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Qiao L, Zhang B, Wu X, Zhang C, Xue Y, Tang H, Tang H, Shi J, Liang Y, Yu B, Wang T. A fetal fraction enrichment method reduces false negatives and increases test success rate of fetal chromosome aneuploidy detection in early pregnancy loss. Lab Invest 2022; 20:345. [PMID: 35918754 PMCID: PMC9344718 DOI: 10.1186/s12967-022-03555-9] [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: 02/08/2022] [Accepted: 07/25/2022] [Indexed: 11/10/2022]
Abstract
OBJECTIVE We and others have previously demonstrated that the size-selection enrichment method could remarkably improve fetal fraction (FF) in the early gestational age (GA, 12-13 weeks), suggesting that 9 or 10 weeks should not be used as a threshold for GA in size-selection noninvasive prenatal screening (NIPS). Here, we assessed whether this method was reliable for detecting fetal chromosomal aneuploidy at the earliest GA (6-8 weeks). METHODS Size-selection NIPS for fetal chromosomal aneuploidy was applied to 208 pregnancy plasma samples (102 male and 106 female fetuses), while the 169 pregnancy samples with male fetuses also underwent standard NIPS. Multivariable linear regression models were used to evaluate the association between fold-change of FF and experimental factors. RESULTS The sensitivity of the cell-free DNA (cfDNA) test in detecting aneuploidy was 100% when screened with FF enrichment, whereas the sensitivity of the same patients was only 62.5% (5/8) without FF enrichment. In the 102 pregnancy samples with male fetuses, FF increased from 6.1% to 15.7%, and the median increase in FF was 2.8-fold with enrichment. Moreover, there was a trend toward an increasing success rate of the cfDNA test from 6 to 13 weeks of gestation, especially when the test success rate reached 100% after 7 weeks with FF enrichment. Multivariate linear regression analysis demonstrated that a lower initial FF, shorter cfDNA size, increased body mass index (BMI), and later GA were all independent predictors of a higher fold-change of FF. Compared with ≤ 120 bp cfDNA fragments, the mean fold-change of FF differences was 0.820 for 121-125 bp, 0.229 for 126-130 bp, - 0.154 for 131-135 bp, - 0.525 for 136-140 bp and - 0.934 for > 140 bp (Ptrend < 0.0001), suggesting that fold-change of FF significantly decreased with cfDNA fragments > 125 bp. These results were statistically significant after adjusting for confounding factors in the models for fold-change of FF. CONCLUSIONS The FF enrichment method is a reasonable strategy to detect fetal chromosomal aneuploidy in early pregnancy loss with reduced false negatives and increased test success rate after 7 weeks of GA and should be recommended for patients with early pregnancy loss.
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Affiliation(s)
- Longwei Qiao
- Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, Jiangsu Province, China
| | - Bin Zhang
- Changzhou Maternal and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, No. 16 Dingxiang road, Changzhou, Jiangsu Province, China
| | - Xiaojuan Wu
- Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, Jiangsu Province, China
| | - Chunhua Zhang
- Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, Jiangsu Province, China
| | - Ying Xue
- Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, Jiangsu Province, China
| | - Hui Tang
- Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, Jiangsu Province, China
| | - Haoyu Tang
- Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, Jiangsu Province, China
| | - Jingye Shi
- Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, Jiangsu Province, China
| | - Yuting Liang
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China.
| | - Bin Yu
- Changzhou Maternal and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, No. 16 Dingxiang road, Changzhou, Jiangsu Province, China.
| | - Ting Wang
- Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, Jiangsu Province, China.
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Gou L, Suo F, Wang Y, Wang N, Wu Q, Hu S, Wang P, Gu L, Zhang M, Wang C, Zhang Y, Yin X, Zhang P, Xu J, Wang X, Gu M. Clinical value for the detection of fetal chromosomal deletions/duplications by noninvasive prenatal testing in clinical practice. Mol Genet Genomic Med 2021; 9:e1687. [PMID: 33951332 PMCID: PMC8222853 DOI: 10.1002/mgg3.1687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/04/2021] [Accepted: 03/23/2021] [Indexed: 01/13/2023] Open
Abstract
Objective This study was to report the experiences on the clinical value of noninvasive prenatal testing (NIPT) for the screening of fetal chromosomal deletions/duplications. Methods We performed a retrospective analysis of a cohort of 20,439 pregnancies undergoing NIPT from March 2017 to September 2020 at a single center. Patients with positive NIPT results for fetal chromosomal deletions or duplications had options of invasive diagnostic testing or no further testing. The data were complied from all cases with positive NIPT results for chromosomal deletions/duplications. The positive predictive value (PPV) was calculated from tabulated data. Results In this cohort, positive NIPT results for fetal chromosomal deletions/duplications were found in 60 pregnant women. Of the positive samples, further invasive testing was performed in 39 cases, in which 9 cases were found to be true positive. The overall PPV for chromosomal deletions/duplications was 23.1%. In addition, fetal structural anomaly was found by ultrasound examination in three cases, in which the chromosomal deletions/duplications of three cases were not verified. Moreover, an unexpected pathogenic 8p23.3 deletion was identified by invasive testing in 1 fetus with a false positive NIPT screen for 3q27.3q29 duplication. Conclusions In summary, positive NIPT results of chromosomal deletions/duplications were not uncommon in clinical practice, whereas the PPV for the testing was low. Hence, potential risks and high percentage of false positives for these abnormal NIPT results might be informed to pregnant women before the choice made of invasive testing.
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Affiliation(s)
- Lingshan Gou
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Feng Suo
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Yi Wang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Na Wang
- Department of Technology, Suzhou Beikang Medical Device Co. Ltd., Suzhou, China
| | - Qin Wu
- Zhejiang Biosan Biochemical Technologies Co. Ltd., Hangzhou, China
| | - Shunan Hu
- Office of Scientific Research & Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Peng Wang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Lize Gu
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Man Zhang
- Zhejiang Biosan Biochemical Technologies Co. Ltd., Hangzhou, China
| | - Chuanxia Wang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Yan Zhang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Xin Yin
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Peng Zhang
- Shenzhen Longgang Institute of Stomatology, Shenzhen Longgang E.N.T. Hospital, Shenzhen, China
| | - Jian Xu
- Shenzhen Longgang Institute of Stomatology, Shenzhen Longgang E.N.T. Hospital, Shenzhen, China
| | - Xingqi Wang
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - Maosheng Gu
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
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Zhang C, Liang B, Qiao L, Xuan L, Li H, He Q, Wu X, Lu J, Yu B, Wang T. Effect quantification and value prediction of factors in noninvasive detection for specific fetal copy number variants by semiconductor sequencing. Mol Genet Genomic Med 2019; 7:e00718. [PMID: 31115175 PMCID: PMC6625335 DOI: 10.1002/mgg3.718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/08/2019] [Accepted: 04/15/2019] [Indexed: 12/20/2022] Open
Abstract
Background The detection limit of noninvasive prenatal testing (NIPT) by next generation sequencing for any given fetal copy number variants (CNV) can be influenced by several factors. In this study, we quantified the effects and predicted the value of parameters for CNVs detection by NIPT. Methods Genomic DNA from patient's leucocytes with 3.16 Mb microdeletion in 22q11.21 was mixed with DNA from aborted fetal tissues without CNV at various concentrations by an enzyme digestion method. Abnormal DNA at 0% served as negative control. Sequencing of mixture samples (at 0%, 4%, 12%, and 20%) by Ion Proton Sequencer was performed at flow 500, with WISECONDOR as the pipeline in CNV‐calling and bin of 500, 750 and 1,000 kb for counting unique reads. The parameters were evaluated with Box–Behnken design. The region with Z score ≦−3 was marked as a potential microdeletion. Results The equation of Z score depending on fetal fraction, unique read number and bin size was obtained by Box–Behnken design. The negative effect was quantified as the coefficient in the equation. The smallest values of these parameters were defined as 4 M unique read number, and 10.08% fetal DNA concentration at bin of 750 kb for detecting subchromosomal microdeletion of 3.16 Mb. Conclusion The quantification of effect and value of parameters as well as the method used in this study can benefit the establishment of quality standards for CNVs detection and interpretation of CNVs detection results.
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Affiliation(s)
- Chunhua Zhang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Bo Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Longwei Qiao
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Liming Xuan
- Basecare Medical Device Co., Ltd, Suzhou, China
| | - Hong Li
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Quanze He
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Xiaojuan Wu
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Jiafeng Lu
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Bin Yu
- Changzhou Women and Children Health Hospital affiliated to Nanjing Medical University, Changzhou, China
| | - Ting Wang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
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