 in the father. Conclusions Our findings not only highlight the significance of diagnostic testing following a positive cfDNA sequencing result but also the necessity for additional analytical and clinical validation before routine use in practice.
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Affiliation(s)
- Yiming Qi
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Jiexia Yang
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Yaping Hou
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Rong Hu
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Dongmei Wang
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Haishan Peng
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
| | - Aihua Yin
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 Guangdong China
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17
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Liu Y, Liu H, He Y, Xu W, Ma Q, He Y, Lei W, Chen G, He Z, Huang J, Liu J, Liu Y, Huang Q, Yu F. Clinical performance of non-invasive prenatal served as a first-tier screening test for trisomy 21, 18, 13 and sex chromosome aneuploidy in a pilot city in China. Hum Genomics 2020; 14:21. [PMID: 32503639 PMCID: PMC7275506 DOI: 10.1186/s40246-020-00268-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 05/10/2020] [Indexed: 12/19/2022] Open
Abstract
Background Cell-free fetal DNA (cffDNA) has opened up new approaches for non-invasive prenatal testing (NIPT), and it is often used as the second-tier test for high-risk pregnant women in detecting trisomy (T) 21, T18, and T13 after serum biochemistry screening. This study aims to discuss the clinical performance of NIPT as an alternative first-tier screening test for pregnant women in detecting T21, T18, T13, and sex chromosome aneuploidies (SCAs) in China. Methods A total of 42,924 samples were recruited. The cell-free plasma DNA was directly sequenced. Each of the chromosome aneuploidies of PPV was analyzed. A total of 22 placental samples were acquired, including 14 FP and 8 TP samples. The placental verification of FP NIPT results was performed. Results Among 42,924 samples, 281 (0.65%) positive cases, including 87 of T21, 31 of T18, 22 of T13, and 141 of SCAs were detected. For the detection of T21, the positive predictive value (PPV) was 78.46%, for trisomy 18, 62.96%, for trisomy 13, 10.00%, for SCAs, 47.22% in the total samples. For trisomy 21, the PPV was 86.67%, for trisomy 18, 80.00%, for trisomy 13, 20.00%, for SCAs, 56.52% in advanced maternal age (AMA) women. The PPV of T21 increased with age. For T18, the PPV showed an overall upward trend. For T13 and SCAs, PPV was raised first and then lowered. Placental verification of false positive (FP) NIPT results confirmed confined placental mosaicism(CPM) was the reason for false positives. Conclusions This study represents the first time that NIPT has been used as a first-tier screening test for fetal aneuploidies in a pilot city with large clinical samples in China. We propose that NIPT could replace serum biochemistry screening as a first-tier test.
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Affiliation(s)
- Yanhui Liu
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, 523112, Guangdong, China
| | - Hailiang Liu
- CapitalBio Genomics Co., Ltd., Dongguan, 523808, China
| | - Yi He
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, 523112, Guangdong, China
| | - Wanfang Xu
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, 523112, Guangdong, China
| | - Qiulin Ma
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, 523112, Guangdong, China
| | - Yuzhen He
- Dongguan Municipal Bureau of Health and Family Planning, Dongguan, 523112, Guangdong, China
| | - Wei Lei
- CapitalBio Genomics Co., Ltd., Dongguan, 523808, China
| | - Guoquan Chen
- Dongguan Municipal Bureau of Health and Family Planning, Dongguan, 523112, Guangdong, China
| | - Zheng He
- CapitalBio Genomics Co., Ltd., Dongguan, 523808, China
| | - Jiayi Huang
- CapitalBio Genomics Co., Ltd., Dongguan, 523808, China
| | - Jianan Liu
- Medical Department, Zunyi Medical College, Zunyi, China
| | - Yuanru Liu
- CapitalBio Genomics Co., Ltd., Dongguan, 523808, China
| | - Quanfei Huang
- CapitalBio Genomics Co., Ltd., Dongguan, 523808, China.
| | - Fubing Yu
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, 523112, Guangdong, China.
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18
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Xu L, Huang H, Lin N, Wang Y, He D, Zhang M, Chen M, Chen L, Lin Y. Non-invasive cell-free fetal DNA testing for aneuploidy: multicenter study of 31 515 singleton pregnancies in southeastern China. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2020; 55:242-247. [PMID: 31364782 DOI: 10.1002/uog.20416] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 07/04/2019] [Accepted: 07/16/2019] [Indexed: 05/27/2023]
Abstract
OBJECTIVE To analyze the non-invasive prenatal testing (NIPT) for aneuploidy results of 31 515 singleton pregnancies in Fujian province, southeastern China, and assess its performance in low-, moderate- and high-risk pregnancies. METHODS Women were categorized into groups according to whether their risk for fetal abnormality was low, moderate or high. Cell-free plasma DNA extracted from peripheral blood samples was subjected to low-coverage whole-genome sequencing. Standard Z-score analysis of the mapped sequencing reads was used to identify fetal aneuploidy, including the three main trisomies (T21, T18 and T13) and sex chromosome aneuploidy (SCA). NIPT-positive results were confirmed by amniocentesis and karyotyping. The performance of NIPT for detection of T21, T18, T13 and SCA was assessed by calculating the sensitivity and specificity. RESULTS The rate of chromosomal abnormality detected by NIPT in the study population was 1.38%. A higher rate of chromosomal abnormality was found in the high-risk group (1.57%) compared to the moderate-risk (1.05%) and low-risk (1.18%) groups (P < 0.05). Sensitivity and specificity, respectively, were 98.96% (95/96) and 99.94% (31 274/31 292) for detection of T21, 100% (25/25) and 99.96% (31 352/31 363) for T18, 100% (7/7) and 99.97% (31 373/31 381) for T13 and 100% (61/61) and 99.74% (31 245/31 327) for SCA. Positive predictive values were high for T21 (84.07%) and T18 (69.44%) and moderate for T13 (46.67%) and SCA (42.66%). CONCLUSION Our findings support the application of NIPT for reliable and accurate testing of the general population of reproductive-age women for clinically significant fetal aneuploidy. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- L Xu
- Prenatal Diagnosis Center of Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, China
| | - H Huang
- Prenatal Diagnosis Center of Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, China
| | - N Lin
- Prenatal Diagnosis Center of Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, China
| | - Y Wang
- Prenatal Diagnosis Center of Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, China
| | - D He
- Prenatal Diagnosis Center of Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, China
| | - M Zhang
- Prenatal Diagnosis Center of Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, China
| | - M Chen
- Prenatal Diagnosis Center of Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, China
| | - L Chen
- Prenatal Diagnosis Center of Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, China
| | - Y Lin
- Prenatal Diagnosis Center of Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, China
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Yang J, Peng CF, Qi Y, Rao XQ, Guo F, Hou Y, He W, Wu J, Chen YY, Zhao X, Wang YN, Peng H, Wang D, Du L, Luo MY, Huang QF, Liu HL, Yin A. Noninvasive prenatal detection of hemoglobin Bart hydrops fetalis via maternal plasma dispensed with parental haplotyping using the semiconductor sequencing platform. Am J Obstet Gynecol 2020; 222:185.e1-185.e17. [PMID: 31394068 DOI: 10.1016/j.ajog.2019.07.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/03/2019] [Accepted: 07/30/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Thalassemia is one of the most common monogenetic diseases in the south of China and Southeast Asia. Hemoglobin Bart's hydrops fetalis syndrome was caused by a homozygous Southeast Asian deletion (-/-) in the HBA gene. Few studies have proved the potential of screen for Bart's hydrops fetalis using fetal cell-free DNA. However, the number of cases is still relatively small. Clinical trials of large samples would be needed. OBJECTIVE In this study, we aimed to develop a noninvasive method of target-captured sequencing and genotyping by the Bayesian method using cell-free fetal DNA to identify the fetal genotype in pregnant women who are at risk of having hemoglobin Bart hydrops fetalis in a large-scale study. STUDY DESIGN In total, 192,173 couples from 30 hospitals were enrolled in our study and 878 couples were recruited, among whom both the pregnant women and their husbands were detected to be carriers of Southeast Asian type (-/αα) of α-thalassemia. Prenatal diagnosis was performed by chorionic villus sampling, amniocentesis, or cordocentesis using gap-polymerase chain reaction considered as the golden standard. RESULTS As a result, we found that the sensitivity and specificity of our noninvasive method were 98.81% and 94.72%, respectively, in the training set as well as 100% and 99.31%, respectively, in the testing set. Moreover, our method could identify all of 885 maternal samples with the Southeast Asian carrier and 36 trisomy samples with 100% of sensitivity in T13, T18, and T21 and 99.89% (1 of 917) and 99.88% (1 of 888) of specificity in T18 and T21, respectively. CONCLUSION Our method opens the possibility of early screening for maternal genotyping of α-thalassemia, fetal aneuploidies in chromosomes 13/18/21, and hemoglobin Bart hydrops fetalis detection in 1 tube of maternal plasma.
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Affiliation(s)
- Jiexia Yang
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Chun-Fang Peng
- CapitalBio Genomics Co, Ltd, Dongguan, and CapitalBio Technology Inc, Beijing, China
| | - Yiming Qi
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Xing-Qiang Rao
- CapitalBio Genomics Co, Ltd, Dongguan, and CapitalBio Technology Inc, Beijing, China
| | - Fangfang Guo
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Yaping Hou
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Wei He
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Jing Wu
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Yang-Yi Chen
- CapitalBio Genomics Co, Ltd, Dongguan, and CapitalBio Technology Inc, Beijing, China
| | - Xin Zhao
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Yu-Nan Wang
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Haishan Peng
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Dongmei Wang
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Li Du
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Ming-Yong Luo
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China
| | - Quan-Fei Huang
- CapitalBio Genomics Co, Ltd, Dongguan, and CapitalBio Technology Inc, Beijing, China
| | - Hai-Liang Liu
- CapitalBio Genomics Co, Ltd, Dongguan, and CapitalBio Technology Inc, Beijing, China.
| | - Aihua Yin
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Beijing, China.
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20
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Evidence of compliance with and effectiveness of guidelines for noninvasive prenatal testing in China: a retrospective study of 189,809 cases. SCIENCE CHINA-LIFE SCIENCES 2020; 63:319-328. [PMID: 31942687 DOI: 10.1007/s11427-019-9600-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/22/2019] [Indexed: 01/28/2023]
Abstract
In China, the medical guidelines recommend performing noninvasive prenatal testing (NIPT) with caution for pregnant women aged 35 years or older. However, the Mother and Child Health Care Law suggests that all primiparous women whose age is older than 35 years undergo prenatal diagnosis. These two inconsistent suggestions/recommendations have made obstetricians confused about whether to offer NIPT to these older pregnant women. To face this issue and find out the solution we performed a retrospective study of 189,809 NIPT samples collected from 28 provincial-leveled administrative units in China. Of 1,564 women with high-risk pregnancies who underwent NIPT, 459 (29.3%) did not participate in follow-up. The compound sensitivity and specificity of NIPT for trisomies 21, 18 and 13 detection was 99.1% (95% CI, 98.0%-99.6%) and 99.9% (95% CI, 98.8%-99.9%), respectively. In secundiparous women, NIPT showed high sensitivity and specificity similar to that in primiparous women. The observed risk for trisomies 21 and 18 significantly increased when the maternal age was 39 and older. After the publication of the current NIPT policy, the follow-up rate at our center was 91.9%; however, a large number of women are not in maternal and infant care networks nationwide, and that makes the follow-up rate outside our center relatively low. Our study shows that to balance the prevention of major aneuploidies and the limited resources for prenatal diagnosis, the cut-off age of 35 for invasive prenatal diagnosis might be unnecessary. Although the NIPT guidelines are well written, how to practice it effectively, especially in less industrialized areas, is worth discussing.
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Chen Y, Yu Q, Mao X, Lei W, He M, Lu W. Noninvasive prenatal testing for chromosome aneuploidies and subchromosomal microdeletions/microduplications in a cohort of 42,910 single pregnancies with different clinical features. Hum Genomics 2019; 13:60. [PMID: 31783780 PMCID: PMC6884830 DOI: 10.1186/s40246-019-0250-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 11/15/2019] [Indexed: 12/24/2022] Open
Abstract
Background Since the discovery of cell-free DNA (cfDNA) in maternal plasma, it has opened up new approaches for non-invasive prenatal testing. With the development of whole-genome sequencing, small subchromosomal deletions and duplications could be found by NIPT. This study is to review the efficacy of NIPT as a screening test for aneuploidies and CNVs in 42,910 single pregnancies. Methods A total of 42,910 single pregnancies with different clinical features were recruited. The cell-free fetal DNA was directly sequenced. Each of the chromosome aneuploidies and the subchromosomal microdeletions/microduplications of PPV were analyzed. Results A total of 534 pregnancies (1.24%) were abnormal results detected by NIPT, and 403 pregnancies had underwent prenatal diagnosis. The positive predictive value (PPV) for trisomy 21(T21), trisomy 18 (T18), trisomy 13 (T13), sex chromosome aneuploidies (SCAs), and other chromosome aneuploidy was 79.23%, 54.84%, 13.79%, 33.04%, and 9.38% respectively. The PPV for CNVs was 28.99%. The PPV for CNVs ≤ 5 Mb is 20.83%, for within 5–10 Mb 50.00%, for > 10 Mb 27.27% respectively. PPVs of NIPT according to pregnancies characteristics are also different. Conclusion Our data have potential significance in demonstrating the usefulness of NIPT profiling not only for common whole chromosome aneuploidies but also for CNVs. However, this newest method is still in its infancy for CNVs. There is still a need for clinical validation studies with accurate detection rates and false positive rates in clinical practice.
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Affiliation(s)
- Yibo Chen
- Ningbo Women and Children Hospital, No.339, Liuting Street, Haishu District Ningbo, Ningbo, 315010, China
| | - Qi Yu
- Ningbo Women and Children Hospital, No.339, Liuting Street, Haishu District Ningbo, Ningbo, 315010, China
| | - Xiongying Mao
- Ningbo Women and Children Hospital, No.339, Liuting Street, Haishu District Ningbo, Ningbo, 315010, China
| | - Wei Lei
- CapitalBio Technology Inc., Beijing, 101111, China
| | - Miaonan He
- Beijing CapitalBio Medical Laboratory, Beijing, 101111, China
| | - Wenbo Lu
- Ningbo Women and Children Hospital, No.339, Liuting Street, Haishu District Ningbo, Ningbo, 315010, China.
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Wu G, Li R, Tong C, He M, Qi Z, Chen H, Deng T, Liu H, Qi H. Non-invasive prenatal testing reveals copy number variations related to pregnancy complications. Mol Cytogenet 2019; 12:38. [PMID: 31485271 PMCID: PMC6716937 DOI: 10.1186/s13039-019-0451-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/21/2019] [Indexed: 12/25/2022] Open
Abstract
Background Pregnancy complications could lead to maternal and fetal morbidity and mortality. Early diagnosing and managing complications have been associated with good outcomes. The placenta was an important organ for development of pregnancy complications. Thus, non-invasive prenatal testing technologies could detect genetic variations, such as aneuploidies and sub-chromosomal copy number variations, reflecting defective placenta by maternal plasma cffDNAs. Maternal cffDNAs had been proved to derive from trophoblast cells of placenta. Results In order to find out the relationship between genetic variations and pregnancy complications, we reviewed NIPT results for subchromosomal copy number variations in a cohort of 3890 pregnancies without complications and 441 pregnancies with pregnancy complications including gestational diabetes mellitus (GDM), pregnancy-induced hypertension (PIH), preterm prelabor rupture of membranes (PPROM) and placenta implantation abnormalities (PIA). For GDMs, we identified three CNV regions containing some members of alpha- and beta-defensins, such as DEFA1, DEFA3, DEFB1. For PIHs, we found three duplication and one deletion region including Pcdhα, Pcdhβ, and Pcdhγ, known as protocadherins, which were complicated by hypertensive disorders. For PPROMs and PIAs, we identified one and two CNV regions, respectively. SFTPA2, SFTPD and SFTPA1, belonging to surfactant protein, was considered to moderated the inflammatory activation within the fetal extra-embryonic compartment, associated to duration of preterm prelabor rupture of fetal membranes, while MEF2C and TM6SF1 could be involved in trophoblast invasion and differentiation. Conclusions Our findings gave a clue to correlation between genetic variations of maternal cell-free DNAs and pregnancy complications. Electronic supplementary material The online version of this article (10.1186/s13039-019-0451-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guangping Wu
- 1Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016 People's Republic of China.,2State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, 400016 People's Republic of China.,3International Collaborative Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016 People's Republic of China
| | - Rong Li
- 1Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016 People's Republic of China.,2State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, 400016 People's Republic of China.,3International Collaborative Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016 People's Republic of China
| | - Chao Tong
- 1Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016 People's Republic of China.,2State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, 400016 People's Republic of China.,3International Collaborative Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016 People's Republic of China
| | - Miaonan He
- Beijing CapitalBio Medical Laboratory, Beijing, 101111 China
| | - Zhiwei Qi
- Beijing CapitalBio Medical Laboratory, Beijing, 101111 China
| | - Huijuan Chen
- Beijing CapitalBio Medical Laboratory, Beijing, 101111 China
| | - Tao Deng
- Beijing CapitalBio Medical Laboratory, Beijing, 101111 China
| | - Hailiang Liu
- CapitalBio Technology Inc., Beijing, 101111 China.,6Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515 Guangdong China
| | - Hongbo Qi
- 1Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016 People's Republic of China.,2State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing, 400016 People's Republic of China.,3International Collaborative Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016 People's Republic of China
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Lee DE, Kim H, Park J, Yun T, Park DY, Kim M, Ryu HM. Clinical Validation of Non-Invasive Prenatal Testing for Fetal Common Aneuploidies in 1,055 Korean Pregnant Women: a Single Center Experience. J Korean Med Sci 2019; 34:e172. [PMID: 31222985 PMCID: PMC6589404 DOI: 10.3346/jkms.2019.34.e172] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 05/28/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Non-invasive prenatal testing (NIPT) using cell-free fetal DNA from maternal plasma for fetal aneuploidy identification is expanding worldwide. The objective of this study was to evaluate the clinical utility of NIPT for the detection of trisomies 21, 18, and 13 of high-risk fetus in a large Korean population. METHODS This study was performed retrospectively, using stored maternal plasma from 1,055 pregnant women with singleton pregnancies who underwent invasive prenatal diagnosis because of a high-risk indication for chromosomal abnormalities. The NIPT results were confirmed by karyotype analysis. RESULTS Among 1,055 cases, 108 cases of fetal aneuploidy, including trisomy 21 (n = 57), trisomy 18 (n = 42), and trisomy 13 (n = 9), were identified by NIPT. In this study, NIPT showed 100% sensitivity and 99.9% specificity for trisomy 21, and 92.9% sensitivity and 100% specificity for trisomy 18, and 100% sensitivity and 99.9% specificity for trisomy 13. The overall positive predictive value (PPV) was 98.1%. PPVs for trisomies 21, 18, and 13 ranged from 90.0% to 100%. CONCLUSION This study demonstrates that our NIPT technology is reliable and accurate when applied to maternal DNA samples collected from pregnant women. Further large prospective studies are needed to adequately assess the performance of NIPT.
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Affiliation(s)
- Da Eun Lee
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Korea
| | - Hyunjin Kim
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul, Korea
| | | | - Taegyun Yun
- Data Analytics CoE, SK Telecom, Seoul, Korea
| | | | - Minhyoung Kim
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women's Healthcare Center, Dankook University College of Medicine, Seoul, Korea
| | - Hyun Mee Ryu
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam, Korea.
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Hu P, Liang D, Chen Y, Lin Y, Qiao F, Li H, Wang T, Peng C, Luo D, Liu H, Xu Z. An enrichment method to increase cell-free fetal DNA fraction and significantly reduce false negatives and test failures for non-invasive prenatal screening: a feasibility study. J Transl Med 2019; 17:124. [PMID: 30975179 PMCID: PMC6460836 DOI: 10.1186/s12967-019-1871-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/03/2019] [Indexed: 12/18/2022] Open
Abstract
Background Noninvasive prenatal screening (NIPS) based on cell-free fetal DNA (cffDNA) has rapidly been applied into clinic. However, the reliability of this method largely depends on the concentration of cffDNA in the maternal plasma. The chance of test failure results or false negative results would increase when cffDNA fraction is low. In this study, we set out to develop a method to enrich the cffDNA for NIPS based on the size difference between cell-free DNA (cfDNA) of fetal origin and maternal origin, and to evaluate whether the new NIPS method can improve the test quality. Methods We utilized 10,000 previous NIPS data to optimize a size-selection strategy for enrichment. Then, we retrospectively performed our new NIPS method with cffDNA enrichment on the 1415 NIPS samples, including 1404 routine cases and 11 false negative cases, and compared the results to the original NIPS results. Results The 10,000 NIPS data revealed the fetal fraction in short cfDNA fragments (< 160 bp) is significantly higher. By using our new NIPS strategy on the 1404 routine cases, the fetal fraction increased from 11.3 ± 4.2 to 22.6 ± 6.6%, and the new method performed a significant decrease of test-failure rate (0.1% vs 0.7%, P < 0.01). Moreover, in 45.5% (5/11) of the false negative cases, fetal trisomies were successfully detected by our new NIPS method. Conclusions We developed an effective method to enrich cffDNA for NIPS, which shows an increased success rate and a reduced chance of false negative comparing to the ordinary NIPS method. Electronic supplementary material The online version of this article (10.1186/s12967-019-1871-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ping Hu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Dong Liang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Yangyi Chen
- CapitalBio Technology Inc., Beijing, 101111, China.,CapitalBio Genomics Co., Ltd., Dongguan, 523808, China.,CapitalBio MedLab, Beijing, 102206, China
| | - Ying Lin
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Fengchang Qiao
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Hang Li
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Ting Wang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215000, Jiangsu, China
| | - Chunfang Peng
- CapitalBio Technology Inc., Beijing, 101111, China.,CapitalBio Genomics Co., Ltd., Dongguan, 523808, China.,CapitalBio MedLab, Beijing, 102206, China
| | - Donghong Luo
- CapitalBio Technology Inc., Beijing, 101111, China.,CapitalBio Genomics Co., Ltd., Dongguan, 523808, China.,CapitalBio MedLab, Beijing, 102206, China
| | - Hailiang Liu
- CapitalBio Technology Inc., Beijing, 101111, China. .,CapitalBio Genomics Co., Ltd., Dongguan, 523808, China. .,CapitalBio MedLab, Beijing, 102206, China.
| | - Zhengfeng Xu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China.
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Hu H, Wang L, Wu J, Zhou P, Fu J, Sun J, Cai W, Liu H, Yang Y. Noninvasive prenatal testing for chromosome aneuploidies and subchromosomal microdeletions/microduplications in a cohort of 8141 single pregnancies. Hum Genomics 2019; 13:14. [PMID: 30871627 PMCID: PMC6419401 DOI: 10.1186/s40246-019-0198-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 02/26/2019] [Indexed: 12/28/2022] Open
Abstract
Background Noninvasive prenatal testing (NIPT) for fetal aneuploidies by scanning cell-free fetal DNA in maternal plasma is rapidly becoming a first-tier aneuploidy screening test in clinical practices. With the development of whole-genome sequencing technology, small subchromosomal deletions and duplications that could not be detected by conventional karyotyping are now able to be detected with NIPT technology. Methods In the present study, we examined 8141 single pregnancies with NIPT to calculate the positive predictive values of each of the chromosome aneuploidies and the subchromosomal microdeletions and microduplications. Results We confirmed that the positive predictive values (PPV) for trisomy 13, trisomy 18, trisomy 21, and sex chromosome aneuploidy were 14.28%, 60%, 80%, and 45.83%, respectively. At the same time, we also found 51 (0.63%) positive cases for chromosomal microdeletions or microduplications but only 13 (36.11%) true-positive cases. These results indicate that NIPT for trisomy 21 detection had the highest accuracy, while accuracy was low for chromosomal microdeletion and microduplications. Conclusions Therefore, it is very important to improve the specificity, accuracy, and sensitivity of NIPT technology for the detection of subchromosomal microdeletions and microduplications.
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Affiliation(s)
- Hua Hu
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Li Wang
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Jiayan Wu
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Peng Zhou
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Jingli Fu
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Jiuchen Sun
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Weiyi Cai
- CapitalBio Technology Inc., Beijing, 101111, China
| | - Hailiang Liu
- CapitalBio Technology Inc., Beijing, 101111, China.
| | - Ying Yang
- Second Affiliated Hospital, Army Military Medical University, Chongqing, 400037, China.
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Liang D, Lin Y, Qiao F, Li H, Wang Y, Zhang J, Liu A, Ji X, Ma D, Jiang T, Hu P, Xu Z. Perinatal outcomes following cell-free DNA screening in >32 000 women: Clinical follow-up data from a single tertiary center. Prenat Diagn 2018; 38:755-764. [PMID: 29966040 DOI: 10.1002/pd.5328] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/24/2018] [Accepted: 06/25/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Dong Liang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Ying Lin
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Fengchang Qiao
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Hang Li
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Yan Wang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Jingjing Zhang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - An Liu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Xiuqing Ji
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Dingyuan Ma
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Tao Jiang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Ping Hu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Zhengfeng Xu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
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Larson NB, Wang C, Na J, Rowsey RA, Highsmith WE, Hoppman NL, Kocher JP, Klee EW. Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models. J Comput Biol 2018; 25:1040-1049. [PMID: 29932737 DOI: 10.1089/cmb.2018.0056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The recent advances in next-generation sequencing (NGS) technologies have enabled the development of effective high-throughput noninvasive prenatal screening (NIPS) assays for fetal genetic abnormalities using maternal circulating cell-free DNA (ccfDNA). An important NIPS quality assurance is quantifying the fetal proportion of the sampled ccfDNA. For methods using allelic read count ratios from targeted sequencing of single-nucleotide polymorphisms (SNPs), systematic biases and errors may reduce accuracy and diminish assay performance. We collected ccfDNA NIPS MiSeq sequencing data from an amplicon-based 92 SNP panel along with complementary low-depth whole-genome sequencing (WGS) on 243 normal male fetus pregnancies along with additional 144 nonpregnant female donor samples. Using fetal fraction estimates based on X and Y chromosome WGS coverage as gold standard, we compared an existing SNP-based approach, FetalQuant, to a more flexible Bayesian hierarchical modeling strategy that borrows information across interrogated SNPs to character SNP-level error rates and biases to improve fetal fraction estimates. Posterior distributions for SNP-level model parameters indicate most SNPs exhibited modest to moderate extrabinomial variation and a consistent underrepresentation of fetal alleles, with some extreme outliers in both regards. Fetal fraction estimates using FetalQuant, naive to these SNP properties, were relatively poor (R2 = 0.14, root mean squared error [RMSE] = 0.050), particularly when the true fetal fraction was low (<5%). In contrast, by quantifying SNP-level biases and error rates, our proposed approach demonstrated improved performance by reducing the bias and variability in fetal fraction estimates (R2 = 0.794, RMSE = 0.025). Using high-depth targeted SNP sequencing data, we identified a high degree of variability in distributional properties across SNP allelic read counts. These results highlight the benefits of leveraging hierarchical modeling for SNP-based fetal quantification assays (FQAs) and the need to properly calibrate FQAs dependent on NGS allelic ratio data.
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Affiliation(s)
- Nicholas B Larson
- 1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic , Rochester, Minnesota
| | - Chen Wang
- 1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic , Rochester, Minnesota
| | - Jie Na
- 1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic , Rochester, Minnesota
| | - Ross A Rowsey
- 2 Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic , Rochester, Minnesota
| | - William Edward Highsmith
- 2 Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic , Rochester, Minnesota
| | - Nicole L Hoppman
- 2 Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic , Rochester, Minnesota
| | - Jean-Pierre Kocher
- 1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic , Rochester, Minnesota
| | - Eric W Klee
- 1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic , Rochester, Minnesota
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Hoon SK, Kang SW, Kwak SH, Kim J. Hypoxia due to positive pressure ventilation in Edwards' syndrome: A case report. J Int Med Res 2017; 46:895-900. [PMID: 29125001 PMCID: PMC5971522 DOI: 10.1177/0300060517734680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Edwards’ syndrome also known as trisomy 18 is a congenital disorder associated with cardiovascular issues including ventricular septal defect (VSD), atrial septal defect (ASD) and patent duct arteriosus (PDA). An emergency colostomy was performed on a neonate born with an imperforate anus. Pre-operative transthoracic echocardiography showed presence of VSD, a patent foramen ovale (PFO) or ASD. Even though the baby had a good general condition and optimal peripheral oxygen saturation (SpO2), during positive pressure ventilation, she suffered severe hypoxia (50% SpO2). The cause of the hypoxia was thought to be the right-left shunt and so during a second attempt at anaesthesia a vasopressor (noradrenaline 0.03 µg/kg/min) was infused to increase systemic vascular resistance. Thereafter, SpO2 increased to 80–90% and the surgery was completed. The baby recovered without any neurological complications. Genetic testing post-partum showed she had Edwards’ syndrome.
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Affiliation(s)
- Sun Kyung Hoon
- 1 Department of Emergency Medicine, 89481 College of Medicine, Chosun University , Gwang-ju, Korea
| | - Seung-Woo Kang
- 2 Deparment of Anaesthesiology and Pain Medicine, Chonnam National University, Medical School, Gwangju, Republic of Korea
| | - Sang-Hyun Kwak
- 2 Deparment of Anaesthesiology and Pain Medicine, Chonnam National University, Medical School, Gwangju, Republic of Korea
| | - Joungmin Kim
- 2 Deparment of Anaesthesiology and Pain Medicine, Chonnam National University, Medical School, Gwangju, Republic of Korea
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Yang J, Qi Y, Guo F, Hou Y, Peng H, Wang D, Oy H, Yin A. A case of placental trisomy 18 mosaicism causing a false negative NIPT result. Mol Cytogenet 2017; 10:40. [PMID: 29093756 PMCID: PMC5658983 DOI: 10.1186/s13039-017-0341-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/23/2017] [Indexed: 11/10/2022] Open
Abstract
Background The non-invasive prenatal testing that evaluates circulating cell free DNA, and has been established as an additional pregnancy test for detecting the common fetal trisomies 21, 18 and 13 is rapidly revolutionizing prenatal screening as a result of its increased sensitivity and specificity. However, false positive and false negative results still exist. Case presentation We presented a case in which the non-invasive prenatal testing results were normal at 15 gestational age (GA), but an ultrasound examination at 30GA showed that the fetus had heart abnormalities, and the third trimester ultrasound at 33GA noted multiple anomalies including a 3.0 mm ventricular septal defect. Along with cordocentesis at 33GA, the cord blood sample cytogenetics analysis showed a mos 47,XN,+18[61]/46,XN[39] T18 karyotype. Six placental biopsies confirmed that the chromosome 18 placenta chimerism ratio had changed from 33% to 72%. Ultimately, the pregnancy was interrupted at 34GA. Conclusions We presented this case to highlight the need to clearly explain false positive or false negative results to patients. We believe that this information will also influence the development of future diagnostic test methodologies.
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Affiliation(s)
- Jiexia Yang
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China
| | - Yiming Qi
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China
| | - Fangfang Guo
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China
| | - Yaping Hou
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China
| | - Haishan Peng
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China
| | - Dongmei Wang
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China
| | - Haoxin Oy
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China
| | - Aihua Yin
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 511400 China
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Gil MM, Accurti V, Santacruz B, Plana MN, Nicolaides KH. Analysis of cell-free DNA in maternal blood in screening for aneuploidies: updated meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2017; 50:302-314. [PMID: 28397325 DOI: 10.1002/uog.17484] [Citation(s) in RCA: 390] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 03/28/2017] [Accepted: 04/03/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVES To review clinical validation or implementation studies of maternal blood cell-free (cf) DNA analysis and define the performance of screening for fetal trisomies 21, 18 and 13 and sex chromosome aneuploidies (SCA). METHODS Searches of PubMed, EMBASE and The Cochrane Library were performed to identify all peer-reviewed articles on cfDNA testing in screening for aneuploidies between January 2011, when the first such study was published, and 31 December 2016. The inclusion criteria were peer-reviewed study reporting on clinical validation or implementation of maternal cfDNA testing in screening for aneuploidies, in which data on pregnancy outcome were provided for more than 85% of the study population. We excluded case-control studies, proof-of-principle articles and studies in which the laboratory scientists carrying out the tests were aware of fetal karyotype or pregnancy outcome. Pooled detection rates (DRs) and false-positive rates (FPRs) were calculated using bivariate random-effects regression models. RESULTS In total, 35 relevant studies were identified and these were used for the meta-analysis on the performance of cfDNA testing in screening for aneuploidies. These studies reported cfDNA results in relation to fetal karyotype from invasive testing or clinical outcome. In the combined total of 1963 cases of trisomy 21 and 223 932 non-trisomy 21 singleton pregnancies, the weighted pooled DR and FPR were 99.7% (95% CI, 99.1-99.9%) and 0.04% (95% CI, 0.02-0.07%), respectively. In a total of 563 cases of trisomy 18 and 222 013 non-trisomy 18 singleton pregnancies, the weighted pooled DR and FPR were 97.9% (95% CI, 94.9-99.1%) and 0.04% (95% CI, 0.03-0.07%), respectively. In a total of 119 cases of trisomy 13 and 212 883 non-trisomy 13 singleton pregnancies, the weighted pooled DR and FPR were 99.0% (95% CI, 65.8-100%) and 0.04% (95% CI, 0.02-0.07%), respectively. In a total of 36 cases of monosomy X and 7676 unaffected singleton pregnancies, the weighted pooled DR and FPR were 95.8% (95% CI, 70.3-99.5%) and 0.14% (95% CI, 0.05-0.38%), respectively. In a combined total of 17 cases of SCA other than monosomy X and 5400 unaffected singleton pregnancies, the weighted pooled DR and FPR were 100% (95% CI, 83.6-100%) and 0.004% (95% CI, 0.0-0.08%), respectively. For twin pregnancies, in a total of 24 cases of trisomy 21 and 1111 non-trisomy 21 cases, the DR was 100% (95% CI, 95.2-100%) and FPR was 0.0% (95% CI, 0.0-0.003%), respectively. CONCLUSIONS Screening by analysis of cfDNA in maternal blood in singleton pregnancies could detect > 99% of fetuses with trisomy 21, 98% of trisomy 18 and 99% of trisomy 13 at a combined FPR of 0.13%. The number of reported cases of SCA is too small for accurate assessment of performance of screening. In twin pregnancies, performance of screening for trisomy 21 is encouraging but the number of cases reported is small. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- M M Gil
- Fetal Medicine Research Institute, King's College Hospital, London, UK
- Obstetrics and Gynecology Department, Torrejon University Hospital, Torrejon de Ardoz, Madrid, Spain
- Obstetrics and Gynecology Department, Universidad Francisco de Vitoria, Pozuelo de Alarcón, Madrid, Spain
| | - V Accurti
- Fetal Medicine Research Institute, King's College Hospital, London, UK
| | - B Santacruz
- Obstetrics and Gynecology Department, Torrejon University Hospital, Torrejon de Ardoz, Madrid, Spain
| | - M N Plana
- Clinical Biostatistics Unit, Ramón y Cajal Hospital (IRYCIS), CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - K H Nicolaides
- Fetal Medicine Research Institute, King's College Hospital, London, UK
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