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Article: Feasibility of Optical Genome Mapping from Placental and Umbilical Cord Sampled after Spontaneous or Therapeutic Pregnancy Termination.

Goumy, Carole / Ouedraogo, Zangbéwendé Guy / Bellemonte, Elodie / Eymard-Pierre, Eleonore / Soler, Gwendoline / Perthus, Isabelle / Pebrel-Richard, Céline / Gouas, Laetitia / Salaun, Gaëlle / Véronèse, Lauren / Laurichesse, Hélène / Darcha, Claude / Tchirkov, Andrei

Diagnostics (Basel, Switzerland)

2023 Volume 13, Issue 23

Abstract: Optical genome mapping (OGM) is an alternative to classical cytogenetic techniques to improve the detection rate of clinically significant genomic abnormalities. The isolation of high-molecular-weight (HMW) DNA is critical for a successful OGM analysis. ... ...

Abstract	Optical genome mapping (OGM) is an alternative to classical cytogenetic techniques to improve the detection rate of clinically significant genomic abnormalities. The isolation of high-molecular-weight (HMW) DNA is critical for a successful OGM analysis. HMW DNA quality depends on tissue type, sample size, and storage conditions. We assessed the feasibility of OGM analysis of DNA from nine umbilical cord (UC) and six chorionic villus (CV) samples collected after the spontaneous or therapeutic termination of pregnancy. We analyzed quality control metrics provided by the Saphyr system (Bionano Genomics) and assessed the length of extracted DNA molecules using pulsed-field capillary electrophoresis. OMG data were successfully analyzed for all six CV samples. Five of the UC samples did not meet the Saphyr quality criteria, mainly due to poor DNA quality. In this regard, we found that DNA quality assessment with pulsed-field capillary electrophoresis can predict a successful OGM analysis. OGM data were fully concordant with the results of standard cytogenetic methods. Moreover, OGM detected an average of 14 additional structural variants involving OMIM genes per sample. On the basis of our results, we established the optimal conditions for sample storage and preparation required for a successful OGM analysis. We recommend checking DNA quality before analysis with pulsed-field capillary electrophoresis if the storage conditions were not ideal or if the quality of the sample is poor. OGM can therefore be performed on fetal tissue harvested after the termination of pregnancy, which opens up the perspective for improved diagnostic yield.
Language	English
Publishing date	2023-11-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662336-5
ISSN	2075-4418
ISSN	2075-4418
DOI	10.3390/diagnostics13233576
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Article ; Online: Clinical, genetic and biochemical signatures of

Plaisancié, Julie / Martinovic, Jelena / Chesneau, Bertrand / Whalen, Sandra / Rodriguez, Diana / Audebert-Bellanger, Séverine / Marzin, Pauline / Grotto, Sarah / Perthus, Isabelle / Holt, Richard James / Bax, Dorine A / Ragge, Nicola / Chassaing, Nicolas

Journal of medical genetics

2023 Volume 61, Issue 1, Page(s) 84–92

Abstract: Background: The retinoic acid (RA) pathway plays a crucial role in both eye morphogenesis and the visual cycle. Individuals with monoallelic and biallelic pathogenic variants in : Methods: We report here seven new families (13 patients) with isolated ...

Abstract	Background: The retinoic acid (RA) pathway plays a crucial role in both eye morphogenesis and the visual cycle. Individuals with monoallelic and biallelic pathogenic variants in Methods: We report here seven new families (13 patients) with isolated and syndromic MAC harbouring heterozygous Results: For the first time, malformations that overlap the clinical spectrum of vitamin A deficiency are reported, providing a link with other RA disorders. Our data support two distinct phenotypes, depending on the nature and mode of inheritance of the variants: dominantly inherited, almost exclusively missense, associated with ocular malformations, in contrast to recessive, mainly truncating, associated with retinal degeneration. Moreover, we also confirm the skewed inheritance and impact of maternal Conclusion: Dominant missense variants in
MeSH term(s)	Pregnancy ; Female ; Humans ; Retinal Degeneration/genetics ; Retinal Degeneration/pathology ; Microphthalmos/genetics ; Anophthalmos/genetics ; Tretinoin/metabolism ; Retinol-Binding Proteins/genetics ; Retinol-Binding Proteins, Plasma/genetics ; Retinol-Binding Proteins, Plasma/chemistry ; Retinol-Binding Proteins, Plasma/metabolism
Chemical Substances	Tretinoin (5688UTC01R) ; Retinol-Binding Proteins ; RBP4 protein, human ; Retinol-Binding Proteins, Plasma
Language	English
Publishing date	2023-12-21
Publishing country	England
Document type	Journal Article
ZDB-ID	220881-7
ISSN	1468-6244 ; 0022-2593
ISSN (online)	1468-6244
ISSN	0022-2593
DOI	10.1136/jmg-2023-109331
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Article ; Online: Optical genome mapping for prenatal diagnosis: A prospective study.

Goumy, Carole / Guy Ouedraogo, Zangbéwendé / Soler, Gwendoline / Eymard-Pierre, Eleonore / Laurichesse, Hélène / Delabaere, Amélie / Gallot, Denis / Bouchet, Pamela / Perthus, Isabelle / Pebrel-Richard, Céline / Gouas, Laetitia / Salaun, Gaëlle / Salse, Jérôme / Véronèse, Lauren / Tchirkov, Andrei

Clinica chimica acta; international journal of clinical chemistry

2023 Volume 551, Page(s) 117594

Abstract: Purpose: Cytogenetic analysis provides important information for prenatal decision-making and genetic counseling. Optical genome mapping (OGM) has demonstrated its performances in retrospective studies. In our prospective study, we assessed the quality ... ...

Abstract	Purpose: Cytogenetic analysis provides important information for prenatal decision-making and genetic counseling. Optical genome mapping (OGM) has demonstrated its performances in retrospective studies. In our prospective study, we assessed the quality of DNA obtained from cultures of amniotic fluid (AF) and chorionic villi (CV) and evaluated the ability of OGM to detect all clinically relevant aberrations identified by standard methods. Methods: A total of 37 prenatal samples from pregnancies with a fetal anomaly on ultrasound were analyzed prospectively by OGM between January 1, 2021 and June 31, 2022. OGM results were interpreted blindly and compared to the results obtained by standard techniques. Results: OGM results were interpretable in 92% of samples. We observed 100% concordance between OGM and karyotype and/or chromosomal microarray results. In addition, OGM identified a median of 30 small (<100 kb) structural variations per case with the involvement of 12 OMIM genes, of which 3 were OMIM morbid genes. Conclusion: This prospective study showed OGM performed well in detecting genomic alterations in cell cultures from prenatal samples. The place of OGM in relation to CMA or exome sequencing remains to be defined in order to optimize the prenatal diagnostic procedure.
MeSH term(s)	Pregnancy ; Female ; Humans ; Prospective Studies ; Retrospective Studies ; Karyotyping ; Cytogenetic Analysis ; Chromosome Mapping ; Prenatal Diagnosis ; Chromosome Aberrations
Language	English
Publishing date	2023-10-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	80228-1
ISSN	1873-3492 ; 0009-8981
ISSN (online)	1873-3492
ISSN	0009-8981
DOI	10.1016/j.cca.2023.117594
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Article: Identification of the First Single

Mansard, Luke / Vaché, Christel / Bianchi, Julie / Baudoin, Corinne / Perthus, Isabelle / Isidor, Bertrand / Blanchet, Catherine / Baux, David / Koenig, Michel / Kalatzis, Vasiliki / Roux, Anne-Françoise

Diagnostics (Basel, Switzerland)

2022 Volume 12, Issue 1

Abstract: ... ...

Abstract	GSDME
Language	English
Publishing date	2022-01-15
Publishing country	Switzerland
Document type	Case Reports
ZDB-ID	2662336-5
ISSN	2075-4418
ISSN	2075-4418
DOI	10.3390/diagnostics12010207
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Article ; Online: Cost and outcomes of the ultrasound screening program for birth defects over time: a population-based study in France.

Ferrier, Clément / Khoshnood, Babak / Dhombres, Ferdinand / Randrianaivo, Hanitra / Perthus, Isabelle / Jouannic, Jean-Marie / Durand-Zaleski, Isabelle

BMJ open

2020 Volume 10, Issue 7, Page(s) e036566

Abstract: Objective: To assess trends in the average costs and effectiveness of the French ultrasound screening programme for birth defects.: Design: A population-based study.: Setting: National Public Health Insurance claim database.: Participants: All ... ...

Abstract	Objective: To assess trends in the average costs and effectiveness of the French ultrasound screening programme for birth defects. Design: A population-based study. Setting: National Public Health Insurance claim database. Participants: All pregnant women in the 'Echantillon Généraliste des Bénéficiaires', a permanent representative sample of 1/97 of the individuals covered by the French Health Insurance System. Main outcomes measures: Trends in the costs and in the average cost-effectiveness ratio (ACER) of the screening programme (in € per case detected antenatally), per year, between 2006 and 2014. incremental cost-effectiveness ratio (ICER) from 1 year to another were also estimated. We assessed costs related to the ultrasound screening programme of birth defects excluding the specific screening of Down's syndrome. The outcome for effectiveness was the prenatal detection rate of birth defects, assessed in a previous study. Linear and logistic regressions were used to analyse time trends. Results: During the study period, there was a slight decrease in prenatal detection rates (from 58.2% in 2006 to 55.2% in 2014; p=0.015). The cost of ultrasound screening increased from €168 in 2006 to €258 per pregnancy in 2014 (p=0.001). We found a 61% increase in the ACER for ultrasound screening during the study period. ACERs increased from €9050 per case detected in 2006 to €14 580 per case detected in 2014 (p=0.001). ICERs had an erratic pattern, with a strong tendency to show that any increment in the cost of screening was highly cost ineffective. Conclusion: Even if the increase in costs may be partly justified, we observed a diminishing returns for costs associated with the prenatal ultrasound screening of birth defects, in France, between 2006 and 2014.
MeSH term(s)	Cost-Benefit Analysis ; Down Syndrome ; Female ; France/epidemiology ; Humans ; Mass Screening ; Pregnancy ; Prenatal Diagnosis
Language	English
Publishing date	2020-07-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2599832-8
ISSN	2044-6055 ; 2044-6055
ISSN (online)	2044-6055
ISSN	2044-6055
DOI	10.1136/bmjopen-2019-036566
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Article ; Online: Familial transmission of chromoanagenesis leads to unpredictable unbalanced rearrangements through meiotic recombination.

Clinical genetics

2023 Volume 103, Issue 4, Page(s) 401–412

Abstract: Chromoanagenesis is a cellular mechanism that leads to complex chromosomal rearrangements (CCR) during a single catastrophic event. It may result in loss and/or gain of genetic material and may be responsible for various phenotypes. These rearrangements ... ...

Abstract	Chromoanagenesis is a cellular mechanism that leads to complex chromosomal rearrangements (CCR) during a single catastrophic event. It may result in loss and/or gain of genetic material and may be responsible for various phenotypes. These rearrangements are usually sporadic. However, some familial cases have been reported. Here, we studied six families in whom an asymptomatic or paucisymptomatic parent transmitted a CCR to its offspring in an unbalanced manner. The rearrangements were characterized by karyotyping, fluorescent in situ hybridization, chromosomal microarray (CMA) and/or whole genome sequencing (WGS) in the carrier parents and offspring. We then hypothesized meiosis-pairing figures between normal and abnormal parental chromosomes that may have led to the formation of new unbalanced rearrangements through meiotic recombination. Our work indicates that chromoanagenesis might be associated with a normal phenotype and normal fertility, even in males, and that WGS may be the only way to identify these events when there is no imbalance. Subsequently, the CCR can be transmitted to the next generation in an unbalanced and unpredictable manner following meiotic recombination. Thereby, prenatal diagnosis using CMA should be proposed to these families to detect any pathogenic imbalances in the offspring.
MeSH term(s)	Male ; Female ; Pregnancy ; Humans ; In Situ Hybridization, Fluorescence ; Gene Rearrangement ; Chromosome Aberrations ; Karyotyping ; Meiosis ; Translocation, Genetic
Language	English
Publishing date	2023-01-19
Publishing country	Denmark
Document type	Journal Article
ZDB-ID	221209-2
ISSN	1399-0004 ; 0009-9163
ISSN (online)	1399-0004
ISSN	0009-9163
DOI	10.1111/cge.14291
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Article ; Online: Trends in resource use and effectiveness of ultrasound detection of fetal structural anomalies in France: a multiple registry-based study.

Ferrier, Clément / Dhombres, Ferdinand / Khoshnood, Babak / Randrianaivo, Hanitra / Perthus, Isabelle / Guilbaut, Lucie / Durand-Zaleski, Isabelle / Jouannic, Jean-Marie

BMJ open

2019 Volume 9, Issue 2, Page(s) e025482

Abstract: Objective: To analyse trends in the number of ultrasound examinations in relation to the effectiveness of prenatal detection of birth defects using population-based data in France.: Design: A multiple registry-based study of time trends in resource ... ...

Abstract	Objective: To analyse trends in the number of ultrasound examinations in relation to the effectiveness of prenatal detection of birth defects using population-based data in France. Design: A multiple registry-based study of time trends in resource use (number of ultrasounds) and effectiveness (proportion of cases prenatally diagnosed). Setting: Three registries of congenital anomalies and claims data on ultrasounds for all pregnant women in France. Participants: There were two samples of pregnant women. Effectiveness was assessed using data from three French birth defect registries. Resource use for ultrasound screening was based on the French national healthcare database. Main outcome measures: The main outcome measures were prenatal diagnosis (effectiveness) and the average number of ultrasounds (resource use). Statistical analyses included linear and logistic regression models to assess trends in resource use and effectiveness of prenatal testing, respectively. Results: The average number of ultrasound examinations per pregnancy significantly increased over the study period, from 2.47 in 2006 to 2.98 in 2014 (p=0.005). However, there was no significant increase in the odds of prenatal diagnosis. The probability of prenatal diagnosis was substantially higher for cases associated with a chromosomal anomaly (91.2%) than those without (51.8%). However, there was no evidence of an increase in prenatal detection of either over time. Conclusions: The average number of ultrasound examinations per pregnancy increased over time, whereas the probability of prenatal diagnosis of congenital anomalies did not. Hence, there is a need to implement policies such as high-quality training programmes which can improve the efficiency of ultrasound examinations for prenatal detection of congenital anomalies.
MeSH term(s)	Congenital Abnormalities/diagnostic imaging ; Congenital Abnormalities/epidemiology ; Female ; France/epidemiology ; Humans ; Linear Models ; Logistic Models ; Pregnancy ; Prenatal Diagnosis/trends ; Registries ; Ultrasonography, Prenatal/statistics & numerical data
Language	English
Publishing date	2019-02-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2747269-3
ISSN	2044-6055 ; 2044-6055 ; 2053-3624
ISSN (online)	2044-6055
ISSN	2044-6055 ; 2053-3624
DOI	10.1136/bmjopen-2018-025482
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Article ; Online: A multidisciplinary and structured investigation of three suspected clusters of transverse upper limb reduction defects in France.

Boudet-Berquier, Julie / Demattei, Christophe / Guldner, Laurence / Gallay, Anne / Manouvrier, Sylvie / Botton, Jérémie / Philippat, Claire / Delva, Fleur / Bloch, Juliette / Semaille, Caroline / Odent, Sylvie / Perthus, Isabelle / Randrianaivo, Hanitra / Babajko, Sylvie / Barjat, Tiphaine / Beneteau, Claire / Brennetot, Naima / Garne, Ester / Haddad, Georges /

European journal of epidemiology

2024

Abstract: Introduction: Between 2019-2021, facing public concern, a scientific expert committee (SEC) reanalysed suspected clusters of transverse upper limb reduction defects (TULRD) in three administrative areas in France, where initial investigations had not ... ...

Abstract	Introduction: Between 2019-2021, facing public concern, a scientific expert committee (SEC) reanalysed suspected clusters of transverse upper limb reduction defects (TULRD) in three administrative areas in France, where initial investigations had not identified any risk exposure. We share here the national approach we developed for managing suspicious clusters of the same group of congenital anomalies occurring in several areas. Methods: The SEC analysed the medical records of TURLD suspected cases and performed spatiotemporal analyses on confirmed cases. If the cluster was statistically significant and included at least three cases, the SEC reviewed exposures obtained from questionnaires, environmental databases, and a survey among farmers living near to cases' homes concerning their plant product use. Results: After case re-ascertainment, no statistically significant cluster was observed in the first administrative areas. In the second area, a cluster of four children born in two nearby towns over two years was confirmed, but as with the initial investigations, no exposure to a known risk factor explaining the number of cases in excess was identified. In the third area, a cluster including just two cases born the same year in the same town was confirmed. Discussion: Our experience highlights that in the event of suspicious clusters occurring in different areas of a country, a coordinated and standardised approach should be preferred.
Language	English
Publishing date	2024-04-27
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	632614-6
ISSN	1573-7284 ; 0393-2990
ISSN (online)	1573-7284
ISSN	0393-2990
DOI	10.1007/s10654-024-01125-5
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Article ; Online: Association between hereditary predisposition to common cancers and congenital multimalformations.

Kwiatkowski, Fabrice / Perthus, Isabelle / Uhrhammer, Nancy / Francannet, Christine / Arbre, Marie / Bidet, Yannick / Bignon, Yves-Jean

Congenital anomalies

2019 Volume 60, Issue 1, Page(s) 22–31

Abstract: In a previous article we reported that mutations favoring cancer at adulthood seemed to improve fertility and limit miscarriages. Because spontaneous abortion may result from anomalies in embryo, we questioned if an increased frequency of congenital ... ...

Abstract	In a previous article we reported that mutations favoring cancer at adulthood seemed to improve fertility and limit miscarriages. Because spontaneous abortion may result from anomalies in embryo, we questioned if an increased frequency of congenital malformation could be evidenced among cancer-prone families. Oncogenetics database (≈193 000 members) of the comprehensive cancer center Jean Perrin was crossed with regional registry of congenital malformations (≈10 000). Among children born between 1986 and 2011, 176 children with malformation matched in both databases. In breast/ovaries cancer-prone families, the risk for malformations was multiplied by 2.4 [1.2-4.5] in case of a BRCA1 mutation. Frequencies of malformation in BRCA2 and MMR mutated families were similar to families without a cancer syndrome. In comparison to malformations concerning a unique anatomical system, multimalformations were significantly more frequent in case of BRCA or MMR mutations: compared to families without cancer syndrome, the risk of multimalformations was multiplied by 4.1 [0.8-21.7] for cancer-prone families but with no known deleterious mutation, by 6.9 [1.2-38.6] in families with a known mutation but an unknown parental mutational status and by 10.4 [2.3-46.0] when one parent carried the familial mutation. No association with the type of anatomical system was found, nor with multiple births. These results suggest that BRCA and MMR genes play an important role in human embryogenesis and that if their function is lowered because of heterozygote mutations, congenital malformations are either more likely (BRCA1 mutations) and/or more susceptible to concern several anatomical systems.
MeSH term(s)	Abortion, Spontaneous/genetics ; Abortion, Spontaneous/pathology ; Adult ; BRCA1 Protein/genetics ; BRCA2 Protein/genetics ; Breast Neoplasms/genetics ; Breast Neoplasms/pathology ; Child ; Congenital Abnormalities/genetics ; Congenital Abnormalities/pathology ; Embryonic Development/genetics ; Female ; Genetic Association Studies ; Genetic Predisposition to Disease ; Germ-Line Mutation/genetics ; Humans ; Ovarian Neoplasms/genetics ; Ovarian Neoplasms/pathology ; Pedigree ; Receptors, Immunologic/genetics
Chemical Substances	BRCA1 Protein ; BRCA1 protein, human ; BRCA2 Protein ; BRCA2 protein, human ; Receptors, Immunologic ; macrophage MHC receptor 1, human
Language	English
Publishing date	2019-03-12
Publishing country	Australia
Document type	Journal Article
ZDB-ID	228664-6
ISSN	1741-4520 ; 0037-2285 ; 0914-3505
ISSN (online)	1741-4520
ISSN	0037-2285 ; 0914-3505
DOI	10.1111/cga.12329
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Article ; Online: In utero exposure to arsenic in tap water and congenital anomalies: A French semi-ecological study.

Marie, Cécile / Léger, Stéphanie / Guttmann, Aline / Marchiset, Nathalie / Rivière, Olivier / Perthus, Isabelle / Lémery, Didier / Vendittelli, Françoise / Sauvant-Rochat, Marie-Pierre

International journal of hygiene and environmental health

2018 Volume 221, Issue 8, Page(s) 1116–1123

Abstract: Introduction: Congenital anomalies (CA) are responsible for high rates of mortality and long-term disabilities. Research on their risk factors including environmental factors is needed. Studies on exposure to arsenic (As) in tap water and the risk of CA ...

Abstract	Introduction: Congenital anomalies (CA) are responsible for high rates of mortality and long-term disabilities. Research on their risk factors including environmental factors is needed. Studies on exposure to arsenic (As) in tap water and the risk of CA have not provided conclusive evidence, particularly when levels of exposure were low (from 10 to 50 μg As/L). The main objective of this study was to assess the association between exposure to As in tap water and the risk of any major CA. The secondary objectives were to assess this association for the most common types of congenital anomalies (in the heart, musculoskeletal, urinary and nervous systems). Methods: A semi-ecological study was conducted from births recorded at the University Hospital of Clermont-Ferrand, France, in 2003, 2006 and 2010. The medico-obstetric data were available at individual level. Children with congenital anomalies were identified from the database of the regional registry of congenital anomalies: the Centre d'Etudes des Malformations Congénitales Auvergne (CEMC-Auvergne). As exposure was estimated from the concentrations of As measured during sanitary control of tap water supplied in the mothers' commune of residence (aggregate data). French guidelines for As in tap water were used to identify the two groups: "≥ 10 μg As/L group" and "[0-10) μg As/L group". Multivariable logistic regression models were fit. Results: 5263 children (5.1% with a CA) were included. In stratified analysis by gender of the child, positive associations between As exposure exceeding 10 μg/L and risk of any major CA (adjusted OR = 2.41; 95%CI: 1.36-4.14) and of congenital heart anomalies (adjusted OR = 3.66; 95%CI: 1.62-7.64) were only shown for girls. No association was found for boys. Conclusion: This French semi-ecological study provides additional arguments for the association between exposure to As exceeding 10 μg/L in tap water and the risk of CA especially in a context of low exposure. Further studies are needed to better understand the interaction between arsenic exposure and child gender.
MeSH term(s)	Adult ; Arsenic/adverse effects ; Arsenic/analysis ; Drinking Water/adverse effects ; Drinking Water/analysis ; Female ; France/epidemiology ; Heart Defects, Congenital/chemically induced ; Heart Defects, Congenital/epidemiology ; Humans ; Infant, Newborn ; Male ; Maternal Exposure ; Maternal-Fetal Exchange ; Odds Ratio ; Pregnancy ; Risk Factors ; Sex Characteristics ; Water Pollutants, Chemical/adverse effects ; Water Pollutants, Chemical/analysis ; Young Adult
Chemical Substances	Drinking Water ; Water Pollutants, Chemical ; Arsenic (N712M78A8G)
Language	English
Publishing date	2018-07-30
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2009176-X
ISSN	1618-131X ; 1438-4639
ISSN (online)	1618-131X
ISSN	1438-4639
DOI	10.1016/j.ijheh.2018.07.012
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