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  1. Article: Optical Genome Mapping in Routine Cytogenetic Diagnosis of Acute Leukemia.

    Soler, Gwendoline / Ouedraogo, Zangbéwendé Guy / Goumy, Carole / Lebecque, Benjamin / Aspas Requena, Gaspar / Ravinet, Aurélie / Kanold, Justyna / Véronèse, Lauren / Tchirkov, Andrei

    Cancers

    2023  Volume 15, Issue 7

    Abstract: Cytogenetic aberrations are found in 65% of adults and 75% of children with acute leukemia. Specific aberrations are used as markers for the prognostic stratification of patients. The current standard cytogenetic procedure for acute leukemias is ... ...

    Abstract Cytogenetic aberrations are found in 65% of adults and 75% of children with acute leukemia. Specific aberrations are used as markers for the prognostic stratification of patients. The current standard cytogenetic procedure for acute leukemias is karyotyping in combination with FISH and RT-PCR. Optical genome mapping (OGM) is a new technology providing a precise identification of chromosomal abnormalities in a single approach. In our prospective study, the results obtained using OGM and standard techniques were compared in 29 cases of acute myeloid (AML) or lymphoblastic leukemia (ALL). OGM detected 73% (53/73) of abnormalities identified by standard methods. In AML cases, two single clones and three subclones were missed by OGM, but the assignment of patients to cytogenetic risk groups was concordant in all patients. OGM identified additional abnormalities in six cases, including one cryptic structural variant of clinical interest and two subclones. In B-ALL cases, OGM correctly detected all relevant aberrations and revealed additional potentially targetable alterations. In T-ALL cases, OGM characterized a complex karyotype in one case and identified additional abnormalities in two others. In conclusion, OGM is an attractive alternative to current multiple cytogenetic testing in acute leukemia that simplifies the procedure and reduces costs.
    Language English
    Publishing date 2023-04-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers15072131
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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

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

    Diagnostics, Vol 13, Iss 23, p

    2023  Volume 3576

    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.
    Keywords optical genome mapping ; umbilical cord biopsies ; chorionic villi ; termination of pregnancy ; birth defect ; Medicine (General) ; R5-920
    Subject code 612
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Reduced telomere length in amniocytes: an early biomarker of abnormal fetal development?

    Goumy, Carole / Veronese, Lauren / Stamm, Rodrigue / Domas, Quentin / Hadjab, Kamil / Gallot, Denis / Laurichesse, Hélène / Delabaere, Amélie / Gouas, Laetitia / Salaun, Gaelle / Perbel-Richard, Céline / Vago, Philippe / Tchirkov, Andrei

    Human molecular genetics

    2022  Volume 31, Issue 16, Page(s) 2669–2677

    Abstract: Telomeres protect chromosome ends and control cell division and senescence. During organogenesis, telomeres need to be long enough to ensure the cell proliferation necessary at this stage of development. Previous studies have shown that telomere ... ...

    Abstract Telomeres protect chromosome ends and control cell division and senescence. During organogenesis, telomeres need to be long enough to ensure the cell proliferation necessary at this stage of development. Previous studies have shown that telomere shortening is associated with growth retardation and congenital malformations. However, these studies were performed in newborns or postnatally, and data on telomere length (TL) during the prenatal period are still very limited. We measured TL using quantitative PCR in amniotic fluid (AF) and chorionic villi (CV) samples from 69 control fetuses with normal ultrasound (52 AF and 17 CV) and 213 fetuses (165 AF and 48 CV) with intrauterine growth retardation (IUGR) or congenital malformations diagnosed by ultrasound. The samples were collected by amniocentesis at the gestational age (GA) of 25.0 ± 5.4 weeks and by CV biopsy at 18.1 ± 6.3 weeks. In neither sample type was TL influenced by GA or fetal sex. In AF, a comparison of abnormal versus normal fetuses showed a significant telomere shortening in cases of IUGR (reduction of 34%, P < 10-6), single (29%, P < 10-6) and multiple (44%, P < 10-6) malformations. Similar TL shortening was also observed in CV from abnormal fetuses but to a lesser extent (25%, P = 0.0002; 18%, P = 0.016; 20%, P = 0.004, respectively). Telomere shortening was more pronounced in cases of multiple congenital anomalies than in fetuses with a single malformation, suggesting a correlation between TL and the severity of fetal phenotype. Thus, TL measurement in fetal samples during pregnancy could provide a novel predictive marker of pathological development.
    MeSH term(s) Biomarkers ; Female ; Fetal Development ; Fetal Growth Retardation/diagnosis ; Fetal Growth Retardation/genetics ; Humans ; Pregnancy ; Telomere/genetics ; Telomere Shortening/genetics
    Chemical Substances Biomarkers
    Language English
    Publishing date 2022-03-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 1108742-0
    ISSN 1460-2083 ; 0964-6906
    ISSN (online) 1460-2083
    ISSN 0964-6906
    DOI 10.1093/hmg/ddac054
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Novel CDK10 variants with multicystic dysplastic kidney, left ventricular non-compaction, and a solitary median maxillary central incisor.

    Darcha, Claude / Laffargue, Fanny / Boutaud, Lucile / Gallot, Denis / Dauphin, Claire / Garcier, Jean Marc / Achaiaa, Amale / Nitschke, Patrick / Fourrage, Cécile / Goumy, Carole / Attie-Bitach, Tania

    Clinical genetics

    2021  Volume 100, Issue 3, Page(s) 348–349

    MeSH term(s) Abnormalities, Multiple/genetics ; Anodontia/enzymology ; Anodontia/genetics ; Cyclin-Dependent Kinases/genetics ; Fatal Outcome ; Humans ; Incisor/abnormalities ; Incisor/enzymology ; Infant ; Isolated Noncompaction of the Ventricular Myocardium/enzymology ; Isolated Noncompaction of the Ventricular Myocardium/genetics ; Male ; Multicystic Dysplastic Kidney/enzymology ; Multicystic Dysplastic Kidney/genetics ; Pedigree
    Chemical Substances CDK10 protein, human (EC 2.7.11.22) ; Cyclin-Dependent Kinases (EC 2.7.11.22)
    Language English
    Publishing date 2021-06-11
    Publishing country Denmark
    Document type Case Reports ; Letter
    ZDB-ID 221209-2
    ISSN 1399-0004 ; 0009-9163
    ISSN (online) 1399-0004
    ISSN 0009-9163
    DOI 10.1111/cge.13996
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Further refining the critical region of 10q26 microdeletion syndrome: A possible involvement of INSYN2 and NPS in the cognitive phenotype.

    Cherik, Florian / Lepage, Mathis / Remerand, Ganaelle / Francannet, Christine / Delabaere, Amélie / Salaun, Gaëlle / Pebrel-Richard, Céline / Gouas, Laetitia / Vago, Philippe / Tchirkov, Andrei / Goumy, Carole

    European journal of medical genetics

    2021  Volume 64, Issue 9, Page(s) 104287

    Abstract: Background: The 10q26 subtelomeric microdeletion syndrome is a rare and clinically heterogeneous disorder. The precise relationships between the causative genes and the phenotype are unclear.: Case presentation: We report two new cases of 860 kb ... ...

    Abstract Background: The 10q26 subtelomeric microdeletion syndrome is a rare and clinically heterogeneous disorder. The precise relationships between the causative genes and the phenotype are unclear.
    Case presentation: We report two new cases of 860 kb deletion of 10q26.2 identified by array CGH in a fetus with intrauterine growth retardation and his mother. The deleted region encompassed only four coding genes, DOCK1, INSYN2, NPS and FOX12. The proband had dysmorphic facies characterized by a high forehead, malformed ears, a prominent nose, and retrognathia. He had bilateral club feet, clinodactily and mild psychomotor retardation. His mother had a short stature, microcephaly, a long face with a high forehead and bitemporal narrowing, arched and sparse eyebrows, strabismus, prominent nose and chin, a thin upper lip and large protruding ears, and mild intellectual disability.
    Conclusions: This study presents the smallest 10q26.2 deletion so far identified, which further refines the minimal critical region associated with the 10q26 microdeletion syndrome. It focuses on three genes potentially responsible for the phenotype: DOCK1, which is the major candidate gene, and INSYN2 and NPS, which could be involved in cognitive functions.
    MeSH term(s) Adult ; Chromosome Deletion ; Chromosomes, Human, Pair 10/genetics ; Cognition ; Facies ; Female ; Humans ; Infant ; Learning Disabilities/genetics ; Learning Disabilities/pathology ; Male ; Neuropeptides/genetics ; Phenotype ; rac GTP-Binding Proteins/genetics
    Chemical Substances DOCK1 protein, human ; Neuropeptides ; neuropeptide S, human ; rac GTP-Binding Proteins (EC 3.6.5.2)
    Language English
    Publishing date 2021-07-09
    Publishing country Netherlands
    Document type Case Reports ; Journal Article
    ZDB-ID 2184135-4
    ISSN 1878-0849 ; 1769-7212
    ISSN (online) 1878-0849
    ISSN 1769-7212
    DOI 10.1016/j.ejmg.2021.104287
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Analysis of the cost effectiveness of different strategies for the antenatal diagnosis of chromosomal aberrations in cases of ultrasound-identified fetal abnormalities.

    Mourgues, Charline / Eymard-Pierre, Eléonore / Laurichesse-Delmas, Hélène / Gerbaud, Laurent / Gouas, Laëtitia / Pébrel-Richard, Céline / Vago, Philippe / Debost-Legrand, Anne / Goumy, Carole

    Annales de biologie clinique

    2020  Volume 78, Issue 5, Page(s) 483–491

    Abstract: Objective: Principal objective of this work was to analyse the cost effectiveness of different sequences of cytogenetic techniques from the hospital's point of view, after prenatal ultrasound has identified fetal malformations.: Methods: Cytogenetic ... ...

    Abstract Objective: Principal objective of this work was to analyse the cost effectiveness of different sequences of cytogenetic techniques from the hospital's point of view, after prenatal ultrasound has identified fetal malformations.
    Methods: Cytogenetic tests were performed for each case in 3 strategies, and their results are reported and compared to one reference strategy. Two new simulated strategies were considered: chromosomal microarrays alone and a direct test + CMA.
    Main outcomes measures: cost-effectiveness ratio.
    Results: A single test result was positive in 234 of the 835 pregnancies studied (28%). CMA alone would have identified 239 abnormalities. In the simulated direct test + CMA sequence, the direct test alone would have been positive for 66.1% of the abnormalities identified. When testing was indicated for NT, reference strategy (Direct + karyotyping) costs 1 084.8 euros by positive test results. Strategies Direct + CMA and CMA alone cost respectively 992.7 and 550.0 euros by positive test results. For OUM indications, reference strategy costs 2 937.8 euros by positive test results. Strategies Direct + CMA and CMA alone cost respectively, 2 118.4 and 1 304.7 euros by positive test results.
    Conclusions: CMA appears to be the most effective test for prenatal cytogenetic diagnosis of fetal abnormalities identified by ultrasound.
    MeSH term(s) Adult ; Algorithms ; Chromosome Aberrations ; Cost-Benefit Analysis ; Cytogenetic Analysis/economics ; Cytogenetic Analysis/methods ; Decision Trees ; Female ; Fetal Diseases/diagnosis ; Fetal Diseases/genetics ; Fetus/abnormalities ; Fetus/diagnostic imaging ; France ; Humans ; Karyotyping/economics ; Karyotyping/methods ; Predictive Value of Tests ; Pregnancy ; Prenatal Diagnosis/economics ; Prenatal Diagnosis/methods ; Retrospective Studies ; Ultrasonography, Prenatal/economics
    Language English
    Publishing date 2020-09-15
    Publishing country France
    Document type Journal Article
    ZDB-ID 418098-7
    ISSN 1950-6112 ; 0003-3898
    ISSN (online) 1950-6112
    ISSN 0003-3898
    DOI 10.1684/abc.2020.1580
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Antenatal ultrasound features of isolated recurrent copy number variation in 7q11.23 (Williams syndrome and 7q11.23 duplication syndrome).

    Courdier, Cécile / Boudjarane, John / Malan, Valérie / Muti, Christine / Sperelakis-Beedham, Brian / Odent, Sylvie / Jaillard, Sylvie / Quelin, Chloé / Le Caignec, Cédric / Patat, Olivier / Dubucs, Charlotte / Julia, Sophie / Schluth-Bolard, Caroline / Goumy, Carole / Redon, Sylvia / Gaillard, Jean-Baptiste / Huynh, Minh Tuan / Dupont, Céline / Tabet, Anne-Claude /
    Cogan, Guillaume / Vialard, François / Dard, Rodolphe / Jedraszak, Guillaume / Jobic, Florence / Lefebvre, Mathilde / Quenum, Geneviève / Inai, Saori / Rama, Mélanie / Sauvestre, Fanny / Coatleven, Frédéric / Thomas, Julie / Rooryck, Caroline

    Prenatal diagnosis

    2023  Volume 43, Issue 6, Page(s) 734–745

    Abstract: Objective: We aimed to gather fetal cases carrying a 7q11.23 copy number variation (CNV) and collect precise clinical data to broaden knowledge of antenatal features in these syndromes.: Methods: We retrospectively recruited unrelated cases with 7q11. ...

    Abstract Objective: We aimed to gather fetal cases carrying a 7q11.23 copy number variation (CNV) and collect precise clinical data to broaden knowledge of antenatal features in these syndromes.
    Methods: We retrospectively recruited unrelated cases with 7q11.23 deletion, known as Williams-Beuren syndrome (WBS), or 7q11.23 duplication who had prenatal ultrasound findings. We collected laboratory and clinical data, fetal ultrasound, cardiac ultrasound and fetal autopsy reports from 18 prenatal diagnostic centers throughout France.
    Results: 40 fetuses with WBS were collected and the most common features were intra-uterine growth retardation (IUGR) (70.0%, 28/40), cardiovascular defects (30.0%, 12/40), polyhydramnios (17.5%, 7/40) and protruding tongue (15.0%, 6/40). Fetal autopsy reports were available for 11 cases and were compared with ultrasound prenatal features. Four cases of fetuses with 7q11.23 microduplication were collected and prenatal ultrasound signs were variable and often isolated.
    Conclusion: This work strengthens the fact that 7q11.23 CNVs are associated with a broad spectrum of antenatal presentations. IUGR and cardiovascular defects were the most frequent ultrasound signs. By reporting the biggest series of antenatal WBS, we aim to better delineate distinctive signs in fetuses with 7q11.23 CNVs.
    MeSH term(s) Humans ; Female ; Pregnancy ; Williams Syndrome/diagnostic imaging ; Williams Syndrome/genetics ; Williams Syndrome/complications ; DNA Copy Number Variations ; Retrospective Studies ; Fetal Growth Retardation ; Ultrasonography
    Language English
    Publishing date 2023-03-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 82031-3
    ISSN 1097-0223 ; 0197-3851
    ISSN (online) 1097-0223
    ISSN 0197-3851
    DOI 10.1002/pd.6340
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  10. Article ; Online: Characterization by microarray and meiotic segregation study of a der(10)t(10;18) in a patient with infertility and normal phenotype.

    Kemeny, Stephan / Brugnon, Florence / Eymard-Pierre, Eléonore / Goumy, Carole / Janny, Laurent / Tchirkov, Andreï / Francannet, Christine / Vago, Philippe / Pebrel-Richard, Céline

    Asian journal of andrology

    2017  Volume 19, Issue 1, Page(s) 135–137

    MeSH term(s) Abortion, Habitual ; Adult ; Chromosomes, Human, Pair 10/genetics ; Chromosomes, Human, Pair 18/genetics ; Humans ; In Situ Hybridization, Fluorescence ; Infertility, Male ; Male ; Meiosis ; Microarray Analysis ; Phenotype ; Spermatozoa/metabolism ; Translocation, Genetic/genetics
    Language English
    Publishing date 2017-01
    Publishing country China
    Document type Case Reports ; Letter
    ZDB-ID 2075824-8
    ISSN 1745-7262 ; 1008-682X
    ISSN (online) 1745-7262
    ISSN 1008-682X
    DOI 10.4103/1008-682X.172818
    Database MEDical Literature Analysis and Retrieval System OnLINE

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