1
|
Anastasiadou K, Silva M, Booth T, Speidel L, Audsley T, Barrington C, Buckberry J, Fernandes D, Ford B, Gibson M, Gilardet A, Glocke I, Keefe K, Kelly M, Masters M, McCabe J, McIntyre L, Ponce P, Rowland S, Ruiz Ventura J, Swali P, Tait F, Walker D, Webb H, Williams M, Witkin A, Holst M, Loe L, Armit I, Schulting R, Skoglund P. Detection of chromosomal aneuploidy in ancient genomes. Commun Biol 2024; 7:14. [PMID: 38212558 PMCID: PMC10784527 DOI: 10.1038/s42003-023-05642-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024] Open
Abstract
Ancient DNA is a valuable tool for investigating genetic and evolutionary history that can also provide detailed profiles of the lives of ancient individuals. In this study, we develop a generalised computational approach to detect aneuploidies (atypical autosomal and sex chromosome karyotypes) in the ancient genetic record and distinguish such karyotypes from contamination. We confirm that aneuploidies can be detected even in low-coverage genomes ( ~ 0.0001-fold), common in ancient DNA. We apply this method to ancient skeletal remains from Britain to document the first instance of mosaic Turner syndrome (45,X0/46,XX) in the ancient genetic record in an Iron Age individual sequenced to average 9-fold coverage, the earliest known incidence of an individual with a 47,XYY karyotype from the Early Medieval period, as well as individuals with Klinefelter (47,XXY) and Down syndrome (47,XY, + 21). Overall, our approach provides an accessible and automated framework allowing for the detection of individuals with aneuploidies, which extends previous binary approaches. This tool can facilitate the interpretation of burial context and living conditions, as well as elucidate past perceptions of biological sex and people with diverse biological traits.
Collapse
Affiliation(s)
- Kyriaki Anastasiadou
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom.
| | - Marina Silva
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Thomas Booth
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Leo Speidel
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
- Genetics Institute, University College London, London, United Kingdom
| | | | - Christopher Barrington
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Jo Buckberry
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, United Kingdom
| | | | - Ben Ford
- Oxford Archaeology, Oxford, United Kingdom
| | | | - Alexandre Gilardet
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Isabelle Glocke
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Katie Keefe
- York Osteoarchaeology, York, United Kingdom
- On-Site Archaeology, York, United Kingdom
| | - Monica Kelly
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Mackenzie Masters
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | - Jesse McCabe
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Paola Ponce
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | | | - Jordi Ruiz Ventura
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | - Pooja Swali
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Frankie Tait
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Helen Webb
- Oxford Archaeology, Oxford, United Kingdom
| | - Mia Williams
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Malin Holst
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | - Louise Loe
- Oxford Archaeology, Oxford, United Kingdom
| | - Ian Armit
- Department of Archaeology, University of York, York, United Kingdom
| | - Rick Schulting
- School of Archaeology, University of Oxford, Oxford, United Kingdom
| | - Pontus Skoglund
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom.
| |
Collapse
|
2
|
Sperling K, Scherb H, Neitzel H. Population monitoring of trisomy 21: problems and approaches. Mol Cytogenet 2023; 16:6. [PMID: 37183244 PMCID: PMC10183086 DOI: 10.1186/s13039-023-00637-1] [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: 12/27/2022] [Accepted: 05/02/2023] [Indexed: 05/16/2023] Open
Abstract
Trisomy 21 (Down syndrome) is the most common autosomal aneuploidy among newborns. About 90% result from meiotic nondisjunction during oogenesis, which occurs around conception, when also the most profound epigenetic modifications take place. Thus, maternal meiosis is an error prone process with an extreme sensitivity to endogenous factors, as exemplified by maternal age. This contrasts with the missing acceptance of causal exogenous factors. The proof of an environmental agent is a great challenge, both with respect to ascertainment bias, determination of time and dosage of exposure, as well as registration of the relevant individual health data affecting the birth prevalence. Based on a few exemplary epidemiological studies the feasibility of trisomy 21 monitoring is illustrated. In the nearer future the methodical premises will be clearly improved, both due to the establishment of electronic health registers and to the introduction of non-invasive prenatal tests. Down syndrome is a sentinel phenotype, presumably also with regard to other congenital anomalies. Thus, monitoring of trisomy 21 offers new chances for risk avoidance and preventive measures, but also for basic research concerning identification of relevant genomic variants involved in chromosomal nondisjunction.
Collapse
Affiliation(s)
- Karl Sperling
- Institute of Medical and Human Genetics, Charité-Universitaetsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.
| | - Hagen Scherb
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Heidemarie Neitzel
- Institute of Medical and Human Genetics, Charité-Universitaetsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| |
Collapse
|
3
|
Tuzimski T, Szubartowski S, Stupak A, Kwaśniewski W, Szultka-Młyńska M, Kwaśniewska A, Buszewski B. The Association between the Bisphenols Residues in Amniotic Fluid and Fetal Abnormalities in Polish Pregnant Women-Its Potential Clinical Application. Int J Mol Sci 2023; 24:ijms24010730. [PMID: 36614173 PMCID: PMC9821541 DOI: 10.3390/ijms24010730] [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: 11/09/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
The present study aimed to investigate the relationship between the concentrations of bisphenols residues in the amniotic fluid (AF) samples collected during amniocentesis and fetal chromosomal abnormalities in pregnant women. A total of 33 pregnant Polish women aged between 24 and 44 years, and screened to detect high risk for chromosomal defects in the first trimester, were included in this study. Samples were collected from these patients during routine diagnostic and treatment procedures at mid-gestation. The concentrations of various bisphenols residues in the samples were determined by liquid chromatography coupled with triple quadrupole tandem mass spectrometry (LC-ESI-QqQ-MS/MS). Residues of eight analytes (BPS, BPF, BPA, BPAF, BADGE, BADGE•2H2O, BADGE•H2O•HCl and BADGE•2HCl) were detected in amniotic fluid samples in the range 0.69 ng/mL to 3.38 ng/mL. Fetuses with chromosomal abnormalities showed a slightly higher frequency of occurrence of selected bisphenols residues in the AF samples collected between 15-26 weeks of pregnancies. Finally, the proposed method was applied in the simultaneous determination of several endocrine-disrupting chemicals from bisphenol group in 33 human AF samples. BADGE•H2O•HCl has been identified in the AF samples taken from women older than average in the examined group. The number of detected compounds has been significant for the following analytes: BPS, BPAF, BADGE•H2O•HCl and BADGE. The proposed method may be an attractive alternative for application in large-scale human biomonitoring studies.
Collapse
Affiliation(s)
- Tomasz Tuzimski
- Department of Physical Chemistry, Medical University of Lublin, 20-093 Lublin, Poland
- Correspondence: ; Tel.: +48-(81)-4487213
| | - Szymon Szubartowski
- Department of Physical Chemistry, Medical University of Lublin, 20-093 Lublin, Poland
- Doctoral School of Medical University of Lublin, Medical University of Lublin, 20-093 Lublin, Poland
| | - Aleksandra Stupak
- Chair and Department of Obstetrics and Pathology of Pregnancy, Independent Public Clinical Hospital No. 1 in Lublin, Medical University of Lublin, 20-081 Lublin, Poland
| | - Wojciech Kwaśniewski
- Department of Gynaecology and Oncology Gynaecology, Independent Public Clinical Hospital No. 1 in Lublin, Medical University of Lublin, 20-081 Lublin, Poland
| | - Małgorzata Szultka-Młyńska
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Anna Kwaśniewska
- Chair and Department of Obstetrics and Pathology of Pregnancy, Independent Public Clinical Hospital No. 1 in Lublin, Medical University of Lublin, 20-081 Lublin, Poland
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Torun, Poland
| |
Collapse
|
4
|
Mothers of children with Down syndrome: a clinical and epidemiological study. J Community Genet 2022; 14:189-195. [PMID: 36562914 PMCID: PMC10104982 DOI: 10.1007/s12687-022-00627-7] [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: 09/15/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Down syndrome is the main genetic cause of intellectual disability. Many studies describe the clinical characteristics of DS patients; however, few have investigated the clinical profile of mothers who have children with DS. Advanced maternal age (≥ 35 years old) is a risk factor for DS. Although there is an overall increase in pregnancies among women with advanced maternal age, there is still a lack of awareness of the increased risk of aneuploidy. Here, we reported the clinical and epidemiological profile of DS children and their mothers in a public reference hospital in the State of Rio de Janeiro, Brazil. For data collection, we performed a face-to-face interview guided by a structured questionnaire with closed-ended questions. A total of 344 individuals, 172 mothers and their DS children, were included in this study. Our results show that 56% of the mothers sampled were ≥ 35 years of age at childbirth. Although 98% of them received prenatal care, only 4% obtained a prenatal diagnosis of DS. Most mothers reported not drinking alcohol or smoking cigarettes during pregnancy. Furthermore, 91% of women took prenatal vitamins and supplements; however, 47% were not aware of their benefits for a healthy pregnancy. Given the strict correlation between advanced maternal age and DS, prenatal care should include genetic counseling for women over 35 years of age. This study highlights the importance of prenatal care and the urgent need for better DS screening allowing for immediate postnatal care, positively impacting the life expectancy of these patients.
Collapse
|
5
|
Czuba B, Mlodawski J, Kajdy A, Sys D, Cnota W, Mlodawska M, Kwiatkowski S, Guzik P, Wielgos M, Rybak-Krzyszkowska M, Fuchs A, Swiercz G, Borowski D. Implementation of the Publicly Funded Prenatal Screening Programme in Poland during the COVID-19 Pandemic: A Cross-Sectional Study. J Clin Med 2022; 11:jcm11051317. [PMID: 35268408 PMCID: PMC8911175 DOI: 10.3390/jcm11051317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 11/23/2022] Open
Abstract
The COVID-19 pandemic in 2020 affected the entire healthcare system in Poland, causing medical personnel to be relocated to other duties and limiting patients’ contacts with healthcare professionals. A large part of the planned diagnostics and treatment was delayed due to lack of equipment and personnel. Against this background, we analysed the implementation of the publicly funded prenatal screening programme (PSP) in Poland compared to the previous year. This is a cross-sectional study. We used nationwide datasets on the implementation of the prenatal testing programme over the period 2019−2020, datasets from the Statistics Poland on birth and the data on the development of the COVID-19 epidemic in Poland. In the year 2020, we observed a 12.41% decrease in woman enrolled to the programme compared to 2019. However, the decrease concerned only women under 35 years of age. With respect to the number of deliveries in the calendar year, the number of patients enrolled in the programme decreased by 3% (31% vs. 34%, p < 0.001). We also observed an increase in estriol measurements per the number of patients included in the programme, and a reduction in the number of PAPP-A tests in the first trimester, which proves an increased share of the triple test in the prenatal diagnosis of chromosomal aberrations. With respect to the number of deliveries, the number of amniocentesis procedures performed under PSP decreased by 0.19% (1.8% vs. 1.99%, p < 0.0001). In 2020, compared to the previous year, the number of patients included in the prenatal testing programme in Poland decreased. In terms of the number of births in Poland, the number of integrated screening tests also decreased, at the expense of increasing the percentage of triple tests. There were also significant reductions in the number of invasive diagnostic tests.
Collapse
Affiliation(s)
- Bartosz Czuba
- Chair and Department of Gynaecology and Obstetrics, Faculty of Health Sciences in Katowice, Medical University of Silesia, 41-703 Ruda Śląska, Poland; (B.C.); (W.C.)
| | - Jakub Mlodawski
- Collegium Medicum, Jan Kochanowski University in Kielce, 25-369 Kielce, Poland; (M.M.); (G.S.)
- Correspondence:
| | - Anna Kajdy
- Department of Reproductive Health, Centre of Postgraduate Medical Education, 01-004 Warsaw, Poland; (A.K.); (D.S.)
| | - Dorota Sys
- Department of Reproductive Health, Centre of Postgraduate Medical Education, 01-004 Warsaw, Poland; (A.K.); (D.S.)
| | - Wojciech Cnota
- Chair and Department of Gynaecology and Obstetrics, Faculty of Health Sciences in Katowice, Medical University of Silesia, 41-703 Ruda Śląska, Poland; (B.C.); (W.C.)
| | - Marta Mlodawska
- Collegium Medicum, Jan Kochanowski University in Kielce, 25-369 Kielce, Poland; (M.M.); (G.S.)
| | - Sebastian Kwiatkowski
- Department Obstetrics and Gynecology, Pommeranian Medical University in Szczecin, 70-111 Szczecin, Poland;
| | - Pawel Guzik
- Clinical Department of Gynecology and Obstetrics, City Hospital, 35-241 Rzeszów, Poland;
| | - Miroslaw Wielgos
- 1st Department of Obstetrics and Genocology, Medical University of Warsaw, 02-015 Warsaw, Poland;
| | - Magda Rybak-Krzyszkowska
- Department of Obstetrics and Perinatology, University Hospital in Krakow, 31-501 Krakow, Poland;
| | - Anna Fuchs
- Chair and Department of Gynecology, Obstetrics and Oncological Gynecology, Medical University of Silesia in Katowice, 40-211 Katowice, Poland;
| | - Grzegorz Swiercz
- Collegium Medicum, Jan Kochanowski University in Kielce, 25-369 Kielce, Poland; (M.M.); (G.S.)
| | - Dariusz Borowski
- Department of Perinatology, Gynaecology and Gynaecologic Oncology, The Faculty of Health Sciences, Collegium Medicum, Nicolaus Coeprnicus University, 85-067 Bydgoszcz, Poland;
| |
Collapse
|
6
|
Benn P, Rebarber A. Non-invasive prenatal testing in the management of twin pregnancies. Prenat Diagn 2021; 41:1233-1240. [PMID: 34170028 PMCID: PMC8518532 DOI: 10.1002/pd.5989] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/03/2021] [Accepted: 06/05/2021] [Indexed: 12/02/2022]
Abstract
Twin pregnancies are common and associated with pregnancy complications and adverse outcomes. Prenatal clinical management is intensive and has been hampered by inferior screening and less acceptable invasive testing. For aneuploidy screening, meta‐analyses show that non‐invasive prenatal testing (NIPT) through analysis of cell‐free DNA (cf‐DNA) is superior to serum and ultrasound‐based tests. The positive predictive value for NIPT is driven strongly by the discriminatory power of the assay and only secondarily by the prior risk. Uncertainties in a priori risks for aneuploidies in twin pregnancies are therefore of lesser importance with NIPT. Additional information on zygosity can be obtained using NIPT. Establishing zygosity can be helpful when chorionicity was not reliably established early in pregnancy or where the there is a concern for one versus two affected fetuses. In dizygotic twin pregnancies, individual fetal fractions can be measured to ensure that both values are satisfactory. Vanishing twins can be identified by NIPT. Although clinical utility of routinely detecting vanishing twins has not yet been demonstrated, there are individual cases where cf‐DNA analysis could be helpful in explaining unusual clinical or laboratory observations. We conclude that cf‐DNA analysis and ultrasound have synergistic roles in the management of multiple gestational pregnancies.
What's already known about this topic?
In singleton pregnancies, non‐invasive prenatal testing (NIPT) for fetal aneuploidy is more effective than conventional serum and ultrasound‐based screening tests. NIPT is more complex in dizygotic twin pregnancies due to the presence of two fetal genotypes. Overall fetal fraction is higher in twin pregnancies but the individual contribution for each fetus is lower.
What does this study add?
A review of cell‐free DNA testing in twin pregnancies. Individual fetal fractions in dizygotic twin pregnancies can be measured. Zygosity can be established using NIPT and this can be particularly useful when there are concerns about chorionicity or determining whether one versus two fetuses are affected. Vanishing twins can be detected through NIPT and this testing could be considered for some apparently singleton pregnancies with complications.
Collapse
Affiliation(s)
- Peter Benn
- Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA
| | - Andrei Rebarber
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Division of Maternal Fetal Medicine, Englewood Hospital, Englewood, New Jersey, USA
| |
Collapse
|
7
|
Levy B, Hoffmann ER, McCoy RC, Grati FR. Chromosomal mosaicism: Origins and clinical implications in preimplantation and prenatal diagnosis. Prenat Diagn 2021; 41:631-641. [PMID: 33720449 DOI: 10.1002/pd.5931] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/03/2021] [Accepted: 03/06/2021] [Indexed: 12/18/2022]
Abstract
The diagnosis of chromosomal mosaicism in the preimplantation and prenatal stage is fraught with uncertainty and multiple factors need to be considered in order to gauge the likely impact. The clinical effects of chromosomal mosaicism are directly linked to the type of the imbalance (size, gene content, and copy number), the timing of the initial event leading to mosaicism during embryogenesis/fetal development, the distribution of the abnormal cells throughout the various tissues within the body as well as the ratio of normal/abnormal cells within each of those tissues. Additional factors such as assay noise and culture artifacts also have an impact on the significance and management of mosaic cases. Genetic counseling is an important part of educating patients about the likelihood of having a liveborn with a chromosome abnormality and these risks differ according to the time of ascertainment and the tissue where the mosaic cells were initially discovered. Each situation needs to be assessed on a case-by-case basis and counseled accordingly. This review will discuss the clinical impact of finding mosaicism through: embryo biopsy, chorionic villus sampling, amniocentesis, and noninvasive prenatal testing using cell-free DNA.
Collapse
Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Eva R Hoffmann
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Francesca R Grati
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays, S.p.A. (Impact Lab), Busto Arsizio, Varese, Italy
| |
Collapse
|