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Abou Tayoun AN, Spinner NB, Rehm HL, Green RC, Bianchi DW. Prenatal DNA Sequencing: Clinical, Counseling, and Diagnostic Laboratory Considerations. Prenat Diagn 2017; 38:26-32. [PMID: 28345240 PMCID: PMC10066604 DOI: 10.1002/pd.5038] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 03/06/2017] [Accepted: 03/12/2017] [Indexed: 12/18/2022]
Abstract
Clinical diagnostic laboratories are producing next-generation sequencing-based test results that are becoming increasingly incorporated into patient care. Whole genome and exome sequencing on fetal material derived from amniocytes, chorionic villi, or products of conception is starting to be offered clinically in specialized centers, but it has not yet become routine practice. The technical, interpretation, and ethical challenges are greatest in the area of prenatal medicine because the fetus has a limited health history, and the physical examination is only indirectly available via prenatal sonography. Here, we provide an overview of these challenges and highlight the clinical utility, reporting, and counseling issues associated with prenatal DNA sequencing. Future considerations are also discussed. © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Ahmad N. Abou Tayoun
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine; The Children's Hospital of Philadelphia, and the Perelman School of Medicine at The University of Pennsylvania Perelman School of Medicine; Philadelphia PA USA
| | - Nancy B. Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine; The Children's Hospital of Philadelphia, and the Perelman School of Medicine at The University of Pennsylvania Perelman School of Medicine; Philadelphia PA USA
| | - Heidi L. Rehm
- Laboratory for Molecular Medicine; Partners Healthcare Personalized Medicine; Cambridge MA USA
- Department of Pathology; Brigham and Women's Hospital, Harvard Medical School; Boston MA USA
- The Broad Institute of MIT and Harvard; Cambridge MA USA
| | - Robert C. Green
- The Broad Institute of MIT and Harvard; Cambridge MA USA
- Division of Genetics, Department of Medicine; Brigham and Women's Hospital, Harvard Medical School; Boston MA USA
| | - Diana W. Bianchi
- Mother Infant Research Institute; Tufts Medical Center; Boston MA USA
- National Human Genome Research Institute; National Institutes of Health; Bethesda MD USA
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Han J, Pan M, Zhen L, Yang X, Ou YM, Liao C, Li DZ. Chorionic villus sampling for early prenatal diagnosis: Experience at a mainland Chinese hospital. J OBSTET GYNAECOL 2014; 34:669-72. [PMID: 24912022 DOI: 10.3109/01443615.2014.920793] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The aim of this study was to describe the experience of transabdominal chorionic villus sampling (CVS) at a mainland Chinese hospital. During a 7-year period, 1,172 pregnant women chose to have CVS for prenatal diagnosis. Details and outcome of all of these cases were reviewed. The median maternal age was 29 years (range 19-45). The median gestational age was 12 weeks (range 10-14). Fetal karyotyping and thalassaemia couples were the main indications (97.2%). Overall, 112 (9.7%) chromosomal abnormalities were identified. There were 91 (7.8%) major chromosomal abnormalities, including autosomal trisomy in 70 patients, sex chromosomal abnormalities in 17, triploidy in two and unbalanced chromosomal rearrangement abnormality in two. Additionally, 137 fetuses with severe thalassaemia syndrome were found, including 86 homozygous β-thalassaemia, and 51 homozygous α-thalassaemia or non-deletional haemoglobin H disease. The procedure failed to obtain an adequate sample in four (0.3%) patients. There were 229 pregnancies terminated for medical indications after CVS. There were three (0.3%) potentially procedure-related fetal losses. CVS is a safe and reliable prenatal diagnostic technique. It should be one of the options available to pregnant women who require prenatal diagnosis.
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Affiliation(s)
- J Han
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University , Guangzhou, Guangdong , China
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3
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Defining the impact of maternal cell contamination on the interpretation of prenatal microarray analysis. Genet Med 2012; 14:914-21. [DOI: 10.1038/gim.2012.77] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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Nagan N, Faulkner NE, Curtis C, Schrijver I. Laboratory guidelines for detection, interpretation, and reporting of maternal cell contamination in prenatal analyses a report of the association for molecular pathology. J Mol Diagn 2010; 13:7-11. [PMID: 21227389 DOI: 10.1016/j.jmoldx.2010.11.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 08/17/2010] [Accepted: 08/23/2010] [Indexed: 11/19/2022] Open
Abstract
This document summarizes laboratory guidelines for the detection, interpretation, and reporting of maternal cell contamination in prenatal analyses.
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Affiliation(s)
- Narasimhan Nagan
- MCC Guidelines Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee, Genzyme Corporation, Westborough, Massachusetts, USA
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Liao C, Yang X, Li FT, Li J, Li DZ. The detection of aneuploidy and maternal contamination by QF-PCR in samples undergoing prenatal diagnosis for thalassemia in Southern China. Eur J Obstet Gynecol Reprod Biol 2009; 144:149-52. [DOI: 10.1016/j.ejogrb.2009.02.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Revised: 01/08/2009] [Accepted: 02/22/2009] [Indexed: 11/29/2022]
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Lemnrau AG, Cardoso S, Creary LE, Brown C, Miretti M, Girdlestone J, Navarrete CV. Human platelet antigen typing of neonatal alloimmune thrombocytopenia patients using whole genome amplified DNA and a 5'-nuclease assay. Transfusion 2009; 49:953-8. [PMID: 19175554 DOI: 10.1111/j.1537-2995.2008.02064.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND A serious constraint in the investigation of the human platelet antigen (HPA) status of potential neonatal alloimmune thrombocytopenia (NAIT) cases is the limited amount of DNA available from the neonates. Whole genome amplification (WGA) of these DNA samples could overcome this problem, but requires validation to ensure that it is sufficiently sensitive and accurate before its application in a clinical diagnostic setting. STUDY DESIGN AND METHODS This study has validated the use of WGA DNA for HPA-1, -2, -3, -4, -5, and -15 genotyping with a panel of six controls and 13 previously HPA-typed samples from neonates together with parental DNA, using a 5'-nuclease (TaqMan) assay. WGA was performed using titrated amounts of genomic and WGA DNA template. HPA typing was performed on genomic and amplified DNA using a 5'-nuclease assay or polymerase chain reaction with sequence-specific primers (PCR-SSP). RESULTS WGA DNA yields were in the suggested range of 400x to 800x, as assessed by spectrophotometry and gel analysis, and did not require further purification. HPA genotyping showed 100 percent concordance when using down to 5 ng of genomic or WGA template. CONCLUSION This study demonstrates that WGA can be used for HPA typing using PCR-SSP or plate-based 5'-nuclease assays. The use of WGA for HPA typing in clinical samples from NAIT patients was validated with 100 percent concordance, and it is suggested that this technology can be used for other analyses where DNA amounts are limited.
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Affiliation(s)
- Alina G Lemnrau
- Histocompatibility & Immunogenetics Department, NHSBT, London, UK
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Schrijver I, Cherny SC, Zehnder JL. Testing for maternal cell contamination in prenatal samples: a comprehensive survey of current diagnostic practices in 35 molecular diagnostic laboratories. J Mol Diagn 2007; 9:394-400. [PMID: 17591939 PMCID: PMC1899411 DOI: 10.2353/jmoldx.2007.070017] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The potential presence of maternal cell contamination (MCC) in chorionic villus or amniotic fluid samples poses a serious preanalytical risk for prenatal misdiagnosis. The aim of this study was to identify current diagnostic practices in the absence of comprehensive practice guidelines. Thirty-five clinical molecular laboratories that conduct prenatal testing agreed to participate in a clinical practice survey. The survey included questions about sample requirements, test indications, assay type, test performance and limitations, criteria and management of uninformative test results, reporting, and billing. Sixty percent of participating laboratories performed testing on direct and cultured amniotic fluid, whereas forty percent tested cultured cells only. Most also accepted chorionic villus samples. Although MCC testing of fetal samples is recommended in guidelines by the American College of Medical Genetics, only 60% of surveyed laboratories performed it without exception. Commercially available assays were used by 75% of participating laboratories, and at least five identity markers were evaluated at 87% of the laboratories. The reported lower limit of MCC detection ranged from 1 to 20% but was not determined in all laboratories. MCC testing was performed in the majority of molecular diagnostic laboratories, but guidelines for standardization are needed to ensure optimal and accurate prenatal patient care.
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Affiliation(s)
- Iris Schrijver
- Department of Pathology and Pediatrics, Stanford University Medical Center, Stanford, CA 94305, USA.
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Larrabee PB, Johnson KL, Pestova E, Lucas M, Wilber K, LeShane ES, Tantravahi U, Cowan JM, Bianchi DW. Microarray analysis of cell-free fetal DNA in amniotic fluid: a prenatal molecular karyotype. Am J Hum Genet 2004; 75:485-91. [PMID: 15252756 PMCID: PMC1182026 DOI: 10.1086/423288] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2004] [Accepted: 06/09/2004] [Indexed: 01/05/2023] Open
Abstract
Metaphase karyotype analysis of fetal cells obtained by amniocentesis or chorionic villus sampling is the current standard for prenatal cytogenetic diagnosis, particularly for the detection of trisomy 21. We previously demonstrated that large quantities of cell-free fetal DNA (cffDNA) are easily extracted from amniotic fluid (AF). In this study, we explored potential clinical applications of AF cffDNA by testing its ability to hybridize to DNA microarrays for comparative genomic hybridization (CGH) analysis. cffDNA isolated from 11 male fetuses showed significantly increased hybridization signals on SRY and decreased signals on X-chromosome markers, compared with female reference DNA. cffDNA isolated from six female fetuses showed the reverse when compared with male reference DNA. cffDNA from three fetuses with trisomy 21 had increased hybridization signals on the majority of the chromosome 21 markers, and cffDNA from a fetus with monosomy X (Turner syndrome) had decreased hybridization signals on most X-chromosome markers, compared with euploid female reference DNA. These results indicate that cffDNA extracted from AF can be analyzed using CGH microarrays to correctly identify fetal sex and aneuploidy. This technology facilitates rapid screening of samples for whole-chromosome changes and may augment standard karyotyping techniques by providing additional molecular information.
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Affiliation(s)
- Paige B Larrabee
- Division of Newborn Medicine, Department of Pediatrics, Tufts-New England Medical Center, Tufts University School of Medicine, Boston, MA 02111, USA
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Pattison S, Pankarican M, Rupar CA, Graham FL, Igdoura SA. Five novel mutations in the lysosomal sialidase gene (NEU1) in type II sialidosis patients and assessment of their impact on enzyme activity and intracellular targeting using adenovirus-mediated expression. Hum Mutat 2004; 23:32-9. [PMID: 14695530 DOI: 10.1002/humu.10278] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Sialidosis is an autosomal recessive disease resulting from a deficiency of lysosomal sialidase. Type II sialidosis is a rare disease characterized clinically by hydrops fetalis, hepatosplenomegaly, and severe psychomotor retardation. Genomic DNA from four unrelated sialidosis patients was screened for mutations within the sialidase gene NEU1. Five novel mutations were identified. Four are missense and one is nonsense: c.674G>C (p.R225P), c.893C>T (p.A298V), c.3G>A (p.M1?), c.941C>G (p.R341G), and c.69G>A (p.W23X). We have used our findings and diagnostic tools to confirm the presence of a homozygous null allele in a neonate sibling. Recombinant adenoviruses expressing the mutant sialidase alleles in primary cell cultures were utilized to assess the impact of each mutation on enzyme activity and intracellular localization. None of the mutant alleles expressed significant enzymatic activity. The p.R341G mutation exerts its pathological effect by perturbing substrate binding, while the p.A298V and p.R225P mutations appear to impair the folding of the sialidase enzyme. Our findings point to mutation-sensitive amino acids involved in catalytic function or structural stability and indicate the potential utility of these mutations for molecular diagnosis of this rare disease.
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Affiliation(s)
- Susan Pattison
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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Antoniadi T, Yapijakis C, Kaminopetros P, Makatsoris C, Velissariou V, Vassilopoulos D, Petersen MB. A simple and effective approach for detecting maternal cell contamination in molecular prenatal diagnosis. Prenat Diagn 2002; 22:425-9. [PMID: 12001201 DOI: 10.1002/pd.325] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The presence of maternal cells in fetal samples constitutes a serious potential source for prenatal misdiagnosis. Here we present our approach for detecting maternal cell contamination (MCC) at prenatal diagnosis for eight monogenic disorders (autosomal recessive: beta-thalassaemia, sickle-cell anaemia, cystic fibrosis, prelingual deafness; autosomal dominant: achondroplasia, Huntington disease, myotonic dystrophy, neurofibromatosis type I; X-linked: spinobulbar muscular atrophy). Our aim was to apply a simple and low-cost approach, which would easily and accurately provide information on the fetal tissue MCC status. MCC testing was applied to cases of recessive inheritance where the primary mutation screening of the fetus revealed the presence of the maternal mutation, to cases concerning dominant inheritance and to cases of multiple gestation. The potential presence of maternal cells was determined by the amplification of the 3'-HVR/APO B, D1S80, THO1 and VNTRI of vWf polymorphic loci, which have previously demonstrated high heterozygosity in Caucasians. Among 135 prenatal diagnoses, 44 finally needed to be tested for MCC (32.6%). MCC was detected in four cases, where DNA was isolated directly from chorionic villi samples (CVS), and in one case with DNA isolated directly from amniotic fluid (AF). In almost 90% of cases a simple test of one polymorphic locus provided sufficient information about MCC. The choice of the appropriate locus is therefore essential, while the simultaneous screening of both parents provides the means for distinguishing non-informative sites about MCC.
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Affiliation(s)
- T Antoniadi
- Laboratory of Molecular Biology, Department of Genetics and Molecular Biology, Mitera Maternity and Surgical Center, Athens, Greece.
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Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) gene studies are now one of the most frequent activities in clinical molecular genetics laboratories. The number of requests is growing, owing to the increasingly wide range of recognized CFTR gene diseases (cystic fibrosis, congenital bilateral absence of the vas deferens, disseminated bronchiectasis, allergic bronchopulmonary aspergillosis and chronic pancreatitis), and the availability of efficient molecular tools for detecting mutations. A growing number of tests capable of simultaneously detecting several frequent CF mutations are being developed, and commercial kits are now available. The most recent kits detect nearly 90% of defective alleles in Caucasians, a rate high enough for carrier screening and for the majority of diagnostic requests. However, because of the wide variety of molecular defects documented in the CFTR gene, only a limited number of laboratories have mastered the entire panoply of necessary techniques, while other laboratories have to refer certain cases to specialized centers with complementary and/or scanning tools at their disposal. A good knowledge of CFTR diseases and their molecular mechanisms, together with expertise in the various techniques, is crucial for interpreting the results. Diagnostic strategies must take into account the indication, the patient's ethnic origin, and the time available in the framework of genetic counseling. This review presents the methods most frequently used for detecting CFTR gene mutations, and discusses the strategies most suited to the different clinical settings.
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Affiliation(s)
- E Girodon-Boulandet
- Service de Biochimie et de Génétique, INSERM U468, Hôpital Henri-Mondor, Créteil, France
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