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Prenatal diagnosis of familial submicroscopic duplication at 18q22.3 without phenotypic abnormalities. Taiwan J Obstet Gynecol 2020; 59:446-450. [PMID: 32416897 DOI: 10.1016/j.tjog.2020.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2020] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVE To report a case of familial submicroscopic duplication at 18q22.3 without phenotypic abnormalities. CASE REPORT Here, we reported two different cases with novel copy number variation at chromosome 18q22.3: one carried a maternally inherited 2.36 Mb microduplication, and the other carried a patrilineally inherited 1.74 Mb microduplication. The HumanCytoSNP-12 array allows for the visualization of the CNVs and maps the breakpoints. Both parents with the microduplication at 18q22.3 as well as their foetuses had normal phenotypes; the infants were regularly followed up after one year of age, and no abnormalities were found, including abnormalities related to growth, intelligence and sexual development. CONCLUSION Our report showed that the duplication of 18q22.3 (chr18:68,606,012-71,287,101) might represent a benign variant.
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Wilkins-Haug L, Zhang C, Cerveira E, Ryan M, Mil-Homens A, Zhu Q, Reddi H, Lee C, Bianchi DW. Biological explanations for discordant noninvasive prenatal test results: Preliminary data and lessons learned. Prenat Diagn 2019; 38:445-458. [PMID: 29633279 DOI: 10.1002/pd.5260] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/25/2018] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Maternal plasma cell-free DNA (cfDNA) analysis is a powerful screening tool for Down syndrome. In a pilot series, we examined biologic causes of discordance between the cfDNA test results and the fetal karyotype. We also explored the feasibility of obtaining trio biospecimens by using parental engagement. METHODS A convenience sample of women with discordant cfDNA results were recruited by their care providers. We provided shipping materials and instructions for biospecimen collection. Maternal, newborn, and placental samples were examined with droplet digital PCR. RESULTS Thirteen of 15 women successfully had biospecimens obtained remotely. High-quality DNA was extracted in 12 of 13 women. Presumed biologic etiologies for discordance were identified in 7 of 12 women: 3 cases from additional clinical review (male renal transplant, vanishing twin, and colon cancer) and 4 cases from additional laboratory investigation using droplet digital PCR (3 with confined placental mosaicism and 1 with true fetal mosaicism). CONCLUSIONS Understanding the biology behind cfDNA-fetal karyotype discordancy is useful for follow-up clinical care. Our study suggests that most cases could be resolved by using a trio biospecimen protocol and parental involvement. To improve accuracy, additional sequencing of biospecimens will be required.
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Affiliation(s)
- Louise Wilkins-Haug
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Eliza Cerveira
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mallory Ryan
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Adam Mil-Homens
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Qihui Zhu
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Honey Reddi
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Charles Lee
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Diana W Bianchi
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA.,Prenatal Genomics and Therapy Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Bianchi DW. Cherchez la femme: maternal incidental findings can explain discordant prenatal cell-free DNA sequencing results. Genet Med 2017; 20:910-917. [PMID: 29215645 PMCID: PMC10082650 DOI: 10.1038/gim.2017.219] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 10/31/2017] [Indexed: 12/19/2022] Open
Abstract
Circulating DNA fragments in a pregnant woman's plasma derive from three sources: placenta, maternal bone marrow, and fetus. Prenatal sequencing to noninvasively screen for fetal chromosome abnormalities is performed on this mixed sample; results can therefore reflect the maternal as well as the fetoplacental DNA. Although it is recommended that pretest counseling include the possibility of detecting maternal genomic imbalance, this seldom occurs. Maternal abnormalities that can affect a prenatal screening test result include disorders that affect the size and metabolism of DNA, such as B12 deficiency, autoimmune disease, and intrahepatic cholestasis of pregnancy. Similarly, maternal tumors, both benign and malignant, can release DNA fragments that contain duplications or deletions. Bioinformatics algorithms can subsequently interpret the raw sequencing data incorrectly, resulting in false-positive test reports of fetal monosomies or test failures. Maternal sex-chromosome abnormalities, both constitutional and somatic, can generate results that are discordant with fetal ultrasound examination or karyotype. Maternal copy-number variants and mosaicism for autosomal aneuploidies can also skew interpretation. A maternal etiology should therefore be considered in the differential diagnosis of prenatal cell-free DNA test failures, false-positive and false-negative sequencing results. Further study is needed regarding the clinical utility of reporting maternal incidental findings.
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Zhou X, Sui L, Xu Y, Song Y, Qi Q, Zhang J, Zhu H, Sun H, Tian F, Xu M, Cram DS, Liu J. Contribution of maternal copy number variations to false-positive fetal trisomies detected by noninvasive prenatal testing. Prenat Diagn 2017; 37:318-322. [PMID: 28152582 DOI: 10.1002/pd.5014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/11/2017] [Accepted: 01/29/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Xiya Zhou
- Department of Obstetrics and Gynecology; Peking Union Medical College Hospital; Beijing China
| | - Lili Sui
- Department of Obstetrics and Gynecology; Peking Union Medical College Hospital; Beijing China
| | - Yalan Xu
- Department of Obstetrics and Gynecology; Peking Union Medical College Hospital; Beijing China
| | - Yijun Song
- Department of Obstetrics and Gynecology; Peking Union Medical College Hospital; Beijing China
| | - Qingwei Qi
- Department of Obstetrics and Gynecology; Peking Union Medical College Hospital; Beijing China
| | | | | | - Huaiyu Sun
- Berry Genomics Corporation; Beijing China
| | - Feng Tian
- Berry Genomics Corporation; Beijing China
| | - Mengnan Xu
- Berry Genomics Corporation; Beijing China
| | | | - Juntao Liu
- Department of Obstetrics and Gynecology; Peking Union Medical College Hospital; Beijing China
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Accuracy and clinical value of maternal incidental findings during noninvasive prenatal testing for fetal aneuploidies. Genet Med 2016; 19:306-313. [PMID: 27584908 DOI: 10.1038/gim.2016.113] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/16/2016] [Indexed: 01/16/2023] Open
Abstract
PURPOSE Genome-wide sequencing of cell-free (cf)DNA of pregnant women aims to detect fetal chromosomal imbalances. Because the largest fraction of cfDNA consists of maternal rather than fetal DNA fragments, maternally derived copy-number variants (CNVs) are also measured. Despite their potential clinical relevance, current analyses do not interpret maternal CNVs. Here, we explore the accuracy and clinical value of maternal CNV analysis. METHODS Noninvasive prenatal testing was performed by whole-genome shotgun sequencing on plasma samples. Following mapping of the sequencing reads, the landscape of maternal CNVs was charted for 9,882 women using SeqCBS analysis. Recurrent CNVs were validated retrospectively by comparing their incidence with published reports. Nonrecurrent CNVs were prospectively confirmed by array comparative genomic hybridization or fluorescent in situ hybridization analysis on maternal lymphocytes. RESULTS Consistent with population estimates, 10% nonrecurrent and 0.4% susceptibility CNVs for low-penetrant genomic disorders were identified. Five clinically actionable variants were reported to the pregnant women, including haploinsufficiency of RUNX1, a mosaicism for segmental chromosome 13 deletion, an unbalanced translocation, and two interstitial chromosome X deletions. CONCLUSION Shotgun sequencing of cfDNA not only enables the detection of fetal aneuploidies but also reveals the presence of maternal CNVs. Some of those variants are clinically actionable or could potentially be harmful for the fetus. Interrogating the maternal CNV landscape can improve overall pregnancy management, and we propose reporting those variants if clinically relevant. The identification and reporting of such CNVs pose novel counseling dilemmas that warrant further discussions and development of societal guidelines.Genet Med 19 3, 306-313.
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Snyder HL, Curnow KJ, Bhatt S, Bianchi DW. Follow-up of multiple aneuploidies and single monosomies detected by noninvasive prenatal testing: implications for management and counseling. Prenat Diagn 2016; 36:203-9. [PMID: 26785403 PMCID: PMC5067681 DOI: 10.1002/pd.4778] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/12/2016] [Accepted: 01/15/2016] [Indexed: 12/17/2022]
Abstract
Objectives To determine the underlying biological basis for noninvasive prenatal testing (NIPT) results of multiple aneuploidies or autosomal monosomies. Methods Retrospective analysis of 113,415 tests to determine the study cohort, consisting of 138 (0.12%) cases reported as a single autosomal monosomy (n = 65), single trisomy with a sex chromosome aneuploidy (n = 36), or with multiple aneuploidies (n = 37). Clinical outcome information was reviewed and stratified into eight categories according to whether the karyotype or sonographic information agreed or disagreed with sequencing results. Results Of 67 cases with fetal or neonatal karyotypes available, 16 (24%) were partially or fully concordant with the NIPT result, 4 (6%) had aneuploidy on a reference chromosome, and 47 (70%) had normal fetal chromosomes, in which 5/47 had maternal malignancies reported. One case of maternal mosaic trisomy 8 was also detected. Of cases with no fetal karyotype information, ten had an abnormal clinical outcome, one was a normal live birth, and one reported maternal malignancy. Conclusions Noninvasive prenatal test results of autosomal monosomy or multiple aneuploidies are rare but have a diversity of underlying biologic causes. Some reflect the fetal karyotype; some reflect the presence of other maternal or fetal chromosome abnormalities, and a small number are linked to maternal disease. © 2016 Illumina. Prenatal Diagnosis published by John Wiley & Sons, Ltd. What's already known about this topic?Noninvasive prenatal testing (NIPT) has been validated for common autosomal trisomies (trisomy 21, 18, and 13), sex chromosome aneuploidies, and a selection of microdeletion syndromes. NIPT findings that are discordant with the fetal karyotype can be because of biological reasons, such as confined placental mosaicism, maternal chromosome abnormalities, and other maternal conditions such as occult malignancy.
What does this study add?Clinical and karyotype outcome information for cases that received an NIPT result indicating an autosomal monosomy or multiple aneuploidies. Some autosomal monosomy and multiple aneuploidy results reflect the true fetal karyotype, and some are explained by other factors, such as other fetal or maternal chromosomal abnormalities or maternal disease. This information will help providers with post‐test counseling for these rare and unusual results.
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Affiliation(s)
| | | | | | - Diana W Bianchi
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
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Kovaleva NV, Cotter PD. Somatic/gonadal mosaicism for structural autosomal rearrangements: female predominance among carriers of gonadal mosaicism for unbalanced rearrangements. Mol Cytogenet 2016; 9:8. [PMID: 26823686 PMCID: PMC4730740 DOI: 10.1186/s13039-015-0211-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/21/2015] [Indexed: 01/23/2023] Open
Abstract
Background Mosaicism for chromosomal structural rearrangements (Rea) is rare and the timing and mechanisms of mosaic Rea formation, maintenance, and clinical manifestation are poorly understood. To date, there are no published data on the cytogenetic profile of mosaic Reas. The question as to whether the proportion of abnormal cells in the carrier’s cultured blood is clinically significant remains unanswered. A previous study showed a strong female preponderance among carriers of mosaicism for Rea with pericentromeric breaks, indicating female-specific instability in early embryos. However, there is no corresponding study on male to female sex ratio (SR) among carriers of somatic and/or gonadal mosaicism for non-centromeric Rea. Population rates of mosaic Rea carriers calculated from consecutive series of patients referred for various reasons and from prenatal samples have not been established. Therefore the objectives of the present study were several-fold: (1) a study on profiles of Rea involved, (2) comparative analysis of the proportion of cells with unbalanced Rea in blood cultures from asymptomatic and affected carriers, (3) comparative analysis of SR in carriers of mosaicism for balanced and unbalanced Rea, and (4) determination of the population frequency of mosaicism for autosomal Rea. Results One hundred and three cases of mosaicism for autosomal non-centromeric Rea (N/Rea; normal line/structural rearrangement) in which the sex of the carrier had been specified were identified in the literature. Among balanced Rea, there was a prevalence of reciprocal translocations (89 %) over inversions (11 %). Among unbalanced Rea, deletions were the most frequent (40 %), followed by duplications (25 %) and rings (16 %). Derivatives and other chromosome abnormalities were less frequent (9 and 10 %). Eight of eleven (73 %) affected carriers of unbalanced Rea displayed a high proportion (>50 %) of abnormal cells compared to 4/37 (11 %) in asymptomatic carriers, p < 0.0001. Among carriers of mosaicism for balanced Rea there was a slight male predominance, 24 M/22 F, unlike the strong female predominance among carriers of mosaicism for unbalanced Rea, 11 M/46 F, p < 0.0001. Among ten carriers of unbalanced Rea with reproductive failure, only one was a male with infertility, and one was a partner of a woman experiencing recurrent spontaneous abortion. Population rates of mosaics for reciprocal translocaton (N/rcp), inversion (N/inv), and unbalanced Rea (N/unbal Rea) calculated from published data on consecutive series of patients with reproductive failures were 0.02 ‰, 0.005 ‰, and 0.002 ‰, correspondingly. Among 30,376 infertile patients three carriers of mosaicism for balanced Rea were identified (two cases of N/rcp and one case of N/inv), whereas among 26,384 patients with habitual abortion seven carriers were detected (five N/rcp and two N/inv). Among all 56,760 tested patients with reproductive failures only one was found to be a carrier of mosaicism for an unbalanced Rea (N/del, mosaicism for deletion). Conclusions A high proportion of Rea cells (>50 %) detected in cultured T-lymphocytes is associated with clinical manifestation of chromosomal imbalance. A strong female prevalence among carriers of mosaicism for unbalanced Rea suggests male-specific selection against abnormal cells rather than impairment of male gametogenesis, as the latter suggests a better prognosis for male fetuses. These findings should be taken into consideration when genetic counseling of patients referred after a diagnosis of mosaicism for an unbalanced rearrangement in a fetus.
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Affiliation(s)
- Natalia V Kovaleva
- Department of Inherited Diseases, The Turner's Scientific and Research Orthopaedic Institute for Children, Parkovaya Str. 64-68, St. Petersburg, 196603 Russian Federation
| | - Philip D Cotter
- Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143 USA ; ResearchDx Inc., Irvine, CA 92618 USA
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Deprest J, Ghidini A, Van Mieghem T, Bianchi DW, Faas B, Chitty LS. In case you missed it: the Prenatal Diagnosis
editors bring you the most significant advances of 2015. Prenat Diagn 2016; 36:3-9. [DOI: 10.1002/pd.4758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jan Deprest
- Department of Obstetrics and Gynecology; University Hospitals Leuven; Leuven Belgium
- Academic Department Development and Regeneration, Biomedical Sciences; KU Leuven; Leuven Belgium
| | - Alessandro Ghidini
- Department of Obstetrics and Gynecology; Georgetown University Hospital; Washington DC USA
| | - Tim Van Mieghem
- Department of Obstetrics and Gynecology; University Hospitals Leuven; Leuven Belgium
- Academic Department Development and Regeneration, Biomedical Sciences; KU Leuven; Leuven Belgium
| | - Diana W. Bianchi
- Mother Infant Research Institute, Tufts Medical Center; Boston MA
- Floating Hospital for Children; Boston MA USA
| | - Brigitte Faas
- Department of Human Genetics; Radboud University Medical Centre; Nijmegen the Netherlands
| | - Lyn S. Chitty
- UCL Institute of Child Health; Great Ormond Street Hospital for Children and NHS Foundation Trust; London UK
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Abstract
Prenatal diagnosis and screening have undergone rapid development in recent years, with advances in molecular technology driving the change. Noninvasive prenatal testing (NIPT) for Down syndrome as a highly sensitive screening test is now available worldwide through the commercial sector with many countries moving toward implementation into their publically funded maternity systems. Noninvasive prenatal diagnosis (NIPD) can now be performed for definitive diagnosis of some recessive and X-linked conditions, rather than just paternally inherited dominant and de novo conditions. NIPD/T offers pregnant couples greater choice during their pregnancy as these safer methods avoid the risk of miscarriage associated with invasive testing. As the cost of sequencing falls and technology develops further, there may well be potential for whole exome and whole genome sequencing of the unborn fetus using cell-free DNA in the maternal plasma. How such assays can or should be implemented into the clinical setting remain an area of significant debate, but it is clear that the progress made to date for safer prenatal testing has been welcomed by expectant couples and their healthcare professionals.
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Chitty LS, Bianchi DW. Next generation sequencing and the next generation: how genomics is revolutionizing reproduction. Prenat Diagn 2015; 35:929-30. [PMID: 26443108 DOI: 10.1002/pd.4679] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Lyn S Chitty
- UCL Institute of Child Health and Great Ormond Street NHS Foundation Trust, London, UK
| | - Diana W Bianchi
- Floating Hospital for Children at Tufts Medical Center, Boston, USA
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