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Harasim T, Neuhann T, Behnecke A, Stampfer M, Holinski-Feder E, Abicht A. Initial Clinical Experience with NIPT for Rare Autosomal Aneuploidies and Large Copy Number Variations. J Clin Med 2022; 11:jcm11020372. [PMID: 35054066 PMCID: PMC8777675 DOI: 10.3390/jcm11020372] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVE Amniocentesis, chorionic villi sampling and first trimester combined testing are able to screen for common trisomies 13, 18, and 21 and other atypical chromosomal anomalies (ACA). The most frequent atypical aberrations reported are rare autosomal aneuploidies (RAA) and copy number variations (CNV), which are deletions or duplications of various sizes. We evaluated the clinical outcome of non-invasive prenatal testing (NIPT) results positive for RAA and large CNVs to determine the clinical significance of these abnormal results. METHODS Genome-wide NIPT was performed on 3664 eligible patient samples at a single genetics center. For patients with positive NIPT reports, the prescribing physician was asked retrospectively to provide clinical follow-up information using a standardized questionnaire. RESULTS RAAs and CNVs (>7 Mb) were detected in 0.5%, and 0.2% of tested cases, respectively. Follow up on pregnancies with an NIPT-positive result for RAA revealed signs of placental insufficiency or intra-uterine death in 50% of the cases and normal outcome at the time of birth in the other 50% of cases. We showed that CNV testing by NIPT allows for the detection of unbalanced translocations and relevant maternal health conditions. CONCLUSION NIPT for aneuploidies of all autosomes and large CNVs of at least 7 Mb has a low "non-reportable"-rate (<0.2%) and allows the detection of additional conditions of clinical significance.
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Pertile MD, Flowers N, Vavrek D, Andrews D, Kalista T, Craig A, Deciu C, Duenwald S, Meier K, Bhatt S. Performance of a Paired-End Sequencing-Based Noninvasive Prenatal Screening Test in the Detection of Genome-Wide Fetal Chromosomal Anomalies. Clin Chem 2021; 67:1210-1219. [PMID: 34077512 DOI: 10.1093/clinchem/hvab067] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/13/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND Noninvasive prenatal tests (NIPTs) detect fetal chromosomal anomalies with high clinical sensitivity and specificity. We examined the performance of a paired-end sequencing-based NIPT in the detection of genome-wide fetal chromosomal anomalies including common trisomies, sex chromosomal aneuploidies (SCA), rare autosomal aneuploidies (RAAs), and partial deletions/duplications ≥7 Mb. METHODS Frozen plasma samples from pregnant women were tested using the VeriSeq NIPT Solution v2 assay. All samples were previously tested with a laboratory-developed NIPT and had known clinical outcomes. Individuals performing the sequencing were blinded to clinical outcome data. Clinical sensitivity and specificity were determined for basic (chromosomes 21, 18, 13, X, and Y) and genome-wide screening modes. RESULTS Of 2335 samples that underwent genome-wide analysis, 28 did not meet QC requirements, resulting in a first-pass assay failure rate of 1.2%. Basic screening analysis, excluding known mosaics, correctly classified 130/130 trisomy 21 samples (sensitivity >99.9%, 95% confidence interval [CI] 97.1%-100%), 41/41 trisomy 18 samples (sensitivity >99.9%, 95% CI 91.4%-100%), and 26/26 trisomy 13 samples (sensitivity >99.9%, 95% CI 87.1%-100%) with 6 false-positive results; specificities ≥99.90% were reported for all 3 trisomies. Concordance for SCAs ranged from 90.5%-100%. Genome-wide screening analysis including known mosaics correctly classified 27/28 RAAs and 20/27 partial deletions/duplications with a specificity of 99.80% for both anomalies, and an overall genome-wide specificity for all anomalies of 99.34%. CONCLUSIONS The VeriSeq NIPT Solution v2 assay enables accurate identification of fetal aneuploidy, allowing detection of genome-wide fetal chromosomal anomalies with high clinical sensitivities and specificities and a low assay failure rate.Clinical Trial Notification [CTN] identification number [ID]: CT-2018-CTN-01585-1 v1, Protocol: NIPT T05 002.
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Affiliation(s)
- Mark D Pertile
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Nicola Flowers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Darcy Vavrek
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Daniel Andrews
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Tasha Kalista
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Andrew Craig
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Cosmin Deciu
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Sven Duenwald
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Kristen Meier
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Sucheta Bhatt
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
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Xie MJ, Liang ZK, He D, Xu WW, Wu YS, Yang XX, Li M. Noninvasive Prenatal Testing of Rare Autosomal Aneuploidies by Semiconductor Sequencing. DNA Cell Biol 2018; 37:174-181. [PMID: 29381401 DOI: 10.1089/dna.2017.4075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rare autosomal aneuploidies (RAAs) can cause miscarriage or other pregnancy complications and lead to inconsistent results of noninvasive prenatal testing (NIPT), but many NIPT providers have not yet started to provide related services. Our aim was to develop a semiconductor sequencing platform (SSP)-based method for detecting RAAs when pregnant women performed NIPT. Fifty-three aneuploidy samples with verified karyotyping or array comparative genomic hybridization (aCGH) results were collected and subjected to RAAs detection using an SSP to develop a method by genomic sequencing. Various trisomies on all chromosomes other than chromosomes 17 and 19, four multiple aneusomies, one monosomy and five sex chromosome abnormalities were got by our method which can directly identify RAAs via a z-score. Then, artificial mixtures of 10% and 5% DNA were created by adding fragmented fifty-three tissue samples and used in an NIPT simulation to develop a bioinformatics analysis method which can use in NIPT. And the results were in accordance with those of karyotyping and aCGH. Therefore, our method has potential for use in NIPT. Finally, 23,823 clinical plasma samples were tested to verify the performance of our approach. Karyotyping or aCGH was performed on the positive clinical samples. In total, 188 of 23,823 clinical samples were positive (T2, n = 1; T7, n = 1; T13, n = 15; T18, n = 45; T21, n = 125; and multiple aneusomies, n = 1) and verified by karyotyping or aCGH; no sample was a false negative. Several false positives were detected, one of which showed maternal copy number variation (CNV). One case of multiple aneusomies was caused by a maternal tumor. The method developed enables detection of RAAs without increasing costs.
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Affiliation(s)
- Mei-Juan Xie
- 1 Institute of Antibody Engineering, School of Laboratory Medical and Biotechnology, Southern Medical University , Guangzhou, China
| | - Zhi-Kun Liang
- 2 Clinical Laboratory Center, Guangzhou Darui Biotechnology, Co., Ltd. , Guangzhou, China
| | - Dan He
- 2 Clinical Laboratory Center, Guangzhou Darui Biotechnology, Co., Ltd. , Guangzhou, China
| | - Wei-Wen Xu
- 1 Institute of Antibody Engineering, School of Laboratory Medical and Biotechnology, Southern Medical University , Guangzhou, China
| | - Ying-Song Wu
- 1 Institute of Antibody Engineering, School of Laboratory Medical and Biotechnology, Southern Medical University , Guangzhou, China
| | - Xue-Xi Yang
- 1 Institute of Antibody Engineering, School of Laboratory Medical and Biotechnology, Southern Medical University , Guangzhou, China
| | - Ming Li
- 1 Institute of Antibody Engineering, School of Laboratory Medical and Biotechnology, Southern Medical University , Guangzhou, China
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