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Wu S, Ma C, Cai J, Yang C, Liu X, Luo C, Yang J, Xiong Z, Cao D, Chen H. A clinically feasible algorithm for the parallel detection of glioma-associated copy number variation markers based on shallow whole genome sequencing. J Pathol Clin Res 2024; 10:e70005. [PMID: 39375998 PMCID: PMC11458885 DOI: 10.1002/2056-4538.70005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 09/06/2024] [Accepted: 09/16/2024] [Indexed: 10/09/2024]
Abstract
Molecular features are incorporated into the integrated diagnostic system for adult diffuse gliomas. Of these, copy number variation (CNV) markers, including both arm-level (1p/19q codeletion, +7/-10 signature) and gene-level (EGFR gene amplification, CDKN2A/B homozygous deletion) changes, have revolutionized the diagnostic paradigm by updating the subtyping and grading schemes. Shallow whole genome sequencing (sWGS) has been widely used for CNV detection due to its cost-effectiveness and versatility. However, the parallel detection of glioma-associated CNV markers using sWGS has not been optimized in a clinical setting. Herein, we established a model-based approach to classify the CNV status of glioma-associated diagnostic markers with a single test. To enhance its clinical utility, we carried out hypothesis testing model-based analysis through the estimation of copy ratio fluctuation level, which was implemented individually and independently and, thus, avoided the necessity for normal controls. Besides, the customization of required minimal tumor fraction (TF) was evaluated and recommended for each glioma-associated marker to ensure robust classification. As a result, with 1× sequencing depth and 0.05 TF, arm-level CNVs could be reliably detected with at least 99.5% sensitivity and specificity. For EGFR gene amplification and CDKN2A/B homozygous deletion, the corresponding TF limits were 0.15 and 0.45 to ensure the evaluation metrics were both higher than 97%. Furthermore, we applied the algorithm to an independent glioma cohort and observed the expected sample distribution and prognostic stratification patterns. In conclusion, we provide a clinically applicable algorithm to classify the CNV status of glioma-associated markers in parallel.
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Affiliation(s)
- Shuai Wu
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghaiPR China
- National Center for Neurological DisordersShanghaiPR China
- Neurosurgical Institute of Fudan UniversityShanghaiPR China
| | - Chenyu Ma
- Genetron Health (Beijing) Co. LtdBeijingPR China
| | - Jiawei Cai
- Department of Neurosurgery, Neurosurgery Research Institute, The First Affiliated HospitalFujian Medical UniversityFuzhouPR China
| | | | - Xiaojia Liu
- Department of Pathology, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghaiPR China
| | - Chen Luo
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghaiPR China
- National Center for Neurological DisordersShanghaiPR China
- Neurosurgical Institute of Fudan UniversityShanghaiPR China
| | - Jingyi Yang
- Genetron Health (Beijing) Co. LtdBeijingPR China
| | - Zhang Xiong
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghaiPR China
- National Center for Neurological DisordersShanghaiPR China
- Neurosurgical Institute of Fudan UniversityShanghaiPR China
| | - Dandan Cao
- Genetron Health (Beijing) Co. LtdBeijingPR China
| | - Hong Chen
- Department of Pathology, Huashan Hospital, Shanghai Medical CollegeFudan UniversityShanghaiPR China
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Sobol M, Aravidis C, Hessel H, Lindqvist A, Baranowska Körberg I. Massive parallel sequencing-based non-invasive prenatal test (NIPT) identifies aberrations on chromosome 13. Eur J Obstet Gynecol Reprod Biol 2024; 302:370-374. [PMID: 39393256 DOI: 10.1016/j.ejogrb.2024.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 10/02/2024] [Accepted: 10/05/2024] [Indexed: 10/13/2024]
Abstract
OBJECTIVE We report data of non-invasive prenatal testing (NIPT) at Uppsala University Hospital between 2017-2022. Furthermore, we illustrate the potential capacity of massive parallel sequencing-based NIPT beyond identification of common trisomies. METHODS Maternal blood samples were analyzed using the Verifi NIPT or VeriSeq NIPT assays. Diagnostic testing, performed on amniotic fluid samples, included QF-PCR, microarray (SNP-array) and metaphase FISH. RESULTS Among 4532 NIPT tests performed between 2017-2022, 125 samples (2.76%) showed increased risk for trisomies 13, 18, 21 and sex chromosome aneuploidy. For three patients with normal NIPT result further microarray indicated other types of chromosomal rearrangement which were not analyzed by NIPT. For another patient (case 1) the Verifi NIPT indicated trisomy 13. Fetal fraction (FF) was estimated to be 10%. Confirmatory microarray detected a segmental duplication on chromosome 13, as well as a terminal duplication and a terminal deletion on chromosome 10. A complex karyotype was observed in the fetus with metaphase FISH. In the second case the VeriSeq NIPT indicated trisomy 13. FF was estimated to be 11%. Confirmatory microarray detected a mosaicism of trisomy 13 in 30 % of cells. CONCLUSION This study illustrates detection of peculiar abnormalities of chromosome 13 and supports potential to screen copy number variations with genome-wide NIPT.
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Affiliation(s)
- Maria Sobol
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Christos Aravidis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Hugo Hessel
- Department of Women's Health, Centralsjukhuset Karlstad, Karlstad, Sweden
| | - Anna Lindqvist
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Izabella Baranowska Körberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden.
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3
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Liu S, Xu Y, Chang Q, Jia B, Li F. Comparison of the performance of NIPT and NIPT-plus for fetal chromosomal aneuploidy and high Z-score increases the positive predictive value. Int J Gynaecol Obstet 2024; 167:273-280. [PMID: 38651210 DOI: 10.1002/ijgo.15535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/13/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024]
Abstract
OBJECTIVE To evaluate non-invasive prenatal testing (NIPT) and expanded non-invasive prenatal testing (NIPT-plus) for detecting aneuploidies at different sequencing depths and assess Z-score accuracy in predicting trisomies 21, 18, 13, 45X, and 47XXX. METHODS Pregnancies with positive NIPT or NIPT-plus results detected at the prenatal diagnosis center of Nanfang Hospital were included in this retrospective study, between January 2017 and December 2022. Invasive prenatal diagnostic results were collected. Logistic regression analyses were used to study the relationship between Z-score and positive predictive value (PPV). Optimal cut-off values were obtained based on receiver operating characteristic analysis, and PPVs were calculated in different groups. RESULTS We evaluated 1348 pregnant women with positive results, including 930 reported by NIPT and 418 reported by NIPT-plus. NIPT reported significantly more rare chromosomal aneuploidies (RCAs), and NIPT-plus had a significantly higher PPV for trisomy 21 (T21). Logistic regression analyses showed a significant association (P < 0.001) between Z-score and PPVs for T21 and trisomy 18 (T18). A linear relationship was observed between fetal fraction (FF) and Z-values in the true positive cases of T21 and T18.The high Z-score group had significantly higher PPVs than the low Z-score group for T21, T18, trisomy 13, and 47XXX, but not for 45X. CONCLUSION The Z-score is helpful in assessing NIPT or NIPT-plus results. Therefore, we suggest including the Z-score and FF in the results. By combining the Z-score, FF, and maternal age, clinicians can interpret NIPT results more accurately and improve personal counsel to reduce patients' anxiety.
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Affiliation(s)
- Siping Liu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yushuang Xu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qingxian Chang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Bei Jia
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fenxia Li
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Li JY, Zuo LP, Xu J, Sun CY. Clinical applications of circulating tumor DNA in hematological malignancies: From past to the future. Blood Rev 2024:101237. [PMID: 39261219 DOI: 10.1016/j.blre.2024.101237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 08/26/2024] [Accepted: 08/27/2024] [Indexed: 09/13/2024]
Abstract
Liquid biopsy, particularly circulating tumor DNA (ctDNA), has drawn a lot of attention as a non- or minimal-invasive detection approach for clinical applications in patients with cancer. Many hematological malignancies are well suited for serial and repeated ctDNA surveillance due to relatively high ctDNA concentrations and high loads of tumor-specific genetic and epigenetic abnormalities. Progress of detecting technology in recent years has improved sensitivity and specificity significantly, thus broadening and strengthening the potential utilities of ctDNA including early diagnosis, prognosis estimation, treatment response evaluation, minimal residual disease monitoring, targeted therapy selection, and immunotherapy surveillance. This manuscript reviews the detection methodologies, clinical application and future challenges of ctDNA in hematological malignancies, especially for lymphomas, myeloma and leukemias.
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Affiliation(s)
- Jun-Ying Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of science and Technology, Wuhan, Hubei, China.
| | - Li-Ping Zuo
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of science and Technology, Wuhan, Hubei, China
| | - Jian Xu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of science and Technology, Wuhan, Hubei, China
| | - Chun-Yan Sun
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of science and Technology, Wuhan, Hubei, China.
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Shirato N, Sekizawa A, Miyagami K, Sakamoto M, Yamada T, Hirose T, Ikebukuro S, Nakamura T, Mizutani A, Ikemoto M, Izum M, Seino H, Yamada S, Suzumori N, Yoshihashi H, Samura O, Sawai H, Sago H, Okuyama T. Impact of the new government-involved noninvasive prenatal testing certification system on the awareness of pregnant women about noninvasive prenatal testing in Japan. J Obstet Gynaecol Res 2024; 50:1542-1551. [PMID: 39143723 DOI: 10.1111/jog.16052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 07/29/2024] [Indexed: 08/16/2024]
Abstract
AIM In Japan, noninvasive prenatal testing (NIPT) has been performed by facilities accredited by the Japanese Society of Obstetrics and Gynecology since 2013. However, since 2016, with the implementation of NIPT, which can only be performed by blood sampling, non-obstetricians have been involved in prenatal testing. Therefore, in July 2022, a new government-involved NIPT certification system based on Health Sciences Council guidelines was introduced to ensure access to prenatal testing information for pregnant women. METHODS This survey was conducted in February 2023 and was the first survey after the certification system implementation. We conducted a web-based survey of 1227 pregnant women and nursing mothers who underwent NIPT after July 2022 to evaluate their experiences. RESULTS Respondents were categorized by certification status as certified (C: 56%), non-certified (non-C: 23%), or uncertain (Q: 20%). The C group with a higher mean age at examination (35.0 ± 4.5 years) paid lower examination fees, received longer pre- and post-examination explanations, and underwent more weekday examinations (80%) than the other groups. Most respondents, 67%, 48%, and 53% in the C, non-C, and Q groups, respectively (p < 0.0001), stated that "NIPT needs to be regulated by the government or academic societies." The non-C group was more likely to say, "Insufficient post-test explanations at the laboratory made me more anxious," than the other groups when the testing results were non-negative (p = 0.015). CONCLUSIONS Despite government regulation, some pregnant women choose convenience over certified facilities, risking inadequate care. The government should ensure that NIPT is a safe option for all pregnant women.
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Affiliation(s)
- Nahoko Shirato
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Akihiko Sekizawa
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Keiko Miyagami
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Miwa Sakamoto
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Takahiro Yamada
- Division of Clinical Genetics, Hokkaido University Hospital, Sapporo, Japan
| | - Tatsuko Hirose
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
- Showa University Graduate School of Health Sciences, Tokyo, Japan
| | - Shin Ikebukuro
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Takeshi Nakamura
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Akane Mizutani
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Mai Ikemoto
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Mikiko Izum
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Hitomi Seino
- Department of Neuropsychiatry, Hyogo Medical University, Nishinomiya, Japan
| | - Shigehito Yamada
- Human Health Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Nobuhiro Suzumori
- Department of Obstetrics and Gynecology, Nagoya City University, Nagoya, Japan
| | - Hiroshi Yoshihashi
- Department of Clinical Genetics, Tokyo Metropolitan Children's Medical Center, Fuchu, Japan
| | - Osamu Samura
- Department of Obstetrics and Gynecology, The Jikei University, Minato, Japan
| | - Hideaki Sawai
- Department of Obstetrics and Gynecology, Hyogo Medical University, Nishinomiya, Japan
| | - Haruhiko Sago
- Center for Medical Genetics, National Center for Child Health and Development, Setagaya, Japan
| | - Torayuki Okuyama
- Department of Clinical Genomics, Saitama Medical University, Saitama, Japan
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Mu Q, Bai L, Xu B, Du H, Jiang Z, Huang S, Gao B, Wu Q, Zhao H, Dai P, Jiang Y. A capture-based method of prenatal cell-free DNA screening for autosomal recessive non-syndromic hearing loss. Prenat Diagn 2024; 44:1043-1052. [PMID: 38488843 DOI: 10.1002/pd.6550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 08/11/2024]
Abstract
OBJECTIVE This study aimed to develop and validate a prenatal cell-free DNA (cfDNA) screening method that uses capture-based enrichment to genotype fetal autosomal recessive disorders. This method was applied in pregnancies at high risk of autosomal recessive non-syndromic hearing loss (ARNSHL) to assess its accuracy and effectiveness. METHODS This assay measured the allele counts in both white blood cell DNA and cfDNA from the blood samples of pregnant women using a capture-based next-generation sequencing method. It then applied a binomial model to infer the fetal genotypes with the maximum likelihood. Ninety-four pregnant couples that were carriers of variants of ARNSHL in GJB2 or SLC26A4 were enrolled. The fetal genotypes deduced using this screening method were compared with the results of genetic diagnosis using amniocentesis. RESULTS Of the 94 couples, 65 carried more than one variant, resulting in 170 single-nucleotide polymorphism (SNP) loci to be inferred in the fetuses. Of the 170 fetal SNP genotypes, 150 (88.2%) had high confidence calls and 139 (92.7%) of these matched the genotypes obtained by amniocentesis result. Out of the remaining 20 (11.8%) cases with low-confidence calls, only 14 (70.0%) were concordant with genetic diagnosis using amniocentesis. The concordance rate was 100% for sites where the maternal genotype was wild-type homozygous. The discordance was site-biased, with each locus showing a consistent direction of discordance. Genetic diagnosis identified a total of 19 wild-type homozygotes, 46 heterozygotes, 19 compound heterozygotes, and 10 pathogenic homozygotes. This screening method correctly genotyped 81.9% (77/94) of fetuses and demonstrated a sensitivity of 89.7% and a specificity of 89.2% for correctly identifying ARNSHL. CONCLUSION This capture-based method of prenatal screening by cfDNA demonstrated strong potential for fetal genotyping of autosomal recessive disorders.
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Affiliation(s)
- Qian Mu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Ling Bai
- Beijing USCI Medical Laboratory, Beijing, China
| | - Bing Xu
- Beijing USCI Medical Laboratory, Beijing, China
| | - Huawen Du
- Department of Gynecology and Obstetrics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Shasha Huang
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Bo Gao
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Qixi Wu
- Beijing USCI Medical Laboratory, Beijing, China
| | | | - Pu Dai
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Yi Jiang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
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7
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Gao B, Jiang Y, Han M, Ji X, Zhang D, Wu L, Gao X, Huang S, Zhao C, Su Y, Yang S, Zhang X, Liu N, Han L, Wang L, Ren L, Yang J, Wu J, Yuan Y, Dai P. Targeted Linked-Read Sequencing for Direct Haplotype Phasing of Parental GJB2/SLC26A4 Alleles: A Universal and Dependable Noninvasive Prenatal Diagnosis Method Applied to Autosomal Recessive Nonsyndromic Hearing Loss in At-Risk Families. J Mol Diagn 2024; 26:638-651. [PMID: 38663495 DOI: 10.1016/j.jmoldx.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/04/2024] [Accepted: 04/10/2024] [Indexed: 05/04/2024] Open
Abstract
Noninvasive prenatal diagnosis (NIPD) for autosomal recessive nonsyndromic hearing loss (ARNSHL) has been rarely reported until recent years. Additionally, the existing method can not be used for challenging genome loci (eg, copy number variations, deletions, inversions, or gene recombinants) or on families without proband genotype. This study assessed the performance of relative haplotype dosage analysis (RHDO)-based NIPD for identifying fetal genotyping in pregnancies at risk of ARNSHL. Fifty couples carrying pathogenic variants associated with ARNSHL in either GJB2 or SLC26A4 were recruited. The RHDO-based targeted linked-read sequencing combined with whole gene coverage probes was used to genotype the fetal cell-free DNA of 49 families who met the quality control standard. Fetal amniocyte samples were genotyped using invasive prenatal diagnosis (IPD) to assess the performance of NIPD. The NIPD results showed 100% (49/49) concordance with those obtained through IPD. Two families with copy number variation and recombination were also successfully identified. Sufficient specific informative single-nucleotide polymorphisms for haplotyping, as well as the fetal cell-free DNA concentration and sequencing depth, are prerequisites for RHDO-based NIPD. This method has the merits of covering the entire genes of GJB2 and SLC26A4, qualifying for copy number variation and recombination analysis with remarkable sensitivity and specificity. Therefore, it has clinical potential as an alternative to traditional IPD for ARNSHL.
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Affiliation(s)
- Bo Gao
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Yi Jiang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Mingyu Han
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | | | - Dejun Zhang
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Lihua Wu
- Department of Otolaryngology, Fujian Medical University ShengLi Clinical College, Fujian Provincial Hospital, Fuzhou, China
| | - Xue Gao
- Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Shasha Huang
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Chaoyue Zhao
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Yu Su
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Suyan Yang
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Xin Zhang
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Na Liu
- MyGenostics Inc., Beijing, China
| | - Lu Han
- MyGenostics Inc., Beijing, China
| | | | - Lina Ren
- MyGenostics Inc., Beijing, China
| | - Jinyuan Yang
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Jian Wu
- MyGenostics Inc., Beijing, China
| | - Yongyi Yuan
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China.
| | - Pu Dai
- Senior Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China.
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Abstract
This review delves into the rapidly evolving landscape of liquid biopsy technologies based on cell-free DNA (cfDNA) and cell-free RNA (cfRNA) and their increasingly prominent role in precision medicine. With the advent of high-throughput DNA sequencing, the use of cfDNA and cfRNA has revolutionized noninvasive clinical testing. Here, we explore the physical characteristics of cfDNA and cfRNA, present an overview of the essential engineering tools used by the field, and highlight clinical applications, including noninvasive prenatal testing, cancer testing, organ transplantation surveillance, and infectious disease testing. Finally, we discuss emerging technologies and the broadening scope of liquid biopsies to new areas of diagnostic medicine.
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Affiliation(s)
- Conor Loy
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA;
| | - Lauren Ahmann
- Department of Pathology, Stanford University, Stanford, California, USA;
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA;
| | - Wei Gu
- Department of Pathology, Stanford University, Stanford, California, USA;
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9
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Gabrielli F, Papa FT, Di Pietro F, Paytuví-Gallart A, Julian D, Sanseverino W, Alfonsi C. MaterniCode: New Bioinformatic Pipeline to Detect Fetal Aneuploidies and Rearrangements Using Next-Generation Sequencing. Int J Genomics 2024; 2024:8859058. [PMID: 38962150 PMCID: PMC11221998 DOI: 10.1155/2024/8859058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 07/05/2024] Open
Abstract
Objective: The present study is aimed at introducing and evaluating MaterniCode, a state-of-the-art bioinformatic pipeline for noninvasive prenatal testing (NIPT) that leverages the Ion Torrent semiconductor sequencing platform. The initiative strives to revolutionize prenatal diagnostics by offering a rapid and cost-effective method without sacrificing accuracy. Methods: Two distinct bioinformatic strategies were employed for fetal sex determination, one of which achieved 100% accuracy. We analyzed 1225 maternal blood samples for fetal aneuploidies, benchmarking against the industry standard Illumina VeriSeq™ NIPT Solution v2. The capability of MaterniCode to detect and characterize complex chromosomal anomalies was also assessed. Results: MaterniCode achieved near-perfect accuracy in fetal sex determination through chromosome Y (chrY )-specific gene analysis, whereas the alternative method, employing the ratio of high-quality mapped reads on chrY relative to all reads, delivered 100% accuracy. For fetal aneuploidy detection, both the integrated WisecondorX and NIPTeR algorithms demonstrated a 100% sensitivity and specificity rate, consistent with Illumina VeriSeq™ NIPT Solution v2. The pipeline also successfully identified and precisely mapped significant chromosomal abnormalities, exemplified by a 2.4 Mb deletion on chromosome 13 and a 3 Mb duplication on chromosome 2. Conclusion: MaterniCode has proven to be an innovative and highly efficient tool in the domain of NIPT, demonstrating excellent sensitivity and specificity. Its robust capability to effectively detect a wide range of complex chromosomal aberrations, including rare and subtle variations, positions it as a promising and valuable addition to prenatal diagnostic technologies. This enhancement to diagnostic precision significantly aids clinicians in making informed decisions during pregnancy management.
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Affiliation(s)
- Federico Gabrielli
- Biolab srl, Laboratorio di Genetica molecolare e Genomica 63100, Ascoli Piceno, Italy
| | - Filomena Tiziana Papa
- Biolab srl, Laboratorio di Genetica molecolare e Genomica 63100, Ascoli Piceno, Italy
| | - Fabio Di Pietro
- Biolab srl, Laboratorio di Genetica molecolare e Genomica 63100, Ascoli Piceno, Italy
| | | | - Daniel Julian
- Sequentia Biotech SL, C/del Dr. Trueta, 179 08005, Barcelona, Spain
| | | | - Cinzia Alfonsi
- Biolab srl, Laboratorio di Genetica molecolare e Genomica 63100, Ascoli Piceno, Italy
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10
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Xue Z, Zhou A, Zhu X, Li L, Zhu H, Jin X, Wang J. NIPT-PG: empowering non-invasive prenatal testing to learn from population genomics through an incremental pan-genomic approach. Brief Bioinform 2024; 25:bbae266. [PMID: 38836702 DOI: 10.1093/bib/bbae266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/03/2024] [Accepted: 05/21/2024] [Indexed: 06/06/2024] Open
Abstract
Non-invasive prenatal testing (NIPT) is a quite popular approach for detecting fetal genomic aneuploidies. However, due to the limitations on sequencing read length and coverage, NIPT suffers a bottleneck on further improving performance and conducting earlier detection. The errors mainly come from reference biases and population polymorphism. To break this bottleneck, we proposed NIPT-PG, which enables the NIPT algorithm to learn from population data. A pan-genome model is introduced to incorporate variant and polymorphic loci information from tested population. Subsequently, we proposed a sequence-to-graph alignment method, which considers the read mis-match rates during the mapping process, and an indexing method using hash indexing and adjacency lists to accelerate the read alignment process. Finally, by integrating multi-source aligned read and polymorphic sites across the pan-genome, NIPT-PG obtains a more accurate z-score, thereby improving the accuracy of chromosomal aneuploidy detection. We tested NIPT-PG on two simulated datasets and 745 real-world cell-free DNA sequencing data sets from pregnant women. Results demonstrate that NIPT-PG outperforms the standard z-score test. Furthermore, combining experimental and theoretical analyses, we demonstrate the probably approximately correct learnability of NIPT-PG. In summary, NIPT-PG provides a new perspective for fetal chromosomal aneuploidies detection. NIPT-PG may have broad applications in clinical testing, and its detection results can serve as a reference for false positive samples approaching the critical threshold.
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Affiliation(s)
- Zhengfa Xue
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
| | - Aifen Zhou
- Institute of Maternal and Child Health, Wuhan Children's Hospital (Wuhan Maternal and Child Health care Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430015, China
- Department of Obstetrics, Wuhan Children's Hospital (Wuhan Maternal and Child Health care Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430015, China
| | - Xiaoyan Zhu
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
| | - Linxuan Li
- BGI Research, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Xin Jin
- BGI Research, Shenzhen 518083, China
- School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Jiayin Wang
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
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11
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Frazer LC, Yamaguchi Y, Singh DK, Akopyants NS, Good M. DNA methylation in necrotizing enterocolitis. Expert Rev Mol Med 2024; 26:e16. [PMID: 38557638 PMCID: PMC11140546 DOI: 10.1017/erm.2024.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 03/05/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Epigenetic modifications, such as DNA methylation, are enzymatically regulated processes that directly impact gene expression patterns. In early life, they are central to developmental programming and have also been implicated in regulating inflammatory responses. Research into the role of epigenetics in neonatal health is limited, but there is a growing body of literature related to the role of DNA methylation patterns and diseases of prematurity, such as the intestinal disease necrotizing enterocolitis (NEC). NEC is a severe intestinal inflammatory disease, but the key factors that precede disease development remain to be determined. This knowledge gap has led to a failure to design effective targeted therapies and identify specific biomarkers of disease. Recent literature has identified altered DNA methylation patterns in the stool and intestinal tissue of neonates with NEC. These findings provide the foundation for a new avenue in NEC research. In this review, we will provide a general overview of DNA methylation and then specifically discuss the recent literature related to methylation patterns in neonates with NEC. We will also discuss how DNA methylation is used as a biomarker for other disease states and how, with further research, methylation patterns may serve as potential biomarkers for NEC.
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Affiliation(s)
- Lauren C. Frazer
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yukihiro Yamaguchi
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dhirendra K. Singh
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalia S. Akopyants
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Misty Good
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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12
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Detection of chromosomal abnormalities and monogenic variants in fetal cfDNA for prenatal diagnosis. Nat Med 2024; 30:352-353. [PMID: 38336835 DOI: 10.1038/s41591-024-02811-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
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13
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Zhang J, Wu Y, Chen S, Luo Q, Xi H, Li J, Qin X, Peng Y, Ma N, Yang B, Qiu X, Lu W, Chen Y, Jiang Y, Chen P, Liu Y, Zhang C, Zhang Z, Xiong Y, Shen J, Liang H, Ren Y, Ying C, Dong M, Li X, Xu C, Wang H, Zhang D, Xu C, Huang H. Prospective prenatal cell-free DNA screening for genetic conditions of heterogenous etiologies. Nat Med 2024; 30:470-479. [PMID: 38253798 DOI: 10.1038/s41591-023-02774-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024]
Abstract
Prenatal cell-free DNA (cfDNA) screening uses extracellular fetal DNA circulating in the peripheral blood of pregnant women to detect prevalent fetal chromosomal anomalies. However, numerous severe conditions with underlying single-gene defects are not included in current prenatal cfDNA screening. In this prospective, multicenter and observational study, pregnant women at elevated risk for fetal genetic conditions were enrolled for a cfDNA screening test based on coordinative allele-aware target enrichment sequencing. This test encompasses the following three of the most frequent pathogenic genetic variations: aneuploidies, microdeletions and monogenic variants. The cfDNA screening results were compared to invasive prenatal or postnatal diagnostic test results for 1,090 qualified participants. The comprehensive cfDNA screening detected a genetic alteration in 135 pregnancies with 98.5% sensitivity and 99.3% specificity relative to standard diagnostics. Of 876 fetuses with suspected structural anomalies on ultrasound examination, comprehensive cfDNA screening identified 55 (56.1%) aneuploidies, 6 (6.1%) microdeletions and 37 (37.8%) single-gene pathogenic variants. The inclusion of targeted monogenic conditions alongside chromosomal aberrations led to a 60.7% increase (from 61 to 98) in the detection rate. Overall, these data provide preliminary evidence that a comprehensive cfDNA screening test can accurately identify fetal pathogenic variants at both the chromosome and single-gene levels in high-risk pregnancies through a noninvasive approach, which has the potential to improve prenatal evaluation of fetal risks for severe genetic conditions arising from heterogenous molecular etiologies. ClinicalTrials.gov registration: ChiCTR2100045739 .
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Affiliation(s)
- Jinglan Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Beijing BioBiggen Technology Co., Ltd, Beijing, China.
| | - Yanting Wu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Qiong Luo
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Xi
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Jianli Li
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaomei Qin
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Ying Peng
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Na Ma
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Bingxin Yang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Qiu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Weiliang Lu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yuan Chen
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Jiang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Panpan Chen
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Yifeng Liu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Chen Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Zhiwei Zhang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Yu Xiong
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jie Shen
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Huan Liang
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yunyun Ren
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chunmei Ying
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Minyue Dong
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Congjian Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Hua Wang
- National Health Commission (NHC) Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.
- NHC Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Women's Reproductive Health of Zhejiang Province, and Zhejiang Provincial Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China.
| | - Chenming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China.
| | - Hefeng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China.
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
- Shanghai Frontiers Science Research Center of Reproduction and Development, Shanghai, China.
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Laššáková S, Šenkyřík P, Pazourková E, Hořínek A, Calda P, Břešťák M, Světnicová K, Neužil P, Korabečná M. Rapid non-invasive prenatal screening test for trisomy 21 based on digital droplet PCR. Sci Rep 2023; 13:22948. [PMID: 38135736 PMCID: PMC10746715 DOI: 10.1038/s41598-023-50330-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 12/19/2023] [Indexed: 12/24/2023] Open
Abstract
Non-invasive prenatal tests for the detection of fetal aneuploidies are predominantly based on the analysis of cell-free DNA (cfDNA) from the plasma of pregnant women by next-generation sequencing. The development of alternative tests for routine genetic laboratories is therefore desirable. Multiplex digital droplet PCR was used to detect 16 amplicons from chromosome 21 and 16 amplicons from chromosome 18 as the reference. Two fluorescently labeled lock nucleic acid probes were used for the detection of reaction products. The required accuracy was achieved by examining 12 chips from each patient using Stilla technology. The plasma cfDNA of 26 pregnant women with euploid pregnancies and 16 plasma samples from pregnancies with trisomy 21 were analyzed to determine the cutoff value for sample classification. The test was validated in a blind study on 30 plasma samples from pregnant patients with a risk for trisomy 21 ranging from 1:4 to 1:801. The results were in complete agreement with the results of the invasive diagnostic procedure (sensitivity, specificity, PPV, and NPV of 100%). Low cost, and speed of analysis make it a potential screening method for implementation into the clinical workflow to support the combined biochemical and ultrasound results indicating a high risk for trisomy 21.
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Affiliation(s)
- Soňa Laššáková
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Pavel Šenkyřík
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Eva Pazourková
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, U Nemocnice 499/2, 128 08, Prague 2, Czech Republic
| | - Aleš Hořínek
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
- 3rd Department of Internal Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, U Nemocnice 1, 128 08, Prague 1, Czech Republic
| | - Pavel Calda
- Department of Gynaecology, Obstetrics and Neonatology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Apolinarska 18, 128 51, Prague, Czech Republic
| | - Miroslav Břešťák
- Department of Gynaecology, Obstetrics and Neonatology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Apolinarska 18, 128 51, Prague, Czech Republic
- Prenatal Diagnosis Center ProfiG2 S.R.O., Vajgarská, 1141, Prague, Czech Republic
| | | | - Pavel Neužil
- Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, Shaanxi, People's Republic of China
| | - Marie Korabečná
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic.
- Department of Laboratory Medicine, Faculty of Health Care and Social Work, University of Trnava in Trnava, Universitne Namestie 1, 918 43, Trnava, Slovak Republic.
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15
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Palomaki GE, Lambert-Messerlian GM, Fullerton D, Hegde M, Conotte S, Saidel ML, Jani JC. Cell-free DNA-based prenatal screening via rolling circle amplification: Identifying and resolving analytic issues. J Med Screen 2023; 30:168-174. [PMID: 37194254 PMCID: PMC10629251 DOI: 10.1177/09691413231173315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/02/2023] [Accepted: 04/11/2023] [Indexed: 05/18/2023]
Abstract
OBJECTIVE A rolling circle amplification (RCA) based commercial methodology using cell-free (cf)DNA to screen for common trisomies became available in 2018. Relevant publications documented high detection but with a higher than expected 1% false positive rate. Preliminary evidence suggested assay variability was an issue. A multi-center collaboration was created to explore this further and examine whether subsequent manufacturer changes were effective. METHODS Three academic (four devices) and two commercial (two devices) laboratories provided run date, chromosome 21, 18, and 13 run-specific standard deviations, number of samples run, and reagent lot identifications. Temporal trends and between-site/device consistency were explored. Proportions of run standard deviations exceeding pre-specified caps of 0.4%, 0.4% and 0.6% were computed. RESULTS Overall, 661 RCA runs between April 2019 and July 30, 2022 tested 39,756 samples. In the first 24, subsequent 9, and final 7 months, proportions of capped chromosome 21 runs dropped from 39% to 22% to 6.0%; for chromosome 18, rates were 76%, 36%, and 4.0%. Few chromosome 13 runs were capped using the original 0.60%, but capping at 0.50%, rates were 28%, 16%, and 7.6%. Final rates occurred after reformulated reagents and imaging software modifications were fully implemented across all devices. Revised detection and false positive rates are estimated at 98.4% and 0.3%, respectively. After repeat testing, failure rates may be as low as 0.3%. CONCLUSION Current RCA-based screening performance estimates are equivalent to those reported for other methods, but with a lower test failure rate after repeat testing.
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Affiliation(s)
- Glenn E Palomaki
- Department of Pathology and Laboratory Medicine, Women & Infants Hospital and Alpert Medical School at Brown University, Providence, RI, USA
| | - Geralyn M Lambert-Messerlian
- Department of Pathology and Laboratory Medicine, Women & Infants Hospital and Alpert Medical School at Brown University, Providence, RI, USA
- Department of Obstetrics and Gynecology, Women & Infants Hospital, Providence, RI, USA
| | - Donna Fullerton
- Department of Clinical Chemistry, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Madhuri Hegde
- Global Laboratory Services, PerkinElmer, Inc, Atlanta, GA, USA
| | - Stéphanie Conotte
- Department of Blood Transfusion, University Hospital Brugmann, Brussels, Belgium
| | | | - Jacques C Jani
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
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Wang Z, Tang X, Yang S, Zhao Y, Yin T, Chen M, Zhang Y, Wang Y, Zhang F, Wang L. Noninvasive prenatal screening with conventional sequencing depth to screen fetal copy number variants: A retrospective study of 19 144 pregnant women. J Obstet Gynaecol Res 2023; 49:2825-2835. [PMID: 37806662 DOI: 10.1111/jog.15805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023]
Abstract
AIM To investigate the detectability of noninvasive prenatal screening (NIPS) with conventional sequencing depth to detect fetal copy number variants. METHODS We performed a retrospective study in a total of 19 144 pregnant women. Their cell-free plasma DNA were assessed for trisomy 21, trisomy 18, trisomy 13, sex chromosome aneuploidies, and genome-wide copy number variants by NIPS at conventional sequencing depth. RESULTS Three hundred seventy-four cases (2.0%, 374/19 144) with abnormal results were detected, which including 84 cases (0.4%, 84/19 144) with high risk of trisomy 21, 18, and 13, 90 cases (0.5%, 90/19 144) with high risk of sex chromosome abnormalities (SCA), and 44 cases (0.2%, 44/19 144) with high risk of other chromosome aneuploidies. One hundred fifty-six cases (0.8%, 156/19 144) with high risk of copy number variations (CNVs) were also detected. In following prenatal diagnosis, composite positive predictive value (PPV) of trisomy 21, 18, and 13 was 69.6% (48/69). The PPV of SCAs was 37.3% (19/51). And the PPVs for CNVs was detected as 51.0% (<5 Mb), 71.4% (5 Mb ≤ CNV ≤10 Mb), 56.5% (>10 Mb). Finally, a follow-up about the pregnancy outcomes were conducted for all available cases. CONCLUSIONS NIPS yielded high PPVs for trisomy 21, 18, and 13 aneuploidies and moderate PPVs for SCAs and CNVs. The screening effectiveness was closely related to the size of CNV fragments. Larger CNVs, especially larger than 5 Mb, could be detected more accurately by NIPS in our analytic technique. Meanwhile, diagnostic confirmation by microarray analysis was highly recommended.
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Affiliation(s)
- Zhiwei Wang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Xinxin Tang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Shuting Yang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Yali Zhao
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Ting Yin
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Min Chen
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Yue Zhang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Yongan Wang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Fang Zhang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Leilei Wang
- Center of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
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Li X, Zhang D, Zhao X, Huang S, Han M, Wang G, Li Y, Kang D, Zhang X, Dai P, Yuan Y. Exploration of a Novel Noninvasive Prenatal Testing Approach for Monogenic Disorders Based on Fetal Nucleated Red Blood Cells. Clin Chem 2023; 69:1396-1408. [PMID: 37963809 DOI: 10.1093/clinchem/hvad165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/21/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND Due to technical issues related to cell-specific capture methods, amplification, and sequencing, noninvasive prenatal testing (NIPT) based on fetal nucleated red blood cells (fNRBCs) has rarely been used for the detection of monogenic disorders. METHODS Maternal peripheral blood was collected from 11 families with hereditary hearing loss. After density gradient centrifugation and cellular immunostaining for multiple biomarkers, candidate individual fetal cells were harvested by micromanipulation and amplified by whole-genome amplification (WGA). Whole-exome sequencing/whole-genome sequencing (WGS) and Sanger sequencing were performed on the identified fNRBCs to determine the fetal genotype. The impact of single-cell and pooled WGA products on the sequencing quality and results was compared. A combined analysis strategy, encompassing whole-exome sequencing/WGS, haplotype analysis, and Sanger sequencing, was used to enhance the NIPT results. RESULTS fNRBCs were harvested and identified in 81.8% (9/11) of families. The results of cell-based-NIPT (cb-NIPT) were consistent with those of invasive prenatal diagnosis in 8 families; the coincidence rate was 88.9% (8/9). The combined analysis strategy improved the success of cb-NIPT. The overall performance of pooled WGA products was better than that of individual cells. Due to a lack of alternative fetal cells or sufficient sequencing data, cb-NIPT failed in 3 families. CONCLUSIONS We developed a novel fNRBC-based NIPT method for monogenic disorders. By combining multiple analysis strategies and multiple fetal cell WGA products, the problem of insufficient genome information in a single cell was remedied. Our method has promising prospects in the field of NIPT for the detection of monogenic disorders.
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Affiliation(s)
- Xiaoge Li
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China
- Key Lab of Hearing Impairment Prevention and Treatment of Beijing, China
| | - Dejun Zhang
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, China
- Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China
- Key Lab of Hearing Impairment Prevention and Treatment of Beijing, China
- The Second Hospital of Jilin University, Changchun, China
| | - Xing Zhao
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China
- Key Lab of Hearing Impairment Prevention and Treatment of Beijing, China
| | - Shasha Huang
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China
- Key Lab of Hearing Impairment Prevention and Treatment of Beijing, China
| | - Mingyu Han
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China
- Key Lab of Hearing Impairment Prevention and Treatment of Beijing, China
| | - Guojian Wang
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China
- Key Lab of Hearing Impairment Prevention and Treatment of Beijing, China
| | - Yingzhuo Li
- Department of Information, Chinese PLA General Hospital, Beijing, China
| | - Dongyang Kang
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China
- Key Lab of Hearing Impairment Prevention and Treatment of Beijing, China
| | - Xin Zhang
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China
- Key Lab of Hearing Impairment Prevention and Treatment of Beijing, China
| | - Pu Dai
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China
- Key Lab of Hearing Impairment Prevention and Treatment of Beijing, China
| | - Yongyi Yuan
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China
- Key Lab of Hearing Impairment Prevention and Treatment of Beijing, China
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18
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Suo F, Wang Y, Wang N, Wang Y, Liao M, Wang J, Wang C, Zhang Y, Zhang M, Zhang C, Gu M, Gou L. Discordant performances of non-invasive prenatal testing for foetal trisomy 21 screening in subgroups of pregnancies. J OBSTET GYNAECOL 2023; 43:2288226. [PMID: 38054928 DOI: 10.1080/01443615.2023.2288226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 11/20/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Non-invasive prenatal testing (NIPT) has been widely adopted as an approach for foetal aneuploidy screening. This study was to evaluate the performance of NIPT for foetal T21 detection in subgroups of pregnancies and the correlation between Z-score and discordant positive predictive values (PPVs). METHODS We retrospectively reviewed the NIPT results among 22361 pregnancies undergoing combined second-trimester screening (cSTS) previously. Sixty-four cases with positive NIPT results for foetal T21 were validated by invasive prenatal diagnosis. RESULTS In pregnancies with cSTS-T21 low-, intermediate-, and high-risk, the PPVs at NIPT were 14.3%, 64.3%, and 86.4%, respectively. Mean Z-scores of positive NIPT cases with cSTS-T21 high- and intermediate-risk were comparable, while were higher than that of cases with pre-test low-risk. Furthermore, PPVs for positive NIPT cases at 3 < Z < 5, 5 ≤ Z < 9, and Z ≥ 9 were 16.7%, 63.2%, and 100.0%, respectively. CONCLUSIONS This study suggested that Z-score value of positive cases might be associated with discordant PPVs for T21 screening in subgroups of pregnancies.
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Affiliation(s)
- Feng Suo
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
- The School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yi Wang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Na Wang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
- Department of Technology, Suzhou Beikang Medical Device Co.Ltd, Suzhou, China
| | - Yawen Wang
- Department of Clinical Medicine, School of Medicine, Yangzhou University, Yangzhou, China
| | - Mingming Liao
- Department of Obstetrics, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Jingjing Wang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Chuanxia Wang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Yan Zhang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Man Zhang
- Department of Technology, Zhejiang Biosan Biochemical Technologies Co., Ltd, Hangzhou, China
| | - Chu Zhang
- Department of Neurobiology, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, China
| | - Maosheng Gu
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Lingshan Gou
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
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19
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Li C, Xiong M, Zhan Y, Zhang J, Qiao G, Li J, Yang H. Clinical Potential of Expanded Noninvasive Prenatal Testing for Detection of Aneuploidies and Microdeletion/Microduplication Syndromes. Mol Diagn Ther 2023; 27:769-779. [PMID: 37689607 DOI: 10.1007/s40291-023-00674-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 09/11/2023]
Abstract
OBJECTIVE We aimed to evaluate the clinical performance of expanded noninvasive prenatal testing (NIPT-Plus) for the detection of aneuploidies and microdeletion/microduplication syndromes. METHODS A total of 7177 pregnant women were enrolled in the study from June 2020 to March 2022 at Xijing Hospital, China. Cases with NIPT-Plus-positive results were further confirmed by chromosomal karyotyping and a chromosomal microarray analysis. RESULTS A total of 112 positive cases (1.56%) were identified by NIPT-Plus, including 60 chromosome aneuploidies and 52 microdeletion/microduplication syndromes. Ninety-five cases were validated by amniocentesis, and 57 were confirmed with true-positive results, comprising 18 trisomy 21, 4 trisomy 18, 1 trisomy 13, 17 sex chromosome aneuploidies, 1 other aneuploidy, and 16 microdeletion/microduplication syndromes. The positive predictive value of total chromosomal abnormalities was 60% (57/95). For trisomy 21, trisomy 18, trisomy 13, sex chromosome aneuploidies, other aneuploidies and microdeletion/microduplication syndromes, the sensitivity was all 100%, the specificity was 100, 99.986, 100, 99.888, 99.958, and 99.636%, and the positive predictive value was 100, 80, 100, 68, 25, and 38.10%, respectively. For all clinical characteristics, the abnormal maternal serum screening group was found to have the highest prevalence of chromosomal abnormalities (1.54%), and the ultrasound abnormality group presented the highest positive predictive value (73.33%). CONCLUSIONS NIPT-Plus has great potential for the detection of aneuploidies and microdeletion/microduplication syndromes owing to its high sensitivity, safety, and specificity, which greatly reduces unnecessary invasive procedures and the risk of miscarriage and allows informed maternal choice.
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Affiliation(s)
- Chunyan Li
- Department of Obstetrics and Gynecology, Xijing Hospital, The Fourth Military Medical University, 127 West ChangLe Road, Xi'an, 710032, Shaanxi, China
| | - Menghua Xiong
- Department of Obstetrics and Gynecology, Xijing Hospital, The Fourth Military Medical University, 127 West ChangLe Road, Xi'an, 710032, Shaanxi, China
| | - Ying Zhan
- Department of Obstetrics and Gynecology, 518 Hospital of PLA, Xi'an, 710043, Shaanxi, China
| | - Jianfang Zhang
- Department of Obstetrics and Gynecology, Xijing Hospital, The Fourth Military Medical University, 127 West ChangLe Road, Xi'an, 710032, Shaanxi, China
| | - Guyuan Qiao
- Department of Obstetrics and Gynecology, Xijing Hospital, The Fourth Military Medical University, 127 West ChangLe Road, Xi'an, 710032, Shaanxi, China
| | - Jia Li
- Department of Obstetrics and Gynecology, Xijing Hospital, The Fourth Military Medical University, 127 West ChangLe Road, Xi'an, 710032, Shaanxi, China
| | - Hong Yang
- Department of Obstetrics and Gynecology, Xijing Hospital, The Fourth Military Medical University, 127 West ChangLe Road, Xi'an, 710032, Shaanxi, China.
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20
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Kobayashi S, Hiwasa T, Kitamura K, Kano M, Hoshino T, Hirano S, Hashimoto M, Seimiya M, Shimada H, Nomura F, Matsubara H, Matsushita K. Combinational antibody detection approach increases the clinical validity of colorectal cancer screening. J Clin Lab Anal 2023; 37:e24978. [PMID: 37964630 PMCID: PMC10749486 DOI: 10.1002/jcla.24978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/27/2023] [Accepted: 10/15/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND At different stages of the disease, biomarkers can help to determine disease progression and recurrence and provide a personalized indicator of therapeutic effectiveness. The serological identification of antigens by recombinant cDNA expression cloning (SEREX) has identified five SEREX antigens. RESULTS Compared with healthy donors, anti-FIRΔexon2 and anti-SOHLH antibodies (Abs) in the sera of patients with colorectal cancer (CRC) were markedly higher. Furthermore, no correlation was noted between five SEREX antigens and the three tumor markers (CEA, CA19-9, and anti-p53 Abs), indicating that anti-FIRΔexon2 Abs are an independent candidate marker for patients with CRC. Generally, the levels of anti-FIRΔexon2 Abs combined with clinically available tumor markers were determined to be significantly higher compared with CEA, CA19-9. Moreover, in early-stage CRC, the levels of anti-FIRΔexon2 Abs combined with existing tumor markers were higher than those of CEA, CA19-9. CONCLUSION Due to the highly heterogeneous nature of CRC, a single tumor marker is unlikely to become a standalone diagnostic test due to its commonly insufficient sensitivity and/or specificity. Using a combination antibody detection approach of tumor markers for CRC diagnosis has the potential to be an effective approach. Therefore, the use of serum protein biomarker candidates holds promise for the development of inexpensive, noninvasive, and inexpensive tests for the detection of CRC.
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Affiliation(s)
- Sohei Kobayashi
- Department of Laboratory Medicine & Division of Clinical GeneticsChiba University HospitalChibaJapan
- Department of Medical Technology & Sciences, School of Health Sciences at NaritaInternational University of Health and WelfareChibaJapan
| | - Takaki Hiwasa
- Department of Neurological Surgery, Graduate School of MedicineChiba UniversityChibaJapan
| | - Kouichi Kitamura
- Department of Laboratory Medicine & Division of Clinical GeneticsChiba University HospitalChibaJapan
| | - Masayuki Kano
- Department of Frontier Surgery, Graduate School of MedicineChiba UniversityChibaJapan
| | - Tyuji Hoshino
- Department of Physical Chemistry, Graduate School of Pharmaceutical SciencesChiba UniversityChibaJapan
| | - Sho Hirano
- Department of Medical Technology & Sciences, School of Health Sciences at NaritaInternational University of Health and WelfareChibaJapan
| | - Mayuko Hashimoto
- Department of Medical Technology & Sciences, School of Health Sciences at NaritaInternational University of Health and WelfareChibaJapan
| | - Masanori Seimiya
- Department of Medical Technology & Sciences, School of Health Sciences at NaritaInternational University of Health and WelfareChibaJapan
| | - Hideaki Shimada
- Department of Gastroenterological Surgery, Graduate School of MedicineToho UniversityTokyoJapan
| | - Fumio Nomura
- Department of Laboratory Medicine & Division of Clinical GeneticsChiba University HospitalChibaJapan
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of MedicineChiba UniversityChibaJapan
| | - Kazuyuki Matsushita
- Department of Laboratory Medicine & Division of Clinical GeneticsChiba University HospitalChibaJapan
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21
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Wei R, Li J, Xia Y, Wang C, Lu X, Fang Y, Zhu J. Application of non-invasive prenatal testing to 91,280 spontaneous pregnancies and 3477 pregnancies conceived by in vitro fertilization. Mol Cytogenet 2023; 16:25. [PMID: 37726793 PMCID: PMC10507956 DOI: 10.1186/s13039-023-00656-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND Many clinical studies based on spontaneous pregnancies (SPs) have demonstrated the superiority of non-invasive prenatal testing (NIPT), and the question of whether this technology is suitable for offspring conceived by assisted reproductive technology has attracted attention. This study aimed to evaluate the application value of NIPT in screening for trisomy (T)21, T18, T13 and sex chromosome aneuploidy (SCA) in pregnant women who conceived by in vitro fertilization (IVF). RESULTS In total, there were 804 high-risk cases [0.88% (804/91280), singleton = 795, twin = 9] in the SP group. Among the 558 invasive prenatal diagnosis (IPD) cases (singleton = 556, twin = 2), 343 (singleton = 342, twin = 1) were true positive, including 213 cases of T21, 28 of T18, 5 of T13 and 97 (singleton = 96, twin = 1) of SCA. The positive predictive values (PPVs) of T21, T18, T13, SCA and T21/T18/T13 combined in singleton pregnancy were 89.12% (213/239), 51.85% (28/54), 21.74% (5/23), 40.00% (96/240), and 77.85% (246/316), respectively, and the PPV of SCA in twin pregnancy was 100.00%. In the IVF group, IPD was performed in 19 (singleton = 16, twin = 3) of the 27 high-risk cases [0.78% (27/3477), singleton = 16, twin = 3], of which 9 (singleton = 8, twin = 1) were true positive, including 5 cases (singleton = 4, twin = 1) of T21 and 4 of SCA. The PPVs of singleton T21, SCA and T21/T18/T13 combined were 66.67% (4/6), 50.00% (4/8) and 57.14% (4/7), respectively, and the PPV of twin T21 was 100.00% (1/1). There were no significant differences in PPV among T21, SCA and T21/T18/T13 combined in singletons between the groups (89.12% vs. 66.67%, p = 0.09; 40.00% vs. 50.00%, p = 0.57; 77.85% vs. 57.14%, p = 0.20). The sensitivity and specificity were higher for singleton and twin pregnancies in the two groups. Based on follow-up results, 1 case of false negative T21 was found in the singleton SP group. Additionally, the mean foetal fraction (FF) of the IVF group was lower than that of the SP group (11.23% vs. 10.51%, p < 0.05). CONCLUSION NIPT has high sensitivity and specificity in screening chromosomal aneuploidies in both IVF pregnancy and spontaneous pregnancy, so it is an ideal screening method for IVF pregnancy.
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Affiliation(s)
- Rong Wei
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei, China
| | - Jingran Li
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China
| | - Yuanyuan Xia
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China
| | - Chaohong Wang
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China
| | - Xinran Lu
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China
| | - Yuqin Fang
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei, China
| | - Jiansheng Zhu
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China.
- The Fifth Clinical Medical College of Anhui Medical University, Hefei, China.
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22
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Benn P, Cuckle H. Overview of Noninvasive Prenatal Testing (NIPT) for the Detection of Fetal Chromosome Abnormalities; Differences in Laboratory Methods and Scope of Testing. Clin Obstet Gynecol 2023; 66:536-556. [PMID: 37650667 DOI: 10.1097/grf.0000000000000803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Although nearly all noninvasive prenatal testing is currently based on analyzing circulating maternal cell-free DNA, the technical methods usedvary considerably. We review the different methods. Based on validation trials and clinical experience, there are mostly relatively small differences in screening performance for trisomies 21, 18, and 13 in singleton pregnancies. Recent reports show low no-call rates for all methods, diminishing its importance when choosing a laboratory. However, method can be an important consideration for twin pregnancies, screening for sex chromosome abnormalities, microdeletion syndromes, triploidy, molar pregnancies, rare autosomal trisomies, and segmental imbalances, and detecting maternal chromosome abnormalities.
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Affiliation(s)
- Peter Benn
- Department of Obstetrics and Gynecology, University of Connecticut Health Center, Farmington, Connecticut
| | - Howard Cuckle
- Department of Obstetrics and Gynecology, Faculty of Medicine, Tel Aviv University, Israel
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23
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He S, Zhang Q, Chen M, Chen X, Liang B, Lin N, Huang H, Xu L. Analysis of retest reliability for pregnant women undergoing cfDNA testing with a no-call result. Mol Biol Rep 2023; 50:7649-7657. [PMID: 37535243 PMCID: PMC10460704 DOI: 10.1007/s11033-023-08591-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 06/13/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND Determining the reasons for unreportable or no-call cell-free DNA (cfDNA) test results has been an ongoing issue, and a consensus on subsequent management is still lacking. This study aimed to explore potential factors related to no-call cfDNA test results and to discuss whether retest results are reliable. METHODS AND RESULTS This was a retrospective study of women with singleton pregnancies undergoing cfDNA testing in 2021. Of the 9871 pregnant patients undergoing cfDNA testing, 111 had a no-call result, and their results were compared to those of 170 control patients. The no-call rate was 1.12% (111/9871), and the primary cause for no-call results was data fluctuation (88.29%, 98/111). Medical conditions were significantly more frequent in the no-call group than in the reportable results group (P < 0.001). After retesting, 107 (107/111, 96.40%) patients had a result, and the false-positive rate (FPR) of retesting was 10.09% (10.09%, 11/109). In addition, placental lesions were more frequent in the no-call group than in the reportable results group (P = 0.037), and 4 patients, all in the no-call group, experienced pregnancy loss. CONCLUSIONS Pregnant women with medical conditions are more likely to have a no-call result. A retest is suggested for patients with a no-call result, but retests have a high FPR. In addition, pregnant women with a no-call result are at increased risk of adverse pregnancy outcomes. In conclusion, more attention should be given to pregnant women for whom a no-call cfDNA result is obtained.
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Affiliation(s)
- Shuqiong He
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Medical University, Fuzhou, China
| | - Qian Zhang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Medical University, Fuzhou, China
| | - Meihuan Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Medical University, Fuzhou, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Medical University, Fuzhou, China
| | - Bin Liang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Medical University, Fuzhou, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Medical University, Fuzhou, China.
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Medical University, Fuzhou, China.
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Medical University, Fuzhou, China.
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24
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Liu S, Chang Q, Yang F, Xu Y, Jia B, Wu R, Li L, Yin A, Chen W, Huang F, Yang X, Li F. Non-invasive prenatal test findings in 41,819 pregnant women: results from a clinical laboratory in southern China. Arch Gynecol Obstet 2023; 308:787-795. [PMID: 36602559 DOI: 10.1007/s00404-022-06908-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 12/27/2022] [Indexed: 01/06/2023]
Abstract
BACKGROUND This paper evaluated the clinical utility of massively parallel sequencing-based non-invasive prenatal testing (NIPT) for detecting trisomy 21 (T21), T18, T13, sex chromosome aneuploidies (SCA), and rare chromosome aneuploidies (RCA) among the data collected by a clinical laboratory in southern China. METHODS In a 3-year period between January 2017 and December 2019, over 40,000 pregnant women underwent NIPT clinical screening test for fetal T21, T18, T13, SCA, and RCA in our laboratory. NIPT samples were processed using the NextSeq CN500 platform. The positive results were confirmed by karyotyping, and chromosomal microarray analysis (CMA) or copy number variants (CNV) sequencing. Details of the pregnancy outcomes were collected via telephone interview. RESULTS NIPT results were available for 41,819 cases; 691 positive cases were reported. The overall sensitivity for detection of T21, T18, T13, SCA, and RCA was 99.21, 100.00, 100.00, 98.55, and 100.00%, and the specificity was 99.95, 99.94, 99.98, 99.69, and 99.92%, respectively. The positive predictive values (PPVs) for detection of T21, T18, T13, SCA, and RCA were 85.62, 45.24, 40.00, 34.17, and 13.51%, respectively, and those for detection of 45,X, 47,XXY, 47,XXX, 47,XYY, and 46,XY(delX) 20.00, 59.18, 28.95, 61.54, and 25.00%, respectively. Regarding pregnancy outcomes, 92.38% of the pregnancies with confirmed aneuploidies were terminated, and 91.20% of those identified as having a false-positive result were carried to term. Among 252 unconfirmed cases, 24.60% of the pregnancies were terminated and 38.10% carried to term, while 37.30% declined interview. CONCLUSIONS NIPT is widely used to screen fetal aneuploidies based on its high sensitivity and specificity. However, in this study, the PPVs of NIPT in terms of detecting T18, T13, XO, XXX and RCA were < 50%. In addition, more than one-third of NIPT-positive women did not accept invasive prenatal diagnosis. Confirmatory diagnosis is strongly recommended for women with positive NIPT outcomes before any further decision is made.
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Affiliation(s)
- Siping Liu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qingxian Chang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fang Yang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yushuang Xu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Bei Jia
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ruifeng Wu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Liyan Li
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ailan Yin
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Weishan Chen
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fodi Huang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xuexi Yang
- Institute of Antibody Engineering, School of Laboratory Medical and Biotechnology, Southern Medical University, Guangzhou, China
| | - Fenxia Li
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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25
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Norton ME. Cell-free DNA Screening for Aneuploidy. Clin Obstet Gynecol 2023; 66:557-567. [PMID: 37650668 DOI: 10.1097/grf.0000000000000796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Cell-free DNA (cfDNA) screening has high detection for the common fetal autosomal aneuploidies, but is not diagnostic. The positive predictive value should be utilized in counseling after a positive cell-free DNA screen, and diagnostic testing should be offered for confirmation. cfDNA screening does not report a result in ~3% of cases; nonreportable results indicate an increased risk for aneuploidy and some adverse perinatal outcomes. False-positive cfDNA screening occurs due to confined placental mosaicism, maternal copy number variants, mosaicism, and cancer. Pretest education and counseling should be provided with emphasis on the potential benefits, risks, and limitations before cfDNA screening.
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Affiliation(s)
- Mary E Norton
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California
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26
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Moufarrej MN, Bianchi DW, Shaw GM, Stevenson DK, Quake SR. Noninvasive Prenatal Testing Using Circulating DNA and RNA: Advances, Challenges, and Possibilities. Annu Rev Biomed Data Sci 2023; 6:397-418. [PMID: 37196360 PMCID: PMC10528197 DOI: 10.1146/annurev-biodatasci-020722-094144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Prenatal screening using sequencing of circulating cell-free DNA has transformed obstetric care over the past decade and significantly reduced the number of invasive diagnostic procedures like amniocentesis for genetic disorders. Nonetheless, emergency care remains the only option for complications like preeclampsia and preterm birth, two of the most prevalent obstetrical syndromes. Advances in noninvasive prenatal testing expand the scope of precision medicine in obstetric care. In this review, we discuss advances, challenges, and possibilities toward the goal of providing proactive, personalized prenatal care. The highlighted advances focus mainly on cell-free nucleic acids; however, we also review research that uses signals from metabolomics, proteomics, intact cells, and the microbiome. We discuss ethical challenges in providing care. Finally, we look to future possibilities, including redefining disease taxonomy and moving from biomarker correlation to biological causation.
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Affiliation(s)
| | - Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development and Section on Prenatal Genomics and Fetal Therapy, Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gary M Shaw
- Department of Pediatrics and March of Dimes Prematurity Research Center at Stanford University, Stanford University School of Medicine, Stanford, California, USA
| | - David K Stevenson
- Department of Pediatrics and March of Dimes Prematurity Research Center at Stanford University, Stanford University School of Medicine, Stanford, California, USA
| | - Stephen R Quake
- Department of Bioengineering and Department of Applied Physics, Stanford University, Stanford, California, USA
- Chan Zuckerberg Initiative, Redwood City, California, USA
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Hong K, Park HJ, Jang HY, Shim SH, Jang Y, Kim SH, Cha DH. A Novel Paradigm for Non-Invasive Prenatal Genetic Screening: Trophoblast Retrieval and Isolation from the Cervix (TRIC). Diagnostics (Basel) 2023; 13:2532. [PMID: 37568895 PMCID: PMC10417081 DOI: 10.3390/diagnostics13152532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
As the prevalence of pregnancies with advanced maternal age increases, the risk of fetal chromosomal abnormalities is on the rise. Therefore, prenatal genetic screening and diagnosis have become essential elements in contemporary obstetrical care. Trophoblast retrieval and isolation from the cervix (TRIC) is a non-invasive procedure that can be utilized for prenatal genetic diagnosis. The method involves the isolation of fetal cells (extravillous trophoblasts) by transcervical sampling; along with its non-invasiveness, TRIC exhibits many other advantages such as its usefulness in early pregnancy at 5 weeks of gestation, and no interference by various fetal and maternal factors. Moreover, the trophoblast yields from TRIC can provide valuable information about obstetrical complications related to abnormal placentation even before clinical symptoms arise. The standardization of this clinical tool is still under investigation, and the upcoming advancements in TRIC are expected to meet the increasing need for a safe and accurate option for prenatal diagnosis.
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Affiliation(s)
- Kirim Hong
- CHA Gangnam Medical Center, Department of Obstetrics and Gynecology, CHA University, Seoul 06125, Republic of Korea; (K.H.); (H.J.P.); (Y.J.)
| | - Hee Jin Park
- CHA Gangnam Medical Center, Department of Obstetrics and Gynecology, CHA University, Seoul 06125, Republic of Korea; (K.H.); (H.J.P.); (Y.J.)
| | - Hee Yeon Jang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (H.Y.J.); (S.H.S.)
| | - Sung Han Shim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (H.Y.J.); (S.H.S.)
| | - Yoon Jang
- CHA Gangnam Medical Center, Department of Obstetrics and Gynecology, CHA University, Seoul 06125, Republic of Korea; (K.H.); (H.J.P.); (Y.J.)
| | - Soo Hyun Kim
- CHA Gangnam Medical Center, Department of Obstetrics and Gynecology, CHA University, Seoul 06125, Republic of Korea; (K.H.); (H.J.P.); (Y.J.)
| | - Dong Hyun Cha
- CHA Gangnam Medical Center, Department of Obstetrics and Gynecology, CHA University, Seoul 06125, Republic of Korea; (K.H.); (H.J.P.); (Y.J.)
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Cai M, Lin N, Chen X, Li Y, Lin M, Fu X, Huang H, He S, Xu L. Non-invasive prenatal testing for the diagnosis of congenital abnormalities: Insights from a large multicenter study in southern China. Braz J Med Biol Res 2023; 56:e12506. [PMID: 37377305 DOI: 10.1590/1414-431x2023e12506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/04/2023] [Indexed: 06/29/2023] Open
Abstract
Although non-invasive prenatal testing (NIPT) is widely used to detect fetal abnormalities, the results of NIPT vary by population, and data for the screening efficiency of NIPT positive predictive value (PPV) from different populations is limited. Herein, we retrospectively analyzed the NIPT results in a large multicenter study involving 52,855 pregnant women. Depending on gestational age, amniotic fluid or umbilical cord blood was extracted for karyotype and/or chromosome microarray analysis (CMA) in NIPT-positive patients, and the PPV and follow-up data were evaluated to determine its clinical value. Among the 52,855 cases, 754 were NIPT-positive, with a positivity rate of 1.4%. Karyotype analysis and/or CMA confirmed 323 chromosomal abnormalities, with a PPV of 45.1%. PPV for trisomy 21 (T21), trisomy 18 (T18), trisomy 13 (T13), sex chromosomal aneuploidies (SCAs), and copy number variations (CNVs) were 78.9, 35.3, 22.2, 36.9, and 32.9%, respectively. The PPVs for T21, T18, and T13 increased with age, whereas the PPVs for SCAs and CNVs had little correlation with age. The PPV was significantly higher in patients with advanced age and abnormal ultrasound. The NIPT results are affected by population characteristics. NIPT had a high PPV for T21 and a low PPV for T13 and T18, and screening for SCAs and CNVs showed clinical significance in southern China.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Min Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xianguo Fu
- Department of Prenatal Diagnosis, Ningde Municipal Hospital, Ningde Normal University, Ningde, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Shuqiong He
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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29
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Hui L, Ellis K, Mayen D, Pertile MD, Reimers R, Sun L, Vermeesch J, Vora NL, Chitty LS. Position statement from the International Society for Prenatal Diagnosis on the use of non-invasive prenatal testing for the detection of fetal chromosomal conditions in singleton pregnancies. Prenat Diagn 2023; 43:814-828. [PMID: 37076973 DOI: 10.1002/pd.6357] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/15/2023] [Indexed: 04/21/2023]
Abstract
Key points
What is already known about this topic?
In 2015, the International Society for Prenatal Diagnosis (ISPD) published its first position statement on the use of non‐invasive prenatal testing (NIPT) to screen for aneuploidy. Widespread uptake across the globe and subsequent published research has shed new light on test performance and implementation issues.
What does this study add?
This new position statement replaces the 2015 statement with updated information on the current technologies, clinical experience, and implementation practices.
As an international organization, ISPD recognizes that there are important population‐specific considerations in the organization of prenatal screening and diagnosis. These opinions are designed to apply to high income settings where prenatal screening for aneuploidy is an established part of antenatal care.
This position statement is not a clinical practice guideline but represents the consensus opinion of the current ISPD Board based on the current state of knowledge and clinical practice.
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Affiliation(s)
- Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, Victoria, Australia
- Department of Obstetrics and Gynaecology, Northern Health, Epping, Victoria, Australia
| | - Katie Ellis
- Illumina ANZ, Sydney, New South Wales, Australia
| | - Dora Mayen
- Genetics Clinic, Hospital Angeles Lomas, Estado de Mexico, Mexico
| | - Mark D Pertile
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Rebecca Reimers
- San Diego Perinatal Center, Rady Children's Hospital, San Diego, California, USA
- Scripps Research Institute, La Jolla, California, USA
| | - Luming Sun
- Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | | | - Neeta L Vora
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Division of Maternal Fetal Medicine, Chapel Hill, North Carolina, USA
| | - Lyn S Chitty
- Great Ormond Street NHS Foundation Trust, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
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30
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Luo Y, Hu B, Long Y, Pan Y, Jiang L, Xiong W, Xu H, Xu L, Wang D. Clinical application of noninvasive prenatal testing in twin pregnancies: a single-center experience. Expert Rev Mol Diagn 2023:1-6. [PMID: 36939534 DOI: 10.1080/14737159.2023.2193291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
OBJECTIVES To evaluate the clinical efficiency of noninvasive prenatal testing (NIPT) for fetal chromosomal aneuploidy screening in twin pregnancies. METHODS A total of 1650 women with twin pregnancies were enrolled in the study, which underwent NIPT at the Southwest Hospital, Army Medical University, Chongqing, China from January 2013 to June 2022. Fetal karyotyping analysis was conducted in high-risk patients, with subsequent follow-up on pregnancy outcomes. RESULTS In 1650 pregnancies, NIPT results showed ten cases of the fetal chromosome aneuploidy, of which six cases were true positive and four cases were false positive. The sensitivity, specificity, positive predictive value (PPV), and false-positive rate (FPR) of trisomy 21 were 100%, 99.79%, 57.14%, and 0.18%, respectively. Sensitivity, specificity, PPV, and FPR of trisomy 18 were 100%, 99.94%, 50%, and 0.06%, respectively. The sensitivity, specificity, PPV, and FPR of trisomy 13 were 100%, 100%, 100%, and 0%, respectively. No false negatives were detected and the negative predictive value (NPV) was 100% of the total. Eleven pregnancies failed the NIPT test with no-call due to the low fetal fraction (< 4%). CONCLUSIONS NIPT is a high-performing routine primary prenatal screening test in twin pregnancies, with high sensitivity and specificity in screening for fetal aneuploidy.
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Affiliation(s)
- Yanmei Luo
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, Sichuan, China
| | - Bin Hu
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, Sichuan, China
| | - Yang Long
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, Sichuan, China
| | - Yan Pan
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, Sichuan, China
| | - Lupin Jiang
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, Sichuan, China
| | - Wei Xiong
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, Sichuan, China
| | - Huanhuan Xu
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, Sichuan, China
| | - Liang Xu
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, Sichuan, China
| | - Dan Wang
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, Sichuan, China
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31
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Quake SR. Prenatal Testing for Non-Medical Traits. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2023; 23:1-2. [PMID: 36919539 DOI: 10.1080/15265161.2023.2179776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
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32
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Combined fetal fraction to analyze the Z-score accuracy of noninvasive prenatal testing for fetal trisomies 13, 18, and 21. J Assist Reprod Genet 2023; 40:803-810. [PMID: 36763299 DOI: 10.1007/s10815-022-02694-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/12/2022] [Indexed: 02/11/2023] Open
Abstract
OBJECTIVE This study aims to evaluate the correlation combined fetal fraction and Z-score for fetal trisomies 13, 18, and 21 of NIPT by the semiconductor sequencing platform and further analyze the differences of different sequencing depths. METHODS A cohort of 61,581 pregnancies were recruited for NIPT. Invasive prenatal diagnostic confirmation is recommended in all high-risk NIPT cases. Logistic regression and rank correlation analysis were applied to analyze the relationship between different parameters. ROC curve analysis was adopted to analyze the cutoff values of Z-score and fetal fraction. RESULTS A total of 278 common trisomy pregnancies were verified in 377 NIPT-positive results. The fitted logistic regression models revealed that Z-scores of NIPT-positive results were significantly associated with PPVs (p < 0.05). The ROC curve analysis showed that the optimal cutoff value of Z-scores for T21, T18, and T13 was 7.597, 4.944, and 9.135 for NIPT and 9.489, 8.004, and 12.4 for NIPT-plus. If combing fetal fraction as another evaluation factor, the PPV of trisomy 21 gradually improved. We analyzed the correlation between the fetal fraction and the PPV, which revealed that the fetal fraction was significantly correlated with PPV. By analyzing the PPV of different groups divided by the associated criteria obtained from ROC curve, the PPV of high Z-score and high fetal fraction is higher in groups of Z-score > the optimal cutoff value. CONCLUSION The results of this study show that the fetal fraction is significantly correlated with the PPV. Combining fetal fraction with Z-score is significantly better than in groups of Z-score-associated criteria; clinicians can give more accurate and efficient prenatal genetic counseling.
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Shaw J, Scotchman E, Paternoster B, Ramos M, Nesbitt S, Sheppard S, Snowsill T, Chitty LS, Chandler N. Non-invasive fetal genotyping for maternal alleles with droplet digital PCR: A comparative study of analytical approaches. Prenat Diagn 2023; 43:477-488. [PMID: 36760169 DOI: 10.1002/pd.6333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/22/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
OBJECTIVES To develop a flexible droplet digital PCR (ddPCR) workflow to perform non-invasive prenatal diagnosis via relative mutation dosage (RMD) for maternal pathogenic variants with a range of inheritance patterns, and to compare the accuracy of multiple analytical approaches. METHODS Cell free DNA (cfDNA) was tested from 124 archived maternal plasma samples: 88 cases for sickle cell disease and 36 for rare Mendelian conditions. Three analytical methods were compared: sequential probability ratio testing (SPRT), Bayesian and z-score analyses. RESULTS The SPRT, Bayesian and z-score analyses performed similarly well with correct prediction rates of 96%, 97% and 98%, respectively. However, there were high rates of inconclusive results for each cohort, particularly for z-score analysis which was 31% overall. Two samples were incorrectly classified by all three analytical methods; a false negative result predicted for a fetus affected with sickle cell disease and a false positive result predicting the presence of an X-linked IDS variant in an unaffected fetus. CONCLUSIONS ddPCR can be applied to RMD for diverse conditions and inheritance patterns, but all methods carry a small risk of erroneous results. Further evaluation is required both to reduce the rate of inconclusive results and explore discordant results in more detail.
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Affiliation(s)
- Joe Shaw
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Ben Paternoster
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Maureen Ramos
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Sarah Nesbitt
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Sophie Sheppard
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | | | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Natalie Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
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Yu SCY, Deng J, Qiao R, Cheng SH, Peng W, Lau SL, Choy LYL, Leung TY, Wong J, Wong VWS, Wong GLH, Jiang P, Chiu RWK, Chan KCA, Lo YMD. Comparison of Single Molecule, Real-Time Sequencing and Nanopore Sequencing for Analysis of the Size, End-Motif, and Tissue-of-Origin of Long Cell-Free DNA in Plasma. Clin Chem 2023; 69:168-179. [PMID: 36322427 DOI: 10.1093/clinchem/hvac180] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 10/03/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Recent studies using single molecule, real-time (SMRT) sequencing revealed a substantial population of analyzable long cell-free DNA (cfDNA) in plasma. Potential clinical utilities of such long cfDNA in pregnancy and cancer have been demonstrated. However, the performance of different long-read sequencing platforms for the analysis of long cfDNA remains unknown. METHODS Size biases of SMRT sequencing by Pacific Biosciences (PacBio) and nanopore sequencing by Oxford Nanopore Technologies (ONT) were evaluated using artificial mixtures of sonicated human and mouse DNA of different sizes. cfDNA from plasma samples of pregnant women at different trimesters, hepatitis B carriers, and patients with hepatocellular carcinoma were sequenced with the 2 platforms. RESULTS Both platforms showed biases to sequence longer (1500 bp vs 200 bp) DNA fragments, with PacBio showing a stronger bias (5-fold overrepresentation of long fragments vs 2-fold in ONT). Percentages of cfDNA fragments 500 bp were around 6-fold higher in PacBio compared with ONT. End motif profiles of cfDNA from PacBio and ONT were similar, yet exhibited platform-dependent patterns. Tissue-of-origin analysis based on single-molecule methylation patterns showed comparable performance on both platforms. CONCLUSIONS SMRT sequencing generated data with higher percentages of long cfDNA compared with nanopore sequencing. Yet, a higher number of long cfDNA fragments eligible for the tissue-of-origin analysis could be obtained from nanopore sequencing due to its much higher throughput. When analyzing the size and end motif of cfDNA, one should be aware of the analytical characteristics and possible biases of the sequencing platforms being used.
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Affiliation(s)
- Stephanie C Y Yu
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Jiaen Deng
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Rong Qiao
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Suk Hang Cheng
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Wenlei Peng
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - So Ling Lau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - L Y Lois Choy
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Tak Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - John Wong
- Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Vincent Wai-Sun Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Grace L H Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Peiyong Jiang
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Rossa W K Chiu
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - K C Allen Chan
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Y M Dennis Lo
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
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Abstract
The options for prenatal genetic testing have evolved rapidly in the past decade, and advances in sequencing technology now allow genetic diagnoses to be made down to the single-base-pair level, even before the birth of the child. This offers women the opportunity to obtain information regarding the foetus, thereby empowering them to make informed decisions about their pregnancy. As genetic testing becomes increasingly available to women, clinician knowledge and awareness of the options available to women is of great importance. Additionally, comprehensive pretest and posttest genetic counselling about the advantages, pitfalls and limitations of genetic testing should be provided to all women. This review article aims to cover the range of genetic tests currently available in prenatal screening and diagnosis, their current applications and limitations in clinical practice as well as what the future holds for prenatal genetics.
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Affiliation(s)
- Karen Mei Xian Lim
- Department of Obstetrics and Gynaecology, National University Health System, Singapore
| | - Aniza Puteri Mahyuddin
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, National University Health System, Singapore,Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Correspondence: A/Prof Mahesh Choolani, Head and Senior Consultant, Department of Obstetrics and Gynaecology, National University Health System, NUHS Tower Block, Level 12, 1E Kent Ridge Road, 119228, Singapore. E-mail:
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Qi Z, Yu J. Synthesis of positive plasmas with known chromosomal abnormalities for validation of non-invasive prenatal screening. Front Genet 2023; 14:971087. [PMID: 36726805 PMCID: PMC9886268 DOI: 10.3389/fgene.2023.971087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
Non-invasive prenatal screening (NIPS) is a DNA sequencing-based screening test for fetal aneuploidies and possibly other pathogenic genomic abnormalities, such as large deletions and duplications. Validation and quality assurance (QA) of this clinical test using plasmas with and without targeted chromosomal abnormalities from pregnant women as negative and positive controls are required. However, the positive plasma controls may not be available for many laboratories that are planning to establish NIPS. Limited synthetic positive plasmas are commercially available, but the types of abnormalities and the number/quantity of synthetic plasmas for each abnormality are insufficient to meet the minimal requirements for the initial validation. We report here a method of making synthetic positive plasmas by adding cell-free DNA (cfDNA) isolated from culture media of prenatal cells with chromosomal abnormalities to the plasmas from non-pregnant women. Thirty-eight positive plasmas with various chromosomal abnormalities, including autosomal and sex chromosomal aneuploidies, large deletions and duplications, were synthesized. The synthetic plasmas were characterized side-by-side with real positive plasmas from pregnant women and commercially available synthetic positive plasmas using the Illumina VeriSeq NIPT v2 system. All chromosomal abnormalities in the synthetic plasmas were correctly identified with the same testing sensitivity and specificity as in the real and commercial synthetic plasmas. The findings demonstrate that the synthetic positive plasmas are excellent alternatives of real positive plasmas for validation and QA of NIPS. The method described here is simple and straightforward, and can be readily used in clinical genetics laboratories with accessibility to prenatal cultures.
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37
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Tian M, Feng L, Li J, Zhang R. Focus on the frontier issue: progress in noninvasive prenatal screening for fetal trisomy from clinical perspectives. Crit Rev Clin Lab Sci 2023; 60:248-269. [PMID: 36647189 DOI: 10.1080/10408363.2022.2162843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The discovery of cell-free fetal DNA (cffDNA) in maternal blood and the rapid development of massively parallel sequencing have revolutionized prenatal testing from invasive to noninvasive. Noninvasive prenatal screening (NIPS) based on cffDNA enables the detection of fetal trisomy through sequencing, comparison, and bioassays. Its accuracy is better than that of traditional screening methods, and it is the most advanced clinical application of high-throughput sequencing technologies. However, the existing sequencing methods are limited by high costs and complex sequencing procedures. These limitations restrict the availability of NIPS for pregnant women. Many amplification methods have been developed to overcome the limitations of sequencing methods. The rapid development of non-sequencing methods has not been accompanied by reviews to summarize them. In this review, we initially describe the detection principles for sequencing-based NIPS. We summarize the rapidly evolving amplification technologies, focusing on the need to reduce costs and simplify the procedures. To ensure that the testing systems are feasible and that the testing processes are reliable, we expand our vision to the clinic. We evaluate the clinical validity of NIPS in terms of sensitivity, specificity, and positive predictive value. Finally, we summarize the application guidelines and discuss the corresponding quality control methods for NIPS. In addition to cffDNA, extracellular vesicle DNA, RNA, protein/peptide, and fetal cells can also be detected as biomarkers of NIPS. With the development of prenatal testing, NIPS has become increasingly important. Notably, NIPS is a screening test instead of a diagnostic test. The testing methods and procedures used in the NIPS process require standardization.
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Affiliation(s)
- Meng Tian
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Peking University Fifth School of Clinical Medicine, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Lei Feng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Peking University Fifth School of Clinical Medicine, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Peking University Fifth School of Clinical Medicine, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
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Noninvasive Prenatal Screening for Common Fetal Aneuploidies Using Single-Molecule Sequencing. J Transl Med 2023; 103:100043. [PMID: 36870287 DOI: 10.1016/j.labinv.2022.100043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 01/11/2023] Open
Abstract
Amplification biases caused by next-generation sequencing (NGS) for noninvasive prenatal screening (NIPS) may be reduced using single-molecule sequencing (SMS), during which PCR is omitted. Therefore, the performance of SMS-based NIPS was evaluated. We used SMS-based NIPS to screen for common fetal aneuploidies in 477 pregnant women. The sensitivity, specificity, positive predictive value, and negative predictive value were estimated. The GC-induced bias was compared between the SMS- and NGS-based NIPS methods. Notably, a sensitivity of 100% was achieved for fetal trisomy 13 (T13), trisomy 18 (T18), and trisomy 21 (T21). The positive predictive value was 46.15% for T13, 96.77% for T18, and 99.07% for T21. The overall specificity was 100% (334/334). Compared with NGS, SMS (without PCR) had less GC bias, a better distinction between T21 or T18 and euploidies, and better diagnostic performance. Overall, our results suggest that SMS improves the performance of NIPS for common fetal aneuploidies by reducing the GC bias introduced during library preparation and sequencing.
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Deng C, Liu J, Liu S, Liu H, Bai T, Jing X, Xia T, Liu Y, Cheng J, Wei X, Xing L, Luo Y, Zhou Q, Zhu Q, Liu S. Maternal and fetal factors influencing fetal fraction: A retrospective analysis of 153,306 pregnant women undergoing noninvasive prenatal screening. Front Pediatr 2023; 11:1066178. [PMID: 37114008 PMCID: PMC10126334 DOI: 10.3389/fped.2023.1066178] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/17/2023] [Indexed: 04/29/2023] Open
Abstract
Background Genetic factors are important causes of birth defects. Noninvasive prenatal screening (NIPS) is widely used for prenatal screening of trisomy 21, trisomy 18, and trisomy 13, which are the three most common fetal aneuploidies. Fetal fraction refers to the proportion of cell-free fetal DNA in maternal plasma, which can influence the accuracy of NIPS. Elucidating the factors that influence fetal fraction can provide guidance for the interpretation of NIPS results and genetic counseling. However, there is currently no broad consensus on the known factors that influence fetal fraction. Objective The study aimed to explore the maternal and fetal factors influencing fetal fraction. Methods A total of 153,306 singleton pregnant women who underwent NIPS were included. Data on gestational age; maternal age; body mass index (BMI); z-scores for chromosomes 21, 18, and 13; and fetal fraction in NIPS were collected from the study population, and the relationships between fetal fraction and these factors were examined. The relationship between fetal fraction and different fetal trisomy types was also analyzed. Results The results showed that the median gestational age, maternal age, and BMI of the pregnant women were 18 (16, 20) weeks, 29 (25, 32) years, and 22.19 (20.40, 24.24) kg/m2, respectively. The median fetal fraction was 11.62 (8.96, 14.7)%. Fetal fraction increased with gestational age and decreased with maternal age and BMI (P < 0.001). Fetal fraction of fetuses with trisomies 21, 18, and 13 was similar to that of the NIPS-negative group. The z-scores of pregnant women with trisomy 21 and 18 fetuses were positively correlated with fetal fraction, but not with that of the trisomy 13 cases. Conclusions The factors that influence fetal fraction need to be taken into consideration before NIPS for quality control and after NIPS for result interpretation.
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Affiliation(s)
- Cechuan Deng
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Jianlong Liu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Sha Liu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Hongqian Liu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Ting Bai
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Xiaosha Jing
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Tianyu Xia
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Yunyun Liu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Jing Cheng
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Xiang Wei
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Lingling Xing
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Yuan Luo
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Quanfang Zhou
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Qian Zhu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- Correspondence: Qian Zhu Shanling Liu
| | - Shanling Liu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- Correspondence: Qian Zhu Shanling Liu
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Clinical impacts of genome-wide noninvasive prenatal testing for rare autosomal trisomy. Am J Obstet Gynecol MFM 2023; 5:100790. [PMID: 36377092 DOI: 10.1016/j.ajogmf.2022.100790] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Genome-wide noninvasive prenatal testing identifies several rare autosomal trisomies in the general obstetrical population, but its use is questioned by its low positive predictive value. Furthermore, the origin of rare autosomal trisomies and the clinical effect of reporting them has not been sufficiently investigated. In addition, professional societies express their need for data assessing the clinical use of genome-wide noninvasive prenatal testing for rare autosomal trisomies for years. OBJECTIVE This study aimed to investigate the origin of rare autosomal trisomies and the clinical effect of disclosing rare autosomal trisomies in clinical settings. STUDY DESIGN Women who received noninvasive prenatal testing between March 2021 and March 2022 were prospectively enrolled. Clinical follow-up and cytogenetic and molecular investigations were performed. Posthoc analysis was performed to investigate the association between placental mosaicism and clinical outcomes. RESULTS Overall, 154 rare autosomal trisomies were identified in 89,242 pregnancies (0.17%) through noninvasive prenatal testing. In the 120 cases in which cytogenetic and molecular investigations were carried out, the rare autosomal trisomies were found to originate from true fetal mosaicism (n=5), uniparental disomy (n=5), maternal mosaic trisomy (n=3), maternal malignancy (n=1), and confined placental mosaicism (n=106). Clinical follow-up showed that 40% of all rare autosomal trisomy cases had adverse perinatal outcomes. In women with false-positive noninvasive prenatal testing results originating from confined placental mosaicism, the frequency of adverse perinatal outcomes was 26%. More importantly, the placental mosaicism ratio revealed by noninvasive prenatal testing was significantly higher in women who experienced adverse perinatal outcomes than those who did not (0.688 vs 0.332; P<.001). CONCLUSION Women with noninvasive prenatal testing results indicative of rare autosomal trisomies are at risk of adverse perinatal outcomes, and that risk can be stratified using chromosomes and the mosaicism ratio revealed by noninvasive prenatal testing. Our data are valuable for obstetrical caregivers advising a patient with a noninvasive prenatal testing result indicative of a rare autosomal trisomy and a false-positive diagnosis and for managing risks during pregnancy.
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41
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Xiang J, Peng Z. Applications of Noninvasive Prenatal Testing for Subchromosomal Copy Number Variations Using Cell-Free DNA. Clin Lab Med 2022; 42:613-625. [PMID: 36368786 DOI: 10.1016/j.cll.2022.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jiale Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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42
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Lannoo L, van Straaten K, Breckpot J, Brison N, De Catte L, Dimitriadou E, Legius E, Peeters H, Parijs I, Tsuiko O, Vancoillie L, Vermeesch JR, Van Buggenhout G, Van Den Bogaert K, Van Calsteren K, Devriendt K. Rare autosomal trisomies detected by non-invasive prenatal testing: an overview of current knowledge. Eur J Hum Genet 2022; 30:1323-1330. [PMID: 35896702 PMCID: PMC9712527 DOI: 10.1038/s41431-022-01147-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/15/2022] [Accepted: 06/30/2022] [Indexed: 12/16/2022] Open
Abstract
Non-invasive prenatal testing has been introduced for the detection of Trisomy 13, 18, and 21. Using genome-wide screening also other "rare" autosomal trisomies (RATs) can be detected with a frequency about half the frequency of the common trisomies in the large population-based studies. Large prospective studies and clear clinical guidelines are lacking to provide adequate counseling and management to those who are confronted with a RAT as a healthcare professional or patient. In this review we reviewed the current knowledge of the most common RATs. We compiled clinical relevant parameters such as incidence, meiotic or mitotic origin, the risk of fetal (mosaic) aneuploidy, clinical manifestations of fetal mosaicism for a RAT, the effect of confined placental mosaicism on placental function and the risk of uniparental disomy (UPD). Finally, we identified gaps in the knowledge on RATs and highlight areas of future research. This overview may serve as a first guide for prenatal management for each of these RATs.
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Affiliation(s)
- Lore Lannoo
- Department of Obstetrics and Gynaecology, Division Woman and Child, University Hospitals Leuven, Leuven, Belgium
| | | | - Jeroen Breckpot
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Nathalie Brison
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Luc De Catte
- Department of Obstetrics and Gynaecology, Division Woman and Child, University Hospitals Leuven, Leuven, Belgium
| | | | - Eric Legius
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Hilde Peeters
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Ilse Parijs
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Olga Tsuiko
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Leen Vancoillie
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | | | | | - Kristel Van Calsteren
- Department of Obstetrics and Gynaecology, Division Woman and Child, University Hospitals Leuven, Leuven, Belgium
| | - Koenraad Devriendt
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium.
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43
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Grati FR, Bestetti I, De Siero D, Malvestiti F, Villa N, Sala E, Crosti F, Parisi V, Nardone AM, Di Giacomo G, Pettinari A, Tortora G, Montaldi A, Calò A, Saccilotto D, Zanchetti S, Celli P, Guerneri S, Silipigni R, Cardarelli L, Lippi E, Cavani S, Malacarne M, Genesio R, Beltrami N, Pittalis MC, Desiderio L, Gentile M, Ficarella R, Recalcati MP, Catusi I, Garzo M, Miele L, Corti C, Ghezzo S, Bertini V, Cambi F, Valetto A, Facchinetti B, Bernardini L, Capalbo A, Balducci F, Pelo E, Minuti B, Pescucci C, Giuliani C, Renieri A, Longo I, Tita R, Castello G, Casalone R, Righi R, Raso B, Civolani A, Muzi MC, di Natale M, Varriale L, Gasperini D, Nuzzi MC, Cellamare A, Casieri P, Busuito R, Ceccarini C, Cesarano C, Privitera O, Melani D, Menozzi C, Falcinelli C, Calabrese O, Battaglia P, Tanzariello A, Stampalija T, Ardisia C, Gasparini P, Benn P, Novelli A. Positive predictive values and outcomes for uninformative cell-free DNA tests: An Italian multicentric Cytogenetic and cytogenomic Audit of diagnOstic testing (ICARO study). Prenat Diagn 2022; 42:1575-1586. [PMID: 36403097 DOI: 10.1002/pd.6271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/21/2022]
Abstract
OBJECTIVES To establish the positive predictive values (PPV) of cfDNA testing based on data from a nationwide survey of independent clinical cytogenetics laboratories. METHODS Prenatal diagnostic test results obtained by Italian laboratories between 2013 and March 2020 were compiled for women with positive non-invasive prenatal tests (NIPT), without an NIPT result, and cases where there was sex discordancy between the NIPT and ultrasound. PPV and other summary data were reviewed. RESULTS Diagnostic test results were collected for 1327 women with a positive NIPT. The highest PPVs were for Trisomy (T) 21 (624/671, 93%) and XYY (26/27, 96.3%), while rare autosomal trisomies (9/47, 19.1%) and recurrent microdeletions (8/55, 14.5%) had the lowest PPVs. PPVs for T21, T18, and T13 were significantly higher when diagnostic confirmation was carried out on chorionic villi (97.5%) compared to amniotic fluid (89.5%) (p < 0.001). In 19/139 (13.9%), of no result cases, a cytogenetic abnormality was detected. Follow-up genetic testing provided explanations for 3/6 cases with a fetal sex discordancy between NIPT and ultrasound. CONCLUSIONS NIPT PPVs differ across the conditions screened and the tissues studied in diagnostic testing. This variability, issues associated with fetal sex discordancy, and no results, illustrate the importance of pre- and post-test counselling.
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Affiliation(s)
- Francesca Romana Grati
- R&D, Cytogenetics, Molecular Genetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A, Busto Arsizio, Italy
| | - Ilaria Bestetti
- Laboratorio di Genetica Medica, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Daria De Siero
- R&D, Cytogenetics, Molecular Genetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A, Busto Arsizio, Italy
| | - Francesca Malvestiti
- R&D, Cytogenetics, Molecular Genetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A, Busto Arsizio, Italy
| | - Nicoletta Villa
- UOS Citogenetica e Genetica Medica - ASST-Monza, Ospedale San Gerardo, Università di Milano-Bicocca, Monza, Italy
| | - Elena Sala
- UOS Citogenetica e Genetica Medica - ASST-Monza, Ospedale San Gerardo, Università di Milano-Bicocca, Monza, Italy
| | - Francesca Crosti
- UOS Citogenetica e Genetica Medica - ASST-Monza, Ospedale San Gerardo, Università di Milano-Bicocca, Monza, Italy
| | - Valentina Parisi
- U.O.C. Laboratorio di Genetica Medica, Ospedale Pediatrico del Bambino Gesù, IRCCS, Roma, Italy
| | - Anna Maria Nardone
- U.O.C. Laboratorio di Genetica Medica, Policlinico Tor Vergata, Roma, Italy
| | | | - Antonella Pettinari
- SOSD Malattie Rare e Citogenetica, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | - Giada Tortora
- SOSD Malattie Rare e Citogenetica, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | | | - Annapaola Calò
- U.O.S. Laboratorio di Genetica, AULSS8 Berica, Vicenza, Italy
| | | | - Sara Zanchetti
- U.O.S. Laboratorio di Genetica, AULSS8 Berica, Vicenza, Italy
| | - Paola Celli
- U.O.S. Laboratorio di Genetica, AULSS8 Berica, Vicenza, Italy
| | - Silvana Guerneri
- Laboratorio di Genetica Medica, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Rosamaria Silipigni
- Laboratorio di Genetica Medica, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Laura Cardarelli
- Laboratorio di Genetica medica, Lifebrain, Gruppo Cerba HealthCare, c/o RDI, Rete Diagnostica Italiana, Limena, Italy
| | - Elisabetta Lippi
- Laboratorio di Genetica medica, Lifebrain, Gruppo Cerba HealthCare, c/o RDI, Rete Diagnostica Italiana, Limena, Italy
| | - Simona Cavani
- U.O.C. Laboratorio di Genetica Umana, IRCCS G. Gaslini, Genova, Italy
| | - Michela Malacarne
- U.O.C. Laboratorio di Genetica Umana, IRCCS G. Gaslini, Genova, Italy
| | - Rita Genesio
- DAI medicina di laboratorio e trasfusionale AOU Federico II, Napoli, Italy
| | | | - Maria Carla Pittalis
- IRCCS Azienda Ospedaliero Universitaria di Bologna, Policlinico di Sant'Orsola, Bologna, Italy
| | - Laura Desiderio
- IRCCS Azienda Ospedaliero Universitaria di Bologna, Policlinico di Sant'Orsola, Bologna, Italy
| | - Mattia Gentile
- Dipartimento di Medicina della Riproduzione, UOC Genetica Medica, ASL BARI, Bari, Italy
| | - Romina Ficarella
- Dipartimento di Medicina della Riproduzione, UOC Genetica Medica, ASL BARI, Bari, Italy
| | - Maria Paola Recalcati
- Laboratorio di Citogenetica e Genetica Molecolare, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Ilaria Catusi
- Laboratorio di Citogenetica e Genetica Molecolare, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | - Maria Garzo
- Laboratorio di Citogenetica e Genetica Molecolare, Istituto Auxologico Italiano, IRCCS, Milano, Italy
| | | | | | - Sara Ghezzo
- Laboratorio di Citogenetica - U.O.C. Genetica Medica, Centro Servizi Pievesestina - Laboratorio Unico, AUSL ROMAGNA, Cesena, Italy
| | - Veronica Bertini
- SOD Citogenetica, Azienda Ospedaliero Universitaria Pisana (AOUP), Pisa, Italy
| | - Francesca Cambi
- SOD Citogenetica, Azienda Ospedaliero Universitaria Pisana (AOUP), Pisa, Italy
| | - Angelo Valetto
- SOD Citogenetica, Azienda Ospedaliero Universitaria Pisana (AOUP), Pisa, Italy
| | - Barbara Facchinetti
- UOSD SMeL 4 Citogenetica e Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Laura Bernardini
- Medical Genetics Division, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Anna Capalbo
- Medical Genetics Division, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Federica Balducci
- TECNOBIOS PRENATALE EUROGENLAB - Gruppo LIFE BRAIN Emilia-Romagna, Bologna, Italy
| | | | | | | | | | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Ilaria Longo
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Rossella Tita
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Giuseppe Castello
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Rosario Casalone
- SSD SMeL Citogenetica e Genetica Medica, ASST dei Settelaghi, Varese, Italy
| | - Rossana Righi
- SSD SMeL Citogenetica e Genetica Medica, ASST dei Settelaghi, Varese, Italy
| | - Barbara Raso
- ASL ROMA 1, Centro S.Anna, Dipartimento dei Laboratori, U.O.S.D. di Genetica medica, Roma, Italy
| | - Alessandro Civolani
- ASL ROMA 1, Centro S.Anna, Dipartimento dei Laboratori, U.O.S.D. di Genetica medica, Roma, Italy
| | - Maria Cristina Muzi
- ASL ROMA 1, Centro S.Anna, Dipartimento dei Laboratori, U.O.S.D. di Genetica medica, Roma, Italy
| | - Manuela di Natale
- ASL ROMA 1, Centro S.Anna, Dipartimento dei Laboratori, U.O.S.D. di Genetica medica, Roma, Italy
| | - Luigia Varriale
- UOSD Diagnostica Alta Complessità, Settore Genetica, Azienda Ospedaliera Ospedali Riuniti Marche Nord-Pesaro, Nord-Pesaro, Italy
| | - Daniela Gasperini
- Laboratorio Genetica e Genomica, Ospedale Microcitemico A.Cao, ARNAS Brotzu Cagliari, Cagliari, Italy
| | - Maria Cristina Nuzzi
- UOC Patologia Clinica - Sezione di Genetica Medica, Ospedale SS. Annunziata Taranto - ASL TARANTO, Taranto, Italy
| | - Angelo Cellamare
- UOC Patologia Clinica - Sezione di Genetica Medica, Ospedale SS. Annunziata Taranto - ASL TARANTO, Taranto, Italy
| | - Paola Casieri
- UOC Patologia Clinica - Sezione di Genetica Medica, Ospedale SS. Annunziata Taranto - ASL TARANTO, Taranto, Italy
| | - Rosa Busuito
- Laboratorio di Genetica Molecolare e Citogenetica - Sezione di Citogenetica, UOC Laboratorio Analisi - ASST Ovest Milanese, Legnano, Italy
| | | | - Carla Cesarano
- U.O.C Genetica Medica, Policlinico Riuniti Foggia, Foggia, Italy
| | - Orsola Privitera
- SOS Genetica e Diagnostica di Laboratorio, Azienda USL Toscana Centro, Presidio Ospedale S. Stefano, Prato, Italy
| | - Daniela Melani
- SOS Genetica e Diagnostica di Laboratorio, Azienda USL Toscana Centro, Presidio Ospedale S. Stefano, Prato, Italy
| | - Cristina Menozzi
- SSD Genetica Medica, Dipartimento Materno Infantile, AOU Policlinico Modena, Modena, Italy
| | - Cristina Falcinelli
- SSD Genetica Medica, Dipartimento Materno Infantile, AOU Policlinico Modena, Modena, Italy
| | - Olga Calabrese
- SSD Genetica Medica, Dipartimento Materno Infantile, AOU Policlinico Modena, Modena, Italy
| | - Paola Battaglia
- Laboratorio di Genetica, UOC Genetica Medica, AUSL Imola, Imola, Italy
| | | | - Tamara Stampalija
- Unit of Fetal Medicine and Prenatal Diagnosis, Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy.,Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Carmela Ardisia
- Genetica Medica IRCCS Ospedale "Burlo Garofolo", Trieste, Italy
| | - Paolo Gasparini
- Genetica Medica IRCCS Ospedale "Burlo Garofolo", Trieste, Italy
| | - Peter Benn
- Department of Obstetrics and Gynecology, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Antonio Novelli
- U.O.C. Laboratorio di Genetica Medica, Ospedale Pediatrico del Bambino Gesù, IRCCS, Roma, Italy
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Barrett AN, Huang Z, Aung S, Ho SSY, Roslan NS, Mahyuddin AP, Biswas A, Choolani M. Whole-Chromosome Karyotyping of Fetal Nucleated Red Blood Cells Using the Ion Proton Sequencing Platform. Genes (Basel) 2022; 13:genes13122257. [PMID: 36553524 PMCID: PMC9778445 DOI: 10.3390/genes13122257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/26/2022] [Accepted: 11/26/2022] [Indexed: 12/02/2022] Open
Abstract
The current gold standard for the definitive diagnosis of fetal aneuploidy uses either chorionic villus sampling (CVS) or amniocentesis, both of which are which are invasive procedures carrying a procedure-related risk of miscarriage of up to 0.1-0.2%. Non-invasive prenatal diagnosis using fetal nucleated red blood cells (FNRBCs) isolated from maternal peripheral venous blood would remove this risk of miscarriage since these cells can be isolated from the mother's blood. We aimed to detect whole-chromosome aneuploidies from single nucleated fetal red blood cells using whole-genome amplification followed by massively parallel sequencing performed on a semiconductor sequencing platform. Twenty-six single cells were picked from the placental villi of twelve patients thought to have a normal fetal genotype and who were undergoing elective first-trimester surgical termination of pregnancy. Following karyotyping, it was subsequently found that two of these cases were also abnormal (one trisomy 15 and one mosaic genotype). One single cell from chorionic villus samples for two patients carrying a fetus with trisomy 21 and two single cells from women carrying fetuses with T18 were also picked. Pooled libraries were sequenced on the Ion Proton and data were analysed using Ion Reporter software. We correctly classified fetal genotype in all 24 normal cells, as well as the 2 T21 cells, the 2 T18 cells, and the two T15 cells. The two cells picked from the fetus with a mosaic result by CVS were classified as unaffected, suggesting that this was a case of confined placental mosaicism. Fetal sex was correctly assigned in all cases. We demonstrated that semiconductor sequencing using commercially available software for data analysis can be achieved for the non-invasive prenatal diagnosis of whole-chromosome aneuploidy with 100% accuracy.
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Affiliation(s)
- Angela N. Barrett
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
| | - Zhouwei Huang
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
| | - Sarah Aung
- iGene Laboratory Pte Ltd., 1 Science Park Road #04-10, The Capricorn, Singapore 117528, Singapore
| | - Sherry S. Y. Ho
- iGene Laboratory Pte Ltd., 1 Science Park Road #04-10, The Capricorn, Singapore 117528, Singapore
| | - Nur Syazana Roslan
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
| | - Aniza P. Mahyuddin
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
| | - Arijit Biswas
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
- Department of Obstetrics & Gynaecology, National University Hospital, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
| | - Mahesh Choolani
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
- Department of Obstetrics & Gynaecology, National University Hospital, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
- Correspondence:
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45
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Yang SY, Kang KM, Kim SY, Lim SY, Jang HY, Hong K, Cha DH, Shim SH, Joung JG. Combined Model-Based Prediction for Non-Invasive Prenatal Screening. Int J Mol Sci 2022; 23:ijms232314990. [PMID: 36499318 PMCID: PMC9737181 DOI: 10.3390/ijms232314990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The risk of chromosomal abnormalities in the child increases with increasing maternal age. Although non-invasive prenatal testing (NIPT) is a safe and effective prenatal screening method, the accuracy of the test results needs to be improved owing to various testing conditions. We attempted to achieve a more accurate and robust prediction of chromosomal abnormalities by combining multiple methods. Here, three different methods, namely standard Z-score, normalized chromosome value, and within-sample reference bin, were used for 1698 reference and 109 test samples of whole-genome sequencing. The logistic regression model combining the three methods achieved a higher accuracy than any single method. In conclusion, the proposed method offers a promising approach for increasing the reliability of NIPT.
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Affiliation(s)
- So-Yun Yang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Kyung Min Kang
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06135, Republic of Korea
| | - Sook-Young Kim
- CHA Future Medicine Research Institute, CHA Bundang Medical Center, Seongnam 13488, Republic of Korea
| | - Seo Young Lim
- Department of Biomedical Engineering, Hankuk University of Foreign Studies, Yongin 17035, Republic of Korea
| | - Hee Yeon Jang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06135, Republic of Korea
| | - Kirim Hong
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul 06135, Republic of Korea
| | - Dong Hyun Cha
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06135, Republic of Korea
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul 06135, Republic of Korea
| | - Sung Han Shim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06135, Republic of Korea
- Correspondence: (S.H.S.); (J.-G.J.); Tel.: +82-31-881-7182 (J.-G.J.); +82-31-881-7148 (S.H.S.)
| | - Je-Gun Joung
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
- CHA Future Medicine Research Institute, CHA Bundang Medical Center, Seongnam 13488, Republic of Korea
- Institute for Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Republic of Korea
- Correspondence: (S.H.S.); (J.-G.J.); Tel.: +82-31-881-7182 (J.-G.J.); +82-31-881-7148 (S.H.S.)
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46
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Lee J, Lee SM, Ahn JM, Lee TR, Kim W, Cho EH, Ki CS. Development and performance evaluation of an artificial intelligence algorithm using cell-free DNA fragment distance for non-invasive prenatal testing (aiD-NIPT). Front Genet 2022; 13:999587. [DOI: 10.3389/fgene.2022.999587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/09/2022] [Indexed: 11/30/2022] Open
Abstract
With advances in next-generation sequencing technology, non-invasive prenatal testing (NIPT) has been widely implemented to detect fetal aneuploidies, including trisomy 21, 18, and 13 (T21, T18, and T13). Most NIPT methods use cell-free DNA (cfDNA) fragment count (FC) in maternal blood. In this study, we developed a novel NIPT method using cfDNA fragment distance (FD) and convolutional neural network-based artificial intelligence algorithm (aiD-NIPT). Four types of aiD-NIPT algorithm (mean, median, interquartile range, and its ensemble) were developed using 2,215 samples. In an analysis of 17,678 clinical samples, all algorithms showed >99.40% accuracy for T21/T18/T13, and the ensemble algorithm showed the best performance (sensitivity: 99.07%, positive predictive value (PPV): 88.43%); the FC-based conventional Z-score and normalized chromosomal value showed 98.15% sensitivity, with 40.77% and 36.81% PPV, respectively. In conclusion, FD-based aiD-NIPT was successfully developed, and it showed better performance than FC-based NIPT methods.
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47
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Kamath V, Chacko MP, Kamath MS. Non-invasive Prenatal Testing in Pregnancies Following Assisted Reproduction. Curr Genomics 2022; 23:326-336. [PMID: 36778193 PMCID: PMC9878858 DOI: 10.2174/1389202923666220518095758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/17/2022] [Accepted: 04/05/2022] [Indexed: 11/22/2022] Open
Abstract
In the decade since non-invasive prenatal testing (NIPT) was first implemented as a prenatal screening tool, it has gained recognition for its sensitivity and specificity in the detection of common aneuploidies. This review mainly focuses on the emerging role of NIPT in pregnancies following assisted reproductive technology (ART) in the light of current evidence and recommendations. It also deals with the challenges, shortcomings and interpretational difficulties related to NIPT in ART pregnancies, with particular emphasis on twin and vanishing twin pregnancies, which are widely regarded as the Achilles' heel of most pre-natal screening platforms. Future directions for exploration towards improving the performance and extending the scope of NIPT are also addressed.
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Affiliation(s)
- Vandana Kamath
- Department of Cytogenetics, Christian Medical College, Vellore 632004, India
| | - Mary Purna Chacko
- Department of Cytogenetics, Christian Medical College, Vellore 632004, India
| | - Mohan S. Kamath
- Department of Reproductive Medicine and Surgery, Christian Medical College, Vellore 632004, India
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48
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Endogenous cell-free DNA in fetal bovine serum introduces artifacts to in vitro cell-free DNA models. Biotechniques 2022; 73:219-226. [DOI: 10.2144/btn-2022-0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Cell-free DNA (cfDNA) is of growing clinical and research significance. In vitro cfDNA models are a useful tool in cfDNA research; however, artifacts in these models may have implications for the interpretation of new and published data. This report aimed to establish how endogenous cfDNA in fetal bovine serum (FBS) may influence in vitro cfDNA measurements. Three commercial cell culture media, supplemented with 10% FBS, were analyzed for the presence of cfDNA, with and without culture with ovarian cancer cell lines. cfDNA from FBS was identified with all three commercial media and contributed a major portion of 167-bp cfDNA. Future studies should account for bovine cfDNA in FBS-supplemented media when conducting in vitro cfDNA research.
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49
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Nardi E, Seravalli V, Serena C, Mecacci F, Massi D, Bertaccini B, Di Tommaso M, Castiglione F. A study on the placenta in stillbirth: an evaluation of molecular alterations through next generation sequencing. Placenta 2022; 129:7-11. [PMID: 36179485 DOI: 10.1016/j.placenta.2022.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/04/2022] [Accepted: 09/12/2022] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Placental dysfunction is one of the most common causes of Intrauterine Fetal Demise (IUFD). Due to its characteristics, the placenta may be the target of molecular research aimed to investigate potential causes of IUFD. In the literature, there are no studies on human placentas that have investigated possible associations between somatic mutations and the occurrence of IUFD. The aim of this study was to identify the presence of gene mutations in placental tissues in a series of cases of IUFD and to evaluate potential correlations with placental microscopic findings. MATERIALS AND METHODS Thirty-seven samples of formalin-fixed and paraffin-embedded placental tissues were retrospectively selected from pregnancies ending in IUFD between 23rd to 40th week. Six control placentas of physiological pregnancies were included as controls. After sampling, made according to standardized protocol and conventional histopathological examination, placental tissues were subjected to DNA extraction and sequencing by means of Next Generation Sequencing with a 56-gene panel. RESULTS The most frequent mutation observed in 32/37 IUFD cases (86.5%) and absent in any of the 6 control placentas was in c-KIT gene, which is implicated in placental tissue differentiation. However, no significant correlation was found between the presence of individual gene mutations and placental histopatological findings. DISCUSSION As the present study found an elevated frequency of c-KIT mutation in IUFD, it further supports the hypothesis that c-KIT is involved in abnormal tissue differentiation leading to altered placental vascularization and function.
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Affiliation(s)
- Eleonora Nardi
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy.
| | - Viola Seravalli
- Department of Health Science, Division of Obstetrics & Gynecology, University of Florence, Florence, Italy
| | - Caterina Serena
- Obstetrics and Gynecology Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Federico Mecacci
- Obstetrics and Gynecology Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Daniela Massi
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Bruno Bertaccini
- Department of Statistics, Informatics, and Application "G. Parenti,", University of Florence, Florence, Italy
| | - Mariarosaria Di Tommaso
- Department of Health Science, Division of Obstetrics & Gynecology, University of Florence, Florence, Italy
| | - Francesca Castiglione
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy
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50
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Xu C, Li J, Chen S, Cai X, Jing R, Qin X, Pan D, Zhao X, Ma D, Xu X, Liu X, Wang C, Yang B, Zhang L, Li S, Chen Y, Pan N, Tang P, Song J, Liu N, Zhang C, Zhang Z, Qiu X, Lu W, Ying C, Li X, Xu C, Wang Y, Wu Y, Huang HF, Zhang J. Genetic deconvolution of fetal and maternal cell-free DNA in maternal plasma enables next-generation non-invasive prenatal screening. Cell Discov 2022; 8:109. [PMID: 36229437 PMCID: PMC9562363 DOI: 10.1038/s41421-022-00457-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
Current non-invasive prenatal screening (NIPS) analyzes circulating fetal cell-free DNA (cfDNA) in maternal peripheral blood for selected aneuploidies or microdeletion/duplication syndromes. Many genetic disorders are refractory to NIPS largely because the maternal genetic material constitutes most of the total cfDNA present in the maternal plasma, which hinders the detection of fetus-specific genetic variants. Here, we developed an innovative sequencing method, termed coordinative allele-aware target enrichment sequencing (COATE-seq), followed by multidimensional genomic analyses of sequencing read depth, allelic fraction, and linked single nucleotide polymorphisms, to accurately separate the fetal genome from the maternal background. Analytical confounders including multiple gestations, maternal copy number variations, and absence of heterozygosity were successfully recognized and precluded for fetal variant analyses. In addition, fetus-specific genomic characteristics, including the cfDNA fragment length, meiotic error origins, meiotic recombination, and recombination breakpoints were identified which reinforced the fetal variant assessment. In 1129 qualified pregnancies tested, 54 fetal aneuploidies, 8 microdeletions/microduplications, and 8 monogenic variants were detected with 100% sensitivity and 99.3% specificity. Using the comprehensive cfDNA genomic analysis tools developed, we found that 60.3% of aneuploidy samples had aberrant meiotic recombination providing important insights into the mechanism underlying meiotic nondisjunctions. Altogether, we show that the genetic deconvolution of the fetal and maternal cfDNA enables thorough and accurate delineation of fetal genome which paves the way for the next-generation prenatal screening of essentially all types of human genetic disorders.
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Affiliation(s)
- Chenming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jianli Li
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaoqiang Cai
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Ruilin Jing
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaomei Qin
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Dong Pan
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xin Zhao
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Dongyang Ma
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiufeng Xu
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaojun Liu
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Can Wang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Bingxin Yang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lanlan Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuyuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiyao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nina Pan
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Tang
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang, China
| | - Jieping Song
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Nian Liu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Chen Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiwei Zhang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiang Qiu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Weiliang Lu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chunmei Ying
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Congjian Xu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yanlin Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanting Wu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.
| | - He-Feng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China. .,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
| | - Jinglan Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Beijing BioBiggen Technology Co., Ltd, Beijing, China.
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