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Pynaker C, McCoy J, Halliday J, Lewis S, Amor DJ, Walker SP, Hui L. Perinatal outcomes after a prenatal diagnosis of a fetal copy number variant: a retrospective population-based cohort study. BMC Pediatr 2024; 24:536. [PMID: 39174956 PMCID: PMC11340052 DOI: 10.1186/s12887-024-05012-6] [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: 02/07/2024] [Accepted: 08/13/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND There are no established guidelines for the follow up of infants born after a prenatal diagnosis of a genomic copy number variant (CNV), despite their increased risk of developmental issues. The aims of this study were (i) to determine the perinatal outcomes of fetuses diagnosed with and without a CNV, and (ii) to establish a population-based paediatric cohort for long term developmental follow up. METHODS An Australian state-wide research database was screened for pregnant individuals who had a prenatal chromosomal microarray (CMA) between 2013-2019 inclusive. Following linkage to laboratory records and clinical referrer details, hospital records were manually reviewed for study eligibility. Eligible participants were mother-child pairs where the pregnancy resulted in a livebirth, the mother was able to provide informed consent in English (did not require a translator) and the mother was the primary caregiver for the child at hospital discharge after birth. Research invitations were sent by registered post at an average of six years after the prenatal diagnostic test. Statistical analysis was performed in Stata17. RESULTS Of 1832 prenatal records examined, 1364 (74.5%) mother-child pairs were eligible for recruitment into the follow up cohort. Of the 468 ineligible, 282 (60.3%) had 'no live pregnancy outcome' (209 terminations of pregnancy (TOP) and 73 miscarriages, stillbirths, and infant deaths), 157 (33.5%) required a translator, and 29 (6.2%) were excluded for other reasons. TOP rates varied by the type of fetal CNV detected: 49.3% (109/221) for pathogenic CNVs, 18.2% (58/319) for variants of uncertain significance and 3.3% (42/1292) where no clinically significant CNV was reported on CMA. Almost 77% of invitation letters were successfully delivered (1047/1364), and the subsequent participation rate in the follow up cohort was 19.2% (201/1047). CONCLUSIONS This study provides Australia's first population-based data on perinatal outcomes following prenatal diagnostic testing with CMA. The relatively high rates of pregnancy loss for those with a prenatal diagnosis of a CNV presented a challenge for establishing a paediatric cohort to examine long term outcomes. Recruiting a mother-child cohort via prenatal ascertainment is a complex and resource-intensive process, but an important step in understanding the impact of a CNV diagnosis in pregnancy and beyond. TRIAL REGISTRATION ACTRN12620000446965p; Registered on April 6, 2020.
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Affiliation(s)
- Cecilia Pynaker
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Jacqui McCoy
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Jane Halliday
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Sharon Lewis
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - David J Amor
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Neurodisability and Rehabilitation Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Susan P Walker
- Department of Obstetrics, Gynaecology and Newborn Health, University of Melbourne, Parkville, VIC, Australia
- Mercy Hospital for Women, Heidelberg, VIC, Australia
| | - Lisa Hui
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, VIC, Australia.
- Department of Obstetrics, Gynaecology and Newborn Health, University of Melbourne, Parkville, VIC, Australia.
- Mercy Hospital for Women, Heidelberg, VIC, Australia.
- Northern Health, Melbourne, VIC, Australia.
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Marchelli G, Mercado C, Gill CS, Kim HKW. Pathogenic Gene Variants Identified in Patients Presenting With Perthes or Perthes-like Hip Disorder. J Pediatr Orthop 2024; 44:e612-e617. [PMID: 38651529 DOI: 10.1097/bpo.0000000000002708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
AIMS Legg-Calve-Perthes disease (LCPD) is a diagnosis of exclusion. Various conditions, such as skeletal dysplasias, can closely mimic LCPD and these must be ruled out to provide appropriate treatment, prognosis, and counseling. Traditionally, genetic testing has not been readily available in pediatric orthopaedic practice. Furthermore, the clinical value of genetic testing patients with LCPD is unclear. With the advance of next-generation sequencing (NGS) technology, genetic testing has become clinically available as a lab test. The purposes of this study were to assess the clinical utility of genetic testing in select patients with LCPD and to determine the patient characteristics of those who tested positive for skeletal dysplasia. METHODS This is an IRB-approved, retrospective study of 63 consecutive patients who presented with Perthes-like symptoms and/or x-ray findings and who had genetic testing. The reason(s) for genetic testing included bilateral hip disease, family history of LCPD, short stature, suspected skeletal dysplasia, atypical radiographic findings, and/or combinations of these reasons. RESULTS Of the 63 patients, 19 patients (30%) were found to have a pathogenic gene variant. In 8 of the 19, a variety of skeletal dysplasia was diagnosed. The remaining 11 patients were found to be carriers of autosomal recessive disorders. All 19 patients were referred for genetic counseling. Of the 8 patients found to have skeletal dysplasia, 3 had bilateral disease, 3 were <10 percentile in height, 1 had a family history of "LCPD," and 3 had atypical x-ray findings. In addition to the pathogenic variants, numerous genetic variants of unknown significance were found with 2 gene variants showing exactly the same variant found in 2 unrelated patients. CONCLUSIONS With 30% of the patients showing pathogenic results, genetic testing of select patients with Perthes-like disease is valuable in detecting an underlying genetic disorder or a carrier status of a genetic disorder.
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Affiliation(s)
| | | | - Corey S Gill
- Center of Excellence in Hip, Scottish Rite for Children
- Department of Orthopedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX
| | - Harry K W Kim
- Center of Excellence in Hip, Scottish Rite for Children
- Department of Orthopedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX
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Wang Y, Liu L, Fu F, Li R, Lei T, Huang R, Li D, Liao C. Chromosome Microarray Analysis and Exome Sequencing: Implementation in Prenatal Diagnosis of Fetuses with Digestive System Malformations. Genes (Basel) 2023; 14:1872. [PMID: 37895220 PMCID: PMC10606699 DOI: 10.3390/genes14101872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
(1) Purpose: Retrospective back-to-back comparisons were performed to evaluate the accuracy, effectiveness, and incremental yield of chromosome microarray analysis (CMA) and exome sequencing (ES) analysis in fetuses with digestive system malformations (DSMs). (2) Methods: In total, 595 women with fetal DSMs who underwent prenatal diagnosis were enrolled. We analyzed the diagnostic yields of CMA and ES and evaluated pregnancy outcomes. Copy number variants (CNVs) were classified according to the American College of Medical Genetics and Genomics guidelines. (3) Results: Pathogenic CNVs were detected in 11/517 (2.12%) fetuses, and variants of unknown significance (VUS) were identified in 69 (13.35%) fetuses using CMA. ES detected 29 pathogenic/likely pathogenic variants in 23/143 (16.08%) fetuses and 26/143 (18.2%) VUS. In those with other ultrasound abnormalities, the detection rate of multiple system structural malformations was 41.2%, followed by skeletal (33.3%), cardiovascular (25.4%), and central nervous system (18.6%) malformations. Of the 391 surviving children, 40 (10.2%) exhibited varying degrees of mental retardation. (4) Conclusion: A correlation exists between DSMs and chromosomal abnormalities. When combined with other systemic abnormalities, the incidence of chromosomal abnormalities increases significantly. Patients with congenital DSM are at risk of developing neurodevelopmental disorders. Combined CMA and ES detection of fetal DSM has good clinical application potential.
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Affiliation(s)
- You Wang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China; (Y.W.); (L.L.)
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
| | - Liyuan Liu
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China; (Y.W.); (L.L.)
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
| | - Fang Fu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
| | - Tingying Lei
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
| | - Ruibin Huang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
| | - Dongzhi Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
| | - Can Liao
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China; (Y.W.); (L.L.)
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
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Shi P, Liang H, Hou Y, Chen D, Ren H, Wang C, Xia Y, Zhang D, Leigh D, Cram DS, Kong X. The uncertainty of copy number variants: pregnancy decisions and clinical follow-up. Am J Obstet Gynecol 2023; 229:170.e1-170.e8. [PMID: 36716986 DOI: 10.1016/j.ajog.2023.01.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/14/2023] [Accepted: 01/21/2023] [Indexed: 01/28/2023]
Abstract
BACKGROUND Next-generation sequencing for copy number variants is often used as a follow-up investigation of unusual fetal ultrasound results and is capable of detecting copy number variations with a resolution of ∼0.1 Mb. In a prenatal setting, observation and subsequent management of pregnancies with a fetal variant of uncertain significance remains problematic for counseling. OBJECTIVE This study aimed to follow the decision-making processes in pregnancies with a fetal variant of uncertain significance and prospectively assess copy number variation interpretations and implications under the newer 2020 American College of Medical Genetics and Genomics guidelines. STUDY DESIGN In a single prenatal unit, prospective chromosome testing using copy number variation sequencing for 8030 fetuses with unexpected noninvasive findings identified 139 pregnancies with a copy number variation classified as a variant of uncertain significance according to the 2015 American College of Medical Genetics and Genomics guidelines current at the time. Parent-of-origin testing was subsequently performed to determine if the copy number variation was inherited or de novo. All couples were offered specialized genetic counseling to assist in pregnancy management decisions. For the continued pregnancies that reached term, newborns were clinically assessed for evidence of any disease at 0 to 10 months and/or at 2 to 4 years of age. RESULTS Of the 139 variants of uncertain significance found, most (78%) were inherited with no evidence of disease in the carrier parent. On the basis of primary ultrasound findings combined with results from noninvasive prenatal screening tests, most inherited variant of uncertain significance pregnancies were continued, whereas most pregnancies involving de novo variants of uncertain significance were terminated. From clinical follow-up of the 113 live births, only 5 showed any evidence of a phenotype that was not apparently related to the original variant of uncertain significance. Prospective reanalysis of the 139 variants of uncertain significance using recent 2020 American College of Medical Genetics and Genomics guidelines changed the status of 24 variants of uncertain significance, with 15 reclassified as benign and 9 as pathogenic. However, the 5 children born with an inherited variant of uncertain significance reclassified as pathogenic showed no evidence of a disease phenotype on clinical follow-up. CONCLUSION The severity of fetal ultrasound findings combined with results from parent-of-origin testing were the key drivers in pregnancy management decisions for patients. According to birth outcomes from continued pregnancies, most variants of uncertain significance proved to be apparently benign in nature and potentially of low risk of adverse disease outcome. There was a discordance rate of 17% for variant of uncertain significance scoring between the 2015 and 2020 American College of Medical Genetics and Genomics guidelines for defining a variant of uncertain significance, suggesting that difficulties remain for predicting true pathogenicity. Nonetheless, with increasing knowledge of population copy number variation polymorphisms, and a more complete assessment for alternative genetic causes, patients having prenatal assessments should feel less anxious when a fetal variant of uncertain significance is identified.
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Affiliation(s)
- Panlai Shi
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongbin Liang
- Genetics and Precision Medicine Centre, First People's Hospital of Kunming, Kunming, China
| | - Yaqin Hou
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Duo Chen
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huanan Ren
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Conghui Wang
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanjie Xia
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Da Zhang
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Don Leigh
- Genetics and Precision Medicine Centre, First People's Hospital of Kunming, Kunming, China
| | - David S Cram
- Genetics and Precision Medicine Centre, First People's Hospital of Kunming, Kunming, China.
| | - Xiangdong Kong
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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Prenatal Diagnosis by Array Comparative Genomic Hybridization in Fetuses with Cardiac Abnormalities. Genes (Basel) 2021; 12:genes12122021. [PMID: 34946970 PMCID: PMC8701951 DOI: 10.3390/genes12122021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Congenital heart defects (CHDs) appear in 8–10 out of 1000 live born newborns and are one of the most common causes of deaths. In fetuses, the congenital heart defects are found even 3–5 times more often. Currently, microarray comparative genomic hybridization (array CGH) is recommended by worldwide scientific organizations as a first-line test in the prenatal diagnosis of fetuses with sonographic abnormalities, especially cardiac defects. We present the results of the application of array CGH in 484 cases with prenatally diagnosed congenital heart diseases by fetal ultrasound scanning (256 isolated CHD and 228 CHD coexisting with other malformations). We identified pathogenic aberrations and likely pathogenic genetic loci for CHD in 165 fetuses and 9 copy number variants (CNVs) of unknown clinical significance. Prenatal array-CGH is a useful method allowing the identification of all unbalanced aberrations (number and structure) with a much higher resolution than the currently applied traditional assessment techniques karyotype. Due to this ability, we identified the etiology of heart defects in 37% of cases.
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Shi P, Xia Y, Li Q, Kong X. Usefulness of copy number variant detection following monogenic disease exclusion in prenatal diagnosis. J Obstet Gynaecol Res 2021; 47:1002-1008. [PMID: 33474820 PMCID: PMC7986431 DOI: 10.1111/jog.14627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/13/2020] [Accepted: 12/12/2020] [Indexed: 12/01/2022]
Abstract
Aim Families with an adverse history of monogenic disease focus on single‐gene diagnosis instead of low‐depth whole‐genome sequence, during subsequent pregnancies. The aim of this study was to assess the potential usefulness of low‐depth whole‐genome sequencing (copy number variant sequencing [CNV‐seq]) detection following monogenic disease exclusion in prenatal diagnosis. Methods A total of 285 families with a history of monogenic disease (of 41 different types; eliminated during the current pregnancy) were recruited and retrospectively analyzed. Low‐depth whole‐genome sequencing (CNV‐Seq, Next‐Seq CN500 platform) was performed for all fetuses. Results The CNV detection results of the 285 samples were as follows: one case of 18‐trisomy chimera (0.35%), one case of pathogenic 3q29 microdeletion syndrome CNV (0.35%), four cases of variant of uncertain significance (VUS) CNVs (1.40%), and four cases of Duchenne muscular dystrophy (DMD) carriers (1.40%); and the remaining samples were normal (96.15%). Of note, 2/285 (0.70%) samples still exhibited pathogenic abnormalities. All positive samples were followed up where the two cases of pathogenic abnormalities elected the pregnancy termination, while the four VUS cases and four DMD‐carrier cases were born healthy. Conclusion In cases where prenatal fetal monogenic disease has been ruled out, CNV detection is still beneficial and should be performed to prevent missed pathogenic CNVs. However, the costs need to be balanced against benefits, and the research will need to assess other types of testing.
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Affiliation(s)
- Panlai Shi
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanjie Xia
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qianqian Li
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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