101
|
Gregg AR, Skotko BG, Benkendorf JL, Monaghan KG, Bajaj K, Best RG, Klugman S, Watson MS. Noninvasive prenatal screening for fetal aneuploidy, 2016 update: a position statement of the American College of Medical Genetics and Genomics. Genet Med 2016; 18:1056-65. [PMID: 27467454 DOI: 10.1038/gim.2016.97] [Citation(s) in RCA: 439] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 06/07/2016] [Indexed: 12/17/2022] Open
Abstract
DISCLAIMER This statement is designed primarily as an educational resource for clinicians to help them provide quality medical services. Adherence to this statement is completely voluntary and does not necessarily assure a successful medical outcome. This statement should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed toward obtaining the same results. In determining the propriety of any specific procedure or test, the clinician should apply his or her own professional judgment to the specific clinical circumstances presented by the individual patient or specimen. Clinicians are encouraged to document the reasons for the use of a particular procedure or test, whether or not it is in conformance with this statement. Clinicians also are advised to take notice of the date this statement was adopted and to consider other medical and scientific information that becomes available after that date. It also would be prudent to consider whether intellectual property interests may restrict the performance of certain tests and other procedures.Noninvasive prenatal screening using cell-free DNA (NIPS) has been rapidly integrated into prenatal care since the initial American College of Medical Genetics and Genomics (ACMG) statement in 2013. New evidence strongly suggests that NIPS can replace conventional screening for Patau, Edwards, and Down syndromes across the maternal age spectrum, for a continuum of gestational age beginning at 9-10 weeks, and for patients who are not significantly obese. This statement sets forth a new framework for NIPS that is supported by information from validation and clinical utility studies. Pretest counseling for NIPS remains crucial; however, it needs to go beyond discussions of Patau, Edwards, and Down syndromes. The use of NIPS to include sex chromosome aneuploidy screening and screening for selected copy-number variants (CNVs) is becoming commonplace because there are no other screening options to identify these conditions. Providers should have a more thorough understanding of patient preferences and be able to educate about the current drawbacks of NIPS across the prenatal screening spectrum. Laboratories are encouraged to meet the needs of providers and their patients by delivering meaningful screening reports and to engage in education. With health-care-provider guidance, the patient should be able to make an educated decision about the current use of NIPS and the ramifications of a positive, negative, or no-call result.Genet Med 18 10, 1056-1065.
Collapse
Affiliation(s)
- Anthony R Gregg
- Department of Obstetrics and Gynecology, University of Florida, Gainesville, Florida, USA
| | - Brian G Skotko
- Department of Pediatrics, Harvard Medical School and Division of Medical Genetics, Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | | | - Komal Bajaj
- New York City Health + Hospitals/Albert Einstein College of Medicine, Bronx, New York, USA
| | - Robert G Best
- University of South Carolina School of Medicine, Greenville Health System, Greenville, South Carolina, USA
| | - Susan Klugman
- Montefiore Medical Center, Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Michael S Watson
- American College of Medical Genetics and Genomics, Bethesda, Maryland, USA
| |
Collapse
|
102
|
Jiang P, Lo YD. The Long and Short of Circulating Cell-Free DNA and the Ins and Outs of Molecular Diagnostics. Trends Genet 2016; 32:360-371. [DOI: 10.1016/j.tig.2016.03.009] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/30/2016] [Indexed: 12/25/2022]
|
103
|
Could Digital PCR Be an Alternative as a Non-Invasive Prenatal Test for Trisomy 21: A Proof of Concept Study. PLoS One 2016; 11:e0155009. [PMID: 27167625 PMCID: PMC4864235 DOI: 10.1371/journal.pone.0155009] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 04/22/2016] [Indexed: 11/21/2022] Open
Abstract
Objective NIPT for fetal aneuploidy by digital PCR has been hampered by the large number of PCR reactions needed to meet statistical requirements, preventing clinical application. Here, we designed an octoplex droplet digital PCR (ddPCR) assay which allows increasing the number of available targets and thus overcomes statistical obstacles. Method After technical optimization of the multiplex PCR on mixtures of trisomic and euploid DNA, we performed a validation study on samples of plasma DNA from 213 pregnant women. Molecular counting of circulating cell-free DNA was performed using a mix of hydrolysis probes targeting chromosome 21 and a reference chromosome. Results The results of our validation experiments showed that ddPCR detected trisomy 21 even when the sample’s trisomic DNA content is as low as 5%. In a validation study of plasma samples from 213 pregnant women, ddPCR discriminated clearly between the trisomy 21 and the euploidy groups. Conclusion Our results demonstrate that digital PCR can meet the requirements for non-invasive prenatal testing of trisomy 21. This approach is technically simple, relatively cheap, easy to implement in a diagnostic setting and compatible with ethical concerns regarding access to nucleotide sequence information. These advantages make it a potential technique of choice for population-wide screening for trisomy 21 in pregnant women.
Collapse
|
104
|
Jiang P, Peng X, Su X, Sun K, Yu SCY, Chu WI, Leung TY, Sun H, Chiu RWK, Lo YMD, Chan KCA. FetalQuant SD: accurate quantification of fetal DNA fraction by shallow-depth sequencing of maternal plasma DNA. NPJ Genom Med 2016; 1:16013. [PMID: 29263813 PMCID: PMC5685300 DOI: 10.1038/npjgenmed.2016.13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/15/2016] [Accepted: 04/04/2016] [Indexed: 12/12/2022] Open
Abstract
Noninvasive prenatal testing using massively parallel sequencing of maternal plasma DNA has been rapidly adopted in clinical use worldwide. Fetal DNA fraction in a maternal plasma sample is an important parameter for accurate interpretations of these tests. However, there is a lack of methods involving low-sequencing depth and yet would allow a robust and accurate determination of fetal DNA fraction in maternal plasma for all pregnancies. In this study, we have developed a new method to accurately quantify the fetal DNA fraction by analysing the maternal genotypes and sequencing data of maternal plasma DNA. Fetal DNA fraction was calculated based on the proportion of non-maternal alleles at single-nucleotide polymorphisms where the mother is homozygous. This new approach achieves a median deviation of 0.6% between predicted fetal DNA fraction and the actual fetal DNA fraction using as low as 0.03-fold sequencing coverage of the human genome. We believe that this method will further enhance the clinical interpretations of noninvasive prenatal testing using genome-wide random sequencing.
Collapse
Affiliation(s)
- Peiyong Jiang
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xianlu Peng
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiaoxi Su
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kun Sun
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Stephanie C Y Yu
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Weng In Chu
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tak Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - Hao Sun
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Rossa W K Chiu
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuk Ming Dennis Lo
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kwan Chee Allen Chan
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
105
|
Matsusaka K, Ishikawa S, Nakayama A, Ushiku T, Nishimoto A, Urabe M, Kaneko N, Kunita A, Kaneda A, Aburatani H, Fujishiro M, Seto Y, Fukayama M. Tumor Content Chart-Assisted HER2/CEP17 Digital PCR Analysis of Gastric Cancer Biopsy Specimens. PLoS One 2016; 11:e0154430. [PMID: 27119558 PMCID: PMC4847903 DOI: 10.1371/journal.pone.0154430] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 04/13/2016] [Indexed: 12/23/2022] Open
Abstract
Evaluating HER2 gene amplification is an essential component of therapeutic decision-making for advanced or metastatic gastric cancer. A simple method that is applicable to small, formalin-fixed, paraffin-embedded biopsy specimens is desirable as an adjunct to or as a substitute for currently used HER2 immunohistochemistry and in situ hybridization protocols. In this study, we developed a microfluidics-based digital PCR method for determining HER2 and chromosome 17 centromere (CEP17) copy numbers and estimating tumor content ratio (TCR). The HER2/CEP17 ratio is determined by three variables—TCR and absolute copy numbers of HER2 and CEP17—by examining tumor cells; only the ratio of the latter two can be obtained by digital PCR using the whole specimen without purifying tumor cells. TCR was determined by semi-automatic image analysis. We developed a Tumor Content chart, which is a plane of rectangular coordinates consisting of HER2/CEP17 digital PCR data and TCR that delineates amplified, non-amplified, and equivocal areas. By applying this method, 44 clinical gastric cancer biopsy samples were classified as amplified (n = 13), non-amplified (n = 25), or equivocal (n = 6). By comparison, 11 samples were positive, 11 were negative, and 22 were equivocally immunohistochemistry. Thus, our novel method reduced the number of equivocal samples from 22 to 6, thereby obviating the need for confirmation by fluorescence or dual-probe in situ hybridization to < 30% of cases. Tumor content chart-assisted digital PCR analysis is also applicable to multiple sites in surgically resected tissues. These results indicate that this analysis is a useful alternative to HER2 immunohistochemistry in gastric cancers that can serve as a basis for the automated evaluation of HER2 status.
Collapse
Affiliation(s)
- Keisuke Matsusaka
- Division of Diagnostic Pathology, the University of Tokyo Hospital, Tokyo, Japan
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shumpei Ishikawa
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
- Department of Genomic Pathology, Medical Research Institute Tokyo Medical and Dental University, Tokyo, Japan
| | - Atsuhito Nakayama
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Aiko Nishimoto
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Masayuki Urabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
- Department of Gastrointestinal Surgery, the University of Tokyo Hospital, Tokyo, Japan
| | - Nobuyuki Kaneko
- Division of Diagnostic Pathology, the University of Tokyo Hospital, Tokyo, Japan
| | - Akiko Kunita
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, the University of Tokyo, Tokyo, Japan
| | - Mitsuhiro Fujishiro
- Department of Endoscopy and Endoscopic Surgery, the University of Tokyo Hospital, Tokyo, Japan
| | - Yasuyuki Seto
- Department of Gastrointestinal Surgery, the University of Tokyo Hospital, Tokyo, Japan
| | - Masashi Fukayama
- Division of Diagnostic Pathology, the University of Tokyo Hospital, Tokyo, Japan
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
- * E-mail:
| |
Collapse
|
106
|
Picoliter Well Array Chip-Based Digital Recombinase Polymerase Amplification for Absolute Quantification of Nucleic Acids. PLoS One 2016; 11:e0153359. [PMID: 27074005 PMCID: PMC4830604 DOI: 10.1371/journal.pone.0153359] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 03/29/2016] [Indexed: 11/28/2022] Open
Abstract
Absolute, precise quantification methods expand the scope of nucleic acids research and have many practical applications. Digital polymerase chain reaction (dPCR) is a powerful method for nucleic acid detection and absolute quantification. However, it requires thermal cycling and accurate temperature control, which are difficult in resource-limited conditions. Accordingly, isothermal methods, such as recombinase polymerase amplification (RPA), are more attractive. We developed a picoliter well array (PWA) chip with 27,000 consistently sized picoliter reactions (314 pL) for isothermal DNA quantification using digital RPA (dRPA) at 39°C. Sample loading using a scraping liquid blade was simple, fast, and required small reagent volumes (i.e., <20 μL). Passivating the chip surface using a methoxy-PEG-silane agent effectively eliminated cross-contamination during dRPA. Our creative optical design enabled wide-field fluorescence imaging in situ and both end-point and real-time analyses of picoliter wells in a 6-cm2 area. It was not necessary to use scan shooting and stitch serial small images together. Using this method, we quantified serial dilutions of a Listeria monocytogenes gDNA stock solution from 9 × 10-1 to 4 × 10-3 copies per well with an average error of less than 11% (N = 15). Overall dRPA-on-chip processing required less than 30 min, which was a 4-fold decrease compared to dPCR, requiring approximately 2 h. dRPA on the PWA chip provides a simple and highly sensitive method to quantify nucleic acids without thermal cycling or precise micropump/microvalve control. It has applications in fast field analysis and critical clinical diagnostics under resource-limited settings.
Collapse
|
107
|
Accurate quantification of supercoiled DNA by digital PCR. Sci Rep 2016; 6:24230. [PMID: 27063649 PMCID: PMC4827127 DOI: 10.1038/srep24230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/15/2016] [Indexed: 11/19/2022] Open
Abstract
Digital PCR (dPCR) as an enumeration-based quantification method is capable of quantifying the DNA copy number without the help of standards. However, it can generate false results when the PCR conditions are not optimized. A recent international comparison (CCQM P154) showed that most laboratories significantly underestimated the concentration of supercoiled plasmid DNA by dPCR. Mostly, supercoiled DNAs are linearized before dPCR to avoid such underestimations. The present study was conducted to overcome this problem. In the bilateral comparison, the National Institute of Metrology, China (NIM) optimized and applied dPCR for supercoiled DNA determination, whereas Korea Research Institute of Standards and Science (KRISS) prepared the unknown samples and quantified them by flow cytometry. In this study, several factors like selection of the PCR master mix, the fluorescent label, and the position of the primers were evaluated for quantifying supercoiled DNA by dPCR. This work confirmed that a 16S PCR master mix avoided poor amplification of the supercoiled DNA, whereas HEX labels on dPCR probe resulted in robust amplification curves. Optimizing the dPCR assay based on these two observations resulted in accurate quantification of supercoiled DNA without preanalytical linearization. This result was validated in close agreement (101~113%) with the result from flow cytometry.
Collapse
|
108
|
Orhant L, Anselem O, Fradin M, Becker PH, Beugnet C, Deburgrave N, Tafuri G, Letourneur F, Goffinet F, Allach El Khattabi L, Leturcq F, Bienvenu T, Tsatsaris V, Nectoux J. Droplet digital PCR combined with minisequencing, a new approach to analyze fetal DNA from maternal blood: application to the non-invasive prenatal diagnosis of achondroplasia. Prenat Diagn 2016; 36:397-406. [PMID: 26850935 DOI: 10.1002/pd.4790] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/29/2015] [Accepted: 02/01/2016] [Indexed: 12/29/2022]
Abstract
BACKGROUND Achondroplasia is generally detected by abnormal prenatal ultrasound findings in the third trimester of pregnancy and then confirmed by molecular genetic testing of fetal genomic DNA obtained by aspiration of amniotic fluid. This invasive procedure presents a small but significant risk for both the fetus and mother. Therefore, non-invasive procedures using cell-free fetal DNA in maternal plasma have been developed for the detection of the fetal achondroplasia mutations. METHODS To determine whether the fetus carries the de novo mis-sense genetic mutation at nucleotide 1138 in FGFR3 gene involved in >99% of achondroplasia cases, we developed two independent methods: digital-droplet PCR combined with minisequencing, which are very sensitive methods allowing detection of rare alleles. RESULTS We collected 26 plasmatic samples from women carrying fetus at risk of achondroplasia and diagnosed to date a total of five affected fetuses in maternal blood. The sensitivity and specificity of our test are respectively 100% [95% confidence interval, 56.6-100%] and 100% [95% confidence interval, 84.5-100%]. CONCLUSIONS This novel, original strategy for non-invasive prenatal diagnosis of achondroplasia is suitable for implementation in routine clinical testing and allows considering extending the applications of these technologies in non-invasive prenatal diagnosis of many other monogenic diseases. © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Lucie Orhant
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France
| | - Olivia Anselem
- Maternité Cochin-Port Royal, HUPC Hôpital Cochin, Paris, France
| | - Mélanie Fradin
- Service de Génétique Médicale, CHU de Rennes, Rennes, France
| | | | - Caroline Beugnet
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France
| | - Nathalie Deburgrave
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France
| | - Gilles Tafuri
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France
| | - Franck Letourneur
- INSERM, U1016, Institut Cochin, CNRS UMR8104, Université Paris Descartes, Paris, France
| | | | | | - France Leturcq
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France
| | - Thierry Bienvenu
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France.,INSERM, U1016, Institut Cochin, CNRS UMR8104, Université Paris Descartes, Paris, France
| | | | - Juliette Nectoux
- Service de Biochimie et Génétique Moléculaire, HUPC Hôpital Cochin, Paris, France.,INSERM, U1016, Institut Cochin, CNRS UMR8104, Université Paris Descartes, Paris, France
| |
Collapse
|
109
|
Li WH, Wang PH, Chuang CM, Chang YW, Yang MJ, Chen CY, Chao KC, Yen MS. Noninvasive prenatal testing for fetal trisomy in a mixed risk factors pregnancy population. Taiwan J Obstet Gynecol 2016; 54:122-5. [PMID: 25951714 DOI: 10.1016/j.tjog.2015.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2015] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE This study assesses the performance of noninvasive prenatal testing (NIPT) for fetal aneuploidies in a mixed risk factors pregnancy population. MATERIALS AND METHODS Data review of 169 pregnant women undergoing prenatal aneuploidy screening in a single tertiary medical center was conducted. Indications included maternal anxiety, advanced maternal age, abnormal nuchal translucency, and high/moderate risk of first trimester Down syndrome screening. Multifetal pregnancies and patients receiving in vitro fertilization were also enrolled for analysis. RESULTS A total of 169 patients were enrolled in this study during a time period from July 2012 to June 2014. For patients' ≥ 34 years, anxiety about amniocentesis was the most common reason for patients selecting NIPT for fetal aneuploidy screening, with 107 (88.4%) patients choosing NIPT for this reason. Among the total patient population, two patients showed a positive result from NIPT. One patient displayed 47, XXY, which was confirmed to be a false-positive result. The other patient displayed trisomy 18, which was confirmed by an amniotic cell culture. The sensitivity for NIPT is 100% with the specificity 99.4%. CONCLUSIONS NIPT for fetal aneuploidy in a mixed risk factors pregnancy population showed high accuracy. NIPT applied to the low risk population might reassure the anxious family.
Collapse
Affiliation(s)
- Wai-Hou Li
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan; National Yang-Ming University, School of Medicine, Taipei, Taiwan
| | - Peng-Hui Wang
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan; National Yang-Ming University, School of Medicine, Taipei, Taiwan
| | - Chi-Mu Chuang
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan; National Yang-Ming University, School of Medicine, Taipei, Taiwan
| | - Yi-Wen Chang
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan; National Yang-Ming University, School of Medicine, Taipei, Taiwan
| | - Ming-Jie Yang
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan; National Yang-Ming University, School of Medicine, Taipei, Taiwan
| | - Chih-Yao Chen
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan; National Yang-Ming University, School of Medicine, Taipei, Taiwan.
| | - Kuan-Chong Chao
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan; National Yang-Ming University, School of Medicine, Taipei, Taiwan
| | - Ming-Shyen Yen
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan; National Yang-Ming University, School of Medicine, Taipei, Taiwan; Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| |
Collapse
|
110
|
Alberti A, Salomon LJ, Le Lorc'h M, Couloux A, Bussières L, Goupil S, Malan V, Pelletier E, Hyon C, Vialard F, Rozenberg P, Bouhanna P, Oury JF, Schmitz T, Romana S, Weissenbach J, Vekemans M, Ville Y. Non-invasive prenatal testing for trisomy 21 based on analysis of cell-free fetal DNA circulating in the maternal plasma. Prenat Diagn 2016; 35:471-6. [PMID: 25643828 DOI: 10.1002/pd.4561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 01/04/2015] [Accepted: 01/14/2015] [Indexed: 12/23/2022]
Abstract
OBJECTIVE By-the-book implementation of non-invasive prenatal test and clinical validation for trisomy 21. STUDY DESIGN Publicly funded prospective study of 225 cases. Women at risk for trisomy 21 > 1/250 based on combined ultrasound and serum markers during first or second trimester were eligible following an informed consent. The technique was established from the available literature and performed on 10 mL of venous blood collected prior to chorionic villus sampling or amniocentesis. Investigators were blinded to the fetal karyotype. Results were expressed in Z-scores of the percentage of each chromosome. RESULTS Among 976 eligible cases, 225 were processed: 8 were used for pretesting phase and 23 to build a reference set. One hundred thirty six euploid cases and 47 with trisomy 21 were then run randomly. Eleven cases yielded no result (4.8%). Z-scores were above 3 (7.58+/-2.41) for chromosome 21 in all 47 trisomies and in none of the euploid cases (0.11+/-1.0). Z-scores were within normal range for the other chromosomes in both groups. Using a cut-off of 3, sensitivity and specificity were of 100% 95% CI [94.1, 100] and 100% 95% CI [98, 100], respectively. CONCLUSION Non-invasive prenatal test for trisomy 21 is a robust strategy that can be translated from seminal publications. Publicly funded studies should refine its indications and cost-effectiveness in prenatal screening and diagnosis. © 2015 John Wiley & Sons, Ltd.
Collapse
|
111
|
Song Q, Gao Y, Zhu Q, Tian Q, Yu B, Song B, Xu Y, Yuan M, Ma C, Jin W, Zhang T, Mu Y, Jin Q. A nanoliter self-priming compartmentalization chip for point-of-care digital PCR analysis. Biomed Microdevices 2015; 17:64. [PMID: 26022215 DOI: 10.1007/s10544-015-9970-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A nanoliter self-priming compartmentalization (SPC) microfluidic chip suited for the digital polymerase chain reaction (dPCR) analysis in point-of-care testing (POCT) has been developed. This dPCR chip is fabricated of polydimethylsiloxane (PDMS). After the dPCR chip is evacuated, there will be a negative pressure environment in the chip because of the gas solubility of PDMS. The negative pressure environment can provide a self-priming power so that the sample solutions can be sucked into each reaction chamber sequentially. The whole sampling process requires no external power and is valve-free. Channels that contain water are designed around each sample panel to prevent the solvent (water) from evaporating during dPCR process. A glass coverslip is also used as a waterproof layer, which is more convenient and more efficient than other waterproof methods seen in literature. This dPCR chip allows three samples to be amplified at the same time. Each sample is distributed into 1040 reaction chambers, and each chamber is only 2.08 nL. Human β-actin DNA solutions of known concentrations are used as the templates for the dPCR analyses to verify the sensitivity and accuracy of the method. Template DNA solutions diluted to concentrations of 300, 100 and 10 copies/μL are tested and shown that this simple, portable and self-priming dPCR chip can be used at any clinic as a real POCT technique.
Collapse
Affiliation(s)
- Qi Song
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, People's Republic of China
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
112
|
Lee SY, Shim SH, Youn JP, Kim SJ, Kim JH, Jung SA, Choi HJ, Oh MJ, Lee KR, Cha DH, Hwang SY. New application methods for chromosomal abnormalities screening test using digital PCR. BIOCHIP JOURNAL 2015. [DOI: 10.1007/s13206-015-9410-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
113
|
Kim HJ, Kim SY, Lim JH, Kwak DW, Park SY, Ryu HM. Quantification and Application of Potential Epigenetic Markers in Maternal Plasma of Pregnancies with Hypertensive Disorders. Int J Mol Sci 2015; 16:29875-88. [PMID: 26694356 PMCID: PMC4691144 DOI: 10.3390/ijms161226201] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/01/2015] [Accepted: 12/08/2015] [Indexed: 12/18/2022] Open
Abstract
The aim of this study was to evaluate quantitative aberrations of novel fetal-specific epigenetic markers in maternal plasma of pregnancies with hypertensive disorders. We compared the concentrations of DSCR3, RASSF1A, and SRY as cell-free fetal DNA markers in 188 normal pregnancies, 16 pregnancies with early-onset preeclampsia (EO-PE), 47 pregnancies with late-onset preeclampsia (LO-PE), and 29 pregnancies with gestational hypertension (GH). The concentrations of all markers were significantly correlated with gestational age (p < 0.001 for all). Strong positive correlations were also observed between DSCR3 and SRY (r = 0.471, p < 0.001), as well as between RASSF1A and SRY (r = 0.326, p = 0.015) and between DSCR3 and RASSF1A (r = 0.673, p < 0.001). The concentrations of DSCR3 and RASSF1A in the EO-PE were significantly higher at 24–32 weeks and onwards (p < 0.05 for both). In the LO-PE, DSCR3 and RASSF1A concentrations were significantly higher only at 33–41 weeks compared with the controls. The concentrations of all markers in the GH group were not significantly different from those in the control group. This study is the first demonstration that DSCR3 is a novel epigenetic marker that can be an alternative to the RASSF1A for the prediction of EO-PE.
Collapse
Affiliation(s)
- Hyun Jin Kim
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul 100-380, Korea.
| | - Shin Young Kim
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul 100-380, Korea.
| | - Ji Hyae Lim
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul 100-380, Korea.
| | - Dong Wook Kwak
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women's Healthcare Center, Dankook University College of Medicine, Seoul 100-380, Korea.
| | - So Yeon Park
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul 100-380, Korea.
| | - Hyun Mee Ryu
- Laboratory of Medical Genetics, Medical Research Institute, Cheil General Hospital and Women's Healthcare Center, Seoul 100-380, Korea.
- Department of Obstetrics and Gynecology, Cheil General Hospital and Women's Healthcare Center, Dankook University College of Medicine, Seoul 100-380, Korea.
| |
Collapse
|
114
|
Mochizuki H, Shapiro SG, Breen M. Detection of BRAF Mutation in Urine DNA as a Molecular Diagnostic for Canine Urothelial and Prostatic Carcinoma. PLoS One 2015; 10:e0144170. [PMID: 26649430 PMCID: PMC4674145 DOI: 10.1371/journal.pone.0144170] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/14/2015] [Indexed: 12/22/2022] Open
Abstract
Urothelial carcinoma (UC) of the lower urinary tract and prostatic carcinoma (PC) are aggressive genitourinary cancers in dogs, characterized by invasion to surrounding tissues and high metastatic potential. Current diagnosis of canine UC and PC requires histopathological examination of a biopsy. Such specimens require specialized medical equipment and are invasive procedures, limiting the availability of diagnosis by histopathology for many canine patients. Access to a non-invasive means to confirm diagnosis is currently an unmet need. Recently, the canine BRAF V595E mutation was detected in ~80% of canine UCs and PCs. In this study, we developed a droplet digital PCR (ddPCR) assay for detection of the canine BRAF V595E mutation in canine urogenital tumors. The assay was evaluated in DNA samples prepared from biopsy specimens of UC (n = 48) and PC (n = 27), as well and non-neoplastic bladder epithelium (n = 38). In addition the assay was assessed for use with DNA isolated from free catch urine samples derived from canine patients with UC (n = 23), PC (n = 3), as well as from dogs with cystitis and healthy controls (n = 37). In all cases the sensitivity to detect the mutant allele was compared with conventional Sanger sequencing. ddPCR had superior sensitivity for detection of the V595E mutation: 75% of UC, 85% of PC, and 0% of control samples were mutation positive, respectively, and the V595E mutation was detected at a level as low as just 1 in 10,000 alleles (~0.01%). Furthermore, the ddPCR assay identified the mutation in free catch urine samples from 83% of canine UC and PC patients, demonstrating its utility as a non-invasive means of diagnosis. We have shown that ddPCR is a sensitive molecular technique with the potential to facilitate accurate and non-invasive means of canine UC and PC diagnosis.
Collapse
Affiliation(s)
- Hiroyuki Mochizuki
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Susan G. Shapiro
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, United States of America
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
115
|
Droplet digital polymerase chain reaction assay for screening of ESR1 mutations in 325 breast cancer specimens. Transl Res 2015; 166:540-553.e2. [PMID: 26434753 DOI: 10.1016/j.trsl.2015.09.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/03/2015] [Accepted: 09/05/2015] [Indexed: 11/21/2022]
Abstract
Droplet digital polymerase chain reaction (ddPCR), which could perform thousands of PCRs on a nanoliter scale simultaneously, would be an attractive method to massive parallel sequencing for identifying and studying the significance of low-frequency rare mutations. Recent evidence has shown that the key potential mechanisms of the failure of aromatase inhibitors-based therapy involve identifying activating mutations affecting the ligand-binding domain of the ESR1 gene. Therefore, the detection of ESR1 mutations may be useful as a biomarker predicting an effect of the treatment. We aimed to develop a ddPCR-based method for the sensitive detection of ESR1 mutations in 325 breast cancer specimens, in which 270 primary and 55 estrogen receptor-positive (ER+) metastatic breast cancer (MBC) specimens. Our ddPCR assay could detect the ESR1 mutant molecules with low concentration of 0.25 copies/μL. According to the selected cutoff, ESR1 mutations occurred in 7 (2.5%) of 270 primary breast cancer specimens and in 11 (20%) of 55 ER+ MBC specimens. Among the 11 MBC specimens, 5 specimens (45.5%) had the most common ESR1 mutation, Y537S, 4 specimens (36.3%) each had D538G, Y537N, and Y537C. Interestingly, 2 patients had 2 ESR1 mutations, Y537N/D538G and Y537S/Y537C, and 2 patients had 3 ESR1 mutations, Y537S/Y537N/D538G. Biopsy was performed in heterochrony in 8 women twice. In 8 women, 4 women had primary breast cancer and MBC specimens and 4 women had 2 specimens when treatment was failure. Four of these 8 women acquired ESR1 mutation, whereas no ESR1 mutation could be identified at first biopsy. ddPCR technique could be a promising tool for the next-generation sequencing-free precise detection of ESR1 mutations in endocrine therapy resistant cases and may assist in determining the treatment strategy.
Collapse
|
116
|
Performance of Droplet Digital PCR in Non-Invasive Fetal RHD Genotyping - Comparison with a Routine Real-Time PCR Based Approach. PLoS One 2015; 10:e0142572. [PMID: 26562517 PMCID: PMC4642940 DOI: 10.1371/journal.pone.0142572] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/25/2015] [Indexed: 02/06/2023] Open
Abstract
Detection and characterization of circulating cell-free fetal DNA (cffDNA) from maternal circulation requires an extremely sensitive and precise method due to very low cffDNA concentration. In our study, droplet digital PCR (ddPCR) was implemented for fetal RHD genotyping from maternal plasma to compare this new quantification alternative with real-time PCR (qPCR) as a golden standard for quantitative analysis of cffDNA. In the first stage of study, a DNA quantification standard was used. Clinical samples, including 10 non-pregnant and 35 pregnant women, were analyzed as a next step. Both methods' performance parameters-standard curve linearity, detection limit and measurement precision-were evaluated. ddPCR in comparison with qPCR has demonstrated sufficient sensitivity for analysing of cffDNA and determination of fetal RhD status from maternal circulation, results of both methods strongly correlated. Despite the more demanding workflow, ddPCR was found to be slightly more precise technology, as evaluated using quantitative standard. Regarding the clinical samples, the precision of both methods equalized with decreasing concentrations of tested DNA samples. In case of cffDNA with very low concentrations, variance parameters of both techniques were comparable. Detected levels of fetal cfDNA in maternal plasma were slightly higher than expected and correlated significantly with gestational age as measured by both methods (ddPCR r = 0.459; qPCR r = 0.438).
Collapse
|
117
|
Eikmans M, van Halteren AGS, van Besien K, van Rood JJ, Drabbels JJM, Claas FHJ. Naturally acquired microchimerism: implications for transplantation outcome and novel methodologies for detection. CHIMERISM 2015; 5:24-39. [PMID: 24762743 DOI: 10.4161/chim.28908] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Microchimerism represents a condition where one individual harbors genetically distinct cell populations, and the chimeric population constitutes <1% of the total number of cells. The most common natural source of microchimerism is pregnancy. The reciprocal cell exchange between a mother and her child often leads to the stable engraftment of hematopoietic and non-hematopoietic stem cells in both parties. Interaction between cells from the mother and those from the child may result in maternal immune cells becoming sensitized to inherited paternal alloantigens of the child, which are not expressed by the mother herself. Vice versa, immune cells of the child may become sensitized toward the non-inherited maternal alloantigens of the mother. The extent of microchimerism, its anatomical location, and the sensitivity of the techniques used for detecting its presence collectively determine whether microchimerism can be detected in an individual. In this review, we focus on the clinical consequences of microchimerism in solid organ and hematopoietic stem cell transplantation, and propose concepts derived from data of epidemiologic studies. Next, we elaborate on the latest molecular methodology, including digital PCR, for determining in a reliable and sensitive way the extent of microchimerism. For the first time, tools have become available to isolate viable chimeric cells from a host background, so that the challenges of establishing the biologic mechanisms and function of these cells may finally be tackled.
Collapse
Affiliation(s)
- Michael Eikmans
- Department of Immunohematology and Blood Transfusion; Leiden University Medical Center; Leiden, the Netherlands
| | - Astrid G S van Halteren
- Immunology Laboratory; Willem Alexander Children's Hospital; Leiden University Medical Center; Leiden, the Netherlands
| | | | - Jon J van Rood
- Department of Immunohematology and Blood Transfusion; Leiden University Medical Center; Leiden, the Netherlands; Europdonor Foundation; Leiden, the Netherlands
| | - Jos J M Drabbels
- Department of Immunohematology and Blood Transfusion; Leiden University Medical Center; Leiden, the Netherlands
| | - Frans H J Claas
- Department of Immunohematology and Blood Transfusion; Leiden University Medical Center; Leiden, the Netherlands
| |
Collapse
|
118
|
Sun K, Jiang P, Chan KCA. The impact of digital DNA counting technologies on noninvasive prenatal testing. Expert Rev Mol Diagn 2015; 15:1261-8. [PMID: 26358092 DOI: 10.1586/14737159.2015.1084227] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The discovery of cell-free DNA molecules in maternal plasma has opened up numerous opportunities for noninvasive prenatal testing. The advent of new digital counting technologies, including digital polymerase chain reaction and massive parallel sequencing, has provided the opportunity to quantify the cell-free DNA molecules in maternal plasma in an unprecedentedly precise manner. Powered by these technologies, prenatal testing of different kinds of hereditary conditions, ranging from monogenic diseases to chromosome aneuploidies, has been shown to be possible through the analysis of maternal plasma DNA. Discussed here are the principles of the approaches used in the noninvasive testing of different fetal conditions, with an emphasis on the impact that different digital DNA counting strategies have made on the development of these tests.
Collapse
Affiliation(s)
- Kun Sun
- a Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- a Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | | |
Collapse
|
119
|
Comparison of digital PCR platforms and semi-nested qPCR as a tool to determine the size of the HIV reservoir. Sci Rep 2015; 5:13811. [PMID: 26350506 PMCID: PMC4563360 DOI: 10.1038/srep13811] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 08/06/2015] [Indexed: 01/04/2023] Open
Abstract
HIV persists in latently infected cells of patients on antiretroviral therapy (ART). This persistent proviral DNA reservoir is an important predictor of viral rebound upon therapy failure or interruption and forms a major obstacle towards cure. Accurate quantification of the low levels of persisting HIV DNA may aid patient monitoring and cure research. Digital PCR is a promising tool that enables direct absolute quantification with high sensitivity. With recent technological advances, several platforms are available to implement digital PCR in a clinical setting. Here, we compared two digital PCR platforms, the Quantstudio 3D (Life Technologies) and the QX100 (Bio-Rad) with a semi-nested qPCR on serial HIV DNA dilutions and DNA isolated from PBMCs of ART-suppressed patients. All three methods were able to detect target to the lowest levels of 2.5 HIV DNA copies. The QX100 excelled in having the least bias and highest precision, efficiency and quantitative linearity. Patient sample quantifications by the QX100 and semi-nested qPCR were highly agreeable by Bland-Altman analysis (0.01±0.32 log10). Due to the observation of false-positive signals with current digital PCR platforms however, semi-nested qPCR may still be preferred in a setup of low quantity detection to discriminate between presence or absence of HIV DNA.
Collapse
|
120
|
Comparison of four digital PCR platforms for accurate quantification of DNA copy number of a certified plasmid DNA reference material. Sci Rep 2015; 5:13174. [PMID: 26302947 PMCID: PMC4548226 DOI: 10.1038/srep13174] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/06/2015] [Indexed: 11/15/2022] Open
Abstract
Digital polymerase chain reaction (dPCR) is a unique approach to measurement of the absolute copy number of target DNA without using external standards. However, the comparability of different dPCR platforms with respect to measurement of DNA copy number must be addressed before dPCR can be classified fundamentally as an absolute quantification technique. The comparability of four dPCR platforms with respect to accuracy and measurement uncertainty was investigated by using a certified plasmid reference material. Plasmid conformation was found to have a significant effect on droplet-based dPCR (QX100 and RainDrop) not shared with chip-based QuantStudio 12k or BioMark. The relative uncertainty of partition volume was determined to be 0.7%, 0.8%, 2.3% and 2.9% for BioMark, QX100, QuantStudio 12k and RainDrop, respectively. The measurements of the certified pNIM-001 plasmid made using the four dPCR platforms were corrected for partition volume and closely consistent with the certified value within the expended uncertainty. This demonstrated that the four dPCR platforms are of comparable effectiveness in quantifying DNA copy number. These findings provide an independent assessment of this method of determining DNA copy number when using different dPCR platforms and underline important factors that should be taken into consideration in the design of dPCR experiments.
Collapse
|
121
|
Chitty LS, Lo YMD. Noninvasive Prenatal Screening for Genetic Diseases Using Massively Parallel Sequencing of Maternal Plasma DNA. Cold Spring Harb Perspect Med 2015; 5:a023085. [PMID: 26187875 PMCID: PMC4561399 DOI: 10.1101/cshperspect.a023085] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The identification of cell-free fetal DNA (cffDNA) in maternal plasma in 1997 heralded the most significant change in obstetric care for decades, with the advent of safer screening and diagnosis based on analysis of maternal blood. Here, we describe how the technological advances offered by next-generation sequencing have allowed for the development of a highly sensitive screening test for aneuploidies as well as definitive prenatal molecular diagnosis for some monogenic disorders.
Collapse
Affiliation(s)
- Lyn S Chitty
- UCL Institute of Child Health, Genetics and Genomic Medicine, London WC1N 1EH, United Kingdom; University College London Hospitals NHS Foundation Trust, London NW1 2PG, United Kingdom; NE Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, 37 Queen Square, London WC1N 3BH, United Kingdom
| | - Y M Dennis Lo
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong SAR, China
| |
Collapse
|
122
|
Kim SK, Hannum G, Geis J, Tynan J, Hogg G, Zhao C, Jensen TJ, Mazloom AR, Oeth P, Ehrich M, van den Boom D, Deciu C. Determination of fetal DNA fraction from the plasma of pregnant women using sequence read counts. Prenat Diagn 2015; 35:810-5. [PMID: 25967380 DOI: 10.1002/pd.4615] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVE This study introduces a novel method, referred to as SeqFF, for estimating the fetal DNA fraction in the plasma of pregnant women and to infer the underlying mechanism that allows for such statistical modeling. METHODS Autosomal regional read counts from whole-genome massively parallel single-end sequencing of circulating cell-free DNA (ccfDNA) from the plasma of 25 312 pregnant women were used to train a multivariate model. The pretrained model was then applied to 505 pregnant samples to assess the performance of SeqFF against known methodologies for fetal DNA fraction calculations. RESULTS Pearson's correlation between chromosome Y and SeqFF for pregnancies with male fetuses from two independent cohorts ranged from 0.932 to 0.938. Comparison between a single-nucleotide polymorphism-based approach and SeqFF yielded a Pearson's correlation of 0.921. Paired-end sequencing suggests that shorter ccfDNA, that is, less than 150 bp in length, is nonuniformly distributed across the genome. Regions exhibiting an increased proportion of short ccfDNA, which are more likely of fetal origin, tend to provide more information in the SeqFF calculations. CONCLUSION SeqFF is a robust and direct method to determine fetal DNA fraction. Furthermore, the method is applicable to both male and female pregnancies and can greatly improve the accuracy of noninvasive prenatal testing for fetal copy number variation.
Collapse
Affiliation(s)
- Sung K Kim
- Sequenom Laboratories, San Diego, CA, USA
| | | | | | - John Tynan
- Sequenom Laboratories, San Diego, CA, USA
| | - Grant Hogg
- Sequenom Laboratories, San Diego, CA, USA
| | - Chen Zhao
- Sequenom Laboratories, San Diego, CA, USA
| | | | | | - Paul Oeth
- Sequenom Laboratories, San Diego, CA, USA
| | | | | | | |
Collapse
|
123
|
Karakas B, Qubbaj W, Al-Hassan S, Coskun S. Noninvasive Digital Detection of Fetal DNA in Plasma of 4-Week-Pregnant Women following In Vitro Fertilization and Embryo Transfer. PLoS One 2015; 10:e0126501. [PMID: 25970589 PMCID: PMC4430227 DOI: 10.1371/journal.pone.0126501] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 04/02/2015] [Indexed: 11/29/2022] Open
Abstract
The discovery of cell-free fetal DNA (cfDNA) circulating in the maternal blood has provided new opportunities for noninvasive prenatal diagnosis (NIPD). However, the extremely low levels of cfDNA within a high background of the maternal DNA in maternal circulation necessitate highly sensitive molecular techniques for its reliable use in NIPD. In this proof of principle study, we evaluated the earliest possible detection of cfDNA in the maternal plasma by a bead-based emulsion PCR technology known as BEAMing (beads, emulsion, amplification, magnetics). Blood samples were collected from in vitro fertilization (IVF) patients at 2 to 6 weeks following embryo transfer (i.e., 4 to 8 week pregnancies) and plasma DNA was extracted. The genomic regions of both X and Y chromosome-specific sequences (AMELX and AMELY) were concurrently amplified in two sequential PCRs; first by conventional PCR then by BEAMing. The positive beads either for AMELX or AMELY gene sequences were counted by a flow cytometer. Our results showed that the pregnancies yielding boys had significantly higher plasma AMELY gene fractions (0.512 ± 0.221) than the ones yielding girls (0.028 ± 0.003) or non-pregnant women (0.020 ± 0.005, P= 0.0059). Here, we clearly demonstrated that the BEAMing technique is capable of reliably detecting cfDNA in the blood circulation of 4-week-pregnant women, which is only two weeks after the embryo transfer. BEAMing technique can also be used to early detect fetal DNA alterations in other pregnancy-associated disorders.
Collapse
Affiliation(s)
- Bedri Karakas
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- * E-mail:
| | - Wafa Qubbaj
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Saad Al-Hassan
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Serdar Coskun
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Alfaisal University, Riyadh, Saudi Arabia
| |
Collapse
|
124
|
Bioinformatics analysis of circulating cell-free DNA sequencing data. Clin Biochem 2015; 48:962-75. [PMID: 25966961 DOI: 10.1016/j.clinbiochem.2015.04.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/30/2015] [Accepted: 04/29/2015] [Indexed: 12/18/2022]
Abstract
The discovery of cell-free DNA molecules in plasma has opened up numerous opportunities in noninvasive diagnosis. Cell-free DNA molecules have become increasingly recognized as promising biomarkers for detection and management of many diseases. The advent of next generation sequencing has provided unprecedented opportunities to scrutinize the characteristics of cell-free DNA molecules in plasma in a genome-wide fashion and at single-base resolution. Consequently, clinical applications of circulating cell-free DNA analysis have not only revolutionized noninvasive prenatal diagnosis but also facilitated cancer detection and monitoring toward an era of blood-based personalized medicine. With the remarkably increasing throughput and lowering cost of next generation sequencing, bioinformatics analysis becomes increasingly demanding to understand the large amount of data generated by these sequencing platforms. In this Review, we highlight the major bioinformatics algorithms involved in the analysis of cell-free DNA sequencing data. Firstly, we briefly describe the biological properties of these molecules and provide an overview of the general bioinformatics approach for the analysis of cell-free DNA. Then, we discuss the specific upstream bioinformatics considerations concerning the analysis of sequencing data of circulating cell-free DNA, followed by further detailed elaboration on each key clinical situation in noninvasive prenatal diagnosis and cancer management where downstream bioinformatics analysis is heavily involved. We also discuss bioinformatics analysis as well as clinical applications of the newly developed massively parallel bisulfite sequencing of cell-free DNA. Finally, we offer our perspectives on the future development of bioinformatics in noninvasive diagnosis.
Collapse
|
125
|
Everett TR, Chitty LS. Cell-free fetal DNA: the new tool in fetal medicine. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2015; 45:499-507. [PMID: 25483938 PMCID: PMC5029578 DOI: 10.1002/uog.14746] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 10/31/2014] [Accepted: 11/25/2014] [Indexed: 06/04/2023]
Affiliation(s)
- T R Everett
- Fetal Medicine Unit, University College London Hospital NHS Foundation Trust, London, UK
| | | |
Collapse
|
126
|
Khalil A, Mahmoodian N, Kulkarni A, Homfray T, Papageorghiou A, Bhide A, Thilaganathan B. Estimation of Detection Rates of Aneuploidy in High-Risk Pregnancy Using an Approach Based on Nuchal Translucency and Non-Invasive Prenatal Testing: A Cohort Study. Fetal Diagn Ther 2015; 38:254-61. [PMID: 25925597 DOI: 10.1159/000381182] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 02/19/2015] [Indexed: 11/19/2022]
Abstract
OBJECTIVES The aim was to investigate aneuploidy detection using an approach based on nuchal translucency (NT) and non-invasive prenatal testing (NIPT). METHODS This was a cohort study including 5,306 high-risk pregnancies with NT measurements and chorionic villus samples (CVS) tested for full karyotype. RESULTS The fetal karyotype was normal in 4,172 (78.6%) cases and abnormal in 1,134 (21.4%), including 1,009 with a likely clinically significant adverse outcome. Universal CVS with full karyotyping would lead to the diagnosis of all clinically significant abnormalities. A policy of relying solely on NIPT would have led to the diagnosis of 88.9% of clinically significant abnormalities. A strategy whereby NIPT is the main method, with CVS reserved for cases with NT ≥3.0 mm, would require CVS in 21.7% of cases, identify 94.8% of significant abnormalities and avoid miscarriage in 41 pregnancies compared to CVS for all. CONCLUSIONS A policy of NIPT for increased-risk cases and CVS with full karyotype if the NT was ≥3.0 mm reduced the risk of miscarriage yet still identified 95% of clinically significant aneuploidy.
Collapse
Affiliation(s)
- Asma Khalil
- Fetal Medicine Unit, Academic Department of Obstetrics and Gynaecology, St George's University of London, London, UK
| | | | | | | | | | | | | |
Collapse
|
127
|
Hudecova I. Digital PCR analysis of circulating nucleic acids. Clin Biochem 2015; 48:948-56. [PMID: 25828047 DOI: 10.1016/j.clinbiochem.2015.03.015] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 03/19/2015] [Indexed: 12/18/2022]
Abstract
Detection of plasma circulating nucleic acids (CNAs) requires the use of extremely sensitive and precise methods. The commonly used quantitative real-time polymerase chain reaction (PCR) poses certain technical limitations in relation to the precise measurement of CNAs whereas the costs of massively parallel sequencing are still relatively high. Digital PCR (dPCR) now represents an affordable and powerful single molecule counting strategy to detect minute amounts of genetic material with performance surpassing many quantitative methods. Microfluidic (chip) and emulsion (droplet)-based technologies have already been integrated into platforms offering hundreds to millions of nanoliter- or even picoliter-scale reaction partitions. The compelling observations reported in the field of cancer research, prenatal testing, transplantation medicine and virology support translation of this technology into routine use. Extremely sensitive plasma detection of rare mutations originating from tumor or placental cells among a large background of homologous sequences facilitates unraveling of the early stages of cancer or the detection of fetal mutations. Digital measurement of quantitative changes in plasma CNAs associated with cancer or graft rejection provides valuable information on the monitoring of disease burden or the recipient's immune response and subsequent therapy treatment. Furthermore, careful quantitative assessment of the viral load offers great value for effective monitoring of antiviral therapy for immunosuppressed or transplant patients. The present review describes the inherent features of dPCR that make it exceptionally robust in precise and sensitive quantification of CNAs. Moreover, I provide an insight into the types of potential clinical applications that have been developed by researchers to date.
Collapse
Affiliation(s)
- Irena Hudecova
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.
| |
Collapse
|
128
|
Digital PCR validates 8q dosage as prognostic tool in uveal melanoma. PLoS One 2015; 10:e0116371. [PMID: 25764247 PMCID: PMC4357379 DOI: 10.1371/journal.pone.0116371] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/08/2014] [Indexed: 12/02/2022] Open
Abstract
Background Uveal melanoma (UM) development and progression is correlated with specific molecular changes. Recurrent mutations in GNAQ and GNA11 initiate UM development while tumour progression is correlated with monosomy of chromosome 3 and gain of chromosome 8q. Hence, molecular analysis of UM is useful for diagnosis and prognosis. The aim of this study is to evaluate the use of digital PCR (dPCR) for molecular analysis of UM. Methods A series of 66 UM was analysed with dPCR for three hotspot mutations in GNAQ/GNA11 with mutation specific probes. The status of chromosomes 3 and 8 were analysed with genomic probes. The results of dPCR analysis were cross-validated with Sanger sequencing, SNP array analysis, and karyotyping. Results Using dPCR, we were able to reconstitute the molecular profile of 66 enucleated UM. With digital PCR, GNAQ/GNA11 mutations were detected in 60 of the 66 UM. Sanger sequencing revealed three rare variants, and, combined, these assays revealed GNAQ/GNA11 mutations in 95% of UM. Monosomy 3 was present in 43 and chromosome 8 aberrations in 52 of the 66 UM. Survival analysis showed that increasing 8q copy numbers were positively correlated with metastasis risk. Conclusion Molecular analysis with dPCR is fast and sensitive. Just like the recurrent genomic aberrations of chromosome 3 and 8, hotspot mutations in GNAQ and GNA11 are effectively detected in heterogeneous samples. Increased sensitivity contributes to the number of mutations and chromosomal aberrations detected. Moreover, quantification of copy number with dPCR validated 8q dosage as a sensitive prognostic tool in UM, of which implementation in disease prediction models will further improve prognostication.
Collapse
|
129
|
Gil MM, Akolekar R, Quezada MS, Bregant B, Nicolaides KH. Analysis of cell-free DNA in maternal blood in screening for aneuploidies: meta-analysis. Fetal Diagn Ther 2015; 35:156-73. [PMID: 24513694 DOI: 10.1159/000358326] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 12/26/2013] [Indexed: 11/19/2022]
Abstract
OBJECTIVE To review clinical validation or implementation studies of maternal blood cell-free (cf) DNA analysis in screening for aneuploidies and to explore the potential use of this method in clinical practice. METHODS Searches of PubMed and MEDLINE were performed to identify all peer-reviewed articles on cfDNA testing in screening for aneuploidies between 2011, when the first such study was published, and 20 December 2013. RESULTS Weighted pooled detection rates (DR) and false-positive rates (FPR) in singleton pregnancies were 99.0% (95% CI 98.2–99.6) and 0.08% (95% CI0.03–0.14), respectively, for trisomy 21; 96.8% (95% CI 94.5–98.4) and 0.15% (95% CI 0.08–0.25) for trisomy 18; 92.1% (95% CI 85.9–96.7) and 0.20% (95% CI 0.04–0.46) for trisomy 13; 88.6% (95% CI 83.0–93.1) and 0.12% (95% CI 0.05–0.24) for monosomy X, and 93.8% (95% CI 85.9–98.7) and 0.12% (95% CI 0.02–0.28) for sex chromosome aneuploidies other than monosomy X. For twin pregnancies, the DR was 94.4% (95% 74.2–99.0) and the FPR was 0% (95% CI 0.00–1.84) for trisomy 21. CONCLUSION An analysis of cfDNA in maternal blood provides effective screening for trisomies.
Collapse
|
130
|
Wong AI, Lo YD. Noninvasive fetal genomic, methylomic, and transcriptomic analyses using maternal plasma and clinical implications. Trends Mol Med 2015; 21:98-108. [DOI: 10.1016/j.molmed.2014.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/12/2014] [Accepted: 12/18/2014] [Indexed: 01/01/2023]
|
131
|
Tian Q, Yu B, Mu Y, Xu Y, Ma C, Zhang T, Jin W, Jin Q. An integrated temporary negative pressure assisted microfluidic chip for DNA isolation and digital PCR detection. RSC Adv 2015. [DOI: 10.1039/c5ra18166f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An integrated DNA purification and digital PCR (dPCR) detection microfluidic chip was developed in this study.
Collapse
Affiliation(s)
- Qingchang Tian
- Research Center for Analytical Instrumentation
- Institute of Cyber Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou 310058
| | - Baodong Yu
- China-Japan Union Hospital of Jilin University
- Changchun
- P. R. China
| | - Ying Mu
- Research Center for Analytical Instrumentation
- Institute of Cyber Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou 310058
| | - Yanan Xu
- Research Center for Analytical Instrumentation
- Institute of Cyber Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou 310058
| | - Congcong Ma
- Research Center for Analytical Instrumentation
- Institute of Cyber Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou 310058
| | - Tao Zhang
- Research Center for Analytical Instrumentation
- Institute of Cyber Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou 310058
| | - Wei Jin
- Research Center for Analytical Instrumentation
- Institute of Cyber Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou 310058
| | - Qinhan Jin
- Research Center for Analytical Instrumentation
- Institute of Cyber Systems and Control
- State Key Laboratory of Industrial Control Technology
- Zhejiang University
- Hangzhou 310058
| |
Collapse
|
132
|
Ferrari M, Carrera P, Lampasona V, Galbiati S. New trend in non-invasive prenatal diagnosis. Clin Chim Acta 2014; 451:9-13. [PMID: 25542529 DOI: 10.1016/j.cca.2014.12.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 12/19/2014] [Indexed: 12/11/2022]
Abstract
The presence of fetal DNA in maternal plasma represents a source of genetic material which can be obtained non-invasively. To date, the translation of noninvasive prenatal diagnosis from research into clinical practice has been rather fragmented, and despite the advances in improving the analytical sensitivity of methods, distinguishing between fetal and maternal sequences remains very challenging. Thus, the field of noninvasive prenatal diagnosis of genetic diseases has yet to attain a routine application in clinical diagnostics. On the contrary, fetal sex determination in pregnancies at high risk of sex-linked disorders, tests for fetal RHD genotyping and non-invasive assessment of chromosomal aneuploidies are now available worldwide.
Collapse
Affiliation(s)
- M Ferrari
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Milan, Italy; Università Vita-Salute San Raffaele, Milan, Italy
| | - P Carrera
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - V Lampasona
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - S Galbiati
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy.
| |
Collapse
|
133
|
Günel T, Hosseini MK, Gümüşoğlu E, Zeybek G, Dölekçap İ, Kalelioğlu İ, Benian A, Ermiş H, Aydınlı K. Current approaches on non-invasive prenatal diagnosis: Prenatal genomics, transcriptomics, personalized fetal diagnosis. Turk J Obstet Gynecol 2014; 11:233-241. [PMID: 28913027 PMCID: PMC5558368 DOI: 10.4274/tjod.26817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 07/26/2014] [Indexed: 12/27/2022] Open
Abstract
Recent developments in molecular genetics improved our knowledge on fetal genome and physiology. Novel scientific innovations in prenatal diagnosis have accelerated in the last decade changing our vision immensely. Data obtained from fetal genomic studies brought new insights to fetal medicine and by the advances in fetal DNA and RNA sequencing technology novel treatment strategies has evolved. Non-invasive prenatal diagnosis found ground in genetics and the results are widely studied in scientific arena. When Lo and colleges proved fetal genetic material can be extracted from maternal plasma and fetal DNA can be isolated from maternal serum, the gate to many exciting discoveries was open. Microarray technology and advances in sequencing helped fetal diagnosis as well as other areas of medicine. Today it is a very crucial prerequisite for physicians practicing prenatal diagnosis to have a profound knowledge in genetics. Prevailing practical use and application of fetal genomic tests in maternal and fetal medicine mandates obstetricians to update their knowledge in genetics. The purpose of this review is to assist physicians to understand and update their knowledge in fetal genetic testing from maternal blood, individualized prenatal counseling and advancements on the subject by sharing our experiences as İstanbul University Fetal Nucleic Acid Research Group.
Collapse
Affiliation(s)
- Tuba Günel
- İstanbul University, Faculty of Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Mohammad Kazem Hosseini
- İstanbul University, Faculty of Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Ece Gümüşoğlu
- İstanbul University, Faculty of Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Görkem Zeybek
- Çanakkale Provincial State Hospital, Clinic of General Obstetrics and Gynecology, Çanakkale, Turkey
| | - İsmail Dölekçap
- İstanbul University, Faculty of Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - İbrahim Kalelioğlu
- İstanbul University İstanbul Faculty of Medicine, Department of Gynecology, İstanbul, Turkey
| | - Ali Benian
- İstanbul University Cerrahpaşa Faculty of Medicine, Department of Gynecology, İstanbul, Turkey
| | - Hayri Ermiş
- İstanbul University İstanbul Faculty of Medicine, Department of Gynecology, İstanbul, Turkey
| | | |
Collapse
|
134
|
Kelley SO, Mirkin CA, Walt DR, Ismagilov RF, Toner M, Sargent EH. Advancing the speed, sensitivity and accuracy of biomolecular detection using multi-length-scale engineering. NATURE NANOTECHNOLOGY 2014; 9:969-80. [PMID: 25466541 PMCID: PMC4472305 DOI: 10.1038/nnano.2014.261] [Citation(s) in RCA: 273] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 10/13/2014] [Indexed: 05/05/2023]
Abstract
Rapid progress in identifying disease biomarkers has increased the importance of creating high-performance detection technologies. Over the last decade, the design of many detection platforms has focused on either the nano or micro length scale. Here, we review recent strategies that combine nano- and microscale materials and devices to produce large improvements in detection sensitivity, speed and accuracy, allowing previously undetectable biomarkers to be identified in clinical samples. Microsensors that incorporate nanoscale features can now rapidly detect disease-related nucleic acids expressed in patient samples. New microdevices that separate large clinical samples into nanocompartments allow precise quantitation of analytes, and microfluidic systems that utilize nanoscale binding events can detect rare cancer cells in the bloodstream more accurately than before. These advances will lead to faster and more reliable clinical diagnostic devices.
Collapse
Affiliation(s)
- Shana O. Kelley
- Department of Pharmaceutical Sciences and Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Correspondence should be addressed to S.O.K.,
| | - Chad A. Mirkin
- Department of Chemistry, International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, USA
| | - David R. Walt
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA
| | - Rustem F. Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Mehmet Toner
- Center for Bioengineering in Medicine, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Edward H. Sargent
- Department of Computer and Electrical Engineering, University of Toronto, Toronto, Ontario M5S 1A4, Canada
| |
Collapse
|
135
|
Wagner AJ, Mitchell ME, Tomita-Mitchell A. Use of cell-free fetal DNA in maternal plasma for noninvasive prenatal screening. Clin Perinatol 2014; 41:957-66. [PMID: 25459783 DOI: 10.1016/j.clp.2014.08.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Noninvasive prenatal testing (NIPT) using cell-free fetal (cfDNA) offers potential as a screening tool for fetal anomalies. All pregnant women should be offered prenatal screening and diagnostic testing based on current guidelines. Adoption of NIPT in high-risk pregnancies suggests a change in the standard of care for genetic screening; there are advantages to an accurate test with results available early in pregnancy. This accuracy decreases the overall number of invasive tests needed for diagnosis, subjecting fewer pregnancies to the risks of invasive procedures. Women undergoing NIPT need informed consent before testing and accurate, sensitive counseling after results are available.
Collapse
Affiliation(s)
- Amy J Wagner
- Division of Pediatric Surgery, Department of Surgery, Medical College of Wisconsin, 999 North 92nd Street, Suite C320, Milwaukee, WI 53226, USA
| | - Michael E Mitchell
- Division of Cardiothoracic Surgery, Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Aoy Tomita-Mitchell
- Division of Cardiothoracic Surgery, Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
| |
Collapse
|
136
|
Huggett JF, Cowen S, Foy CA. Considerations for digital PCR as an accurate molecular diagnostic tool. Clin Chem 2014; 61:79-88. [PMID: 25338683 DOI: 10.1373/clinchem.2014.221366] [Citation(s) in RCA: 302] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Digital PCR (dPCR) is an increasingly popular manifestation of PCR that offers a number of unique advantages when applied to preclinical research, particularly when used to detect rare mutations and in the precise quantification of nucleic acids. As is common with many new research methods, the application of dPCR to potential clinical scenarios is also being increasingly described. CONTENT This review addresses some of the factors that need to be considered in the application of dPCR. Compared to real-time quantitative PCR (qPCR), dPCR clearly has the potential to offer more sensitive and considerably more reproducible clinical methods that could lend themselves to diagnostic, prognostic, and predictive tests. But for this to be realized the technology will need to be further developed to reduce cost and simplify application. Concomitantly the preclinical research will need be reported with a comprehensive understanding of the associated errors. dPCR benefits from a far more predictable variance than qPCR but is as susceptible to upstream errors associated with factors like sampling and extraction. dPCR can also suffer systematic bias, particularly leading to underestimation, and internal positive controls are likely to be as important for dPCR as they are for qPCR, especially when reporting the absence of a sequence. SUMMARY In this review we highlight some of the considerations that may be needed when applying dPCR and discuss sources of error. The factors discussed here aim to assist in the translation of dPCR to diagnostic, predictive, or prognostic applications.
Collapse
Affiliation(s)
- Jim F Huggett
- LGC, Teddington, UK; Research Department of Infection, Division of Infection and Immunity, UCL, London, UK.
| | | | | |
Collapse
|
137
|
Affiliation(s)
- Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences and Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China. Fax +852-2636-5090; e-mail
| |
Collapse
|
138
|
Barrett AN, Thadani HA, Laureano-Asibal C, Ponnusamy S, Choolani M. Stability of cell-free DNA from maternal plasma isolated following a single centrifugation step. Prenat Diagn 2014; 34:1283-8. [DOI: 10.1002/pd.4468] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 06/19/2014] [Accepted: 07/21/2014] [Indexed: 12/27/2022]
Affiliation(s)
- Angela N. Barrett
- Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine; National University of Singapore; Singapore Singapore
| | - Henna A. Thadani
- Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine; National University of Singapore; Singapore Singapore
| | - Cecille Laureano-Asibal
- Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine; National University of Singapore; Singapore Singapore
| | - Sukumar Ponnusamy
- Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine; National University of Singapore; Singapore Singapore
| | - Mahesh Choolani
- Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine; National University of Singapore; Singapore Singapore
| |
Collapse
|
139
|
Gekas J, Langlois S, Ravitsky V, Audibert F, van den Berg DG, Haidar H, Rousseau F. Identification of trisomy 18, trisomy 13, and Down syndrome from maternal plasma. APPLICATION OF CLINICAL GENETICS 2014; 7:127-31. [PMID: 25053891 PMCID: PMC4104725 DOI: 10.2147/tacg.s35602] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Current prenatal diagnosis for fetal aneuploidies (including trisomy 21 [T21]) generally relies on an initial biochemical serum-based noninvasive prenatal testing (NIPT) after which women who are deemed to be at high risk are offered an invasive confirmatory test (amniocentesis or chorionic villi sampling for a fetal karyotype), which is associated with a risk of fetal miscarriage. Recently, genomics-based NIPT (gNIPT) was proposed for the analysis of fetal genomic DNA circulating in maternal blood. The diffusion of this technology in routine prenatal care could be a major breakthrough in prenatal diagnosis, since initial research studies suggest that this novel approach could be very effective and could reduce substantially the number of invasive procedures. However, the limitations of gNIPT may be underappreciated. In this review, we examine currently published literature on gNIPT to highlight advantages and limitations. At this time, the performance of gNIPT is relatively well-documented only in high-risk pregnancies for T21 and trisomy 18. This additional screening test may be an option for women classified as high-risk of aneuploidy who wish to avoid invasive diagnostic tests, but it is crucial that providers carefully counsel patients about the test's advantages and limitations. The gNIPT is currently not recommended as a first-tier prenatal screening test for T21. Since gNIPT is not considered as a diagnostic test, a positive gNIPT result should always be confirmed by an invasive test, such as amniocentesis or chorionic villus sampling. Validation studies are needed to optimally introduce this technology into the existing routine workflow of prenatal care.
Collapse
Affiliation(s)
- Jean Gekas
- Prenatal Diagnosis Unit, Department of Medical Genetics and Pediatrics, Faculty of Medicine, Laval University, Québec City, Quebec, Canada ; Department of Medical Biology, Centre Hospitalier Universitaire de Québec, Québec City, Quebec, Canada
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Vardit Ravitsky
- Bioethics Program, Department of Social and Preventive Medicine, School of Public Health, University of Montreal, Montreal, Canada
| | - François Audibert
- Department of Obstetrics and Gynecology, Sainte Justine Hospital, Montreal, Canada
| | - David-Gradus van den Berg
- Department of Social and Preventive Medicine, Faculty of Medicine, Laval University, Québec City, Quebec, Canada
| | - Hazar Haidar
- Bioethics Program, Department of Social and Preventive Medicine, School of Public Health, University of Montreal, Montreal, Canada
| | - François Rousseau
- Department of Medical Biology, Centre Hospitalier Universitaire de Québec, Québec City, Quebec, Canada ; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec City, Quebec, Canada
| |
Collapse
|
140
|
Xiang Y, Zhang J, Li Q, Zhou X, Wang T, Xu M, Xia S, Xing Q, Wang L, He L, Zhao X. DNA methylome profiling of maternal peripheral blood and placentas reveal potential fetal DNA markers for non-invasive prenatal testing. Mol Hum Reprod 2014; 20:875-84. [PMID: 24996894 DOI: 10.1093/molehr/gau048] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Utilizing epigenetic (DNA methylation) differences to differentiate between maternal peripheral blood (PBL) and fetal (placental) DNA has been a promising strategy for non-invasive prenatal testing (NIPT). However, the differentially methylated regions (DMRs) have yet to be fully ascertained. In the present study, we performed genome-wide comparative methylome analysis between maternal PBL and placental DNA from pregnancies of first trimester by methylated DNA immunoprecipitation-sequencing (MeDIP-Seq) and Infinium HumanMethylation450 BeadChip assays. A total of 36 931 DMRs and 45 804 differentially methylated sites (DMSs) covering the whole genome, exclusive of the Y chromosome, were identified via MeDIP-Seq and Infinium 450k array, respectively, of which 3759 sites in 2188 regions were confirmed by both methods. Not only did we find the previously reported potential fetal DNA markers in our identified DMRs/DMSs but also we verified fully the identified DMRs/DMSs in the validation round by MassARRAY EpiTYPER. The screened potential fetal DNA markers may be used for NIPT on aneuploidies and other chromosomal diseases, such as cri du chat syndrome and velo-cardio-facial syndrome. In addition, these potential markers may have application in the early diagnosis of placental dysfunction, such as pre-eclampsia.
Collapse
Affiliation(s)
- Yuqian Xiang
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
| | - Junyu Zhang
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
| | - Qiaoli Li
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
| | - Xinyao Zhou
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
| | - Teng Wang
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
| | - Mingqing Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Shihui Xia
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
| | - Qinghe Xing
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
| | - Lei Wang
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
| | - Lin He
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Xinzhi Zhao
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
| |
Collapse
|
141
|
Zhou Q, Pan L, Chen S, Chen F, Hwang R, Yang X, Wang W, Jiang J, Xu J, Huang H, Xu C. Clinical application of noninvasive prenatal testing for the detection of trisomies 21, 18, and 13: a hospital experience. Prenat Diagn 2014; 34:1061-5. [PMID: 24899146 DOI: 10.1002/pd.4428] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 05/28/2014] [Accepted: 06/02/2014] [Indexed: 12/28/2022]
Affiliation(s)
- Qiyin Zhou
- Department of Reproductive Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
142
|
New MI, Tong YK, Yuen T, Jiang P, Pina C, Chan KCA, Khattab A, Liao GJW, Yau M, Kim SM, Chiu RWK, Sun L, Zaidi M, Lo YMD. Noninvasive prenatal diagnosis of congenital adrenal hyperplasia using cell-free fetal DNA in maternal plasma. J Clin Endocrinol Metab 2014; 99:E1022-30. [PMID: 24606108 PMCID: PMC4037720 DOI: 10.1210/jc.2014-1118] [Citation(s) in RCA: 236] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Congenital adrenal hyperplasia (CAH) is an autosomal recessive condition that arises from mutations in CYP21A2 gene, which encodes for the steroidogenic enzyme 21-hydroxylase. To prevent genital ambiguity in affected female fetuses, prenatal treatment with dexamethasone must begin on or before gestational week 9. Currently used chorionic villus sampling and amniocentesis provide genetic results at approximately 14 weeks of gestation at the earliest. This means that mothers who want to undergo prenatal dexamethasone treatment will be unnecessarily treating seven of eight fetuses (males and three of four unaffected females), emphasizing the desirability of earlier genetic diagnosis in utero. OBJECTIVE The objective of the study was to develop a noninvasive method for early prenatal diagnosis of fetuses at risk for CAH. PATIENTS Fourteen families, each with a proband affected by phenotypically classical CAH, were recruited. DESIGN Cell-free fetal DNA was obtained from 3.6 mL of maternal plasma. Using hybridization probes designed to capture a 6-Mb region flanking CYP21A2, targeted massively parallel sequencing (MPS) was performed to analyze genomic DNA samples from parents and proband to determine parental haplotypes. Plasma DNA from pregnant mothers also underwent targeted MPS to deduce fetal inheritance of parental haplotypes. RESULTS In all 14 families, the fetal CAH status was correctly deduced by targeted MPS of DNA in maternal plasma, as early as 5 weeks 6 days of gestation. CONCLUSIONS MPS on 3.6 mL plasma from pregnant mothers could potentially provide the diagnosis of CAH, noninvasively, before the ninth week of gestation. Only affected female fetuses will thus be treated. Our strategy represents a generic approach for noninvasive prenatal testing for an array of autosomal recessive disorders.
Collapse
|
143
|
Devonshire AS, Whale AS, Gutteridge A, Jones G, Cowen S, Foy CA, Huggett JF. Towards standardisation of cell-free DNA measurement in plasma: controls for extraction efficiency, fragment size bias and quantification. Anal Bioanal Chem 2014; 406:6499-512. [PMID: 24853859 PMCID: PMC4182654 DOI: 10.1007/s00216-014-7835-3] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/26/2014] [Accepted: 04/14/2014] [Indexed: 01/01/2023]
Abstract
Circulating cell-free DNA (cfDNA) is becoming an important clinical analyte for prenatal testing, cancer diagnosis and cancer monitoring. The extraction stage is critical in ensuring clinical sensitivity of analytical methods measuring minority nucleic acid fractions, such as foetal-derived sequences in predominantly maternal cfDNA. Consequently, quality controls are required for measurement of extraction efficiency, fragment size bias and yield for validation of cfDNA methods. We evaluated the utility of an external DNA spike for monitoring these parameters in a study comparing three specific cfDNA extraction methods [QIAamp® circulating nucleic acid (CNA) kit, NucleoSpin® Plasma XS (NS) kit and FitAmp™ plasma/serum DNA isolation (FA) kit] with the commonly used QIAamp DNA blood mini (DBM) kit. We found that the extraction efficiencies of the kits ranked in the order CNA kit > DBM kit > NS kit > FA kit, and the CNA and NS kits gave a better representation of smaller DNA fragments in the extract than the DBM kit. We investigated means of improved reporting of cfDNA yield by comparing quantitative PCR measurements of seven different reference gene assays in plasma samples and validating these with digital PCR. We noted that the cfDNA quantities based on measurement of some target genes (e.g. TERT) were, on average, more than twofold higher than those of other assays (e.g. ERV3). We conclude that analysis and averaging of multiple reference genes using a GeNorm approach gives a more reliable estimate of total cfDNA quantity. Comparison of single and multiple reference gene normalisation for quantification of plasma cell free DNA ![]()
Collapse
Affiliation(s)
- Alison S Devonshire
- Molecular and Cell Biology Team, LGC Ltd, Queen's Road, Teddington, TW11 0LY, UK,
| | | | | | | | | | | | | |
Collapse
|
144
|
Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing. Proc Natl Acad Sci U S A 2014; 111:8583-8. [PMID: 24843150 DOI: 10.1073/pnas.1406103111] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Noninvasive prenatal testing using fetal DNA in maternal plasma is an actively researched area. The current generation of tests using massively parallel sequencing is based on counting plasma DNA sequences originating from different genomic regions. In this study, we explored a different approach that is based on the use of DNA fragment size as a diagnostic parameter. This approach is dependent on the fact that circulating fetal DNA molecules are generally shorter than the corresponding maternal DNA molecules. First, we performed plasma DNA size analysis using paired-end massively parallel sequencing and microchip-based capillary electrophoresis. We demonstrated that the fetal DNA fraction in maternal plasma could be deduced from the overall size distribution of maternal plasma DNA. The fetal DNA fraction is a critical parameter affecting the accuracy of noninvasive prenatal testing using maternal plasma DNA. Second, we showed that fetal chromosomal aneuploidy could be detected by observing an aberrant proportion of short fragments from an aneuploid chromosome in the paired-end sequencing data. Using this approach, we detected fetal trisomy 21 and trisomy 18 with 100% sensitivity (T21: 36/36; T18: 27/27) and 100% specificity (non-T21: 88/88; non-T18: 97/97). For trisomy 13, the sensitivity and specificity were 95.2% (20/21) and 99% (102/103), respectively. For monosomy X, the sensitivity and specificity were both 100% (10/10 and 8/8). Thus, this study establishes the principle of size-based molecular diagnostics using plasma DNA. This approach has potential applications beyond noninvasive prenatal testing to areas such as oncology and transplantation monitoring.
Collapse
|
145
|
Gregg AR, Van den Veyver IB, Gross SJ, Madankumar R, Rink BD, Norton ME. Noninvasive prenatal screening by next-generation sequencing. Annu Rev Genomics Hum Genet 2014; 15:327-47. [PMID: 24849140 DOI: 10.1146/annurev-genom-090413-025341] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Noninvasive prenatal screening (NIPS) has emerged as a highly accurate method of screening for fetal Down syndrome, with a detection rate and specificity approaching 100%. Challenging the widespread use of this technology are cost and the paradigm shift in counseling that accompanies any emerging technology. The expense of the test is expected to decrease with increased utilization, and well beyond the current NIPS technology, its components (fetal genome measurements, sequencing technology, and bioinformatics) will be utilized alone or in combinations to interrogate the fetal genome. The end goal is simple: to offer patients information early in pregnancy about fetal genomes without incurring procedural risks. This will allow patients an opportunity to make informed reproductive and pregnancy management decisions based on precise fetal genomic information.
Collapse
Affiliation(s)
- Anthony R Gregg
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, University of Florida College of Medicine, Gainesville, Florida 32610;
| | | | | | | | | | | |
Collapse
|
146
|
Nepomnyashchaya YN, Artemov AV, Roumiantsev SA, Roumyantsev AG, Zhavoronkov A. Non-invasive prenatal diagnostics of aneuploidy using next-generation DNA sequencing technologies, and clinical considerations. Clin Chem Lab Med 2014; 51:1141-54. [PMID: 23023923 DOI: 10.1515/cclm-2012-0281] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/29/2012] [Indexed: 02/02/2023]
Abstract
Rapidly developing next-generation sequencing (NGS) technologies produce a large amount of data across the whole human genome and allow a large number of DNA samples to be analyzed simultaneously. Screening cell-free fetal DNA (cffDNA) obtained from maternal blood using NGS technologies has provided new opportunities for non-invasive prenatal diagnosis (NIPD) of fetal aneuploidies. One of the major challenges to the analysis of fetal abnormalities is the development of accurate and reliable algorithms capable of analyzing large numbers of short sequence reads. Several such algorithms have recently been developed. Here, we provide a review of recent NGS-based NIPD methods as well as the available algorithms for short-read sequence analysis. We furthermore introduce the practical application of these algorithms for the detection of different types of fetal aneuploidies, and compare the performance, cost and complexity of each approach for clinical deployment. Our review identifies several main technologies and trends in NGS-based NIPD. The main considerations for clinical development for NIPD and screening tests using DNA sequencing are: accuracy, intellectual property, cost and the ability to screen for a wide range of chromosomal abnormalities and genetic defects. The cost of the diagnostic test depends on the sequencing method, diagnostic algorithm and volume of the tests. If the cost of sequencing equipment and reagents remains at or around current levels, targeted approaches for sequencing-based aneuploidy testing and SNP-based methods are preferred.
Collapse
Affiliation(s)
- Yana N Nepomnyashchaya
- Bioinformatics and Medical Information Technology Laboratory, Federal Clinical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | | | | | | | | |
Collapse
|
147
|
Manoj P. Droplet digital PCR technology promises new applications and research areas. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:742-6. [PMID: 24779593 DOI: 10.3109/19401736.2014.913168] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Digital Polymerase Chain Reaction (dPCR) is used to quantify nucleic acids and its applications are in the detection and precise quantification of low-level pathogens, rare genetic sequences, quantification of copy number variants, rare mutations and in relative gene expressions. Here the PCR is performed in large number of reaction chambers or partitions and the reaction is carried out in each partition individually. This separation allows a more reliable collection and sensitive measurement of nucleic acid. Results are calculated by counting amplified target sequence (positive droplets) and the number of partitions in which there is no amplification (negative droplets). The mean number of target sequences was calculated by Poisson Algorithm. Poisson correction compensates the presence of more than one copy of target gene in any droplets. The method provides information with accuracy and precision which is highly reproducible and less susceptible to inhibitors than qPCR. It has been demonstrated in studying variations in gene sequences, such as copy number variants and point mutations, distinguishing differences between expression of nearly identical alleles, assessment of clinically relevant genetic variations and it is routinely used for clonal amplification of samples for NGS methods. dPCR enables more reliable predictors of tumor status and patient prognosis by absolute quantitation using reference normalizations. Rare mitochondrial DNA deletions associated with a range of diseases and disorders as well as aging can be accurately detected with droplet digital PCR.
Collapse
Affiliation(s)
- P Manoj
- a Rajiv Gandhi Centre for Biotechnology , Thycaud P.O. , Thiruvananthapuram , Kerala , India
| |
Collapse
|
148
|
Bills V, Soothill P. Fetal blood grouping using cell free DNA – An improved service for RhD negative pregnant women. Transfus Apher Sci 2014; 50:148-53. [DOI: 10.1016/j.transci.2014.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
149
|
Milachich T. New advances of preimplantation and prenatal genetic screening and noninvasive testing as a potential predictor of health status of babies. BIOMED RESEARCH INTERNATIONAL 2014; 2014:306505. [PMID: 24783200 PMCID: PMC3982254 DOI: 10.1155/2014/306505] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/13/2014] [Accepted: 02/15/2014] [Indexed: 11/18/2022]
Abstract
The current morphologically based selection of human embryos for transfer cannot detect chromosome aneuploidies. So far, only biopsy techniques have been able to screen for chromosomal aneuploidies in the in vitro fertilization (IVF) embryos. Preimplantation genetic diagnosis (PGD) or screening (PGS) involves the biopsy of oocyte polar bodies or embryonic cells and has become a routine clinical procedure in many IVF clinics worldwide, including recent development of comprehensive chromosome screening of all 23 pairs of chromosomes by microarrays for aneuploidy screening. The routine preimplantation and prenatal genetic diagnosis (PND) require testing in an aggressive manner. These procedures may be invasive to the growing embryo and fetus and potentially could compromise the clinical outcome. Therefore the aim of this review is to summarize not only the new knowledge on preimplantation and prenatal genetic diagnosis in humans, but also on the development of potential noninvasive embryo and fetal testing that might play an important role in the future.
Collapse
Affiliation(s)
- Tanya Milachich
- SAGBAL Dr. Shterev, IVF Unit, Hristo Blagoev 25-31, 1330 Sofia, Bulgaria
| |
Collapse
|
150
|
Zhu Q, Qiu L, Yu B, Xu Y, Gao Y, Pan T, Tian Q, Song Q, Jin W, Jin Q, Mu Y. Digital PCR on an integrated self-priming compartmentalization chip. LAB ON A CHIP 2014; 14:1176-85. [PMID: 24481046 DOI: 10.1039/c3lc51327k] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
An integrated on-chip valve-free and power-free microfluidic digital PCR device is for the first time developed by making use of a novel self-priming compartmentalization and simple dehydration control to realize 'divide and conquer' for single DNA molecule detection. The high gas solubility of PDMS is exploited to provide the built-in power of self-priming so that the sample and oil are sequentially sucked into the device to realize sample self-compartmentalization based on surface tension. The lifespan of its self-priming capability was about two weeks tested using an air-tight packaging bottle sealed with a small amount of petroleum jelly, which is significant for a practical platform. The SPC chip contains 5120 independent 5 nL microchambers, allowing the samples to be compartmentalized completely. Using this platform, three different abundances of lung cancer related genes are detected to demonstrate the feasibility and flexibility of the microchip for amplifying a single nucleic acid molecule. For maximal accuracy, within less than 5% of the measurement deviation, the optimal number of positive chambers is between 400 and 1250 evaluated by the Poisson distribution, which means one panel can detect an average of 480 to 4804 template molecules. This device without world-to-chip connections eliminates the constraint of the complex pipeline control, and is an integrated on-chip platform, which would be a significant improvement to digital PCR automation and more user-friendly.
Collapse
Affiliation(s)
- Qiangyuan Zhu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, PR China.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|