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Li YY, Tse WT, Kong CW, Wong NKL, Leung TY, Choy KW, To WWK, Cao Y. Prenatal Diagnosis and Pregnancy Outcomes of Fetuses With Orofacial Cleft: A Retrospective Cohort Study in Two Centres in Hong Kong. Cleft Palate Craniofac J 2024; 61:391-399. [PMID: 36128746 DOI: 10.1177/10556656221128436] [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] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE To evaluate the local incidence of orofacial cleft (OFC) encountered in fetal morphology scan and prenatal diagnosis, genetic etiology of fetuses with or without other structural abnormalities, and their pregnancy outcomes. DESIGN Retrospective cohort study. SETTING Two maternal fetal medicine units, tertiary hospitals, Hong Kong. PARTICIPANTS All pregnant women with antenatal diagnosis of fetal OFC between January 2016 and December 2020 (N = 66). RESULTS OFC has an incidence of 0.13% among pregnancies in Hong Kong and 28.8% (19/66) were syndromic cleft that exhibited other fetal structural anomalies. There were 55 cases (84.6%) who opted for invasive prenatal diagnostic testing. Genetic defects were identified in 25.8% (17/66) of this cohort, including 14 pathogenic variants. The detection rate in the syndromic cases is 68.4% (13/19) which was significantly higher than 8.5% (4/47) among non-syndromic cases. Aneuploidies would be the most common cause, accounting for 9.1% (6/66). Chromosomal microarray analysis (CMA) provided an incremental diagnostic yield of 6.1% compared to conventional karyotyping. A total of 29 live births including 3 cases of a variant of uncertain significance and 26 cases without genetic abnormalities detected have continued pregnancy to birth. There were 87.5% (21/24) without detectable pathogenic genetic abnormality reported good long-term outcomes. The chance of OFC fetuses having a good long-term outcome was significantly higher if no genomic variant was detected (P < .001). CONCLUSIONS Invasive prenatal tests with CMA should be offered to pregnancies with OFC regardless of the type. It has provided incremental diagnostic yield over conventional karyotyping and helped in prenatal and genetic counseling. A negative result in non-syndromic OFC favors couples to keep the pregnancy.
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Affiliation(s)
- Yan Yu Li
- Department of Obstetrics and Gynaecology, United Christian Hospital, Hong Kong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong
| | - Wing Ting Tse
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong
| | - Choi Wah Kong
- Department of Obstetrics and Gynaecology, United Christian Hospital, Hong Kong
| | - Natalie Kwun Long Wong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong
| | - William Wing Kee To
- Department of Obstetrics and Gynaecology, United Christian Hospital, Hong Kong
| | - Ye Cao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong
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Cai M, Chen X, Li Y, Lin N, Huang H, Xu L. Genetic analysis, ultrasound phenotype, and pregnancy outcomes of fetuses with Xp22.33 or Yp11.32 microdeletions. J Perinat Med 2024; 52:96-101. [PMID: 37846158 DOI: 10.1515/jpm-2023-0190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/27/2023] [Indexed: 10/18/2023]
Abstract
OBJECTIVES The phenotypes of Xp22.33 or Yp11.32 microdeletions comprising the short-stature homeobox (SHOX) gene have been extensively described in adults and children. Herein, the prenatal ultrasound phenotype and pregnancy outcomes of fetuses with Xp22.33/Yp11.32 microdeletions were analyzed to improve our understanding, diagnosis, and monitoring of this genetic condition in the fetal stage. METHODS A total of 9,100 pregnant women referred to tertiary units for prenatal diagnosis were evaluated by chromosomal microarray analysis(CMA). RESULTS Seven (0.08 %) fetuses had Xp22.33/Yp11.32 microdeletions, ranging from 243 kb to 1.1 Mb, that comprised SHOX. The ultrasonic phenotypes differed among these fetuses, with three fetuses presenting abnormal bone development, one had labial-palatal deformity and strawberry head, two had an abnormal ultrasonic soft marker, and one had no abnormalities. After genetic counseling, only one couple underwent pedigree assessment, which confirmed the paternal origin of the microdeletion. This infant presented delayed speech development, whereas other three infants showed a typical postnatal development. In three cases, the parents chose to terminate the pregnancy. CONCLUSIONS The ultrasonic phenotype of fetuses with Xp22.33/Yp11.32 microdeletions resulting in SHOX heterozygosity loss is variable. Prenatal CMA can quickly and effectively diagnose Xp22.33/Yp11.32 microdeletions and SHOX loss, which may help prenatal counseling.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, P.R. China
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Cai M, Guo N, Fu M, Chen Y, Liang B, Que Y, Ji Q, Huang H, Xu L, Lin N. Prenatal diagnosis of genetic aberrations in fetuses with pulmonary stenosis in southern China: a retrospective analysis. BMC Med Genomics 2023; 16:119. [PMID: 37248535 DOI: 10.1186/s12920-023-01548-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 05/15/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND The genetic etiology of congenital pulmonary stenosis (PS) in fetuses remains inadequately studied. We used karyotype analysis and chromosomal microarray analysis (CMA) to investigate the genetic aberrations associated with PS in human fetuses. METHODS A retrospective analysis was performed on 84 fetuses with congenital PS in southern China. Fetal amniotic fluid and umbilical cord blood samples were obtained for chromosomal karyotype analysis and CMA. RESULTS The rate of pathogenic copy number variation (CNV) was 15.5% (13/84) after karyotyping and CMA. An abnormal karyotype was detected in five cases (6.0%, 5/84) via karyotyping, whereas pathogenic CNVs were detected in 13 cases (15.5%, 13/84) via CMA. In addition to the five abnormal karyotypes detected using karyotype analysis, eight additional chromosomal microduplications and microdeletions were detected using CMA, comprising three cases of 22q11.21 microdeletion; two cases of 16p11.2 microdeletion; one case of simultaneous 18q23 microdeletion and 22q13.33 microduplication; one case of 15q24.1q24.2 microdeletion; and one case of 1q21.1q21.2 microduplication. The rate of pathogenic CNV occurrence was 11.5% in fetuses with isolated PS and 17.2% in fetuses with PS combined with other ultrasound abnormalities. This difference between the two experimental groups was statistically significant. Among 84 fetuses with PS, 39 pregnancies were terminated, and five were lost to follow-up. CONCLUSIONS CMA was not only conducive to detect PS-related pathogenic genomic abnormalities but also to accurately evaluate fetal prognosis in genetic counseling. The early detection of PS and genomic abnormalities will exerta positive impact on fetal intervention and the related prognosis of PS in perinatal infants.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Nan Guo
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Meimei Fu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yuqing Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Bin Liang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yanting Que
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Qingqiang Ji
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China.
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China.
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China.
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Dudakovic A, Bayram B, Bettencourt JW, Limberg AK, Galvan ML, Carrasco ME, Stans B, Thaler R, Morrey ME, Sanchez-Sotelo J, Berry DJ, van Wijnen AJ, Abdel MP. The epigenetic regulator BRD4 is required for myofibroblast differentiation of knee fibroblasts. J Cell Biochem 2023; 124:320-334. [PMID: 36648754 PMCID: PMC9990907 DOI: 10.1002/jcb.30368] [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: 12/21/2022] [Accepted: 12/30/2022] [Indexed: 01/18/2023]
Abstract
Arthrofibrosis, which is characterized by excessive scar tissue and limited motion, can complicate the daily functioning of patients after total knee arthroplasty (TKA). Molecular hallmarks of arthrofibrosis include pathologic accumulation of myofibroblasts and disproportionate collagen deposition. Epigenetic mechanisms, including posttranslation modification of histones, control gene expression and may regulate fibrotic events. This study assessed the role of the bromodomain and extra-terminal (BET) proteins on myofibroblast differentiation. This group of epigenetic regulators recognize acetylated lysines and are targeted by a class of drugs known as BET inhibitors. RNA-seq analysis revealed robust mRNA expression of three BET members (BRD2, BRD3, and BRD4) while the fourth member (BRDT) is not expressed in primary TKA knee outgrowth fibroblasts. RT-qPCR and western blot analyses revealed that BET inhibition with the small molecule JQ1 impairs TGFβ1-induced expression of ACTA2, a key myofibroblast marker, in primary outgrowth knee fibroblasts. Similarly, JQ1 administration also reduced COL3A1 mRNA levels and collagen deposition as monitored by picrosirius red staining. Interestingly, the inhibitory effects of JQ1 on ACTA2 mRNA and protein expression, as well as COL3A1 expression and collagen deposition, were paralleled by siRNA-mediated depletion of BRD4. Together, these data reveal that BRD4-mediated epigenetic events support TGFβ1-mediated myofibroblast differentiation and collagen deposition as seen in arthrofibrosis. To our knowledge, these are the first studies that assess epigenetic regulators and their downstream events in the context of arthrofibrosis. Future studies may reveal clinical utility for drugs that target epigenetic pathways, specifically BET proteins, in the prevention and treatment of arthrofibrosis.
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Affiliation(s)
- Amel Dudakovic
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Banu Bayram
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | | | - Afton K. Limberg
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - M. Lizeth Galvan
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | | | - Britta Stans
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Roman Thaler
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Mark E. Morrey
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | | | - Daniel J. Berry
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Andre J. van Wijnen
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, VT, USA
| | - Matthew P. Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
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Lansdon LA, Dickinson A, Arlis S, Liu H, Hlas A, Hahn A, Bonde G, Long A, Standley J, Tyryshkina A, Wehby G, Lee NR, Daack-Hirsch S, Mohlke K, Girirajan S, Darbro BW, Cornell RA, Houston DW, Murray JC, Manak JR. Genome-wide analysis of copy-number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes. Am J Hum Genet 2023; 110:71-91. [PMID: 36493769 PMCID: PMC9892779 DOI: 10.1016/j.ajhg.2022.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is a common birth defect with a complex, heterogeneous etiology. It is well established that common and rare sequence variants contribute to the formation of CL/P, but the contribution of copy-number variants (CNVs) to cleft formation remains relatively understudied. To fill this knowledge gap, we conducted a large-scale comparative analysis of genome-wide CNV profiles of 869 individuals from the Philippines and 233 individuals of European ancestry with CL/P with three primary goals: first, to evaluate whether differences in CNV number, amount of genomic content, or amount of coding genomic content existed within clefting subtypes; second, to assess whether CNVs in our cohort overlapped with known Mendelian clefting loci; and third, to identify unestablished Mendelian clefting genes. Significant differences in CNVs across cleft types or in individuals with non-syndromic versus syndromic clefts were not observed; however, several CNVs in our cohort overlapped with known syndromic and non-syndromic Mendelian clefting loci. Moreover, employing a filtering strategy relying on population genetics data that rare variants are on the whole more deleterious than common variants, we identify several CNV-associated gene losses likely driving non-syndromic clefting phenotypes. By prioritizing genes deleted at a rare frequency across multiple individuals with clefts yet enriched in our cohort of individuals with clefts compared to control subjects, we identify COBLL1, RIC1, and ARHGEF38 as clefting genes. CRISPR-Cas9 mutagenesis of these genes in Xenopus laevis and Danio rerio yielded craniofacial dysmorphologies, including clefts analogous to those seen in human clefting disorders.
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Affiliation(s)
- Lisa A Lansdon
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Department of Biology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; Department of Pathology, University of Missouri - Kansas City School of Medicine, Kansas City, MO 64108, USA
| | | | - Sydney Arlis
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Huan Liu
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Arman Hlas
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Alyssa Hahn
- Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - Greg Bonde
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Abby Long
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Jennifer Standley
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | | | - George Wehby
- College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Nanette R Lee
- Office of Population Studies Foundation, Inc., University of San Carlos, Cebu City, Philippines
| | | | - Karen Mohlke
- University of North Carolina, Chapel Hill, NC 27514, USA
| | | | - Benjamin W Darbro
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - Robert A Cornell
- Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA; Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Douglas W Houston
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
| | - J Robert Manak
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA; Department of Biology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA.
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Zhang Y, Li J, Ji Y, Cheng Y, Fu X. Mutations in the TBX15-ADAMTS2 pathway associate with a novel soft palate dysplasia. Hum Mutat 2022; 43:2102-2115. [PMID: 36124393 DOI: 10.1002/humu.24473] [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: 06/07/2022] [Revised: 08/29/2022] [Accepted: 09/15/2022] [Indexed: 01/25/2023]
Abstract
We reported de novo variants in specific exons of the TBX15 and ADAMTS2 genes in a hitherto undescribed class of patients with unique craniofacial developmental defects. The nine unrelated patients represent unilateral soft palate hypoplasia, lost part of the sphenoid bone in the pterygoid process, but the uvula developed completely. Interestingly, these clinical features are contrary to the palate's anterior-posterior (A-P) developmental direction. Based on developmental characteristics, we suggested that these cases correspond to a novel craniofacial birth defect different from cleft palate, and we named it soft palate dysplasia (SPD). However, little is known about the molecular mechanism of the ADAMTS2 and TBX15 genes in the regulation of soft palate development. Phylogenetic analysis showed that the sequences around these de novo mutation sites are conserved between species. Through cellular co-transfections and chromatin immunoprecipitation assays, we demonstrate that TBX15 binds to the promoter regions of the ADAMTS2 gene and activates the promoter activity. Furthermore, we show that TBX15 and ADAMTS2 are colocalization in the posterior palatal mesenchymal cells during soft palate development in E13.5 mice embryos. Based on these data, we propose that the disruption of the TBX15-ADAMTS2 signaling pathway during embryogenesis leads to a novel SPD.
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Affiliation(s)
- Yuying Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China.,The Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jian Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China.,The Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yaoting Ji
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yibin Cheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Xiazhou Fu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
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Zhou X, Ji C, Sun L, Yin L, Deng X, Pan Q, Zhang J, Yang Z, Zheng C, Ling C, Shi L, Wu Y. Clinical value of fetal facial profile markers during the first trimester. BMC Pregnancy Childbirth 2022; 22:738. [PMID: 36184592 PMCID: PMC9526988 DOI: 10.1186/s12884-022-05028-9] [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: 03/28/2022] [Accepted: 09/05/2022] [Indexed: 11/11/2022] Open
Abstract
Objectives To study the correlations between facial profile markers and crown-lump length (CRL) in a Chinese population, and to evaluate the clinical value of these markers for abnormal fetuses during the first trimester (11 to 13+6 gestational weeks). Methods The facial profile markers were as followings: inferior facial angle (IFA), maxilla-nasion-mandible (MNM) angle, facial maxillary angle (FMA), frontal space (FS) distance and profile line (PL) distance. These markers were measured in facial mid-sagittal section through ViewPoint 6 software. The diagnostic value of these markers for abnormal fetuses was assessed by receiver operating characteristic (ROC) curves. Results According to the first-trimester scanning (FTS) and follow-up, 31 fetuses were enrolled in the abnormal group, including 14 cases of trisomy 21, 7 cases of trisomy 18, 10 cases with cleft lip and palate (CLP), and 1000 normal fetuses were selected. Among the normal fetuses, the IFA, FS distance and PL distance had negative correlations with CRL. The MNM angle and FMA had positive correlations with CRL. The mean IFA values for fetuses with trisomy 21 and trisomy 18 were 74.11° (standard deviation (SD) 7.48) and 69.88° (SD 7.08), respectively, which were significantly smaller than the normal fetuses (p = 0.013; p = 0.003). The mean MNM angle of fetuses with trisomy 18 and CLP were 6.98° (SD 2.61) and 9.41° (SD 2.57), respectively, which were significantly greater than the normal fetuses (p = 0.005; p < 0.001). The mean FMA values of trisomy 18 fetuses were 63.95° (SD 4.77), which was significantly smaller than the normal fetuses (p < 0.001). The mean FS distance of CLP fetuses was -0.22 mm (SD 1.38), which was significantly smaller than the normal fetuses (p < 0.001). The mean PL distance of trisomy 21, trisomy 18 and CLP fetuses were 2.89 mm (SD 0.41), 2.91 mm (SD 0.56) and 2.71 mm (SD 0.37), respectively. The difference with the normal fetuses had no statistical significance (p = 0.56; p = 0.607; p = 0.54). Conclusions Fetal facial profile markers had excellent correlations with CRL during the first trimester. IFA had certain clinical significance in detecting trisomy 21. FMA, IFA and MNM angle were reliable indicators for screening trisomy 18. The abnormal MNM angle and FS distance could be used as sensitive indicators for CLP. However, PL distance was not the best markers for trisomy 21, trisomy 18 and CLP. Supplementary Information The online version contains supplementary material available at 10.1186/s12884-022-05028-9.
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Affiliation(s)
- Xiaofeng Zhou
- Department of Ultrasound, Changshu Hospital Affiliated to Nanjing University of Chinese Medicine, No. 6 Huanghe Street, Changshu, 215500, Jiangsu, China
| | - Chunya Ji
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, No. 26 Daoqian Street, Suzhou, 215002, Jiangsu, China
| | - Lingling Sun
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, No. 26 Daoqian Street, Suzhou, 215002, Jiangsu, China
| | - Linliang Yin
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, No. 26 Daoqian Street, Suzhou, 215002, Jiangsu, China.
| | - Xuedong Deng
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, No. 26 Daoqian Street, Suzhou, 215002, Jiangsu, China.
| | - Qi Pan
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, No. 26 Daoqian Street, Suzhou, 215002, Jiangsu, China
| | - Jun Zhang
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, No. 26 Daoqian Street, Suzhou, 215002, Jiangsu, China
| | - Zhong Yang
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, No. 26 Daoqian Street, Suzhou, 215002, Jiangsu, China
| | - Chenhan Zheng
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, No. 26 Daoqian Street, Suzhou, 215002, Jiangsu, China
| | - Chen Ling
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, No. 26 Daoqian Street, Suzhou, 215002, Jiangsu, China
| | - Liping Shi
- Department of Ultrasound, Changshu Hospital Affiliated to Nanjing University of Chinese Medicine, No. 6 Huanghe Street, Changshu, 215500, Jiangsu, China
| | - Yanqing Wu
- Department of Ultrasound, Changshu Hospital Affiliated to Nanjing University of Chinese Medicine, No. 6 Huanghe Street, Changshu, 215500, Jiangsu, China
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Fitzsimons KJ, Hamilton MJ, van der Meulen J, Medina J, Wahedally M, Park MH, Russell C. Range and Frequency of Congenital Malformations Among Children With Cleft Lip and/or Palate. Cleft Palate Craniofac J 2022:10556656221089160. [PMID: 35382604 DOI: 10.1177/10556656221089160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
To assess the range and frequency of additional congenital malformations identified among children born alive with CL/P. Analysis of patient-level data from a national registry of cleft births linked to national administrative data of hospital admissions. National Health Service, England. Children born between 2000 and 2012 receiving cleft care in English NHS hospitals. The proportion of children with ICD-10 codes for additional congenital malformations, according to cleft type. The study included 9403 children. Of these 2114 (22.5%) had CL±A, 4509 (48.0%) had CP, 1896 (20.2%) had UCLP, and 884 (9.4%) had BCLP. A total of 3653 (38.8%) children had additional congenital malformations documented in their hospital admission records. The prevalence of additional congenital malformations was greatest among children with CP (53.0%), followed by those with BCLP (33.5%), UCLP (26.3%), and then CL±A (22.2%) (P < .001). Among those with UCLP, children with right-sided clefts were more likely to have additional malformations than those with left-sided clefts (31.6% vs 23.0%, P < .001). Malformations of the skeletal system and circulatory system were most common, affecting 10.5% and 10.2% of the included children, respectively. A total of 16.8% of children had additional congenital malformations affecting 2 or more structural systems. Congenital malformations are common among children born alive with a cleft, affecting over half of some cleft subgroups. Given the frequency of certain structural malformations, clinicians should consider standardized screening for these children. Establishing good links with pediatric and genetic services is recommended.
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Affiliation(s)
- K J Fitzsimons
- Clinical Effectiveness Unit, 14211Royal College of Surgeons of England, London, UK
| | - M J Hamilton
- West of Scotland Centre for Genomic Medicine, 473300Queen Elizabeth University Hospital, Glasgow, UK
| | - J van der Meulen
- Department of Health Services Research and Policy, 4906London School of Hygiene and Tropical Medicine, London, UK
| | - J Medina
- Clinical Effectiveness Unit, 14211Royal College of Surgeons of England, London, UK
| | - Mah Wahedally
- Clinical Effectiveness Unit, 14211Royal College of Surgeons of England, London, UK
| | - M H Park
- Department of Health Services Research and Policy, 4906London School of Hygiene and Tropical Medicine, London, UK
| | - Cjh Russell
- 59842Royal Hospital for Children, 473300Queen Elizabeth University Hospital, Glasgow, UK
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9
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Mastromoro G, Guadagnolo D, Khaleghi Hashemian N, Marchionni E, Traversa A, Pizzuti A. Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis. Diagnostics (Basel) 2022; 12:575. [PMID: 35328129 PMCID: PMC8947110 DOI: 10.3390/diagnostics12030575] [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: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.
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Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (N.K.H.); (E.M.); (A.T.); (A.P.)
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10
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Paradise CR, Galvan ML, Pichurin O, Jerez S, Kubrova E, Dehghani SS, Carrasco ME, Thaler R, Larson AN, van Wijnen AJ, Dudakovic A. Brd4 is required for chondrocyte differentiation and endochondral ossification. Bone 2022; 154:116234. [PMID: 34700039 PMCID: PMC9014208 DOI: 10.1016/j.bone.2021.116234] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 01/03/2023]
Abstract
Differentiation of multi-potent mesenchymal stromal cells (MSCs) is directed by the activities of lineage-specific transcription factors and co-factors. A subset of these proteins controls the accessibility of chromatin by recruiting histone acetyl transferases or deacetylases that regulate acetylation of the N-termini of H3 and H4 histone proteins. Bromodomain (BRD) proteins recognize these acetylation marks and recruit the RNA pol II containing transcriptional machinery. Our previous studies have shown that Brd4 is required for osteoblast differentiation in vitro. Here, we investigated the role of Brd4 on endochondral ossification in C57BL/6 mice and chondrogenic differentiation in cell culture models. Conditional loss of Brd4 in the mesenchyme (Brd4 cKO, Brd4fl/fl: Prrx1-Cre) yields smaller mice that exhibit alteration in endochondral ossification. Importantly, abnormal growth plate morphology and delayed long bone formation is observed in juvenile Brd4 cKO mice. One week old Brd4 cKO mice have reduced proliferative and hypertrophic zones within the physis and exhibit a delay in the formation of the secondary ossification center. At the cellular level, Brd4 function is required for chondrogenic differentiation and maturation of both ATDC5 cells and immature mouse articular chondrocytes. Mechanistically, Brd4 loss suppresses Sox9 levels and reduces expression of Sox9 and Runx2 responsive endochondral genes (e.g., Col2a1, Acan, Mmp13 and Sp7/Osx). Collectively, our results indicate that Brd4 is a key epigenetic regulator required for normal chondrogenesis and endochondral ossification.
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Affiliation(s)
- Christopher R Paradise
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA; Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, USA
| | - M Lizeth Galvan
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Oksana Pichurin
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Sofia Jerez
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Eva Kubrova
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | | | | | - Roman Thaler
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - A Noelle Larson
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Andre J van Wijnen
- Department of Biochemistry, University of Vermont, Burlington, VT, USA; Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Amel Dudakovic
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
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11
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Ji C, Yang Z, Yin L, Deng X, Pan Q, Lu B, Zhang J, Jiang W, Jiang X. The application of three-dimensional ultrasound with reformatting technique in the diagnosis of fetal cleft lip/palate. JOURNAL OF CLINICAL ULTRASOUND : JCU 2021; 49:307-314. [PMID: 33665816 DOI: 10.1002/jcu.22994] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/22/2021] [Accepted: 02/11/2021] [Indexed: 06/12/2023]
Abstract
OBJECTIVE To evaluate the clinical value of three-dimensional ultrasound (3D-US) with reformatting technique in the diagnosis of fetal cleft lip/palate (CL/P), especially those involving the secondary palate. METHODS A total of 113 fetuses suspected with cleft lip (CL) on two-dimensional ultrasound (2D-US) were further evaluated by 2D-US and 3D-US with reformatting technique, in order to clarify the type of oral cleft. Lesions were classified as cleft lip (CL), cleft lip and alveolus (CLA), and cleft lip and palate (CLP) (including primary and secondary palate). All fetuses were followed until birth or termination of pregnancy. The diagnostic accuracies of 2D-US and 3D-US with reformatting technology were compared. RESULTS Both 2D-US and 3D-US with reformatting successfully detected CLs in the final 103 participants. Among these, 29, 25, and 49 cases were confirmed to have CL, CLA, and CLP, respectively. CL, CLA, and CLP were diagnosed by 2D-US in 34, 66, and 3 cases, respectively, and by 3D-US with reformatting technology in 31, 27, and 45 cases, respectively. The sensitivities of 2D-US and 3D-US with reformatting technology in the diagnosis of CLA were 80% (20/25) and 92.0% (23/25), respectively, and the difference was not statistically significant. For CLP, however, the sensitivities were 6.1% (3/49) and 91.8% (45/49), respectively (P < .001). CONCLUSIONS Both 2D-US and 3D-US with reformatting technique have high diagnostic accuracy for CL and CLA. However, 3D-US has a much higher diagnostic accuracy for CLP.
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Affiliation(s)
- Chunya Ji
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu, China
| | - Zhong Yang
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu, China
| | - Linliang Yin
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu, China
| | - Xuedong Deng
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu, China
| | - Qi Pan
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu, China
| | - Bing Lu
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu, China
| | - Jun Zhang
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu, China
| | - Wei Jiang
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu, China
| | - Xiaoli Jiang
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu, China
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12
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Ji C, Jiang X, Yin L, Deng X, Yang Z, Pan Q, Zhang J, Liang Q. Ultrasonographic study of fetal facial profile markers during the first trimester. BMC Pregnancy Childbirth 2021; 21:324. [PMID: 33894762 PMCID: PMC8070329 DOI: 10.1186/s12884-021-03813-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/20/2021] [Indexed: 01/20/2023] Open
Abstract
Background To establish reference ranges of fetal facial profile markers and study their correlations with crown-rump length (CRL) during the first trimester (11 ~ 13+ 6 weeks’ gestation) in a Chinese population. Methods Ultrasonographic images of measuring fetal nuchal translucency (NT) were retrospectively selected randomly in normal fetuses whose parents were both Chinese. The facial markers included inferior facial angle (IFA), maxilla-nasion-mandible (MNM) angle, facial maxillary angle (FMA) and profile line (PL) distance. These markers were measured through ViewPoint 6 software by two experienced sonographers. Results Three hundred and eighty fetuses were selected. The ICCs (95 % CI) of intra-operator 1 reproducibility of IFA, MNM angle, FMA, PL distance were 0.944 (0.886 ~ 0.973), 0.804 (0.629 ~ 0.902), 0.834 (0.68 ~ 0.918) and 0.935 (0.868 ~ 0.969), respectively. The ICCs (95 % CI) of intra-operator 2 reproducibility of IFA, MNM angle, FMA, PL distance were 0.931 (0.857 ~ 0.967), 0.809 (0.637 ~ 0.904), 0.786 (0.600 ~ 0.892) and 0.906 (0.813 ~ 0.954), respectively. The ICCs (95 % CI) of inter-operator reproducibility of IFA, MNM angle, FMA, PL distance were 0.885 (0.663 ~ 0.953), 0.829 (0.672 ~ 0.915), 0.77 (0.511 ~ 0.891) and 0.844 (0.68 ~ 0.925), respectively. The average ± SD of IFA, MNM angle, FMA and PL distance were 80.2°±7.25°, 4.17°±1.19°, 75.36°±5.31°, 2.78 ± 0.54 mm, respectively. IFA and PL distance significantly decreased with CRL, while MNM angle and FMA significantly increased with CRL. Conclusions It was feasible to measure fetal facial markers during the first trimester. In Chinese population, the reference ranges of IFA, MNM angle, FMA and PL distance were 80.2°±7.25°, 4.17°±1.19°, 75.36°±5.31°, 2.78 ± 0.54 mm, respectively, and the measurements were found to correlate with CRL.
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Affiliation(s)
- Chunya Ji
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, No. 26 Daoqian Street, 215002, Suzhou, Jiangsu, China
| | - Xiaoli Jiang
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, No. 26 Daoqian Street, 215002, Suzhou, Jiangsu, China
| | - Linliang Yin
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, No. 26 Daoqian Street, 215002, Suzhou, Jiangsu, China.
| | - Xuedong Deng
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, No. 26 Daoqian Street, 215002, Suzhou, Jiangsu, China.
| | - Zhong Yang
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, No. 26 Daoqian Street, 215002, Suzhou, Jiangsu, China
| | - Qi Pan
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, No. 26 Daoqian Street, 215002, Suzhou, Jiangsu, China
| | - Jun Zhang
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, No. 26 Daoqian Street, 215002, Suzhou, Jiangsu, China
| | - Qing Liang
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, No. 26 Daoqian Street, 215002, Suzhou, Jiangsu, China
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13
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Hui AS, Chau MHK, Chan YM, Cao Y, Kwan AH, Zhu X, Kwok YK, Chen Z, Lao TT, Choy KW, Leung TY. The role of chromosomal microarray analysis among fetuses with normal karyotype and single system anomaly or nonspecific sonographic findings. Acta Obstet Gynecol Scand 2020; 100:235-243. [PMID: 32981064 DOI: 10.1111/aogs.14003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/19/2020] [Accepted: 09/17/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Chromosomal microarray analysis is recommended as the first-tier test for the evaluation of fetuses with structural anomalies. This study aims to investigate the incremental diagnostic yield of chromosomal microarray over conventional karyotyping analysis in fetuses with anomalies restricted to one anatomic system and those with nonspecific anomalies detected by sonography. MATERIAL AND METHODS This is a retrospective cohort analysis of 749 fetuses undergoing prenatal diagnosis for abnormal ultrasound findings isolated to one anatomic system and normal karyotype, utilizing chromosomal microarray. Overall, 495 (66%) fetuses had anomalies confined to one anatomic system and 254 (34%) had other nonspecific anomalies including increased nuchal translucency (≥3.5 mm), cystic hygroma, intrauterine growth restriction and hydrops fetalis. RESULTS Fetuses with ultrasound anomalies restricted to one anatomic system had a 3.0% risk of carrying a pathogenic copy number variant; the risk varied dependent on the anatomic system affected. Fetuses with confined anomalies of the cardiac system had the highest diagnostic yield at 4.6%, but there were none in the urogenital system. Fetuses with nonspecific ultrasound anomalies had the highest diagnostic yield in fetuses with an intrauterine growth restriction at 5.9%. Overall, fetuses with a nonspecific ultrasound anomaly were affected with pathogenic copy number variants in 1.6% in the cases. CONCLUSIONS The diagnostic yield of chromosomal microarray in fetuses with normal karyotype and ultrasound abnormality confined to a single anatomic system was highest if it involved cardiac defects or intrauterine growth restriction. This diagnostic yield ranges from 0% to 4.6% depending on the anatomic system involved. Chromosomal microarray has considerable diagnostic value in these pregnancies.
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Affiliation(s)
- Annie Sy Hui
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Matthew Hoi Kin Chau
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yiu Man Chan
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Adept Medical Center, Hong Kong SAR, China
| | - Ye Cao
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Angel Hw Kwan
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiaofan Zhu
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yvonne K Kwok
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zihan Chen
- Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Terence T Lao
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kwong Wai Choy
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, China, Hong Kong SAR, China
| | - Tak Yeung Leung
- Department of Obstetrics and gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Key Laboratory for Regenerative Medicine, Ministry of Education (Shenzhen Base), Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, China, Hong Kong SAR, China
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Li W, Hu J, Shi B, Palomba F, Digman MA, Gratton E, Jiang H. Biophysical properties of AKAP95 protein condensates regulate splicing and tumorigenesis. Nat Cell Biol 2020; 22:960-972. [PMID: 32719551 PMCID: PMC7425812 DOI: 10.1038/s41556-020-0550-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 06/24/2020] [Indexed: 12/14/2022]
Abstract
It remains unknown if biophysical or material properties of biomolecular condensates regulate cancer. Here we show that AKAP95, a nuclear protein that regulates transcription and RNA splicing, plays an important role in tumorigenesis by supporting cancer cell growth and suppressing oncogene-induced senescence. AKAP95 forms phase-separated and liquid-like condensates in vitro and in nucleus. Mutations of key residues to different amino acids perturb AKAP95 condensation in opposite directions. Importantly, the activity of AKAP95 in splice regulation is abolished by disruption of condensation, significantly impaired by hardening of condensates, and regained by substituting its condensation-mediating region with other condensation-mediating regions from irrelevant proteins. Moreover, the abilities of AKAP95 in regulating gene expression and supporting tumorigenesis require AKAP95 to form condensates with proper liquidity and dynamicity. These results link phase separation to tumorigenesis and uncover an important role of appropriate biophysical properties of protein condensates in gene regulation and cancer.
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Affiliation(s)
- Wei Li
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Jing Hu
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Bi Shi
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Francesco Palomba
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Michelle A Digman
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Enrico Gratton
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA.
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15
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Li L, He Z, Huang X, Lin S, Wu J, Huang L, Wan Y, Fang Q. Chromosomal abnormalities detected by karyotyping and microarray analysis in twins with structural anomalies. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2020; 55:502-509. [PMID: 30977228 DOI: 10.1002/uog.20287] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 02/19/2019] [Accepted: 03/30/2019] [Indexed: 06/09/2023]
Abstract
OBJECTIVES To evaluate the incidence and types of chromosomal abnormalities detected in twins with structural anomalies and compare their distribution according to chorionicity and amnionicity and by structural-anomaly type. The added value of chromosomal microarray analysis (CMA) over conventional karyotyping in twins was also estimated. METHODS This was a single-center, retrospective analysis of 534 twin pregnancies seen over an 11-year period, in which one or both fetuses were diagnosed with congenital structural anomalies on ultrasound. The ultrasound findings and invasive prenatal diagnostic results were reviewed. Twin pregnancies were categorized as monochorionic monoamniotic (MCMA), monochorionic diamniotic (MCDA) or dichorionic diamniotic (DCDA). Chromosomal abnormalities detected by G-banding karyotyping and/or CMA were analyzed by chorionicity and amnionicity and by structural-anomaly type. RESULTS The 534 twin pairs analyzed comprised 25 pairs of MCMA, 112 pairs of MCDA and 397 pairs of DCDA twins. Of the 549 fetuses affected by structural anomalies, 432 (78.7%) underwent invasive prenatal testing and cytogenetic results were obtained. The incidence of overall chromosomal abnormalities in the DCDA fetuses (25.4%) was higher than that in the MCMA (3.7%) and MCDA (15.3%) fetuses. The incidence of aneuploidy was significantly higher in the DCDA group (22.8%) than in the MCMA (0.0%) and MCDA (12.4%) groups. The incidence of chromosomal abnormalities detected in fetuses, with anomalies of the cardiovascular, faciocervical, musculoskeletal, genitourinary and gastrointestinal systems, was higher in the DCDA group than in the MCDA group. In both the DCDA and MCDA groups, hydrops fetalis was associated with the highest incidence of chromosomal abnormality; of these fetuses, 67.6% had Turner syndrome (45,X). Pathogenic copy-number variations (CNVs) undetectable by karyotyping were identified by CMA in five (2.0%; 95% CI, 0.3-3.7%) DCDA fetuses. No pathogenic CNVs were found in MCMA and MCDA twins. CONCLUSIONS Dichorionic twins with structural anomalies have a higher risk of chromosomal abnormalities, especially aneuploidies, than do monochorionic twins. The incremental diagnostic yield of CMA over karyotyping seems to be lower (2.0%) in twins than that reported in singleton pregnancy. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- L Li
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Z He
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - X Huang
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - S Lin
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - J Wu
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - L Huang
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Y Wan
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Q Fang
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Alesi V, Dentici ML, Loddo S, Genovese S, Orlando V, Calacci C, Pompili D, Dallapiccola B, Digilio MC, Novelli A. Confirmation of BRD4 haploinsufficiency role in Cornelia de Lange-like phenotype and delineation of a 19p13.12p13.11 gene contiguous syndrome. Ann Hum Genet 2018; 83:100-109. [PMID: 30302754 DOI: 10.1111/ahg.12289] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 08/14/2018] [Accepted: 09/24/2018] [Indexed: 12/16/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is a genetically and clinical heterogeneous condition characterized by congenital malformation, intellectual disability, and peculiar dysmorphic features. Recently, BRD4 (19p13.12) was proposed as a new critical gene associated with a mild CdLS because of a similar presentation of the patients carrying point mutations and of its involvement in the NIPBL pathway. Patients harboring a 19p interstitial deletion shared some physical features with BRD4 mutation carriers, which results in a more complex phenotype because of the involvement of several neighboring genes. We report a new 19p deletion in a patient clinically diagnosed as CdLS, partially overlapping with previously published cases with the aim to support the role of BRD4 haploinsufficiency in a CdL-like phenotype and to improve the delineation of 19p13.12p13.11 deletion as a new nonrecurrent gene contiguous syndrome, spanning GIPC1, NOTCH3, BRD4, AKAP8, AKAP8L, CASP14, and EPS15L1 genes. Previously described cases are reviewed, attempting to delineate a genotype-phenotype correlation.
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Affiliation(s)
- Viola Alesi
- Medical Genetics Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Maria Lisa Dentici
- Medical Genetics Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Sara Loddo
- Medical Genetics Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Silvia Genovese
- Medical Genetics Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Valeria Orlando
- Medical Genetics Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Chiara Calacci
- Medical Genetics Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Daniele Pompili
- Medical Genetics Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Bruno Dallapiccola
- Medical Genetics Department, Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Antonio Novelli
- Medical Genetics Department, Bambino Gesù Children's Hospital, Rome, Italy
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17
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Jin H, Yingqiu C, Zequn L, Yanjun H, Yunyan Z, Shufan Z, Yiyang C, Ru L, Li Z, Yongling Z, Hongtao W, Can L. Chromosomal microarray analysis in the prenatal diagnosis of orofacial clefts: Experience from a single medical center in mainland China. Medicine (Baltimore) 2018; 97:e12057. [PMID: 30142861 PMCID: PMC6112896 DOI: 10.1097/md.0000000000012057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The aim of this study was to investigate the value of chromosomal microarray analysis (CMA) for the prenatal diagnosis of orofacial clefts.A total of 143 fetuses with oral clefts were detected by ultrasound during prenatal exam between 2012 and 2017 in our center. We categorized the cases into 4 groups: isolated cleft lip (CL) (CL only), isolated cleft palate (CP only), isolated cleft lip and palate (CLP) (CLP only), and syndromic CLP (combined with other malformations). The CMA was performed in all cases, while 139 fetuses were referred for G-banded chromosome analysis.There were 42 male and 10 female fetuses were born, with a sex ratio of 4.2:1. The isolated CLP group accounted for 74.1% (106/143) of cases, while the isolated CL, isolated CP, and syndromic CP groups accounted for 13.9% (20/143), 2% (3/143), and 10% (14/143), respectively. A total of 11 fetuses had pathogenic copy number variants (CNVs, 7.7%), including isolated CP (1/143, 0.7%), isolated CLP (5/143, 3.5%), and syndromic CLP (5/143, 3.5%). Compared with the CMA results, 5 fetuses were found to have an abnormal karyotype (5/139, 3.6%). However, no abnormalities were found in either karyotype analysis or CMA in the isolated CL group.CMA is a valuable tool for identifying submicroscopic chromosomal abnormalities in the prenatal diagnosis of oral clefts. An excellent outcome can be expected for fetuses with isolated CL that are negative for chromosomal abnormalities.
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Affiliation(s)
- Han Jin
- Department of Prenatal Diagnostic Center
| | - Cui Yingqiu
- Department of Oral and Maxillofacial Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Liu Zequn
- Department of Prenatal Diagnostic Center
| | | | - Zhang Yunyan
- Department of Oral and Maxillofacial Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Zhao Shufan
- Department of Oral and Maxillofacial Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Chen Yiyang
- Department of Oral and Maxillofacial Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Li Ru
- Department of Prenatal Diagnostic Center
| | - Zhen Li
- Department of Prenatal Diagnostic Center
| | | | - Wang Hongtao
- Department of Oral and Maxillofacial Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Liao Can
- Department of Prenatal Diagnostic Center
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18
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Wang H, Chau MHK, Cao Y, Kwok KY, Choy KW. Chromosome copy number variants in fetuses with syndromic malformations. Birth Defects Res 2018; 109:725-733. [PMID: 28568742 DOI: 10.1002/bdr2.1054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chromosome copy number variants (CNVs; gains and losses of DNA sequences >1 kb) are wide-spread throughout the genome of healthy individuals. Laboratory studies show that a subset of CNVs are pathogenic, and not only can be responsible for the pathogenesis of major birth defects and cancer, but are also associated with neurodevelopmental disorders at birth. The characteristics of the pathogenic microdeletions and microduplications are important for both clinical implications and genetic counselling regarding test selection for prenatal screening and diagnosis. Unfortunately, our knowledge of the phenotypic effects of most CNV is still minimal, leading to the classification of many CNVs as "genomic imbalances of unknown clinical significance". Microdeletions and microduplications can occur in all pregnancies and the spectrum of pathogenic CNVs in fetuses with syndromic malformations is not well studied. This review summarizes our current understanding of CNVs, the common detection methods, and the characteristics of pathogenic CNVs identified in fetuses with syndromic malformations. Birth Defects Research 109:725-733, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Huilin Wang
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China.,Shenzhen Research Institute, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shenzhen, China
| | - Matthew Hoi Kin Chau
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ye Cao
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China.,Shenzhen Research Institute, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shenzhen, China
| | - Ka Yin Kwok
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China.,Shenzhen Research Institute, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shenzhen, China
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19
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Chromosomal microarray analysis in developmental delay and intellectual disability with comorbid conditions. BMC Med Genomics 2018; 11:49. [PMID: 29793483 PMCID: PMC5968608 DOI: 10.1186/s12920-018-0368-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 05/15/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Developmental delay (DD) and intellectual disability (ID) are frequently associated with a broad spectrum of additional phenotypes. Chromosomal microarray analysis (CMA) has been recommended as a first-tier test for DD/ID in general, whereas the diagnostic yield differs significantly among DD/ID patients with different comorbid conditions. METHODS To investigate the genotype-phenotype correlation, we examined the characteristics of identified pathogenic copy number variations (pCNVs) and compared the diagnostic yields among patient subgroups with different co-occurring conditions. RESULTS This study is a retrospective review of CMA results generated from a mixed cohort of 710 Chinese patients with DD/ID. A total of 247 pCNVs were identified in 201 patients (28%). A large portion of these pCNVs were copy number losses, and the size of copy number losses was generally smaller than gains. The diagnostic yields were significantly higher in subgroups with co-occurring congenital heart defects (55%), facial dysmorphism (39%), microcephaly (34%) or hypotonia (35%), whereas co-occurring conditions of skeletal malformation (26%), brain malformation (24%) or epilepsy (24%) did not alter the yield. In addition, the diagnostic yield nominally correlated with ID severity. CONCLUSION Varied yields exist in DD/ID patients with different phenotypic presentation. The presence of comorbid conditions can be among factors to consider when planning CMA.
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20
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Lansdon LA, Darbro BW, Petrin AL, Hulstrand AM, Standley JM, Brouillette RB, Long A, Mansilla MA, Cornell RA, Murray JC, Houston DW, Manak JR. Identification of Isthmin 1 as a Novel Clefting and Craniofacial Patterning Gene in Humans. Genetics 2018; 208:283-296. [PMID: 29162626 PMCID: PMC5753863 DOI: 10.1534/genetics.117.300535] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 11/20/2017] [Indexed: 12/26/2022] Open
Abstract
Orofacial clefts are one of the most common birth defects, affecting 1-2 per 1000 births, and have a complex etiology. High-resolution array-based comparative genomic hybridization has increased the ability to detect copy number variants (CNVs) that can be causative for complex diseases such as cleft lip and/or palate. Utilizing this technique on 97 nonsyndromic cleft lip and palate cases and 43 cases with cleft palate only, we identified a heterozygous deletion of Isthmin 1 in one affected case, as well as a deletion in a second case that removes putative 3' regulatory information. Isthmin 1 is a strong candidate for clefting, as it is expressed in orofacial structures derived from the first branchial arch and is also in the same "synexpression group" as fibroblast growth factor 8 and sprouty RTK signaling antagonist 1a and 2, all of which have been associated with clefting. CNVs affecting Isthmin 1 are exceedingly rare in control populations, and Isthmin 1 scores as a likely haploinsufficiency locus. Confirming its role in craniofacial development, knockdown or clustered randomly interspaced short palindromic repeats/Cas9-generated mutation of isthmin 1 in Xenopus laevis resulted in mild to severe craniofacial dysmorphologies, with several individuals presenting with median clefts. Moreover, knockdown of isthmin 1 produced decreased expression of LIM homeobox 8, itself a gene associated with clefting, in regions of the face that pattern the maxilla. Our study demonstrates a successful pipeline from CNV identification of a candidate gene to functional validation in a vertebrate model system, and reveals Isthmin 1 as both a new human clefting locus as well as a key craniofacial patterning gene.
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Affiliation(s)
- Lisa A Lansdon
- Department of Pediatrics
- Department of Biology
- Interdisciplinary Graduate Program in Genetics
| | - Benjamin W Darbro
- Department of Pediatrics
- Interdisciplinary Graduate Program in Genetics
| | - Aline L Petrin
- Department of Pediatrics
- College of Dentistry, University of Iowa, Iowa 52242 and
| | | | | | | | | | | | - Robert A Cornell
- Interdisciplinary Graduate Program in Genetics
- Department of Anatomy and Cell Biology, and
| | - Jeffrey C Murray
- Department of Pediatrics
- Department of Biology
- Department of Anatomy and Cell Biology, and
- Interdisciplinary Graduate Program in Genetics
- College of Dentistry, University of Iowa, Iowa 52242 and
| | | | - J Robert Manak
- Department of Pediatrics,
- Department of Biology
- Interdisciplinary Graduate Program in Genetics
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21
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Dong Z, Xie W, Chen H, Xu J, Wang H, Li Y, Wang J, Chen F, Choy KW, Jiang H. Copy-Number Variants Detection by Low-Pass Whole-Genome Sequencing. ACTA ACUST UNITED AC 2017; 94:8.17.1-8.17.16. [PMID: 28696555 DOI: 10.1002/cphg.43] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Emerging studies have demonstrated that whole-genome sequencing (WGS) is an efficient tool for copy-number variants (CNV) detection, particularly in probe-poor regions, as compared to chromosomal microarray analysis (CMA). However, the cost of testing is beyond economical for routine usage and the lengthy turn-around time is not ideal for clinical implementation. In addition, the demand for computational resources also reduces the probability of clinical integration into each laboratory. Herein, a protocol providing CNV detection from low-pass, whole-genome sequencing (0.25×) in a clinical laboratory setting is described. The cost is reduced to less than $200 USD per sample and the turn-around time is within an acceptable clinically workable time-frame (7 days). © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Zirui Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Weiwei Xie
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Haixiao Chen
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Jinjin Xu
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Huilin Wang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Bao'an Maternal and Child Health Hospital, Shenzhen, China
| | - Yun Li
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
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22
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Li M, Carey J, Cristiano S, Susztak K, Coresh J, Boerwinkle E, Kao WHL, Beaty TH, Köttgen A, Scharpf RB. Genome-Wide Association of Copy Number Polymorphisms and Kidney Function. PLoS One 2017; 12:e0170815. [PMID: 28135296 PMCID: PMC5279752 DOI: 10.1371/journal.pone.0170815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 01/11/2017] [Indexed: 01/08/2023] Open
Abstract
Genome-wide association studies (GWAS) using single nucleotide polymorphisms (SNPs) have identified more than 50 loci associated with estimated glomerular filtration rate (eGFR), a measure of kidney function. However, significant SNPs account for a small proportion of eGFR variability. Other forms of genetic variation have not been comprehensively evaluated for association with eGFR. In this study, we assess whether changes in germline DNA copy number are associated with GFR estimated from serum creatinine, eGFRcrea. We used hidden Markov models (HMMs) to identify copy number polymorphic regions (CNPs) from high-throughput SNP arrays for 2,514 African (AA) and 8,645 European ancestry (EA) participants in the Atherosclerosis Risk in Communities (ARIC) study. Separately for the EA and AA cohorts, we used Bayesian Gaussian mixture models to estimate copy number at regions identified by the HMM or previously reported in the HapMap Project. We identified 312 and 464 autosomal CNPs among individuals of EA and AA, respectively. Multivariate models adjusted for SNP-derived covariates of population structure identified one CNP in the EA cohort near genome-wide statistical significance (Bonferroni-adjusted p = 0.067) located on chromosome 5 (876-880kb). Overall, our findings suggest a limited role of CNPs in explaining eGFR variability.
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Affiliation(s)
- Man Li
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Jacob Carey
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Stephen Cristiano
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Welch Center for Prevention, Epidemiology and Clinical Research, Baltimore, Maryland, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Wen Hong L. Kao
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Welch Center for Prevention, Epidemiology and Clinical Research, Baltimore, Maryland, United States of America
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Division of Genetic Epidemiology, Medical Center–University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Robert B. Scharpf
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
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23
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Oneda B, Rauch A. Microarrays in prenatal diagnosis. Best Pract Res Clin Obstet Gynaecol 2017; 42:53-63. [PMID: 28215395 DOI: 10.1016/j.bpobgyn.2017.01.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 12/13/2016] [Accepted: 01/04/2017] [Indexed: 01/09/2023]
Abstract
In prenatal diagnosis, chromosomal microarray (CMA) has not yet fully replaced conventional karyotyping but has rapidly become the recommended test in pregnancies with ultrasound abnormalities. In this review, we provide an overview of the published data concerning this technology and the controversies concerning its use in the prenatal setting. There is abundant evidence indicating the added detection of pathogenic abnormalities with CMA in comparison to the traditional karyotyping, especially in fetuses with multiple or isolated ultrasound abnormalities such as congenital heart disease, increased nuchal translucency, or oral cleft. On the other hand, there is also a risk to detect variants of unknown significance, late-onset disorders, and variants in susceptibility loci. However, it has been shown that pregnant couples tend to prefer a maximum of information about the health of their unborn child. Taken together, CMA has considerable diagnostic and prognostic values during pregnancy and should therefore be the test of choice.
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Affiliation(s)
- Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland.
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
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