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Luo J, Wang S, Zhang S, He Y, Li S, Han J, Xu M, Deng G. Performance of ImproGene Cell-Free DNA Tubes for Stabilization and Analysis of cfDNA in Blood Samples. Fetal Pediatr Pathol 2022; 41:771-780. [PMID: 34547970 DOI: 10.1080/15513815.2021.1979143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND With the development of liquid biopsy technology, the demand for noninvasive prenatal testing (NIPT) is increasing rapidly. The aim of the study is to evaluate the effects of different blood collection tubes on plasma cfDNA and NIPT quality control. METHODS We investigated hemolysis, cfDNA concentration, and fragment distribution within blood samples stored in EDTA, ImproGene, and Streck tubes. The effects of ImproGene and Streck tubes on NIPT quality control were evaluated. RESULTS The ImproGene tubes prevented the time-dependent increase of cfDNA concentration and preserved the cfDNA fragment size distribution. For NIPT quality control, there is no significant difference in cfDNA, library concentration, and fetal fraction between ImproGene and Streck tubes samples. GC content of the samples in ImproGene tubes was closer to the human genome. CONCLUSION The ImproGene cfDNA tube has excellent performance and is an effective choice for storing blood samples for NIPT testing or other cfDNA analysis.
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Affiliation(s)
- Jianglan Luo
- Enterprise Key Laboratory, Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Guangdong, China
| | - Sina Wang
- Enterprise Key Laboratory, Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Guangdong, China
| | - Shu Zhang
- Enterprise Key Laboratory, Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Guangdong, China
| | - Ye He
- Enterprise Key Laboratory, Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Guangdong, China
| | - Siyun Li
- Enterprise Key Laboratory, Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Guangdong, China
| | - Jianhong Han
- Enterprise Key Laboratory, Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Guangdong, China
| | - Mingfei Xu
- Enterprise Key Laboratory, Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Guangdong, China
| | - Guanhua Deng
- Enterprise Key Laboratory, Enterprise Key Laboratory for Blood Compatibility of Medical Materials, Guangdong, China
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Guo Y, Yu D, Zhou K, Wang J, Lei D, Xu Z, Tang W, Wu M, Fang X, Shen J, Peng Z, Xiang J. The effect of hemolysis on quality control metrics for noninvasive prenatal testing. BMC Med Genomics 2022; 15:125. [PMID: 35659298 PMCID: PMC9167518 DOI: 10.1186/s12920-022-01280-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/23/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Noninvasive prenatal testing (NIPT) is the testing of blood samples from pregnant women to screen for fetal risk of chromosomal disorders. Even though in vitro hemolysis of blood specimens is common in clinical laboratories, its influence on NIPT has not been well investigated. METHODS Peripheral blood samples were collected from 205 pregnant women and categorized according to the concentration of free hemoglobin in the plasma. After performing NIPT using massively parallel sequencing, the quality control metrics were analyzed and compared with samples that did not undergo hemolysis or samples redrawn from the same women. RESULTS The specimens were divided into four groups based on the concentration of free hemoglobin: Group I (0-1 g/L, n = 53), Group II (1-2 g/L, n = 97), Group III (2-4 g/L, n = 30), and Group IV (> 4 g/L, n = 25). There was no significant difference in the quality control metrics of clinical samples with slight or moderate hemolysis (Group II and III). However, samples with severe hemolysis (Group IV) showed a significantly increased rate of duplicated reads (duplication rate) and fetal fraction, as well as decreased library concentration compared with samples without hemolysis. Moreover, the increase in fetal fraction caused by hemolysis was confirmed by redrawing blood samples in Group IV. CONCLUSION For NIPT using massively parallel sequencing, samples with slight or moderate hemolysis (≤ 4 g/L) are acceptable. However, careful consideration should be taken regarding the use of severely hemolyzed samples (> 4 g/L), since they might increase the risk of test failure.
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Affiliation(s)
- Yaya Guo
- BGI College, Zhengzhou University, Zhengzhou, 450007, China
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450052, China
| | - Dandan Yu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Kaisu Zhou
- Department of Obstetrics, Shenzhen Second People's Hospital, Shenzhen, 518000, China
| | - Jie Wang
- Department of Genetics, Inner Mongolia Maternity and Child Health Care Hospital, Hohhot, 010020, China
| | - Dongzhu Lei
- Center of Prenatal Diagnosis, Chenzhou No.1 People's Hospital, Chenzhou, 423000, China
| | - Zhenpeng Xu
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 430074, China
| | - Weijiang Tang
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 430074, China
| | - Miaofeng Wu
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xingxing Fang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jiankun Shen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhiyu Peng
- BGI College, Zhengzhou University, Zhengzhou, 450007, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiale Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Cao J, Qiao L, Jin J, Zhang S, Chen P, Tang H, Yu Z, Shi J, Wang T, Liang Y. Lipid Metabolism Affects Fetal Fraction and Screen Failures in Non-invasive Prenatal Testing. Front Med (Lausanne) 2022; 8:811385. [PMID: 35096900 PMCID: PMC8790535 DOI: 10.3389/fmed.2021.811385] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: To assess the association between lipid metabolism and fetal fraction, which is a critical factor in ensuring a highly accurate non-invasive prenatal testing (NIPT), and on the rate of screen failures or “no calls” in NIPT. Methods: A total of 4,514 pregnant women at 12–26 weeks of gestation underwent NIPT sequencing and serum lipid measurements. Univariate analysis and multivariate regression models were used to evaluate the associations of serum lipid concentrations with the fetal fraction and the rate of screen failures. Results: The fetal fraction decreased with increased low-density lipoprotein cholesterol and triglyceride (TG) levels, which were significant factors (standardized coefficient: −0.11). Conversely, high-density lipoprotein cholesterol and the interval between the two tests were positively correlated with the fetal fraction. The median fetal fraction was 10.88% (interquartile range, 8.28–13.89%) and this decreased with TG from 11.56% at ≤1.10 mmol/L to 9.51% at >2.30 mmol/L. Meanwhile, multivariate logistic regression analysis revealed that increased TG levels were independently associated with the risk of screen failures. The rate of screen failures showed an increase with TG levels from 1.20% at ≤1.70 mmol/L to 2.41% at >2.30 mmol/L. Conclusions: The fetal fraction and the rate of screen failures in NIPT are affected by TG levels. Meanwhile, in pregnant women with high TG levels, delaying the time between NIPT blood collections can significantly increase the fetal fraction.
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Affiliation(s)
- Jun Cao
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Longwei Qiao
- School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, China
| | - Jieyu Jin
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Sheng Zhang
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ping Chen
- School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, China
| | - Haoyu Tang
- School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, China
| | - Zheng Yu
- School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, China
| | - Jingye Shi
- School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, China
| | - Ting Wang
- School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, China
| | - Yuting Liang
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China.,Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Deng C, Liu S. Factors Affecting the Fetal Fraction in Noninvasive Prenatal Screening: A Review. Front Pediatr 2022; 10:812781. [PMID: 35155308 PMCID: PMC8829468 DOI: 10.3389/fped.2022.812781] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/03/2022] [Indexed: 12/03/2022] Open
Abstract
A paradigm shift in noninvasive prenatal screening has been made with the discovery of cell-free fetal DNA in maternal plasma. Noninvasive prenatal screening is primarily used to screen for fetal aneuploidies, and has been used globally. Fetal fraction, an important parameter in the analysis of noninvasive prenatal screening results, is the proportion of fetal cell-free DNA present in the total maternal plasma cell-free DNA. It combines biological factors and bioinformatics algorithms to interpret noninvasive prenatal screening results and is an integral part of quality control. Maternal and fetal factors may influence fetal fraction. To date, there is no broad consensus on the factors that affect fetal fraction. There are many different approaches to evaluate this parameter, each with its advantages and disadvantages. Different fetal fraction calculation methods may be used in different testing platforms or laboratories. This review includes numerous publications that focused on the understanding of the significance, influencing factors, and interpretation of fetal fraction to provide a deeper understanding of this parameter.
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Affiliation(s)
- Cechuan Deng
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Shanling Liu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
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Bingulac-Popović J, Babić I, Đogić V, Kundid R, Simović Medica J, Mišković B, Jukić I. Prenatal RHD genotyping in Croatia: preliminary results. Transfus Clin Biol 2020; 28:38-43. [PMID: 33227453 DOI: 10.1016/j.tracli.2020.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/23/2020] [Accepted: 10/30/2020] [Indexed: 11/17/2022]
Abstract
OBJECTIVES Croatian Institute of Transfusion Medicine (CITM) implemented non-invasive fetal RHD genotyping as a request for targeted antenatal anti-D prophylaxis. The diagnostic performance of in-house RT-PCR method for fetal RHD genotyping and preliminary results are analyzed. MATERIALS AND METHODS Evaluation included results of RHD genotyping for 205 RhD negative pregnant women, 12-36th week of gestation, whose samples were received in period between 2015 and 2020. QIAsymphony SP DSP Virus Midi Kit was used for cffDNA extraction on QIAsymphony SP platform (Qiagen, Germany). Fragments of RHD exons 7 and 10 and later exon 5 were RT-PCR amplified. As internal controls, amplification of SRY gene or RASSF1A fragment and β-actin genes digested with BsTUI were used. RESULTS We identified 70.72% (145/205) positive and 28.78% (59/205) negative fetal RHD genotypes. We had one inconclusive result (0.50%) due to the interference of maternal DNA with variant genotype RHD*09.02.00/01/*01N.01. When compared to newborns RhD phenotypes, no false negative and three false positive results (3/199, 1.50%) were observed. The test yielded 100% sensitivity and 95.08% specificity, while diagnostic accuracy was 98.48%. We were able to determine one case of fetal variant genotype RHD*04.04/*01N.01 inherited from the father. The negative and positive predictive test values were 100% and 97.86%, respectively. CONCLUSION Automated cffDNA extraction and RT-PCR amplification of fetal RHD exons 5,7,10 and fragments of SRY, RASSF1A genes represents highly reliable system for determining fetal RHD status which enables targeted antenatal anti-D prophylaxis. To obtain high specificity of cffDNA extraction, strict and thoroughly cleaning procedures are required.
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Affiliation(s)
- J Bingulac-Popović
- Department of Molecular Diagnostics, Croatian Institute of Transfusion Medicine, Petrova 3, 10000 Zagreb, Croatia.
| | - I Babić
- Department of Molecular Diagnostics, Croatian Institute of Transfusion Medicine, Petrova 3, 10000 Zagreb, Croatia.
| | - V Đogić
- Department of Molecular Diagnostics, Croatian Institute of Transfusion Medicine, Petrova 3, 10000 Zagreb, Croatia.
| | - R Kundid
- Department of Molecular Diagnostics, Croatian Institute of Transfusion Medicine, Petrova 3, 10000 Zagreb, Croatia.
| | - J Simović Medica
- Department of Transfusion Medicine, General Hospital Pula, Santoriova 24a, 52100 Pula, Croatia.
| | - B Mišković
- Department of Obstetrics and Gynecology, Clinical Hospital "Holy Spirit", 64 Holy Spirit, 10000 Zagreb, Croatia.
| | - I Jukić
- Medical Department, Croatian Institute of Transfusion Medicine, Petrova 3, 10000 Zagreb, Croatia; Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Cara Hadrijana 10/E, 31000 Osijek, Croatia.
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