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Liu G. Chromosomal aberration analysis: Novel noninvasive techniques for early-stage cancer screening. Clin Chim Acta 2024; 560:119736. [PMID: 38763468 DOI: 10.1016/j.cca.2024.119736] [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: 04/12/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/21/2024]
Abstract
OBJECTIVE Chromosome breakage is a catastrophic event that leads to the progressive development and progression of cancer. In order to analyze the changes of peripheral blood microenvironment of tumor patients, to explore the indicators of non-specific non-invasive tumor early screening. This paper presents a new idea of whether the gene sequence near the DNA damage break point is the gene sequence that controls the unrestricted growth of normal cells. METHODS The chromosomal aberrations of peripheral blood lymphocytes were analysed in 60 healthy adult and 49 cancer patients before radiotherapy. RESULTS The detection rate of chromosomal aberrations was high in tumor patients, and "dicentric + translocations" of chromosomes were detected in 36 patients (73.47 %). The chi-square test showed statistically significant differences (P < 0.01), and chromosome adhesion and dissolution were observed. CONCLUSIONS "Dicentric + Translocation" chromosome can be used as a nonspecific early screening indicator for cancer. This is worthy of further study. This index can be used to determine the genetic basis of various cancers at the gene level to modify the base sequence and prevent the occurrence of cancer. It is worthy of further study, and it can provide a new method for gene therapy of tumors.
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Affiliation(s)
- Gang Liu
- Gansu Provincial Center for Disease Control and Prevention, (Joint Laboratory of Institute of Radiology, Chinese Academy of Medical Sciences), NO.310 Donggang West Road, Lanzhou, Gansu, China.
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Soster E, Dyr B, Caldwell S, Sussman A, Magharyous H. Prenatal cfDNA Screening for Emanuel Syndrome and Other Unbalanced Products of Conception in Carriers of the Recurrent Balanced Translocation t(11;22): One Laboratory's Retrospective Experience. Genes (Basel) 2023; 14:1924. [PMID: 37895273 PMCID: PMC10606745 DOI: 10.3390/genes14101924] [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: 08/31/2023] [Revised: 09/25/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Prenatal cell-free DNA screening (cfDNA) can identify fetal chromosome abnormalities beyond common trisomies. Emanuel syndrome (ES), caused by an unbalanced translocation between chromosomes 11 and 22, has lacked a reliable prenatal screening option for families with a carrier parent. A cohort of cases (n = 46) sent for cfDNA screening with indications and/or results related to ES was queried; diagnostic testing and pregnancy outcomes were requested and analyzed. No discordant results were reported or suspected; there were ten true positives with diagnostic confirmation, six likely concordant positives based on known translocations and consistent cfDNA data, and twenty-six true negatives, by diagnostic testing or birth outcomes. For cases with parental testing, all affected ES cases had maternal translocation carriers. Expanded cfDNA may provide reassurance for t(11;22) carriers with screen negative results, and screen positive results appear to reflect a likely affected fetus, especially with a known maternal translocation. Current society guidelines support the use of expanded cfDNA screening in specific circumstances, such as for translocation carriers, with appropriate counseling. Diagnostic testing is recommended for prenatal diagnosis of ES and other chromosome abnormalities in pregnancy. To our knowledge, this cohort is the largest published group of cases with prenatal screening for carriers of t(11;22).
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Affiliation(s)
- Erica Soster
- Labcorp, La Jolla, San Diego, 92121 CA, USA; (B.D.); (S.C.); (H.M.)
| | - Brittany Dyr
- Labcorp, La Jolla, San Diego, 92121 CA, USA; (B.D.); (S.C.); (H.M.)
| | | | | | - Hany Magharyous
- Labcorp, La Jolla, San Diego, 92121 CA, USA; (B.D.); (S.C.); (H.M.)
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van Zutven LJCM, Mijalkovic J, van Veghel-Plandsoen M, Goense M, Polak M, Knapen MFCM, de Weerd S, Joosten M, Diderich KEM, Hoefsloot LH, Van Opstal D, Srebniak MI. What proportion of couples with a history of recurrent pregnancy loss and with a balanced rearrangement in one parent can potentially be identified through cell-free DNA genotyping? Mol Cytogenet 2023; 16:26. [PMID: 37775759 PMCID: PMC10543837 DOI: 10.1186/s13039-023-00657-x] [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: 07/07/2023] [Accepted: 09/14/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Balanced chromosome aberrations are reported in about 1:30 couples with recurrent pregnancy loss (RPL). Karyotyping of both parents is necessary to identify these aberrations. Genome-wide non-invasive prenatal testing (NIPT) in case of recurrent pregnancy loss could be a more efficient way to identify couples at increased risk for carrying a balanced chromosome rearrangement. The aim of this study was to evaluate whether the potential fetal imbalances caused by parental balanced aberrations detected in our center are large enough to be detectable by genome-wide non-invasive prenatal testing (NIPT). MATERIAL AND METHODS From January 1970 until May 2020 our laboratory received 30,863 unique requests for karyotyping due to RPL. We have identified 16,045 couples and evaluated all abnormal cytogenetic results to assess the minimal size of the involved chromosomal segments in potential unbalanced products of the rearrangements. RESULTS In the presented cohort we detected 277 aberrant balanced translocations/inversions in females and 185 in males amongst 16,045 couples with RPL, which can be translated to a risk of 1:35 (2.9%, 95% CI 2.6-3.2%). Our study showed that the vast majority (98.7%, 95% CI 97.1-99.5%) of these balanced aberrations will potentially cause a fetal imbalance > 10 Mb, which is detectable with genome-wide NIPT if it was performed during one of the miscarriages. CONCLUSIONS Our study suggests that genome-wide NIPT is able to reveal most unbalanced products of balanced chromosomal rearrangements carried by couples with RPL and therefore can potentially identify balanced chromosomal aberration carriers. Moreover, our data suggest that these couples can be offered NIPT in case they decline invasive testing in future pregnancies.
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Affiliation(s)
- Laura J C M van Zutven
- Department of Clinical Genetics, Erasmus Medical Centre, Dr Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Jona Mijalkovic
- Department of Clinical Genetics, Erasmus Medical Centre, Dr Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Monique van Veghel-Plandsoen
- Department of Clinical Genetics, Erasmus Medical Centre, Dr Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Margaret Goense
- Department of Clinical Genetics, Erasmus Medical Centre, Dr Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Marike Polak
- Department of Psychology, Education & Child Studies (DPECS), Erasmus University, Rotterdam, The Netherlands
| | - Maarten F C M Knapen
- Department of Obstetrics and Prenatal Medicine, Erasmus Medical Centre, Wytemaweg 80, Na-1517, 3015 GE, Rotterdam, The Netherlands
| | - Sabina de Weerd
- Department of Obstetrics and Gynaecology, Albert Schweitzer Hospital, Albert Schweitzerplaats 25, 3318 AT, Dordrecht, The Netherlands
| | - Marieke Joosten
- Department of Clinical Genetics, Erasmus Medical Centre, Dr Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus Medical Centre, Dr Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Lies H Hoefsloot
- Department of Clinical Genetics, Erasmus Medical Centre, Dr Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Diane Van Opstal
- Department of Clinical Genetics, Erasmus Medical Centre, Dr Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Malgorzata I Srebniak
- Department of Clinical Genetics, Erasmus Medical Centre, Dr Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
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Kleinfinger P, Brechard M, Luscan A, Trost D, Boughalem A, Mylene Valduga, Serero DR S, Costa JM, Lohmann L. Case Report: How whole-genome sequencing-based cell-free DNA prenatal testing can help identify a marker mhromosome. Front Genet 2022; 13:926290. [PMID: 36226188 PMCID: PMC9549001 DOI: 10.3389/fgene.2022.926290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
A supernumerary marker chromosome (SMC) is a structurally abnormal chromosome that cannot be characterized by conventional banding cytogenetics. Marker chromosomes are present in 0.075% of prenatal cases. They are associated with variable phenotypes, ranging from normal to severely abnormal, and the prognosis is largely dependent on the results of further cytogenomic analysis. Here, we report the identification and characterization of a marker chromosome following prenatal screening in a 39-year-old pregnant patient. The patient had a normal first trimester ultrasound but was high-risk for fetal chromosome anomalies based on the results of maternal serum parameters. Chorionic villus sampling was performed, and analysis of chorionic villi revealed the presence of two identical marker chromosomes. In the interest of a rapid identification of the markers, we performed noninvasive prenatal testing (NIPT) together with chorionic villus sampling. A pericentromeric 29 Mb duplication of chromosome 20: dup (20) (p13q11.21) was identified and thereafter confirmed by targeted metaphasic FISH. Whole-genome sequencing-based NIPT was instrumental in rapid characterization of the SMCs and allowed us to obviate the need for multiple expensive and time-consuming FISH analyses.
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Zhang YL, Jing XY, Wan JH, Pan M, Li DZ. Prenatal Silver-Russell Syndrome in a Chinese Family Identified by Non-Invasive Prenatal Testing. Mol Syndromol 2022; 13:323-327. [PMID: 36158051 PMCID: PMC9421674 DOI: 10.1159/000520389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/21/2021] [Indexed: 01/03/2023] Open
Abstract
Russell-Silver syndrome (SRS) is a rare condition characterized by poor growth before and after birth along with multiple physical and psychosocial characteristics such as short stature, characteristic facial features, body asymmetry, feeding difficulties, and learning disabilities. In this study, we report a family with 2 recurrent SRS pregnancies due to a derivative chromosome 15 that is the result of a maternally derived t(11;15) translocation, detected by non-invasive prenatal testing (NIPT). The 2 SRS fetuses were diagnosed by chromosomal microarray analysis, but a balanced, reciprocal translocation of the mother was disclosed by the combination of routine karyotyping and FISH. This study demonstrates that NIPT has the ability to identify submicroscopic copy number variations (CNVs) in fetuses, which in some cases may result from a parent being a balanced rearrangement carrier. Because of the differences in resolution and the various benefits and limitations of each genetic technique, great care must be taken when deciding on which test(s) to employ in family studies.
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Harasim T, Neuhann T, Behnecke A, Stampfer M, Holinski-Feder E, Abicht A. Initial Clinical Experience with NIPT for Rare Autosomal Aneuploidies and Large Copy Number Variations. J Clin Med 2022; 11:jcm11020372. [PMID: 35054066 PMCID: PMC8777675 DOI: 10.3390/jcm11020372] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVE Amniocentesis, chorionic villi sampling and first trimester combined testing are able to screen for common trisomies 13, 18, and 21 and other atypical chromosomal anomalies (ACA). The most frequent atypical aberrations reported are rare autosomal aneuploidies (RAA) and copy number variations (CNV), which are deletions or duplications of various sizes. We evaluated the clinical outcome of non-invasive prenatal testing (NIPT) results positive for RAA and large CNVs to determine the clinical significance of these abnormal results. METHODS Genome-wide NIPT was performed on 3664 eligible patient samples at a single genetics center. For patients with positive NIPT reports, the prescribing physician was asked retrospectively to provide clinical follow-up information using a standardized questionnaire. RESULTS RAAs and CNVs (>7 Mb) were detected in 0.5%, and 0.2% of tested cases, respectively. Follow up on pregnancies with an NIPT-positive result for RAA revealed signs of placental insufficiency or intra-uterine death in 50% of the cases and normal outcome at the time of birth in the other 50% of cases. We showed that CNV testing by NIPT allows for the detection of unbalanced translocations and relevant maternal health conditions. CONCLUSION NIPT for aneuploidies of all autosomes and large CNVs of at least 7 Mb has a low "non-reportable"-rate (<0.2%) and allows the detection of additional conditions of clinical significance.
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Reexamining the optimal nuchal translucency cutoff for diagnostic testing in the cell-free DNA and microarray era: results from the Victorian Perinatal Record Linkage study. Am J Obstet Gynecol 2021; 225:527.e1-527.e12. [PMID: 33957116 DOI: 10.1016/j.ajog.2021.03.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/11/2021] [Accepted: 03/09/2021] [Indexed: 01/27/2023]
Abstract
BACKGROUND The American College of Obstetricians and Gynecologists and the Society for Maternal-Fetal Medicine recently recommended offering genetic counseling and diagnostic testing for enlarged nuchal translucency at ≥3.0 mm, regardless of previous negative screening with noninvasive prenatal testing. OBJECTIVE This study aimed to perform a population-based, individual record linkage study to determine the optimal definition of an enlarged nuchal translucency for the detection of atypical chromosome abnormalities. STUDY DESIGN This was a retrospective study of women resident in Victoria, Australia, undergoing combined first-trimester screening during the 24-month period from January 2015 to December 2016. Linkages between statewide results for combined first-trimester screening, prenatal diagnostic procedures, and postnatal cytogenetic results from products of conception and infants up to 12 months of age were used to ascertain the frequency and type of chromosome abnormality by gestation and nuchal translucency measurement. An atypical chromosome abnormality was defined as any major chromosome abnormality other than whole chromosome aneuploidy involving chromosomes 21, 18, 13, X, and Y. RESULTS Of the 81,244 singleton pregnancies undergoing combined first-trimester screening, 491 (0.60%) had a nuchal translucency of ≥3.5 mm, 534 (0.66%) had a nuchal translucency of 3.0 to 3.4 mm, and 80,219 (98.74%) had a nuchal translucency of < 3.0 mm. When grouped by nuchal translucency multiples of the median (MoM), 192 (0.24%) had a nuchal translucency of ≥3.0 MoM, 513 (0.63%) had a nuchal translucency of 1.9 to 2.9 MoM, and 80,539 (99.13%) had a nuchal translucency of <1.9 MoM. A total of 1779 pregnancies underwent prenatal or postnatal diagnostic testing, of which 89.60% were performed by whole-genome single-nucleotide polymorphism chromosomal microarray. The frequency of total major chromosome abnormalities was significantly higher in the group with a nuchal translucency of ≥3.5 mm (147 of 491, 29.94%) than the group with a nuchal translucency of 3.0 to 3.4 mm (21 of 534, 3.93%) or a nuchal translucency of <3.0 mm (71 of 80,219, 0.09%) (P<.001). There were 93 atypical chromosome abnormalities in the total screened cohort. The frequency of an atypical chromosome abnormality was 4.07% (95% confidence interval, 2.51-6.22), 0.37% (95% confidence interval, 0.05-1.35), and 0.09% (95% confidence interval, 0.07-0.11) in the groups with a nuchal translucency of ≥3.5 mm, 3.0 to 3.4 mm, and <3.0 mm, respectively. The frequency of atypical chromosome abnormalities was 4.69% (95% confidence interval, 2.17-8.71), 2.53% (95% confidence interval, 1.36-4.29), and 0.09% (95% confidence interval, 0.07-0.11) in the groups with a nuchal translucency of ≥3.0 MoM, 1.9 to 2.9 MoM, and <1.9 MoM, respectively. When defining thresholds for offering diagnosis with chromosomal microarray at 11 to 13 weeks, both a nuchal translucency threshold of 1.9 MoM and a fixed threshold of 3.0 mm captured 22 of 93 fetuses (23.7%) with an atypical chromosome abnormality. Of these, 50.0% had a coexisting fetal abnormality on ultrasound. However, the gestation-specific threshold of 1.9 MoM had a better specificity than 3.0 mm. The positive predictive value of an enlarged nuchal translucency for any atypical chromosome abnormality was 1 in 47 for nuchal translucency of >3.0 mm and 1 in 32 for nuchal translucency of >1.9 MoM. Our nuchal translucency threshold of 1.9 MoM captured 0.87% of fetuses, thus approximating the 99th centile. CONCLUSION A gestational age-adjusted nuchal translucency threshold of 1.9 MoM or 99th centile is superior to the fixed cutoff of 3.0 mm for the identification of atypical chromosome abnormalities. The risk of an atypical chromosome abnormality in a fetus with an enlarged nuchal translucency is more than tripled in the presence of an additional ultrasound abnormality.
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Srebniak MI, Jehee FS, Joosten M, Boter M, de Valk WG, van der Helm R, Sistermans EA, Voorhoeve E, Bhola S, Hoffer MJV, den Hollander N, Macville MVE, Van Opstal D. Non-invasive prenatal diagnosis for translocation carriers-YES please or NO go? Acta Obstet Gynecol Scand 2021; 100:2036-2043. [PMID: 34472080 DOI: 10.1111/aogs.14256] [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: 05/04/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 11/28/2022]
Abstract
INTRODUCTION The presence of an unbalanced familial translocation can be reliably assessed in the cytotrophoblast of chorionic villi. However, carriers of a balanced translocation often decline invasive testing. This study aimed to investigate whether an unbalanced translocation can also be diagnosed in cell free DNA by whole-genome non-invasive prenatal screening (NIPS). MATERIAL AND METHODS Pregnant women carrying a fetus with an unbalanced familial translocation, for whom NIPS as well as microarray data were available, were included in this retrospective assessment. NIPS was performed in the course of the TRIDENT study. RESULTS In 12 cases, both NIPS and microarray data were available. In 10 of 12 cases the unbalanced translocation was correctly identified by NIPS without prior knowledge on parental translocation. One was missed because the fetal fraction was too low. One was missed because of technical restrictions in calling 16p gains. CONCLUSIONS This study supports the hypothesis that routine NIPS may be used for prenatal diagnosis of unbalanced inheritance of familial translocations, especially with prior knowledge of the translocation allowing focused examination of the involved chromosomal regions. Our study showed that routine shallow sequencing designed for aneuploidy detection in cell free DNA may be sufficient for higher resolution NIPS, if specialized copy number software is used and if sufficient fetal fraction is present.
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Affiliation(s)
| | - Fernanda S Jehee
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marieke Joosten
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marjan Boter
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Walter G de Valk
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robert van der Helm
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Erik A Sistermans
- Department of Clinical Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Els Voorhoeve
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Shama Bhola
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mariette J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Merryn V E Macville
- Department of Clinical Genetics, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Diane Van Opstal
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
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Song H, Shi H, Yang ET, Bu ZQ, Jin ZQ, Huo MZ, Zhang YL. Effects of Gender of Reciprocal Chromosomal Translocation on Blastocyst Formation and Pregnancy Outcome in Preimplantation Genetic Testing. Front Endocrinol (Lausanne) 2021; 12:704299. [PMID: 34367071 PMCID: PMC8334865 DOI: 10.3389/fendo.2021.704299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 07/08/2021] [Indexed: 11/13/2022] Open
Abstract
Objective To determine the effect of gender of reciprocal chromosomal translocation on blastocyst formation and pregnancy outcome in preimplantation genetic testing, including different parental ages. Methods This was a retrospective cohort study that enrolled 1034 couples undergoing preimplantation genetic testing-structural rearrangement on account of a carrier of reciprocal chromosomal translocation from the Reproductive Medicine Center of the First Affiliated Hospital of Zhengzhou University from January 2015 to December 2019. Group A represented 528 couples in which the man was the carrier of reciprocal translocation and group B represented 506 couples in which the woman was the carrier of reciprocal translocation. All patients were divided into two groups according to their age: female age<35 and female age≥35. Furthermore, the differences in blastocyst condition and pregnancy outcome between male and female carriers in each group were further explored according to their father's age. Results The blastocyst formation rate of group A (55.3%) is higher than that of group B (50%) and the results were statistically significant (P<0.05). The blastocyst formation rate of group A is higher than that of group B, no matter in young maternal age or in advanced maternal age (P<0.05). The blastocyst formation rate in maternal age<35y and paternal age<30y in group A(57.1%) is higher than that of Group B(50%); Similarly, the blastocyst formation rate in maternal age≥35 and paternal age≥38y(66.7%) is higher than that of Group B(33.3%)(all P<0.05). There was no difference in fertilization rate, aeuploidy rate, clinical pregnancy rate, miscarriage rate and live birth rate between Group A and Group B. Conclusion When the carrier of reciprocal translocation is male, the blastocyst formation rate is higher than that of female carrier. While there is no significant difference between the two in terms of fertilization rate, aeuploidy rate, clinical pregnancy rate, miscarriage rate and live birth rate.
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Affiliation(s)
- Hui Song
- Reproductive Medicine Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hao Shi
- Reproductive Medicine Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - En-tong Yang
- Reproductive Medicine Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhi-qin Bu
- Reproductive Medicine Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zi-qi Jin
- Reproductive Medicine Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ming-zhu Huo
- Reproductive Medicine Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yi-le Zhang
- Reproductive Medicine Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Ali TM, Mateu-Brull E, Balaguer N, Dantas C, Borges HR, de Oliveira MQG, Rodrigo L, Campos-Galindo I, Navarro R, Milán M. Inherited unbalanced reciprocal translocation with 3q duplication and 5p deletion in a foetus revealed by cell-free foetal DNA (cffDNA) testing: a case report. Eur J Med Res 2021; 26:64. [PMID: 34187576 PMCID: PMC8243479 DOI: 10.1186/s40001-021-00535-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/18/2021] [Indexed: 11/17/2022] Open
Abstract
Background Since 2011, screening maternal blood for cell-free foetal DNA (cffDNA) fragments has offered a robust clinical tool to classify pregnancy as low or high-risk for Down, Edwards, and Patau syndromes. With recent advances in molecular biology and improvements in data analysis algorithms, the screening’s scope of analysis continues to expand. Indeed, screening now encompassess additional conditions, including aneuploidies for sex chromosomes, microdeletions and microduplications, rare autosomal trisomies, and, more recently, segmental deletions and duplications called copy number variations (CNVs). Yet, the ability to detect CNVs creates a new challenge for cffDNA analysis in couples in which one member carries a structural rearrangement such as a translocation or inversion. Case presentation We report a segmental duplication of the long arm of chromosome 3 and a segmental deletion of the short arm of chromosome 5 detected by cffDNA analysis in a 25-year-old pregnant woman. The blood sample was sequenced on a NextSeq 550 (Illumina) using the VeriSeq NIPT Solution v1 assay. G-band karyotyping in amniotic fluid only detected an abnormality in chromosome 5. Next-generation sequencing in amniocytes confirmed both abnormalities and identified breakpoints in 3q26.32q29 and 5p13.3p15. The foetus died at 21 weeks of gestation due to multiple abnormalities, and later G-band karyotyping in the parents revealed that the father was a carrier of a balanced reciprocal translocation [46,XY,t(3;5)(q26.2;p13)]. Maternal karyotype appeared normal. Conclusion This case provides evidence that extended cffDNA can detect, in addition to aneuploidies for whole chromosomes, large segmental aneuploidies. In some cases, this may indicate the presence of chromosomal rearrangements in a parent. Such abnormalities are outside the scope of standard cffDNA analysis targeting chromosomes 13, 18, 21, X, and Y, potentially leading to undiagnosed congenital conditions.
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Affiliation(s)
- Taccyanna M Ali
- Laboratório Igenomix, Laboratório de Genética E Medicina Reprodutiva, Sao Paulo, Sao Paulo, Brazil
| | - Emilia Mateu-Brull
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Nuria Balaguer
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Camila Dantas
- Laboratório Igenomix, Laboratório de Genética E Medicina Reprodutiva, Sao Paulo, Sao Paulo, Brazil
| | | | | | - Lorena Rodrigo
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Inmaculada Campos-Galindo
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Roser Navarro
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Miguel Milán
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain.
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Pertile MD, Flowers N, Vavrek D, Andrews D, Kalista T, Craig A, Deciu C, Duenwald S, Meier K, Bhatt S. Performance of a Paired-End Sequencing-Based Noninvasive Prenatal Screening Test in the Detection of Genome-Wide Fetal Chromosomal Anomalies. Clin Chem 2021; 67:1210-1219. [PMID: 34077512 DOI: 10.1093/clinchem/hvab067] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/13/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND Noninvasive prenatal tests (NIPTs) detect fetal chromosomal anomalies with high clinical sensitivity and specificity. We examined the performance of a paired-end sequencing-based NIPT in the detection of genome-wide fetal chromosomal anomalies including common trisomies, sex chromosomal aneuploidies (SCA), rare autosomal aneuploidies (RAAs), and partial deletions/duplications ≥7 Mb. METHODS Frozen plasma samples from pregnant women were tested using the VeriSeq NIPT Solution v2 assay. All samples were previously tested with a laboratory-developed NIPT and had known clinical outcomes. Individuals performing the sequencing were blinded to clinical outcome data. Clinical sensitivity and specificity were determined for basic (chromosomes 21, 18, 13, X, and Y) and genome-wide screening modes. RESULTS Of 2335 samples that underwent genome-wide analysis, 28 did not meet QC requirements, resulting in a first-pass assay failure rate of 1.2%. Basic screening analysis, excluding known mosaics, correctly classified 130/130 trisomy 21 samples (sensitivity >99.9%, 95% confidence interval [CI] 97.1%-100%), 41/41 trisomy 18 samples (sensitivity >99.9%, 95% CI 91.4%-100%), and 26/26 trisomy 13 samples (sensitivity >99.9%, 95% CI 87.1%-100%) with 6 false-positive results; specificities ≥99.90% were reported for all 3 trisomies. Concordance for SCAs ranged from 90.5%-100%. Genome-wide screening analysis including known mosaics correctly classified 27/28 RAAs and 20/27 partial deletions/duplications with a specificity of 99.80% for both anomalies, and an overall genome-wide specificity for all anomalies of 99.34%. CONCLUSIONS The VeriSeq NIPT Solution v2 assay enables accurate identification of fetal aneuploidy, allowing detection of genome-wide fetal chromosomal anomalies with high clinical sensitivities and specificities and a low assay failure rate.Clinical Trial Notification [CTN] identification number [ID]: CT-2018-CTN-01585-1 v1, Protocol: NIPT T05 002.
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Affiliation(s)
- Mark D Pertile
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Nicola Flowers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Darcy Vavrek
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Daniel Andrews
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Tasha Kalista
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Andrew Craig
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Cosmin Deciu
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Sven Duenwald
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Kristen Meier
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Sucheta Bhatt
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
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12
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Christiaens L, Chitty LS, Langlois S. Current controversies in prenatal diagnosis: Expanded NIPT that includes conditions other than trisomies 13, 18, and 21 should be offered. Prenat Diagn 2021; 41:1316-1323. [PMID: 33829520 DOI: 10.1002/pd.5943] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/06/2021] [Accepted: 03/22/2021] [Indexed: 11/11/2022]
Abstract
Non-invasive prenatal testing (NIPT) based on analysis of cell free DNA circulating in the maternal plasma has been available clinically to screen for chromosomal abnormalities since 2011. There is significant evidence to suggest that NIPT has revolutionised prenatal screening for the common trisomies 13, 18, and 21. However, the evidence in favour of its extended use to screen for conditions other than these trisomies remains a topic of debate with no national or international organisation supporting clinical implementation for these indications. In the debate presented here - "Expanded NIPT that includes conditions other than trisomies 13, 18, and 21 should be offered" - we will see the pros and cons of screening for a wider range of chromosomal problems. The discussion presented swung the vote from 65% in favour and 35% against before the arguments were voiced to 41% in favour and 59% against. This significant swing in the vote indicates that the majority of our community feel more evidence is required before clinical implementation of extended NIPT.
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Affiliation(s)
- Lieve Christiaens
- Illumina Inc., San Diego, California, USA.,University Hospital of Utrecht, Utrecht, Netherlands
| | - Lyn S Chitty
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,The UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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13
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Chitty LS, Ghidini A, Deprest J, Van Mieghem T, Levy B, Hui L, Bianchi DW. Right or wrong? Looking through the retrospectoscope to analyse predictions made a decade ago in prenatal diagnosis and fetal surgery. Prenat Diagn 2020; 40:1627-1635. [PMID: 33231306 DOI: 10.1002/pd.5870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK.,UCL Great Ormond Street Institute of Child Health, London, UK
| | - Alessandro Ghidini
- Department of Obstetrics and Gynecology, Georgetown University Hospital, Washington, DC.,Antenatal Testing Center, Inova Alexandria Hospital, Alexandria, VA
| | - Jan Deprest
- Department of Obstetrics and Gynaecology, University of Leuven, Leuven, Belgium and the Institute for Women's Health, UCL, London
| | - Tim Van Mieghem
- Fetal Medicine Unit and Ontario Fetal Centre, Department of Obstetrics and Gynaecology, Mount Sinai Hospital and University of Toronto, Toronto, Ontario, Canada
| | - Brynn Levy
- Division of Personalized Genomic Medicine, Columbia University Medical Center & the New York Presbyterian Hospital, New York, New York, USA
| | - Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Victoria, Australia.,Mercy Hospital for Women, Heidelberg, Victoria, Australia.,Murdoch Children's Research Institute, Parkville, Victoria, Australia.,The Northern Hospital, Epping, Victoria, Australia
| | - Diana W Bianchi
- Division of Prenatal Genomics and Fetal Therapy, Medical Genomics and Metabolic Genetics Branch, National Human Genome Institute, National Human Genome Institute, National Institutes of Health, Bethesda, Maryland, USA
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