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Ren H, Liu Z, Chen C, Shi Y, Zhang J, Chen Y, Jia L, Liu Y, Yan J. Case reports on uniparental disomy of chromosomes 6 and 3 in paternity testing. Forensic Sci Res 2024; 9:owae027. [PMID: 38774862 PMCID: PMC11106219 DOI: 10.1093/fsr/owae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 04/09/2024] [Indexed: 05/24/2024] Open
Abstract
In paternity testing, when there are Mendelian errors in the alleles between the child and the parents, a slippage mutation, or silent allele may not fully explain the phenomenon. Sometimes, it is attributed to chromosomal abnormalities, such as uniparental disomy (UPD). Here, we present the investigation of two cases of suspected UPD in paternity testing based on short tandem repeat (STR) detection (capillary electrophoresis platform). Case 1 involves a trio, where all genotypes detected on chromosome 6 in the child are homozygous and found in the father. Case 2 is a duo (mother and child), where all genotypes on chromosome 3 in the child are homozygous and not always found in the mother. At the same time, Mendelian error alleles were also observed at specific loci in these two chromosomes. Furthermore, we used the MGIEasy Signature Identification Library Prep Kit for sequencing on the massively parallel sequencing platform, which included common autosomal, X and Y chromosomes, and mitochondrial genetic markers used in forensic practice. The results showed that the genotypes of shared STRs on the two platforms were consistent, and STRs and single nucleotide polymorphisms (SNPs) on these two chromosomes were homozygous. All other genetic markers followed the laws of inheritance. A comprehensive analysis supported the parent-child relationship between the child and the alleged parent, and the observed genetic anomalies can be attributed to UPD. UPD occurrences are rare, and ignoring its presence can lead to erroneous exclusions in paternity testing, particularly when multiple loci on a chromosome exhibit homozygosity.
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Affiliation(s)
- He Ren
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, Academy of Forensic Science, Shanghai, China
- Beijing Police College, Beijing, China
| | - Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chong Chen
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing, China
| | - Yan Shi
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing, China
| | - Jiarong Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, China
| | - Ying Chen
- Fangshan Branch of Beijing Public Security Bureau, Beijing, China
| | - Li Jia
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing, China
| | - Yacheng Liu
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, China
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Ma Y, Wang J, Wen T, Xu Y, Huang L, Mai Q, Xu Y. An Incidental Detection of a Rare UPD in SNP-Array Based PGT-SR: A Case Report. Reprod Sci 2024:10.1007/s43032-024-01598-5. [PMID: 38780745 DOI: 10.1007/s43032-024-01598-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Uniparental disomies (UPD) refers to the inheritance of both homologs of a chromosome from only one parent with no representative copy from the other parent. UPD was with an estimated prevalence of 0.15‰ in population. Current understanding of UPD was limited to subjects for which UPD was associated with clinical manifestation due to imprinting disorders or recessive diseases. Segmental UPD was rare, especially for a segmental UPD with a combination of hetero- and isodisomy. This paper presents a couple with reciprocal translocation 46,XY, t(14;22)(q32.3;q12.2) for PGT-SR. Among 8 biopsied blastocysts, one euploid blastocyst (No.4) with segmental loss of heterozygosity (LOH)(22) [arr[hg19] q12.1q22.3 (28,160,407 - 35,407,682)] was detected by B allele frequency. We found the chromosome contained both UPiD(22) [arr[hg19] q12.1q22.3 (28,160,407 - 35,407,682) ×2 hmz mat] and UPhD(22) [arr[hg19] q22.3qter(35,407,682 - 51,169,045) ×2 htz mat] by haplotype analysis. UPDtool software confirmed the result. What's more, the segmental UPD and reciprocal translocation shared the same breakpoint, chr22q12.1 (28,160,407), while the breakpoint between iso- and heterodisomy was chr22q22.3 (35,407,682). We reported the first segmental UPD with a combination of hetero- and isodisomy, which may result from aneuploidy rescue. This case emphasizes the importance of the combination of comprehensive chromosome screening and haplotype analysis to reduce the risk of misdiagnosis.
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Affiliation(s)
- Yuanlin Ma
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road No. 1, Yuexiu District, 510080, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Yuexiu District, 510080, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for obstetrical and gynecological diseases, Yuexiu District, 510080, Guangzhou, Guangdong, China
| | - Jing Wang
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road No. 1, Yuexiu District, 510080, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Yuexiu District, 510080, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for obstetrical and gynecological diseases, Yuexiu District, 510080, Guangzhou, Guangdong, China
| | - Tianrui Wen
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road No. 1, Yuexiu District, 510080, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Yuexiu District, 510080, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for obstetrical and gynecological diseases, Yuexiu District, 510080, Guangzhou, Guangdong, China
| | - Yan Xu
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road No. 1, Yuexiu District, 510080, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Yuexiu District, 510080, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for obstetrical and gynecological diseases, Yuexiu District, 510080, Guangzhou, Guangdong, China
| | - Linhuan Huang
- Fetal Medicine Centre, The First Affiliated Hospital of Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Qingyun Mai
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road No. 1, Yuexiu District, 510080, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Yuexiu District, 510080, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for obstetrical and gynecological diseases, Yuexiu District, 510080, Guangzhou, Guangdong, China
| | - Yanwen Xu
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road No. 1, Yuexiu District, 510080, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Yuexiu District, 510080, Guangzhou, Guangdong, China.
- Guangdong Provincial Clinical Research Center for obstetrical and gynecological diseases, Yuexiu District, 510080, Guangzhou, Guangdong, China.
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Ma D, Ye M, Hu W, Gao H, Wang L, Song Y, Nie R, Hu Z, Guo H. Large regions of homozygosity in prenatal diagnosis. Am J Med Genet A 2024:e63712. [PMID: 38757552 DOI: 10.1002/ajmg.a.63712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/26/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
Chromosomal microarrays (CMA) incorporate single nucleotide polymorphisms to enable the detection of regions of homozygosity (ROH). Here, we retrospectively analyzed 6288 prenatal cases who performed CMA to explored the clinical implications of large ROH in prenatal diagnosis. We analyzed cases with ROH larger than 10 megabases and reviewed the ultrasound findings; karyotype results and pregnancy follow-up data. Cases with possible imprinting disorders were assessed by methylation-specific multiplex ligation-dependent probe amplification. In total, we identified 50 cases with large ROH and chromosomes 1 and 2 were the most affected. About 59.18% of the ROH cases had ultrasound abnormalities, with the most common findings being ultrasound soft-marker abnormalities. There were seven fetuses had ROH which covered almost the entire chromosome and four had terminal ROH that involved almost the entire long arm of the chromosomes, which indicated uniparental disomy (UPD), of which 70% showed abnormal ultrasound findings. Ten cases with multiple ROH on different chromosomes indicated the third to fifth degree of consanguinity. In this study, we highlighted the clinical relevance of large ROH related to UPD. The analysis of ROH allowed us to gain further understanding of complex cytogenetic and disease mechanisms in prenatal diagnosis.
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Affiliation(s)
- Di Ma
- Forensic Evidence Laboratory, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Mei Ye
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Clinical Medical Research Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Wenlong Hu
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Clinical Medical Research Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Hui Gao
- Forensic Evidence Laboratory, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Lijuan Wang
- Forensic Evidence Laboratory, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Yaqin Song
- Forensic Evidence Laboratory, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Rui Nie
- Forensic Evidence Laboratory, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Zhiyang Hu
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Department of Obstetrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Hui Guo
- Forensic Evidence Laboratory, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Genetic and Prenatal Disease Diagnosis Center, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
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Wu CY, Zhou Y, Yin X, Peng R, Xie HN. Prenatal ultrasound findings and clinical outcomes of uniparental disomy: a retrospective study. BMC Pregnancy Childbirth 2024; 24:288. [PMID: 38637738 PMCID: PMC11027273 DOI: 10.1186/s12884-024-06493-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/07/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Uniparental disomy is the inheritance of a homologous chromosome pair or part of homologous chromosomes from only one parent. However, the clinical significance of uniparental disomy and the difference among the prognosis of involvement of different chromosomes remain unclear. OBJECTIVE To assess the associated prenatal ultrasound presentations and clinical outcomes of uniparental disomy on different chromosomes and to analyze the relationship between prenatal ultrasound markers and clinical outcomes. STUDY DESIGN We retrospectively analyzed data from fetuses with uniparental disomy diagnosed using chromosome microarray analysis with the Affymetrix CytoScan HD array at our institution between January 2013 and September 2022. The relationship between prenatal ultrasound findings, the involved chromosome(s), and clinical outcomes was evaluated. RESULTS During the study period, 36 fetuses with uniparental disomy were diagnosed, and two cases were excluded for non-available postnatal data. Finally, 34 fetuses were included in our study, of which 30 (88.2%) had uniparental disomy occurring on a single chromosome, while four (11.8%) were identified with uniparental disomy on different chromosomes. The most frequently involved chromosomes were chromosomes 16, X and 2, which presented in 8 (23.5%), 5 (14.7%) and 4 (11.8%), respectively. Prenatal ultrasound abnormalities were detected in 21 fetuses, with the most common category being multiple abnormalities (12 (57.1%)). Fetal growth restriction was identified in 14 (41.2%) fetuses, all of which coexisted with other abnormal findings. The rate of adverse perinatal outcomes in patients with uniparental disomy and fetal abnormalities was significantly higher than those without abnormalities (76.2% versus 15.4%, P = 0.002). The incidence of fetal or neonatal death was significantly higher in fetuses with fetal growth restriction than those without (85.7% versus 30.0%, P = 0.004). CONCLUSIONS The prognosis of fetuses with uniparental disomy combined with fetal abnormalities, especially fetal growth restriction, was much poorer than those without.
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Affiliation(s)
- Cui-Yi Wu
- Department of Ultrasonic Medicine, Fetal Medical Centre, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yi Zhou
- Department of Obstetrics, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xia Yin
- Department of Ultrasonic Medicine, Fetal Medical Centre, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ruan Peng
- Department of Ultrasonic Medicine, Fetal Medical Centre, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Hong-Ning Xie
- Department of Ultrasonic Medicine, Fetal Medical Centre, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
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5
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Ma D, Lin Y, Zhang R, Wang S, Hu W, Ye M, Gao H, Wang L, Song Y, Guo H. Effect of uniparental disomy in parentage testing. Leg Med (Tokyo) 2024; 67:102381. [PMID: 38154315 DOI: 10.1016/j.legalmed.2023.102381] [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: 04/22/2023] [Revised: 11/21/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
Uniparental disomy (UPD) is a rare type of chromosomal aberration that may hinder the analysis of kinship during forensic identification. Here, we investigated these genetic findings to avoid false exclusions during parentage testing. Thirty-nine fluorescently labeled, autosomal short tandem repeats (STR) were amplified in three cases, to detect parent-child relationships. Twenty-three fluorescently labeled Y-chromosome STRs were also employed. These were subjected to capillary electrophoresis. The parentage index was calculated by the bipartite or tripartite model. Single nucleotide polymorphism (SNP) microarrays were performed to further investigate the genetic mechanisms. The conclusions supported the biological mother-child relationship in three cases. However, in all cases, the alleged father and child had three autosomal STR markers, constrained to a single chromosome, which did not conform to Mendelian inheritance rules. The genotyping of 23 Y-chromosome STRs did not reveal any violations of Mendelian law. The combination of STR profiling and SNP microarrays suggested that two children had maternal UPD of chromosome 7, whilst one had UPD of chromosome 2. After excluding the three incompatible loci, the conclusions supported the biological father-child relationship in all cases. The same results were obtained when parentage testing of trios was used. Uniparental disomy may complicate the judgment of kinship in parentage testing. The possibility of UPD should be considered when incompatible STR loci are found on the same chromosome. Genetic evidence obtained through additional molecular techniques can provide better interpretation of kinship in the presence of UPD and avoid false exclusions of biological relationships.
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Affiliation(s)
- Di Ma
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - YuMei Lin
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - RuanZhang Zhang
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Shayan Wang
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Wenlong Hu
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Mei Ye
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Hui Gao
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Lijuan Wang
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Yaqin Song
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Hui Guo
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China.
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Chaves TF, Ocampos M, Barbato IT, de Camargo Pinto LL, de Luca GR, Barbato Filho JH, Bernardi P, Costa Netto Muniz Y, Francesca Maris A. A cohort study of neurodevelopmental disorders and/or congenital anomalies using high resolution chromosomal microarrays in southern Brazil highlighting the significance of ASD. Sci Rep 2024; 14:3762. [PMID: 38355898 PMCID: PMC10867078 DOI: 10.1038/s41598-024-54385-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/12/2024] [Indexed: 02/16/2024] Open
Abstract
Chromosomal microarray (CMA) is the reference in evaluation of copy number variations (CNVs) in individuals with neurodevelopmental disorders (NDDs), such as intellectual disability (ID) and/or autism spectrum disorder (ASD), which affect around 3-4% of the world's population. Modern platforms for CMA, also include probes for single nucleotide polymorphisms (SNPs) that detect homozygous regions in the genome, such as long contiguous stretches of homozygosity (LCSH). These regions result from complete or segmental chromosomal homozygosis and may be indicative of uniparental disomy (UPD), inbreeding, population characteristics, as well as replicative DNA repair events. In this retrospective study, we analyzed CMA reading files requested by geneticists and neurologists for diagnostic purposes along with available clinical data. Our objectives were interpreting CNVs and assess the frequencies and implications of LCSH detected by Affymetrix CytoScan HD (41%) or 750K (59%) platforms in 1012 patients from the south of Brazil. The patients were mainly children with NDDs and/or congenital anomalies (CAs). A total of 206 CNVs, comprising 132 deletions and 74 duplications, interpreted as pathogenic, were found in 17% of the patients in the cohort and across all chromosomes. Additionally, 12% presented rare variants of uncertain clinical significance, including LPCNVs, as the only clinically relevant CNV. Within the realm of NDDs, ASD carries a particular importance, owing to its escalating prevalence and its growing repercussions for individuals, families, and communities. ASD was one clinical phenotype, if not the main reason for referral to testing, for about one-third of the cohort, and these patients were further analyzed as a sub-cohort. Considering only the patients with ASD, the diagnostic rate was 10%, within the range reported in the literature (8-21%). It was higher (16%) when associated with dysmorphic features and lower (7%) for "isolated" ASD (without ID and without dysmorphic features). In 953 CMAs of the whole cohort, LCSH (≥ 3 Mbp) were analyzed not only for their potential pathogenic significance but were also explored to identify common LCSH in the South Brazilians population. CMA revealed at least one LCSH in 91% of the patients. For about 11.5% of patients, the LCSH suggested consanguinity from the first to the fifth degree, with a greater probability of clinical impact, and in 2.8%, they revealed a putative UPD. LCSH found at a frequency of 5% or more were considered common LCSH in the general population, allowing us to delineate 10 regions as potentially representing ancestral haplotypes of neglectable clinical significance. The main referrals for CMA were developmental delay (56%), ID (33%), ASD (33%) and syndromic features (56%). Some phenotypes in this population may be predictive of a higher probability of indicating a carrier of a pathogenic CNV. Here, we present the largest report of CMA data in a cohort with NDDs and/or CAs from the South of Brazil. We characterize the rare CNVs found along with the main phenotypes presented by each patient and show the importance and usefulness of LCSH interpretation in CMA results that incorporate SNPs, as well as we illustrate the value of CMA to investigate CNV in ASD.
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Affiliation(s)
- Tiago Fernando Chaves
- Laboratório de Polimorfismos Genéticos (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
- Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
| | - Maristela Ocampos
- Laboratory Neurogene (former), Florianopolis, SC, Brazil
- Mercolab Diagnóstica (actual), Florianopolis, SC, Brazil
| | | | | | | | | | - Priscila Bernardi
- University Hospital Professor Polydoro Ernani de São Thiago, Florianópolis, SC, Brazil
| | - Yara Costa Netto Muniz
- Laboratório de Polimorfismos Genéticos (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Angelica Francesca Maris
- Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
- Children's Hospital Joana de Gusmão, Florianópolis, SC, Brazil.
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Xu C, Li M, Gu T, Xie F, Zhang Y, Wang D, Peng J. Chromosomal microarray analysis for prenatal diagnosis of uniparental disomy: a retrospective study. Mol Cytogenet 2024; 17:3. [PMID: 38291465 PMCID: PMC10826057 DOI: 10.1186/s13039-023-00668-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/28/2023] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Chromosomal microarray analysis (CMA) is a valuable tool in prenatal diagnosis for the detection of chromosome uniparental disomy (UPD). This retrospective study examines fetuses undergoing invasive prenatal diagnosis through Affymetrix CytoScan 750 K array analysis. We evaluated both chromosome G-banding karyotyping data and CMA results from 2007 cases subjected to amniocentesis. RESULTS The detection rate of regions of homozygosity (ROH) ≥ 10 Mb was 1.8% (33/2007), with chromosome 11 being the most frequently implicated (17.1%, 6/33). There were three cases where UPD predicted an abnormal phenotype based on imprinted gene expression. CONCLUSION The integration of UPD detection by CMA offers a more precise approach to prenatal genetic diagnosis. CMA proves effective in identifying ROH and preventing the birth of children affected by imprinting diseases.
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Affiliation(s)
- Chenxia Xu
- Prenatal Diagnosis Center, Boai Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Miaoyuan Li
- Department of Urology, The People's Hospital of Zhongshan, Zhongshan, Guangdong, China
- The First School of Clinical Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Tiancai Gu
- Prenatal Diagnosis Center, Boai Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Fenghua Xie
- Prenatal Diagnosis Center, Boai Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Yanfang Zhang
- Prenatal Diagnosis Center, Boai Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Degang Wang
- Prenatal Diagnosis Center, Boai Hospital of Zhongshan, Zhongshan, Guangdong, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Jianming Peng
- Prenatal Diagnosis Center, Boai Hospital of Zhongshan, Zhongshan, Guangdong, China.
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8
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Li M, Hao N, Jiang Y, Xue H, Dai Y, Wang M, Bai J, Lv Y, Qi Q, Zhou X. Contribution of uniparental disomy to fetal growth restriction: a whole-exome sequencing series in a prenatal setting. Sci Rep 2024; 14:238. [PMID: 38168635 PMCID: PMC10762123 DOI: 10.1038/s41598-023-50584-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
Fetal growth restriction (FGR), a leading cause of perinatal morbidity and mortality, is caused by fetal, maternal, and placental factors. Uniparental disomy (UPD) is a rare condition that leads to imprinting effects, low-level mosaic aneuploidies and homozygosity for pathogenic variants. In the present study, UPD events were detected in 5 women with FGR by trio exome sequencing (trio-WES) of a cohort of 150 FGR cases. Furthermore, noninvasive prenatal testing results of the 5 patients revealed a high risk of rare autosomal trisomy. Trio-WES showed no copy-number variations (CNVs) or nondisease-causing mutations associated with FGR. Among the 5 women with FGR, two showed gene imprinting, and two exhibited confined placental mosaicism (CPM) by copy number variant sequencing (CNV-seq). The present study showed that in FGR patients with UPD, the detection of imprinted genes and CPM could enhance the genetic diagnosis of FGR.
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Affiliation(s)
- Mengmeng Li
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Na Hao
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yulin Jiang
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Huili Xue
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian, 350001, China
| | - Yifang Dai
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian, 350001, China
| | - Mingming Wang
- GenoDecode (Beijing) Co. Ltd., Beijing, 101160, China
| | - Junjie Bai
- Be Creative Lab (Beijing) Co. Ltd., Beijing, 100176, China
| | - Yan Lv
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Qingwei Qi
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xiya Zhou
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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9
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Campos G, Sciorio R, Fleming S. Healthy Live Births after the Transfer of Mosaic Embryos: Self-Correction or PGT-A Overestimation? Genes (Basel) 2023; 15:18. [PMID: 38275600 PMCID: PMC10815078 DOI: 10.3390/genes15010018] [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: 12/04/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
The implementation of next generation sequencing (NGS) in preimplantation genetic testing for aneuploidy (PGT-A) has led to a higher prevalence of mosaic diagnosis within the trophectoderm (TE) sample. Regardless, mosaicism could potentially increase the rate of live-born children with chromosomic syndromes, though available data from the transfer of embryos with putative PGT-A mosaicism are scarce but reassuring. Even with lower implantation and higher miscarriage rates, mosaic embryos can develop into healthy live births. Therefore, this urges an explanation for the disappearance of aneuploid cells throughout development, to provide guidance in the management of mosaicism in clinical practice. Technical overestimation of mosaicism, together with some sort of "self-correction" mechanisms during the early post-implantation stages, emerged as potential explanations. Unlike the animal model, in which the elimination of genetically abnormal cells from the future fetal lineage has been demonstrated, in human embryos this capability remains unverified even though the germ layer displays an aneuploidy-induced cell death lineage preference with higher rates of apoptosis in the inner cell mass (ICM) than in the TE cells. Moreover, the reported differential dynamics of cell proliferation and apoptosis between euploid, mosaic, and aneuploid embryos, together with pro-apoptosis gene products (cfDNA and mRNA) and extracellular vesicles identified in the blastocoel fluid, may support the hypothesis of apoptosis as a mechanism to purge the preimplantation embryo of aneuploid cells. Alternative hypotheses, like correction of aneuploidy by extrusion of a trisomy chromosome or by monosomic chromosome duplication, are even, though they represent an extremely rare phenomenon. On the other hand, the technical limitations of PGT-A analysis may lead to inaccuracy in embryo diagnoses, identifying as "mosaic" those embryos that are uniformly euploid or aneuploid. NGS assumption of "intermediate copy number profiles" as evidence of a mixture of euploid and aneuploid cells in a single biopsy has been reported to be poorly predictive in cases of mosaicism diagnosis. Additionally, the concordance found between the TE and the ICM in cases of TE biopsies displaying mosaicism is lower than expected, and it correlates differently depending on the type (whole chromosome versus segmental) and the level of mosaicism reported. Thus, in cases of low-/medium-level mosaicism (<50%), aneuploid cells would rarely involve the ICM and other regions. However, in high-level mosaics (≥50%), abnormal cells in the ICM should display higher prevalence, revealing more uniform aneuploidy in most embryos, representing a technical variation in the uniform aneuploidy range, and therefore might impair the live birth rate.
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Affiliation(s)
- Gerard Campos
- Geisinger Medical Center, Women’s Health Fertility Clinic, Danville, PA 17821, USA;
- GIREXX Fertility Clinics, C. de Cartagena, 258, 08025 Girona, Spain
| | - Romualdo Sciorio
- Fertility Medicine and Gynaecological Endocrinology Unit, Department Woman-Mother-Child, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Steven Fleming
- Discipline of Anatomy & Histology, School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia;
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10
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Moch J, Radtke M, Gburek-Augustat J, Karnstedt M, Schönnagel S, Drukewitz SH, Pilgram L, Hentschel J, Schumann I. Case report: Complete paternal isodisomy on chromosome 18 induces methylation changes in PARD6G-AS1 promotor in a case with arthrogryposis. Front Genet 2023; 14:1297754. [PMID: 38188501 PMCID: PMC10768175 DOI: 10.3389/fgene.2023.1297754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Uniparental disomy (UPD) is the inheritance of both alleles of a chromosome from only one parent. So far, the detection of UPDs in sequencing data is not well established and a known gap in next-generation sequencing (NGS) diagnostics. By developing a new tool for UPD detection, we re-evaluated an eight-year-old individual presenting with scoliosis, muscle weakness and global developmental delay. Previous panel analysis identified a homozygous likely pathogenic loss-of-function variant in the PIEZO2-gene associated with arthrogryposis (OMIM # 617146). Interestingly, during a re-evaluation process, we identified a region of homozygosity (ROH) covering over 95% of chromosome 18. Segregation and microsatellite analysis within the family revealed that only the father is a heterozygous carrier of the variant in PIEZO2 and confirmed paternal uniparental isodisomy (iUPD) on chromosome 18 in the individual. Further methylation analysis indicated demethylation of the promotor region of PARD6G-AS1, which is described to be maternally imprinted and could possibly influence the individuals' phenotype. Our report describes the first complete iUPD on chromosome 18 and highlights that UPDs can be a cause for homozygous pathogenic variants, which reduces the risk of reoccurrence in case of a new pregnancy in comparison to an autosomal recessive inheritance trait significantly.
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Affiliation(s)
- Johanna Moch
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Maximilian Radtke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Janina Gburek-Augustat
- Division of Neuropaediatrics, Hospital for Children and Adolescents, University of Leipzig Medical Center, Leipzig, Germany
| | - Maike Karnstedt
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Senta Schönnagel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Stephan H. Drukewitz
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Laura Pilgram
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Isabell Schumann
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
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11
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Beal F, Coward R, Platt C. How to solve a clinical conundrum: Have you tried a trio exome analysis? Arch Dis Child Educ Pract Ed 2023; 108:456-462. [PMID: 37407083 DOI: 10.1136/archdischild-2021-322910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 06/13/2023] [Indexed: 07/07/2023]
Abstract
The following report describes the clinical journey of a 5-month-old male infant who presented with a significant kidney injury following a diarrhoeal illness. His course was complicated by severe hypertension and a number of acute life-threatening events necessitating periods of time on the intensive care unit, where he received ventilatory support and underwent renal replacement therapy and treatment with a monoclonal antibody therapy.We take the reader on a stepwise journey from presentation through to final diagnosis, discussing important biochemical, haematological and radiological features where learning points are discussed. Guidance on the use of genomic testing strategies for the non-geneticist is provided in some detail with a particular focus on the trio exome analysis that identified the diagnosis for this young boy.This complex case not only provides a number of excellent learning opportunities but also highlights the importance of early involvement of the clinical genetics team and the relevance of the trio exome analysis for rapid identification of rare monogenic diseases.
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Affiliation(s)
- Felicity Beal
- Paediatric Education Fellow, Bristol Royal Hospital for Children, Bristol, UK
| | - Richard Coward
- School of clinical Sciences, University of Bristol Academic Renal Unit, Bristol, UK
- Department of Paediatric Nephrology, Bristol Royal Hospital for Children, Bristol, UK
| | - Caroline Platt
- Department of Paediatric Nephrology, Bristol Royal Hospital for Children, Bristol, UK
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12
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Semikhodskii A, Makarova T, Sutyagina D. Maternal uniparental disomy of chromosome 21 as a cause of pseudo-exclusion from paternity. Mol Genet Genomics 2023; 298:1389-1394. [PMID: 37656271 DOI: 10.1007/s00438-023-02064-8] [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: 01/02/2023] [Accepted: 08/18/2023] [Indexed: 09/02/2023]
Abstract
Uniparental disomy (UPD) is a rare chromosomal condition, which apart from its importance in medical genetics can affect an outcome of parentage DNA testing, often causing pseudo exclusions. We describe a case of trio paternity test using 24 informative STR loci with potential exclusion at 2 systems located on chromosome 21. Consequent genotyping of an additional 25 autosomal and 27 Y-specific STRs revealed one other inconsistency, also located on this chromosome. All three inconsistent markers had the same heteroallelic state between the child and the biological mother providing evidence for maternal heterodisomy of chromosome 21. The case highlights the importance of considering UPD as a cause of genetic inconsistencies, especially when the inconsistent marker systems are located on the same chromosome.
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Affiliation(s)
| | - Tatiana Makarova
- Medical Genomics LLC, 48 Zhelyabov Str, Tver, 170100, Russian Federation
| | - Daria Sutyagina
- Medical Genomics LLC, 48 Zhelyabov Str, Tver, 170100, Russian Federation
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13
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Bu X, Li X, Peng C, Li H, Zhou S, Zhu Z, He J, Linpeng S. Case report: Paternal uniparental disomy on chromosome 7 and homozygous SUGCT mutation in a fetus with overweight after birth. Front Genet 2023; 14:1272028. [PMID: 37920852 PMCID: PMC10619901 DOI: 10.3389/fgene.2023.1272028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/04/2023] [Indexed: 11/04/2023] Open
Abstract
Background: Paternal uniparental disomy (UPD) of chromosome 7 is extremely rare, and only a few postnatal cases have been reported. The effects on growth were discordant in these cases, and the relevance of paternal UPD(7) to growth caused by imprinting remains questionable. Case presentation: Here, we report a prenatal case that underwent invasive prenatal diagnosis due to the high risk of Down's syndrome and failed noninvasive prenatal screening. The fetus had a normal karyotype and no apparent copy number variation. Homozygous copy-neutral regions on chromosome 7 were identified using a single nucleotide polymorphism (SNP) array; the data for the parent-child trios showed that the fetus carried the whole paternal isodisomy of chromosome 7. Whole exome and Sanger sequencing revealed a homozygous frameshift mutation in SUGCT at 7p14.1, from the heterozygous carrier father, with no contribution from the mother. The parents decided to continue with the pregnancy after genetic counseling, and the neonate had normal physical findings at birth and showed overweight after birth during a long-term intensive follow-up. Conclusion: We report the first prenatal case who carried paternal UPD(7) and homozygous SUGCT mutation with an overweight phenotype after birth. The overweight may be caused by paternal UPD(7) or homozygous frameshift mutation of SUGCT, or both of them, but it is unclear which contributes more.
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Affiliation(s)
- Xiufen Bu
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China
| | - Xu Li
- Department of Physiology, Changsha Health Vocational College, Changsha, China
| | - Can Peng
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China
| | - Hongyu Li
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China
| | - Shihao Zhou
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China
| | - Zesen Zhu
- Technical Support Center, Zhejiang Biosan Biochemical Technologies Co., Ltd., Hangzhou, China
| | - Jun He
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China
| | - Siyuan Linpeng
- Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, China
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14
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Chen Q, Chen Y, Shi L, Tao Y, Li X, Zhu X, Yang Y, Xu W. Uniparental disomy: expanding the clinical and molecular phenotypes of whole chromosomes. Front Genet 2023; 14:1232059. [PMID: 37860673 PMCID: PMC10582337 DOI: 10.3389/fgene.2023.1232059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/22/2023] [Indexed: 10/21/2023] Open
Abstract
Uniparental disomy (UPD) refers to as both homologous chromosomes inherited from only one parent without identical copies from the other parent. Studies on clinical phenotypes in UPDs are usually focused on the documented UPD 6, 7, 11, 14, 15, and 20, which directly lead to imprinting disorders. This study describes clinical phenotypes and genetic findings of three patients with UPD 2, 9, and 14, respectively. Chromosomal microarray (CMA), UPDtool, methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) and whole-exome sequencing (WES) analysis were performed to characterize the genetic etiology. The CMA revealed a homozygous region involving the whole chromosome 2 and 9, a partial region of homozygosity in chromosome 14. UPD-tool revealed a paternal origin of the UPD2. MS-MLPA showed hypomethylation of imprinting gene MEG3 from maternal origin in the UPD14 case. In addition, UPD14 case displayed complex symptoms including growth failure, hypotonia and acute respiratory distress syndrome (ARDS), accompanied by several gene mutations with heterozygous genotype by WES analysis. Furthermore, we reviewed the documented UPDs and summarized the clinical characteristics and prognosis. This study highlighted the importance to confirm the diagnosis and origin of UPD using genetic testing. Therefore, it is suggested that expanding of the detailed phenotypes and genotypes provide effective guidance for molecule testing and genetic counseling, and promote further biological investigation to the underlying mechanisms of imprinted disorders and accompanied copy number variations.
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Affiliation(s)
- Qi Chen
- Genetic and Prenatal Diagnosis Center, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yunpeng Chen
- Genetic and Prenatal Diagnosis Center, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Lin Shi
- Department of Ultrasound, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Ying Tao
- Genetic and Prenatal Diagnosis Center, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Xiaoguang Li
- Genetic and Prenatal Diagnosis Center, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Xiaolan Zhu
- Reproductive Medicine Center, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yan Yang
- Genetic and Prenatal Diagnosis Center, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
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15
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Tan X, Liu B, Yan T, Wei X, Qin Y, Zeng D, Yuan D. Prenatal diagnosis of paternal uniparental disomy for chromosome 2 in two fetuses with intrauterine growth restriction. Mol Cytogenet 2023; 16:20. [PMID: 37612666 PMCID: PMC10464012 DOI: 10.1186/s13039-023-00647-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/20/2023] [Indexed: 08/25/2023] Open
Abstract
Uniparental disomy (UPD) is when all or part of the homologous chromosomes are inherited from only one of the two parents. Currently, UPD has been reported to occur for almost all chromosomes. In this study, we report two cases of UPD for chromosome 2 (UPD2) encountered during prenatal diagnosis. The ultrasound findings of the fetuses from two unrelated families showed intrauterine growth restriction. The karyotype analyses were normal. The two fetuses both had complete paternal chromosome 2 uniparental disomy detected by whole-exome sequencing, but their clinical outcomes were significantly different, with fetal arrest in case 1 and birth in case 2. In this report, we analyzed and discussed the phenotypes of the fetuses in these two cases and reviewed the literature on UPD2.
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Affiliation(s)
- Xuemei Tan
- Department of Medical Genetics, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Thalassemia Prevention and Control, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, China
- Department of Medical Genetics, Liuzhou Hospital of Guangzhou Women and Children's Medical Center, Liuzhou, China
| | - Bailing Liu
- Department of Perinatal Health, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, China
| | - Tizhen Yan
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, China.
| | - Xiaobao Wei
- Department of Medical Genetics, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Thalassemia Prevention and Control, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, China
| | - Yanfeng Qin
- Department of Perinatal Health, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, China
| | - Dingyuan Zeng
- Department of Gynecology, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, China
| | - Dejian Yuan
- Department of Medical Genetics, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, China.
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, China.
- Liuzhou Key Laboratory of Thalassemia Prevention and Control, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, China.
- Department of Medical Genetics, Liuzhou Hospital of Guangzhou Women and Children's Medical Center, Liuzhou, China.
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16
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Chen CP, Wu FT, Pan YT, Chern SR, Wu PS, Chiu CL, Lee CC, Chen WL, Wang W. Prenatal diagnosis of mosaic trisomy 18 and maternal uniparental disomy 18 by amniocentesis in a pregnancy associated with cytogenetic discrepancy in various tissues and a favorable fetal outcome. Taiwan J Obstet Gynecol 2023; 62:606-610. [PMID: 37407205 DOI: 10.1016/j.tjog.2023.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2023] [Indexed: 07/07/2023] Open
Abstract
OBJECTIVE We present prenatal diagnosis of mosaic trisomy 18 and maternal uniparental disomy (UPD) 18 in a pregnancy with a favorable fetal outcome. CASE REPORT A 34-year-old woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age, and the result was 47,XY,+18 [4]/46,XY [25] in cultured amniocytes. Simultaneous array comparative genomic hybridization (aCGH) on uncultured amniocytes revealed 65% mosaicism for trisomy 18. Prenatal ultrasound was normal. She consulted our hospital and underwent repeat amniocentesis at 22 weeks of gestation, and the result revealed a karyotype of 47,XY,+18 [9]/46,XY [12] in cultured amniocytes. Simultaneous aCGH on uncultured amniocytes revealed arr 18p11.32q23 × 2.4 (log2 ratio = 0.3) consistent with 40% mosaicism for trisomy 18. Parental karyotypes were normal. Quantitative fluorescent polymerase chain reaction (QF-PCR) analysis on the DNA extracted from parental bloods and uncultured amniocytes confirmed maternal uniparental heterodisomy of chromosome 18. At 26 weeks of gestation, she underwent the third amniocentesis which revealed a karyotype of 47,XY,+18 [7]/46,XY [19] in cultured amniocytes. Simultaneous aCGH on uncultured amniocytes revealed arr 18p11.32q23 × 2.4 (log2 ratio = 0.27) consistent with 40% mosaicism for trisomy 18. Interphase fluorescence in situ hybridization (FISH) on uncultured amniocytes revealed 38% (38/100 cells) mosaicism for trisomy 18. The woman was advised to continue the pregnancy, and a 2620-g phenotypically normal male baby was delivered at 40 weeks of gestation. At birth, the karyotypes of cord blood, umbilical cord and placenta were 47,XY,+18 [14]/46,XY [26], 47,XY,+18 [9]/46,XY [31] and 47,XY,+18 (40/40 cells), respectively. When follow-up at age 2½ months, the neonate was phenotypically normal. The peripheral blood had a karyotype of 47,XY,+18 [28]/46,XY [12], and interphase FISH analysis on buccal mucosal cells detected 6.4% (7/93 cells) mosaicism for trisomy 18, compared with 0% (0/100 cells) in the normal control. When follow-up at age seven months, the neonate was normal in development, and the peripheral blood had a karyotype of 47,XY,+18 [18]/46,XY [22]. CONCLUSIONS Mosaic trisomy 18 at amniocentesis can be associated with cytogenetic discrepancy in various tissues, UPD 18 and a favorable fetal outcome. Prenatal diagnosis of mosaic trisomy 18 should alert the possibility of UPD 18 and include UPD testing.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medical and Health Science, Asia University, Taichung, Taiwan.
| | - Fang-Tzu Wu
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Yen-Ting Pan
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Chien-Ling Chiu
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chen-Chi Lee
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wen-Lin Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
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17
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Liu YD, Tan DD, Song DY, Fan YB, Fu XN, Ge L, Wei W, Xiong H. Uniparental disomy for chromosome 1 with POMGNT1 splice-site variant causes muscle-eye-brain disease. Front Genet 2023; 14:1170089. [PMID: 37342771 PMCID: PMC10277930 DOI: 10.3389/fgene.2023.1170089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/25/2023] [Indexed: 06/23/2023] Open
Abstract
POMGNT1, encoding protein O-mannose beta-1,2-N-acetylglucosaminyltransferase 1, is one of the genes responsible for dystroglycanopathy (DGP), which includes multiple phenotypes such as muscle-eye-brain disease (MEB), congenital muscular dystrophy with intellectual disability, and limb-girdle muscular dystrophy Here, we report a case of MEB that is the result of a homozygous variant of POMGNT1 that is revealed through uniparental disomy (UPD). An 8-month-old boy was admitted with mental and motor retardation, hypotonia, esotropia, early onset severe myopia, and structural brain abnormalities. A panel testing of genetic myopathy-related genes was used to identify a homozygous c.636C>T (p.Phe212Phe) variant in exon 7 of POMGNT1 in the patient, a heterozygous c.636C>T variant in the father, and the wild type in the mother. Quantitative polymerase chain reaction (q-PCR) revealed no abnormal copy numbers in exon 7. Trio-based whole-exome sequencing (trio-WES) revealed a possible paternal UPD on chromosome 1 of the patient. Chromosomal microarray analysis (CMA) revealed a 120,451 kb loss of heterozygosity (LOH) on 1p36.33-p11.2, encompassing POMGNT1, and a 99,319 kb loss of heterozygosity on 1q21.2-q44, which indicated UPD. Moreover, RNA sequencing (RNA-seq) verified that the c.636C>T variant was a splice-site variant, leading to skipping of exon 7 (p.Asp179Valfs*23). In conclusion, to the best of our knowledge, we present the first case of MEB caused by UPD, providing valuable insights into the genetic mechanisms underlying this condition.
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Affiliation(s)
- Yi-Dan Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Dan-Dan Tan
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Dan-Yu Song
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yan-Bin Fan
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiao-Na Fu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Lin Ge
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Wei Wei
- Beijing Kangso Medical Inspection Co., Ltd., Beijing, China
| | - Hui Xiong
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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18
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Hara-Isono K, Matsubara K, Nakamura A, Sano S, Inoue T, Kawashima S, Fuke T, Yamazawa K, Fukami M, Ogata T, Kagami M. Risk assessment of assisted reproductive technology and parental age at childbirth for the development of uniparental disomy-mediated imprinting disorders caused by aneuploid gametes. Clin Epigenetics 2023; 15:78. [PMID: 37147716 PMCID: PMC10163687 DOI: 10.1186/s13148-023-01494-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/26/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Our previous study suggested that assisted reproductive technology (ART) may be a possible risk factor for the development of epimutation-mediated imprinting disorders (epi-IDs) for mothers aged ≥ 30 years. However, whether ART or advanced parental age facilitates the development of uniparental disomy-mediated IDs (UPD-IDs) has not yet been investigated. RESULTS We enrolled 130 patients with aneuploid UPD-IDs including various IDs confirmed by molecular studies and obtained ART data of the general population and patients with epi-IDs from a robust nationwide database and our previous report, respectively. We compared the proportion of ART-conceived livebirths and maternal childbearing age between patients with UPD-IDs and the general population or patients with epi-IDs. The proportion of ART-conceived livebirths in patients with aneuploid UPD-IDs was consistent with that in the general population of maternal age ≥ 30 years and was lower than that in the patients with epi-IDs, although there was no significant difference. The maternal childbearing age of patients with aneuploid UPD-IDs was skewed to the increased ages with several cases exceeding the 97.5th percentile of maternal childbearing age of the general population and significantly higher than that of patients with epi-IDs (P < 0.001). In addition, we compared the proportion of ART-conceived livebirths and parental age at childbirth between patients with UPD-IDs caused by aneuploid oocytes (oUPD-IDs) and that by aneuploid sperm (sUPD-IDs). Almost all ART-conceived livebirths were identified in patients with oUPD-IDs, and both maternal age and paternal age at childbirth were significantly higher in patients with oUPD-IDs than in patients with sUPD-IDs. Because maternal age and paternal age were strongly correlated (rs = 0.637, P < 0.001), higher paternal age in oUPD-IDs was explained by the higher maternal age in this group. CONCLUSIONS Different from the case of epi-IDs, ART itself is not likely to facilitate the development of aneuploid UPD-IDs. We demonstrated that advanced maternal age can be a risk factor for the development of aneuploid UPD-IDs, particularly oUPD-IDs.
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Affiliation(s)
- Kaori Hara-Isono
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-Ku, Tokyo, 157-8535, Japan
- Department of Pediatrics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-Ku, Tokyo, 157-8535, Japan
| | - Akie Nakamura
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-Ku, Tokyo, 157-8535, Japan
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-Ku, Sapporo, 060-8648, Japan
| | - Shinichiro Sano
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-Ku, Tokyo, 157-8535, Japan
- Department of Endocrinology and Metabolism, Shizuoka Children's Hospital, 860 Urushiyama, Aoi-Ku, Shizuoka, 420-8660, Japan
| | - Takanobu Inoue
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-Ku, Tokyo, 157-8535, Japan
| | - Sayaka Kawashima
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-Ku, Tokyo, 157-8535, Japan
| | - Tomoko Fuke
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-Ku, Tokyo, 157-8535, Japan
| | - Kazuki Yamazawa
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-Ku, Tokyo, 157-8535, Japan
- Medical Genetics Center, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-Ku, Tokyo, 152-8902, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-Ku, Tokyo, 157-8535, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-Ku, Tokyo, 157-8535, Japan
- Department of Biochemistry, Hamamatsu University School of Medicine, 1‑20‑1 Handayama, Higashi‑ku, Hamamatsu, 431‑3192, Japan
- Department of Pediatrics, Hamamatsu Medical Center, 328 Tomizuka Cho, Naka-Ku, Hamamatsu, 432-8580, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-Ku, Tokyo, 157-8535, Japan.
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19
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Polonis K, Lopes JL, Cabral H, Babcock HE, Kline L, Ruiz KM, Schwartz S, Hasadsri L, Rowsey RA, Hoppman NL. Uniparental disomy of multiple chromosomes in two cases with a complex phenotype. Am J Med Genet A 2023. [PMID: 37134191 DOI: 10.1002/ajmg.a.63224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023]
Abstract
Uniparental disomy (UPD) is the inheritance of both chromosomal homologs from one parent. Depending on the chromosome involved and the parental origin, UPD may result in phenotypic abnormalities due to aberrant methylation patterns or unmasking recessive conditions in isodisomic regions. UPD primarily originates from somatic rescue of a single meiotically-derived aneuploidy, most commonly a trisomy. Double UPD is exceedingly rare and triple UPD has not been previously described. Here, we report two unrelated clinical cases with UPD of multiple chromosomes; an 8-month-old male with maternal isodisomy of chromosome 7 and paternal isodisomy of chromosome 9, and a 4-week-old female with mixed paternal UPD for chromosomes 4, 10, and 14. These cases also demonstrate that although extremely rare, the detection of AOH on two or more chromosomes may warrant additional clinical and laboratory investigation such as methylation and STR marker analysis, especially when involving chromosomes known to be associated with imprinting disorders.
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Affiliation(s)
- Katarzyna Polonis
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jaime L Lopes
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Huong Cabral
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Holly E Babcock
- Rare Disease Institute, Children's National Hospital, Washington, DC, USA
| | - Laura Kline
- Women's Health and Genetics, Laboratory Corporation of America, Burlington, North Carolina, USA
| | - Kaylee M Ruiz
- Valley Children's Healthcare, Madera, California, USA
| | - Stuart Schwartz
- Women's Health and Genetics, Laboratory Corporation of America, Burlington, North Carolina, USA
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ross A Rowsey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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20
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Gong T, McNally FJ. Caenorhabditis elegans spermatocytes can segregate achiasmate homologous chromosomes apart at higher than random frequency during meiosis I. Genetics 2023; 223:iyad021. [PMID: 36792551 PMCID: PMC10319977 DOI: 10.1093/genetics/iyad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/05/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
Chromosome segregation errors during meiosis are the leading cause of aneuploidy. Faithful chromosome segregation during meiosis in most eukaryotes requires a crossover which provides a physical attachment holding homologs together in a "bivalent." Crossovers are critical for homologs to be properly aligned and partitioned in the first meiotic division. Without a crossover, individual homologs (univalents) might segregate randomly, resulting in aneuploid progeny. However, Caenorhabditis elegans zim-2 mutants, which have crossover defects on chromosome V, have fewer dead embryos than that expected from random segregation. This deviation from random segregation is more pronounced in zim-2 males than that in females. We found three phenomena that can explain this apparent discrepancy. First, we detected crossovers on chromosome V in both zim-2(tm574) oocytes and spermatocytes, suggesting a redundant mechanism to make up for the ZIM-2 loss. Second, after accounting for the background crossover frequency, spermatocytes produced significantly more euploid gametes than what would be expected from random segregation. Lastly, trisomy of chromosome V is viable and fertile. Together, these three phenomena allow zim-2(tm574) mutants with reduced crossovers on chromosome V to have more viable progeny. Furthermore, live imaging of meiosis in spo-11(me44) oocytes and spermatocytes, which exhibit crossover failure on all 6 chromosomes, showed 12 univalents segregating apart in roughly equal masses in a homology-independent manner, supporting the existence of a mechanism that segregates any 2 chromosomes apart.
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Affiliation(s)
- Ting Gong
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Francis J McNally
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
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21
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Verebi C, Caumes R, Chantot-Bastaraud S, Deburgrave N, Orhant L, Vaucouleur N, Cuisset L, Bienvenu T, Leturcq F, Nectoux J. How a paternal uniparental isodisomy of chromosome 17 leads to autosomal recessive limb-girdle muscular dystrophy-3. Neuromuscul Disord 2023; 33:367-370. [PMID: 36996638 DOI: 10.1016/j.nmd.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023]
Abstract
Uniparental isodisomy is a condition where both chromosomes of a pair are inherited from one parental homologue. If a deleterious variant is present on the duplicated chromosome, its homozygosity can reveal an autosomal recessive disorder in the offspring of a heterozygous carrier. Limb-girdle muscular dystrophy (LGMD) R3 is an autosomal recessive inherited disease that is associated with alpha-sarcoglycan gene (SGCA) variants. We report the first published case of LGMDR3 due to a homozygous variant in SGCA unmasked by uniparental isodisomy. The patient is an 8-year-old who experienced delayed motor milestones but normal cognitive development. He presented with muscle pain and elevated plasma creatine kinase. Sequencing of the SGCA gene showed a homozygous pathogenic variant. Parents were not related and only the father was heterozygous for the pathogenic variant. A chromosomal microarray revealed a complete chromosome 17 copy number neutral loss of heterozygosity encompassing SGCA, indicating paternal uniparental isodisomy.
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22
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Lü Y, Jiang Y, Zhou X, Hao N, Lü G, Guo X, Guo R, Liu W, Xu C, Chang J, Li M, Zhang H, Zhou J, Zhang W(V, Qi Q. Evaluation and Analysis of Absence of Homozygosity (AOH) Using Chromosome Analysis by Medium Coverage Whole Genome Sequencing (CMA-seq) in Prenatal Diagnosis. Diagnostics (Basel) 2023; 13:diagnostics13030560. [PMID: 36766665 PMCID: PMC9914714 DOI: 10.3390/diagnostics13030560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE Absence of homozygosity (AOH) is a genetic characteristic known to cause human diseases mainly through autosomal recessive or imprinting mechanisms. The importance and necessity of accurate AOH detection has become more clinically significant in recent years. However, it remains a challenging task for sequencing-based methods thus far. METHODS In this study, we developed and optimized a new bioinformatic algorithm based on the assessment of minimum sequencing coverage, optimal bin size, the Z-score threshold of four types of allele count and the frequency for accurate genotyping using 28 AOH negative samples, and redefined the AOH detection cutoff value. We showed the performance of chromosome analysis by five-fold coverage whole genome sequencing (CMA-seq) for AOH identification in 27 typical prenatal/postnatal AOH positive samples, which were previously confirmed by chromosomal microarray analysis with single nucleotide polymorphism array (CMA/SNP array). RESULTS The blinded study indicated that for all three forms of AOH, including whole genomic AOH, single chromosomal AOH and segmental AOH, and all kinds of sample types, including chorionic villus sampling, amniotic fluid, cord blood, peripheral blood and abortive tissue, CMA-seq showed equivalent detection power to that of routine CMA/SNP arrays (750K). The subtle difference between the two methods is that CMA-seq is prone to detect small inconsecutive AOHs, while CMA/SNP array reports it as a whole. CONCLUSION Based on our newly developed bioinformatic algorithm, it is feasible to detect clinically significant AOH using CMA-seq in prenatal diagnosis.
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Affiliation(s)
- Yan Lü
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yulin Jiang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiya Zhou
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Na Hao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Guizhen Lü
- AmCare Genomics Lab, Guangzhou 510335, China
| | | | - Ruidong Guo
- AmCare Genomics Lab, Guangzhou 510335, China
| | - Wenjie Liu
- AmCare Genomics Lab, Guangzhou 510335, China
| | - Chenlu Xu
- AmCare Genomics Lab, Guangzhou 510335, China
| | - Jiazhen Chang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Mengmeng Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Hanzhe Zhang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jing Zhou
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | - Qingwei Qi
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
- Correspondence: ; Tel.: +86-1851-066-6066
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23
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Lopour MQ, Schimmenti LA, Boczek NJ, Kearney HM, Drack AV, Brodsky MC. Alström syndrome caused by maternal uniparental disomy. Am J Ophthalmol Case Rep 2022; 29:101745. [PMID: 36636630 PMCID: PMC9829691 DOI: 10.1016/j.ajoc.2022.101745] [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: 07/21/2022] [Revised: 10/13/2022] [Accepted: 11/01/2022] [Indexed: 01/02/2023] Open
Abstract
Purpose To describe a case of Alström syndrome arising from maternal uniparental disomy. Observations A 13-month-old boy with poor vision and nystagmus was diagnosed with Alström syndrome based on genetic testing that identified a homozygous pathogenic variant, ALMS1 c.2141_2141del (p.Ser714Tyrfs*6), that was only found in his mother and not his father. In contrast to the usual autosomal recessive inheritance pattern in which a child inherits a variant from each parent, multi-step genetic testing of the child and both parents confirmed uniparental disomy as the mechanism of inheritance. Conclusions and Importance Confirmation of uniparental disomy in autosomal recessive disorders allows for parental assurance that future offspring will be unaffected.
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Affiliation(s)
| | - Lisa A. Schimmenti
- Department of Clinical Genomics and Department of Otolaryngology, Biochemistry and Molecular Biology, and Ophthalmology, Mayo Clinic, Rochester, MN, USA
| | - Nicole J. Boczek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Hutton M. Kearney
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Arlene V. Drack
- Department of Ophthalmology, University of Iowa and the University of Iowa Institute for Vision Research, Iowa City, IA, USA
| | - Michael C. Brodsky
- Department of Ophthalmology and Department of Neurology, Mayo Clinic, Rochester, MN, USA,Corresponding author. Department of Ophthalmology and Department of Neurology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA.
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24
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López-Garrido MP, Carrascosa-Romero MC, Montero-Hernández M, Serrano-Martínez CM, Sánchez-Sánchez F. Case Report: Precision genetic diagnosis in a case of Dyggve-Melchior-Clausen syndrome reveals paternal isodisomy and heterodisomy of chromosome 18 with imprinting clinical implications. Front Genet 2022; 13:1005573. [PMID: 36468000 PMCID: PMC9716064 DOI: 10.3389/fgene.2022.1005573] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/02/2022] [Indexed: 02/19/2024] Open
Abstract
A twelve-year-old patient with a previous clinical diagnosis of spondylocostal skeletal dysplasia and moderate intellectual disability was genetically analyzed through next generation sequencing of a targeted gene panel of 179 genes associated to skeletal dysplasia and mucopolysaccharidosis in order to stablish a precision diagnosis. A homozygous nonsense [c.62C>G; p.(Ser21Ter)] mutation in DYM gene was identified in the patient. Null mutations in DYM have been associated to Dyggve-Melchior-Clausen syndrome, which is a rare autosomal-recessive disorder characterized by skeletal dysplasia and mental retardation, compatible with the patient´s phenotype. To confirm the pathogenicity of this mutation, a segregation analysis was carried out, revealing that the mutation p(Ser21Ter) was solely inherited from the father, who is a carrier of the mutation, while the mother does not carry the mutation. With the suspicion that a paternal disomy could be causing the disease, a series of microsatellite markers in chromosome 18, where the DYM gene is harbored, was analyzed in all the members of the family. Haplotype analysis provided strong evidence of paternal isodisomy and heterodisomy in that chromosome, confirming the pathological effect of this mutation. Furthermore, the patient may have a compromised expression of the ELOA3 gene due to modifications in the genomic imprinting that may potentially increase the risk of digestive cancer. All these results highlight the importance of obtaining a precision diagnosis in rare diseases.
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Affiliation(s)
- María-Pilar López-Garrido
- Laboratorio de Genética Médica, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Facultad de Medicina de Ciudad Real, Universidad de Castilla-La Mancha (UCLM), Albacete, Spain
| | | | - Minerva Montero-Hernández
- Laboratorio de Genética Médica, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha (UCLM), Spain
| | - Caridad-María Serrano-Martínez
- Laboratorio de Genética Médica, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha (UCLM), Spain
| | - Francisco Sánchez-Sánchez
- Laboratorio de Genética Médica, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha (UCLM), Spain
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25
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Chao Y, Qin Y, Zou X, Wang X, Hu C, Xia F, Zou C. Promising therapeutic aspects in human genetic imprinting disorders. Clin Epigenetics 2022; 14:146. [PMID: 36371218 PMCID: PMC9655922 DOI: 10.1186/s13148-022-01369-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon of monoallelic gene expression pattern depending on parental origin. In humans, congenital imprinting disruptions resulting from genetic or epigenetic mechanisms can cause a group of diseases known as genetic imprinting disorders (IDs). Genetic IDs involve several distinct syndromes sharing homologies in terms of genetic etiologies and phenotypic features. However, the molecular pathogenesis of genetic IDs is complex and remains largely uncharacterized, resulting in a lack of effective therapeutic approaches for patients. In this review, we begin with an overview of the genomic and epigenomic molecular basis of human genetic IDs. Notably, we address ethical aspects as a priority of employing emerging techniques for therapeutic applications in human IDs. With a particular focus, we delineate the current field of emerging therapeutics for genetic IDs. We briefly summarize novel symptomatic drugs and highlight the key milestones of new techniques and therapeutic programs as they stand today which can offer highly promising disease-modifying interventions for genetic IDs accompanied by various challenges.
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Affiliation(s)
- Yunqi Chao
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Yifang Qin
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Xinyi Zou
- grid.13402.340000 0004 1759 700XZhejiang University City College, Hangzhou, 310015 Zhejiang China
| | - Xiangzhi Wang
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Chenxi Hu
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Fangling Xia
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Chaochun Zou
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
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26
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Trost B, Thiruvahindrapuram B, Chan AJS, Engchuan W, Higginbotham EJ, Howe JL, Loureiro LO, Reuter MS, Roshandel D, Whitney J, Zarrei M, Bookman M, Somerville C, Shaath R, Abdi M, Aliyev E, Patel RV, Nalpathamkalam T, Pellecchia G, Hamdan O, Kaur G, Wang Z, MacDonald JR, Wei J, Sung WWL, Lamoureux S, Hoang N, Selvanayagam T, Deflaux N, Geng M, Ghaffari S, Bates J, Young EJ, Ding Q, Shum C, D'Abate L, Bradley CA, Rutherford A, Aguda V, Apresto B, Chen N, Desai S, Du X, Fong MLY, Pullenayegum S, Samler K, Wang T, Ho K, Paton T, Pereira SL, Herbrick JA, Wintle RF, Fuerth J, Noppornpitak J, Ward H, Magee P, Al Baz A, Kajendirarajah U, Kapadia S, Vlasblom J, Valluri M, Green J, Seifer V, Quirbach M, Rennie O, Kelley E, Masjedi N, Lord C, Szego MJ, Zawati MH, Lang M, Strug LJ, Marshall CR, Costain G, Calli K, Iaboni A, Yusuf A, Ambrozewicz P, Gallagher L, Amaral DG, Brian J, Elsabbagh M, Georgiades S, Messinger DS, Ozonoff S, Sebat J, Sjaarda C, Smith IM, Szatmari P, Zwaigenbaum L, Kushki A, Frazier TW, Vorstman JAS, Fakhro KA, Fernandez BA, Lewis MES, Weksberg R, Fiume M, Yuen RKC, Anagnostou E, Sondheimer N, Glazer D, Hartley DM, Scherer SW. Genomic architecture of autism from comprehensive whole-genome sequence annotation. Cell 2022; 185:4409-4427.e18. [PMID: 36368308 PMCID: PMC10726699 DOI: 10.1016/j.cell.2022.10.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/30/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022]
Abstract
Fully understanding autism spectrum disorder (ASD) genetics requires whole-genome sequencing (WGS). We present the latest release of the Autism Speaks MSSNG resource, which includes WGS data from 5,100 individuals with ASD and 6,212 non-ASD parents and siblings (total n = 11,312). Examining a wide variety of genetic variants in MSSNG and the Simons Simplex Collection (SSC; n = 9,205), we identified ASD-associated rare variants in 718/5,100 individuals with ASD from MSSNG (14.1%) and 350/2,419 from SSC (14.5%). Considering genomic architecture, 52% were nuclear sequence-level variants, 46% were nuclear structural variants (including copy-number variants, inversions, large insertions, uniparental isodisomies, and tandem repeat expansions), and 2% were mitochondrial variants. Our study provides a guidebook for exploring genotype-phenotype correlations in families who carry ASD-associated rare variants and serves as an entry point to the expanded studies required to dissect the etiology in the ∼85% of the ASD population that remain idiopathic.
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Affiliation(s)
- Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | - Ada J S Chan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Edward J Higginbotham
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jennifer L Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Livia O Loureiro
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Miriam S Reuter
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; CGEn, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Delnaz Roshandel
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Joe Whitney
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | - Cherith Somerville
- Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Rulan Shaath
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Mona Abdi
- Department of Human Genetics, Sidra Medicine, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Rohan V Patel
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Omar Hamdan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Gaganjot Kaur
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Zhuozhi Wang
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jeffrey R MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - John Wei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Wilson W L Sung
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ny Hoang
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Thanuja Selvanayagam
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Nicole Deflaux
- Verily Life Sciences, South San Francisco, CA 94080, USA
| | - Melissa Geng
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Siavash Ghaffari
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - John Bates
- Verily Life Sciences, South San Francisco, CA 94080, USA
| | - Edwin J Young
- Genome Diagnostics, Department of Paediatric Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Qiliang Ding
- Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Carole Shum
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Lia D'Abate
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Clarrisa A Bradley
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Annabel Rutherford
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Vernie Aguda
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Beverly Apresto
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Nan Chen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sachin Desai
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Xiaoyan Du
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Matthew L Y Fong
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sanjeev Pullenayegum
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Kozue Samler
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ting Wang
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Karen Ho
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Tara Paton
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sergio L Pereira
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jo-Anne Herbrick
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | - Olivia Rennie
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Elizabeth Kelley
- Department of Psychology, Queen's University, Kingston, ON K7L 3N6, Canada; Department of Psychiatry, Queen's University, Kingston, ON K7L 7X3, Canada
| | - Nina Masjedi
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Catherine Lord
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Michael J Szego
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Family and Community Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Ma'n H Zawati
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Michael Lang
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Lisa J Strug
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Statistical Sciences, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Christian R Marshall
- Genome Diagnostics, Department of Paediatric Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gregory Costain
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Kristina Calli
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada; BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Alana Iaboni
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada
| | - Afiqah Yusuf
- Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Patricia Ambrozewicz
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Psychology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Louise Gallagher
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 2, Ireland; Department of Psychiatry, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Child, Youth and Family Services, The Centre for Addiction and Mental Health, Toronto, ON M6J 1H4, Canada; Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - David G Amaral
- MIND Institute, University of California, Davis, Sacramento, CA 95817, USA; Department of Psychiatry and Behavioral Sciences, University of California, Davis, Sacramento, CA 95817, USA
| | - Jessica Brian
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada; Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada
| | - Mayada Elsabbagh
- Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Stelios Georgiades
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON L8N 3K7, Canada
| | | | - Sally Ozonoff
- MIND Institute, University of California, Davis, Sacramento, CA 95817, USA; Department of Psychiatry and Behavioral Sciences, University of California, Davis, Sacramento, CA 95817, USA
| | - Jonathan Sebat
- Department of Psychiatry and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Calvin Sjaarda
- Department of Psychiatry, Queen's University, Kingston, ON K7L 7X3, Canada; Queen's Genomics Lab at Ongwanada, Queen's University, Kingston, ON K7M 8A6, Canada
| | - Isabel M Smith
- Department of Pediatrics, Dalhousie University, Halifax, NS B3H 4R2, Canada; IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Peter Szatmari
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada; Centre for Addiction and Mental Health, Toronto, ON M6J 1H4, Canada
| | - Lonnie Zwaigenbaum
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Azadeh Kushki
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Thomas W Frazier
- Autism Speaks, Princeton, NJ 08540, USA; Department of Psychology, John Carroll University, Cleveland, OH 44118, USA
| | - Jacob A S Vorstman
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar; Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Bridget A Fernandez
- Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90033, USA
| | - M E Suzanne Lewis
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada; BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | | | - Ryan K C Yuen
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Evdokia Anagnostou
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada; Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada
| | - Neal Sondheimer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA 94080, USA
| | | | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; McLaughlin Centre, Toronto, ON M5G 0A4, Canada.
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27
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Martínez-Hernández A, Martínez-Anaya D, Durán-McKinster C, Del Castillo-Ruiz V, Navarrete-Meneses P, Córdova EJ, Villegas-Torres BE, Ruiz-Herrera A, Juárez-Velázquez R, Yokoyama-Rebollar E, Cervantes-Barragán D, Pedraza-Meléndez A, Orozco L, Pérez-Vera P, Salas-Labadía C. Pigmentary mosaicism as a recurrent clinical manifestation in three new patients with mosaic trisomy 12 diagnosed postnatally: cases report and literature review. BMC Med Genomics 2022; 15:224. [PMCID: PMC9620619 DOI: 10.1186/s12920-022-01382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/22/2022] [Indexed: 11/10/2022] Open
Abstract
Background To date, only twenty-one cases diagnosed postnatally with mosaic trisomy 12 have been reported. The most frequent phenotypic manifestations are developmental delay, dysmorphic facial features, congenital heart defects, digital alterations, and pigmentary disorders. In the present report, detailed clinical and genetic profiles of three unrelated new patients with mosaic trisomy 12 are described and compared with previously reported cases. Case presentation In the present report, we include the clinical, cytogenetic, and molecular description of three Mexican patients diagnosed postnatally with mosaic trisomy 12. At phenotypic level, the three patients present with developmental delay, dysmorphic facial features, congenital heart defects and skin pigmentary anomalies. Particularly, patient 1 showed unique eye alterations as bilateral distichiasis, triple rows of upper lashes, and digital abnormalities. In patient 2 redundant skin, severe hearing loss, and hypotonia were observed, and patient 3 presented with hypertelorism and telecanthus. Hyperpigmentation with disseminated pigmentary anomalies is a common trait in all of them. The cytogenetic study was carried out under the strict criteria of analysis, screening 50–100 metaphases from three different tissues, showing trisomy 12 mosaicism in at least one of the three different tissues analyzed. With SNParray, the presence of low-level mosaic copy number variants not previously detected by cytogenetics, and uniparental disomy of chromosome 12, was excluded. STR markers allowed to confirm the absence of uniparental disomy as well as to know the parental origin of supernumerary chromosome 12. Conclusions The detailed clinical, cytogenetic, and molecular description of these three new patients, contributes with relevant information to delineate more accurately a group of patients that show a heterogeneous phenotype, although sharing the same chromosomal alteration. The possibility of detecting mosaic trisomy 12 is directly associated with the sensitivity of the methodology applied to reveal the low-level chromosomal mosaicism, as well as with the possibility to perform the analysis in a suitable tissue.
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Affiliation(s)
- A. Martínez-Hernández
- grid.452651.10000 0004 0627 7633Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica SS, Ciudad de Mexico, México
| | - D. Martínez-Anaya
- grid.419216.90000 0004 1773 4473Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, 04530 México
| | - C. Durán-McKinster
- grid.419216.90000 0004 1773 4473Departamento de Dermatología, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - V. Del Castillo-Ruiz
- grid.419216.90000 0004 1773 4473Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - P. Navarrete-Meneses
- grid.419216.90000 0004 1773 4473Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, 04530 México
| | - E. J. Córdova
- grid.452651.10000 0004 0627 7633Consorcio de Oncogenómica, Instituto Nacional de Medicina Genómica SS, Ciudad de Mexico, México
| | - B. E. Villegas-Torres
- grid.452651.10000 0004 0627 7633Instituto Nacional de Medicina Genómica SS, Ciudad de Mexico, México
| | - A. Ruiz-Herrera
- grid.414465.6Hospital de Especialidades Pediátrico de León, León, Guanajuato, México
| | - R. Juárez-Velázquez
- grid.419216.90000 0004 1773 4473Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, 04530 México
| | - E. Yokoyama-Rebollar
- grid.419216.90000 0004 1773 4473Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - D. Cervantes-Barragán
- grid.502779.e0000 0004 0633 6373Hospital Central Sur de Alta Especialidad, PEMEX, Ciudad de Mexico, México
| | - A. Pedraza-Meléndez
- grid.9486.30000 0001 2159 0001Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
| | - L. Orozco
- grid.452651.10000 0004 0627 7633Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica SS, Ciudad de Mexico, México
| | - P. Pérez-Vera
- grid.419216.90000 0004 1773 4473Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, 04530 México
| | - C. Salas-Labadía
- grid.419216.90000 0004 1773 4473Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, 04530 México
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28
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Molloy B, Jones ER, Linhares ND, Buckley PG, Leahy TR, Lynch B, Knerr I, King MD, Gorman KM. Uniparental disomy screen of Irish rare disorder cohort unmasks homozygous variants of clinical significance in the TMCO1 and PRKRA genes. Front Genet 2022; 13:945296. [PMID: 36186440 PMCID: PMC9515794 DOI: 10.3389/fgene.2022.945296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/23/2022] [Indexed: 11/20/2022] Open
Abstract
A uniparental disomy (UPD) screen using whole genome sequencing (WGS) data from 164 trios with rare disorders in the Irish population was performed to identify large runs of homozygosity of uniparental origin that may harbour deleterious recessive variants. Three instances of whole chromosome uniparental isodisomy (UPiD) were identified: one case of maternal isodisomy of chromosome 1 and two cases of paternal isodisomy of chromosome 2. We identified deleterious homozygous variants on isodisomic chromosomes in two probands: a novel p (Glu59ValfsTer20) variant in TMCO1, and a p (Pro222Leu) variant in PRKRA, respectively. The overall prevalence of whole chromosome UPiD in our cohort was 1 in 55 births, compared to 1 in ∼7,500 births in the general population, suggesting a higher frequency of UPiD in rare disease cohorts. As a distinct mechanism underlying homozygosity compared to biallelic inheritance, the identification of UPiD has important implications for family planning and cascade testing. Our study demonstrates that UPD screening may improve diagnostic yields by prioritising UPiD chromosomes during WGS analysis.
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Affiliation(s)
- B. Molloy
- Genuity Science, Dublin, Ireland
- *Correspondence: B. Molloy,
| | | | | | | | - T. R. Leahy
- Department of Paediatric Immunology, Children’s Health Ireland at Crumlin, Dublin, Ireland
- Department of Paediatrics, Trinity College, University of Dublin, Dublin, Ireland
| | - B. Lynch
- Department of Paediatric Neurology and Clinical Neurophysiology, Children’s Health Ireland at Temple Street, Dublin, Ireland
- School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - I. Knerr
- School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
- National Centre for Inherited Metabolic Disorders, Children’s Health Ireland at Temple Street, Dublin, Ireland
| | - M. D. King
- Department of Paediatric Neurology and Clinical Neurophysiology, Children’s Health Ireland at Temple Street, Dublin, Ireland
- School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - K. M. Gorman
- Department of Paediatric Neurology and Clinical Neurophysiology, Children’s Health Ireland at Temple Street, Dublin, Ireland
- School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
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29
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Maternal uniparental disomy of chromosome 7 underlying argininosuccinic aciduria and Silver-Russell syndrome. Hum Genome Var 2022; 9:32. [PMID: 36097158 PMCID: PMC9468177 DOI: 10.1038/s41439-022-00211-y] [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: 08/02/2022] [Revised: 08/15/2022] [Accepted: 08/15/2022] [Indexed: 01/12/2023] Open
Abstract
We describe a patient presenting with argininosuccinic aciduria and Silver-Russell syndrome (SRS). SRS was caused by maternal uniparental disomy of chromosome 7 (UPD(7)mat). UPD(7)mat also unmasked a maternally inherited splicing variant in ASL on chromosome 7, leading to the onset of argininosuccinic aciduria. The phenotype of the present case was more severe than that of a previous case, demonstrating a phenotypic variation in the combination of argininosuccinic aciduria and SRS.
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30
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Capalbo A, Poli M, Jalas C, Forman EJ, Treff NR. On the reproductive capabilities of aneuploid human preimplantation embryos. Am J Hum Genet 2022; 109:1572-1581. [PMID: 36055209 PMCID: PMC9502046 DOI: 10.1016/j.ajhg.2022.07.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/05/2022] [Indexed: 12/01/2022] Open
Abstract
In IVF cycles, the application of aneuploidy testing at the blastocyst stage is quickly growing, and the latest reports estimate almost half of cycles in the US undergo preimplantation genetic testing for aneuploidies (PGT-A). Following PGT-A cycles, understanding the predictive value of an aneuploidy result is paramount for making informed decisions about the embryo's fate and utilization. Compelling evidence from non-selection trials strongly supports that embryos diagnosed with a uniform whole-chromosome aneuploidy very rarely result in the live birth of a healthy baby, while their transfer exposes women to significant risks of miscarriage and chromosomally abnormal pregnancy. On the other hand, embryos displaying low range mosaicism for whole chromosomes have shown reproductive capabilities somewhat equivalent to uniformly euploid embryos, and they have comparable clinical outcomes and gestational risks. Therefore, given their clearly distinct biological origin and clinical consequences, careful differentiation between uniform and mosaic aneuploidy is critical in both the clinical setting when counseling individuals and in the research setting when presenting aneuploidy studies in human embryology. Here, we focus on the evidence gathered so far on PGT-A diagnostic predictive values and reproductive outcomes observed across the broad spectrum of whole-chromosome aneuploidies detected at the blastocyst stage to obtain evidence-based conclusions on the clinical management of aneuploid embryos in the quickly growing PGT-A clinical setting.
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31
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Zhang L, Hu Y, Lu J, Zhao P, Zhang X, Tan L, Li J, Xiao C, Zeng L, He X. Identification of the first congenital ichthyosis case caused by a homozygous deletion in the ALOX12B gene due to chromosome 17 mixed uniparental disomy. Front Genet 2022; 13:931833. [PMID: 36003334 PMCID: PMC9393266 DOI: 10.3389/fgene.2022.931833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/27/2022] [Indexed: 11/18/2022] Open
Abstract
Uniparental disomy (UPD) is a rare genetic event caused by errors during gametogenesis and fertilization leading to two copies of a chromosome or chromosomal region inherited from one parent. MixUPD is one type of UPD that contains isodisomic and heterodisomic parts because of meiotic recombination. Using whole-exome sequencing (WES), we identified the first case of ichthyosis due to a maternal mixUPD on chromosome 17, which results in a homozygous deletion of partial intron 8 to exon 10 in ALOX12B, being predicted to lead to an internal protein deletion of 97 amino acids. We also performed a retrospective analysis of 198 patients with ALOX12B mutations. The results suggested that the exon 9 and 10 are located in the mutational hotspots of ALOX12B. In addition, our patient has microtia and congenital stenosis of the external auditory canals, which is very rare in patients with ALOX12B mutations. Our study reports the first case of autosomal recessive congenital ichthyosis (ARCI) due to a mixUPD of chromosome 17 and expands the spectrum of clinical manifestations of ARCI caused by mutations in the ALOX12B gene.
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Affiliation(s)
- Lei Zhang
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Yanqiu Hu
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Jingjing Lu
- Dermatology Department, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Peiwei Zhao
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Xiankai Zhang
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Li Tan
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Jun Li
- Otolaryngology Department, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Cuiping Xiao
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- *Correspondence: Xuelian He, ; Cuiping Xiao, ; Linkong Zeng,
| | - Linkong Zeng
- Neonatology Department, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- *Correspondence: Xuelian He, ; Cuiping Xiao, ; Linkong Zeng,
| | - Xuelian He
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- *Correspondence: Xuelian He, ; Cuiping Xiao, ; Linkong Zeng,
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Prenatal diagnosis of fetuses with region of homozygosity detected by single nucleotide polymorphism array: a retrospective cohort study. J Hum Genet 2022; 67:629-638. [PMID: 35896820 DOI: 10.1038/s10038-022-01062-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/01/2022] [Accepted: 06/23/2022] [Indexed: 11/09/2022]
Abstract
Region of homozygosity (ROH) is classified as uniparental disomy (UPD) or identity by descent, depending on its origin. To explore the clinical relevance of ROH in prenatal diagnoses, we reviewed 5063 fetal samples subjected to single nucleotide polymorphism array at our center over 5 years. ROH cases meeting our reporting threshold were further analyzed. ROHs were detected in 22 fetuses (0.43%, 22/5063), of which, 77.3% (17/22) showed a ROH on a single chromosome and 22.7% (5/22) showed multiple ROHs on different chromosomes. Among 5063 fetuses undergoing invasive prenatal diagnoses owing to various indications, five cases were identified as UPDs with a rate of ~1/1000. We observed clinically relevant UPDs in two cases related to Prader-Willi syndrome and transient neonatal diabetes mellitus. Of note, one case showed 50% mosaicism for trisomy 2 in amniotic fluid, whereas a complete UPD (2) was observed in umbilical cord blood. Trio whole-exome sequencing was performed for three cases. Clinically relevant variants were identified in two cases, one of which, NM_000302:c.2071_2072insCC (p.R693Qfs*122) in PLOD1 located in the ROH, may be related to Ehlers-Danlos syndrome, kyphoscoliotic type, 1. Overall, 72.7% (16/22) of the ROH carriers showed ultrasound abnormalities, of whom eight (50%, 8/16) had adverse perinatal outcomes. Our study demonstrates that the clinical relevance of ROHs should be examined regarding fetuses with ROHs occurring on imprinted chromosomes or those derived from consanguineous parents in prenatal diagnoses; imprinting disorders and/or autosomal recessive diseases attributed to ROHs should be considered during genetic counseling.
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Liu X, Liu S, Wang H, Hu T. Potentials and challenges of chromosomal microarray analysis in prenatal diagnosis. Front Genet 2022; 13:938183. [PMID: 35957681 PMCID: PMC9360565 DOI: 10.3389/fgene.2022.938183] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/11/2022] [Indexed: 11/19/2022] Open
Abstract
Introduction: For decades, conventional karyotyping analysis has been the gold standard for detecting chromosomal abnormalities during prenatal diagnosis. With the development of molecular cytogenetic methods, this situation has dramatically changed. Chromosomal microarray analysis (CMA), a method of genome-wide detection with high resolution, has been recommended as a first-tier test for prenatal diagnosis, especially for fetuses with structural abnormalities. Methods: Based on the primary literature, this review provides an updated summary of the application of CMA for prenatal diagnosis. In addition, this review addresses the challenges that CMA faces with the emergence of genome sequencing techniques, such as copy number variation sequencing, genome-wide cell-free DNA testing, and whole exome sequencing. Conclusion: The CMA platform is still suggested as priority testing methodology in the prenatal setting currently. However, pregnant women may benefit from genome sequencing, which enables the simultaneous detection of copy number variations, regions of homozygosity and single-nucleotide variations, in near future.
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Affiliation(s)
- Xijing Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Shanling Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - He Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- *Correspondence: Ting Hu,
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Pignata L, Cecere F, Verma A, Hay Mele B, Monticelli M, Acurzio B, Giaccari C, Sparago A, Hernandez Mora JR, Monteagudo-Sánchez A, Esteller M, Pereda A, Tenorio-Castano J, Palumbo O, Carella M, Prontera P, Piscopo C, Accadia M, Lapunzina P, Cubellis MV, de Nanclares GP, Monk D, Riccio A, Cerrato F. Novel genetic variants of KHDC3L and other members of the subcortical maternal complex associated with Beckwith-Wiedemann syndrome or Pseudohypoparathyroidism 1B and multi-locus imprinting disturbances. Clin Epigenetics 2022; 14:71. [PMID: 35643636 PMCID: PMC9148495 DOI: 10.1186/s13148-022-01292-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/16/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Beckwith-Wiedemann syndrome (BWS) and Pseudohypoparathyroidism type 1B (PHP1B) are imprinting disorders (ID) caused by deregulation of the imprinted gene clusters located at 11p15.5 and 20q13.32, respectively. In both of these diseases a subset of the patients is affected by multi-locus imprinting disturbances (MLID). In several families, MLID is associated with damaging variants of maternal-effect genes encoding protein components of the subcortical maternal complex (SCMC). However, frequency, penetrance and recurrence risks of these variants are still undefined. In this study, we screened two cohorts of BWS patients and one cohort of PHP1B patients for the presence of MLID, and analysed the positive cases for the presence of maternal variants in the SCMC genes by whole exome-sequencing and in silico functional studies. RESULTS We identified 10 new cases of MLID associated with the clinical features of either BWS or PHP1B, in which segregate 13 maternal putatively damaging missense variants of the SCMC genes. The affected genes also included KHDC3L that has not been associated with MLID to date. Moreover, we highlight the possible relevance of relatively common variants in the aetiology of MLID. CONCLUSION Our data further add to the list of the SCMC components and maternal variants that are involved in MLID, as well as of the associated clinical phenotypes. Also, we propose that in addition to rare variants, common variants may play a role in the aetiology of MLID and imprinting disorders by exerting an additive effect in combination with rarer putatively damaging variants. These findings provide useful information for the molecular diagnosis and recurrence risk evaluation of MLID-associated IDs in genetic counselling.
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Affiliation(s)
- Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", Caserta, Italy
- Institute of Genetics and Biophysics (IGB), "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), Naples, Italy
| | - Ankit Verma
- Institute of Genetics and Biophysics (IGB), "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), Naples, Italy
| | - Bruno Hay Mele
- Department of Biology, Università Degli Studi Di Napoli "Federico II", Naples, Italy
| | - Maria Monticelli
- Department of Biology, Università Degli Studi Di Napoli "Federico II", Naples, Italy
| | - Basilia Acurzio
- Institute of Genetics and Biophysics (IGB), "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), Naples, Italy
| | - Carlo Giaccari
- Institute of Genetics and Biophysics (IGB), "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), Naples, Italy
| | - Angela Sparago
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Jose Ramon Hernandez Mora
- Cancer Epigenetic and Biology Program (PEBC), Imprinting and Cancer Group, Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ana Monteagudo-Sánchez
- Cancer Epigenetic and Biology Program (PEBC), Imprinting and Cancer Group, Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukeamia Research Institute, Can Ruti, Cami de les Escoles, Badalona, Barcelona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Arrate Pereda
- Molecular (Epi)Genetics Laboratory, Rare Diseases Research Group, Bioaraba Health Research Institute, Araba University Hospital-Txagorritxu, C/Jose Atxotegi s/n, 01009, Vitoria-Gasteiz, Spain
| | - Jair Tenorio-Castano
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Institute of Medical and Molecular Genetics, INGEMM-Idipaz, Madrid, Spain
- ITHACA, European Reference Network, Brussels, Belgium
| | - Orazio Palumbo
- Division of Medical Genetics, Fondazione IRCCS "Casa Sollievo Della Sofferenza", 71013, San Giovanni Rotondo, FG, Italy
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS "Casa Sollievo Della Sofferenza", 71013, San Giovanni Rotondo, FG, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University and Hospital of Perugia, Perugia, Italy
| | - Carmelo Piscopo
- Medical and Laboratory Genetics Unit, "Antonio Cardarelli" Hospital, 80131, Naples, Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital "Cardinale G. Panico", 73039, Tricase, Lecce, Italy
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Institute of Medical and Molecular Genetics, INGEMM-Idipaz, Madrid, Spain
- ITHACA, European Reference Network, Brussels, Belgium
| | | | - Guiomar Perez de Nanclares
- Molecular (Epi)Genetics Laboratory, Rare Diseases Research Group, Bioaraba Health Research Institute, Araba University Hospital-Txagorritxu, C/Jose Atxotegi s/n, 01009, Vitoria-Gasteiz, Spain
| | - David Monk
- Cancer Epigenetic and Biology Program (PEBC), Imprinting and Cancer Group, Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TG, UK
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", Caserta, Italy.
- Institute of Genetics and Biophysics (IGB), "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), Naples, Italy.
| | - Flavia Cerrato
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", Caserta, Italy.
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35
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Tuveri S, Debackere K, Marcelis L, Dierckxsens N, Demeulemeester J, Dimitriadou E, Dierickx D, Lefesvre P, Deraedt K, Graux C, Michaux L, Cools J, Tousseyn T, Vermeesch JR, Wlodarska I. Primary mediastinal large B-cell lymphoma is characterized by large-scale copy-neutral loss of heterozygosity. Genes Chromosomes Cancer 2022; 61:603-615. [PMID: 35611992 DOI: 10.1002/gcc.23069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 11/07/2022] Open
Abstract
Development of primary mediastinal B-cell lymphoma (PMBL) is driven by cumulative genomic aberrations. We discovered a unique copy-neutral loss of heterozygosity (CN-LOH) landscape of PMBL which distinguishes this tumour from other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma. Using single nucleotide polymorphism array analysis we identified large-scale CN-LOH lesions in 91% (30/33) of diagnostic PMBLs and both investigated PMBL-derived cell lines. Altogether, the cohort showed 157 extra-large (25.3-248.4 Mb) CN-LOH lesions affecting up to 14 chromosomes per case (mean of 4.4) and resulting in a reduction of heterozygosity an average of 9.9% (range 1.3-51%) of the genome. Predominant involvement of terminal chromosomal segments suggests the implication of B-cell specific crossover events in the pathogenesis of PMBL. Notably, CN-LOH stretches non-randomly clustered on 6p (60%), 15 (37.2%) and 17q (40%), and frequently co-occurred with homozygous mutations in the MHC I (6p21), B2M (15q15) and GNA13 (17q23) genes, respectively, as shown by preliminary whole-exome/genome sequencing data. Altogether, our findings implicate CN-LOH as a novel and distinct mutational process contributing to the molecular pathogenesis of PMBL. The aberration acting as 'second hit' in the Knudson hypothesis, ranks as the major mechanism converting to homozygosity the PMBL-related driver genes. Screening of the cohort of 199 B cell leukamia/lymphoma whole-genomes revealed significant differences in the CN-LOH landscape of PMBL and other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma.
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Affiliation(s)
| | - Koen Debackere
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Lukas Marcelis
- Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | | | - Jonas Demeulemeester
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | | | - Daan Dierickx
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Pierre Lefesvre
- Department of Pathology, Free University Hospital, Brussels, Belgium
| | - Karen Deraedt
- Anatomo-Pathology, Hospital East Limburg, Genk, Belgium
| | - Carlos Graux
- Department of Hematology, Mont-Godinne University Hospital, Yvoir, Belgium
| | | | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Thomas Tousseyn
- Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
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36
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Cranston T, Boon H, Olesen MK, Ryan FJ, Shears D, London R, Rostom H, Elajnaf T, Thakker RV, Hannan FM. Spectrum of germline AIRE mutations causing APS-1 and familial hypoparathyroidism. Eur J Endocrinol 2022; 187:111-122. [PMID: 35521792 PMCID: PMC9175554 DOI: 10.1530/eje-21-0730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 05/04/2022] [Indexed: 11/21/2022]
Abstract
Objective The autoimmune polyendocrine syndrome type 1 (APS-1) is an autosomal recessive disorder characterised by immune dysregulation and autoimmune endocrine gland destruction. APS-1 is caused by biallelic mutations affecting the autoimmune regulator (AIRE) gene on chromosome 21q22.3, which facilitates immunological self-tolerance. The objective was to investigate >300 probands with suspected APS-1 or isolated hypoparathyroidism for AIRE abnormalities. Methods Probands were assessed by DNA sequence analysis. Novel variants were characterised using 3D modelling of the AIRE protein. Restriction enzyme and microsatellite analysis were used to investigate for uniparental isodisomy. Results Biallelic AIRE mutations were identified in 35 probands with APS-1 and 5 probands with isolated hypoparathyroidism. These included a novel homozygous p.(His14Pro) mutation, predicted to disrupt the N-terminal caspase activation recruitment domain of the AIRE protein. Furthermore, an apparently homozygous AIRE mutation, p.Leu323fs, was identified in an APS-1 proband, who is the child of non-consanguineous asymptomatic parents. Microsatellite analysis revealed that the proband inherited two copies of the paternal mutant AIRE allele due to uniparental isodisomy. Hypoparathyroidism was the most common endocrine manifestation in AIRE mutation-positive probands and >45% of those harbouring AIRE mutations had at least two diseases out of the triad of candidiasis, hypoparathyroidism, and hypoadrenalism. In contrast, type 1 diabetes and hypothyroidism occurred more frequently in AIRE mutation-negative probands with suspected APS-1. Around 30% of AIRE mutation-negative probands with isolated hypoparathyroidism harboured mutations in other hypoparathyroid genes. Conclusions This study of a large cohort referred for AIRE mutational analysis expands the spectrum of genetic abnormalities causing APS-1.
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Affiliation(s)
- Treena Cranston
- Oxford Genetics Laboratories, Churchill Hospital, Oxford, UK
| | - Hannah Boon
- Oxford Genetics Laboratories, Churchill Hospital, Oxford, UK
| | - Mie K Olesen
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Fiona J Ryan
- Paediatric Endocrinology, Children's Hospital, John Radcliffe Hospital, Oxford, UK
| | - Deborah Shears
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford, UK
| | - Rosemary London
- Paediatric Endocrinology, Children's Hospital, John Radcliffe Hospital, Oxford, UK
| | - Hussam Rostom
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | - Taha Elajnaf
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | - Rajesh V Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - Fadil M Hannan
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
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37
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Yu W, Cao L, Lin P. Neuronal Ceroid Lipofuscinosis Owing to Complete Maternal Uniparental Disomy. JAMA Neurol 2022; 79:720-721. [PMID: 35576013 DOI: 10.1001/jamaneurol.2022.1008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Wenfei Yu
- Cheeloo College of Medicine, Department of Neurology, Qilu Hospital, Shandong University, Jinan, China.,University of Health and Rehabilitation Sciences, Qingdao, China
| | - Lili Cao
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, China
| | - Pengfei Lin
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, China
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38
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Ashenhurst JR, Sazonova OV, Svrchek O, Detweiler S, Kita R, Babalola L, McIntyre M, Aslibekyan S, Fontanillas P, Shringarpure S, Pollard JD, Koelsch BL. A Polygenic Score for Type 2 Diabetes Improves Risk Stratification Beyond Current Clinical Screening Factors in an Ancestrally Diverse Sample. Front Genet 2022; 13:871260. [PMID: 35559025 PMCID: PMC9086969 DOI: 10.3389/fgene.2022.871260] [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: 02/08/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
A substantial proportion of the adult United States population with type 2 diabetes (T2D) are undiagnosed, calling into question the comprehensiveness of current screening practices, which primarily rely on age, family history, and body mass index (BMI). We hypothesized that a polygenic score (PGS) may serve as a complementary tool to identify high-risk individuals. The T2D polygenic score maintained predictive utility after adjusting for family history and combining genetics with family history led to even more improved disease risk prediction. We observed that the PGS was meaningfully related to age of onset with implications for screening practices: there was a linear and statistically significant relationship between the PGS and T2D onset (-1.3 years per standard deviation of the PGS). Evaluation of U.S. Preventive Task Force and a simplified version of American Diabetes Association screening guidelines showed that addition of a screening criterion for those above the 90th percentile of the PGS provided a small increase the sensitivity of the screening algorithm. Among T2D-negative individuals, the T2D PGS was associated with prediabetes, where each standard deviation increase of the PGS was associated with a 23% increase in the odds of prediabetes diagnosis. Additionally, each standard deviation increase in the PGS corresponded to a 43% increase in the odds of incident T2D at one-year follow-up. Using complications and forms of clinical intervention (i.e., lifestyle modification, metformin treatment, or insulin treatment) as proxies for advanced illness we also found statistically significant associations between the T2D PGS and insulin treatment and diabetic neuropathy. Importantly, we were able to replicate many findings in a Hispanic/Latino cohort from our database, highlighting the value of the T2D PGS as a clinical tool for individuals with ancestry other than European. In this group, the T2D PGS provided additional disease risk information beyond that offered by traditional screening methodologies. The T2D PGS also had predictive value for the age of onset and for prediabetes among T2D-negative Hispanic/Latino participants. These findings strengthen the notion that a T2D PGS could play a role in the clinical setting across multiple ancestries, potentially improving T2D screening practices, risk stratification, and disease management.
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39
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PGDIS Position Statement on the Transfer of Mosaic Embryos 2021. Reprod Biomed Online 2022; 45:19-25. [DOI: 10.1016/j.rbmo.2022.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/15/2022] [Accepted: 03/06/2022] [Indexed: 11/17/2022]
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40
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Chien SC, Chen CP, Liou JD. Prenatal diagnosis and genetic counseling of uniparental disomy. Taiwan J Obstet Gynecol 2022; 61:210-215. [DOI: 10.1016/j.tjog.2022.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 10/18/2022] Open
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41
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Corominas J, Smeekens SP, Nelen MR, Yntema HG, Kamsteeg EJ, Pfundt R, Gilissen C. Clinical exome sequencing - mistakes and caveats. Hum Mutat 2022; 43:1041-1055. [PMID: 35191116 PMCID: PMC9541396 DOI: 10.1002/humu.24360] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 01/11/2022] [Accepted: 02/18/2022] [Indexed: 11/30/2022]
Abstract
Massive parallel sequencing technology has become the predominant technique for genetic diagnostics and research. Many genetic laboratories have wrestled with the challenges of setting up genetic testing workflows based on a completely new technology. The learning curve we went through as a laboratory was accompanied by growing pains while we gained new knowledge and expertise. Here we discuss some important mistakes that have been made in our laboratory through 10 years of clinical exome sequencing but that have given us important new insights on how to adapt our working methods. We provide these examples and the lessons that we learned to help other laboratories avoid to make the same mistakes.
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Affiliation(s)
- Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sanne P Smeekens
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marcel R Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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42
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Liehr T. Uniparental disomy is a chromosomic disorder in the first place. Mol Cytogenet 2022; 15:5. [PMID: 35177099 PMCID: PMC8851757 DOI: 10.1186/s13039-022-00585-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 01/31/2022] [Indexed: 02/07/2023] Open
Abstract
Background Uniparental disomy (UPD) is well-known to be closely intermingled with imprinting disorders. Besides, UPD can lead to a disease by ‘activation’ of a recessive gene mutation or due to incomplete (cryptic) trisomic rescue. Corresponding to all common theories how UPD forms, it takes place as a consequence of a “chromosomic problem”, like an aneuploidy or a chromosomal rearrangement. Nonetheless, UPD is rarely considered as a cytogenetic, but most often as a molecular genetic problem. Results Here a review on the ~ 4900 published UPD-cases is provided, and even though being biased as discussed in the paper, the following insights have been given from that analysis: (1) the rate of maternal to paternal UPD is 2~3 to 1; (2) at most only ~ 0.03% of the available UPD cases are grasped scientifically, yet; (3) frequencies of single whole-chromosome UPDs are non-random, with UPD(16) and UPD(15) being most frequent in clinically healthy and diseased people, respectively; (4) there is a direct correlation of UPD frequency and known frequent first trimester trisomies, except for chromosomes 1, 5, 11 and 18 (which can be explained); (5) heterodisomy is under- and UPD-mosaicism is over-represented in recent reports; and (6) cytogenetics is not considered enough when a UPD is identified. Conclusions As UPD is diagnosed using molecular genetic approaches, and thus by specialists considering chromosomes at best as a whim of nature, most UPD reports lack the chromosomal aspect. Here it is affirmed and substantiated by corresponding data that UPD is a chromosomic disorder in the first place and cytogenetic analyses is indicated in each diagnosed UPD-case. Supplementary Information The online version contains supplementary material available at 10.1186/s13039-022-00585-2.
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Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, 07747, Jena, Germany.
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43
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Zaletaev DV, Nemtsova MV, Strelnikov VV. Epigenetic Regulation Disturbances on Gene Expression in Imprinting Diseases. Mol Biol 2022. [DOI: 10.1134/s0026893321050149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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44
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Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology. Genes (Basel) 2022; 13:genes13020333. [PMID: 35205378 PMCID: PMC8871714 DOI: 10.3390/genes13020333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
During the last decade, genetic testing has emerged as an important etiological diagnostic tool for Mendelian diseases, including pediatric neurological conditions. A genetic diagnosis has a considerable impact on disease management and treatment; however, many cases remain undiagnosed after applying standard diagnostic sequencing techniques. This review discusses various methods to improve the molecular diagnostic rates in these genomic cold cases. We discuss extended analysis methods to consider, non-Mendelian inheritance models, mosaicism, dual/multiple diagnoses, periodic re-analysis, artificial intelligence tools, and deep phenotyping, in addition to integrating various omics methods to improve variant prioritization. Last, novel genomic technologies, including long-read sequencing, artificial long-read sequencing, and optical genome mapping are discussed. In conclusion, a more comprehensive molecular analysis and a timely re-analysis of unsolved cases are imperative to improve diagnostic rates. In addition, our current understanding of the human genome is still limited due to restrictions in technologies. Novel technologies are now available that improve upon some of these limitations and can capture all human genomic variation more accurately. Last, we recommend a more routine implementation of high molecular weight DNA extraction methods that is coherent with the ability to use and/or optimally benefit from these novel genomic methods.
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Li Q, Zhu X, Yu C, Shang L, Li R, Wang X, Yang Y, Meng J, Kong X. Case Report: A Novel Homozygous Mutation in MYF5 Due to Paternal Uniparental Isodisomy of Chromosome 12 in a Case of External Ophthalmoplegia With Rib and Vertebral Anomalies. Front Genet 2022; 12:780363. [PMID: 35186005 PMCID: PMC8851471 DOI: 10.3389/fgene.2021.780363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/30/2021] [Indexed: 12/01/2022] Open
Abstract
External ophthalmoplegia with rib and vertebral anomalies (EORVA) is characterized by congenital nonprogressive external ophthalmoplegia, ptosis, scoliosis, torticollis, vertebral, and rib anomalies, caused by homozygous mutations in the myogenic factor 5 gene (MYF5) located on chromosome 12q21.31. Uniparental disomy (UPD) is a rare inheritance of a pair of chromosomes originating from only one parent. This study describes a case of an 8-year-old boy with ptosis, scoliosis, and dysmorphic hypoplastic ribs with fusion anomalies. Trio-based exome sequencing (trio-ES) identified a novel homozygous mutation c.191delC (p.Ala64Valfs*33) in MYF5 in the proband, with the father being heterozygous and the mother wild-type, as verified by Sanger sequencing. UPD identified from trio-ES variant call format data suggested the possibility of paternal UPD of chromosome 12 (UPD12pat) in the proband, further confirmed to be a complete isodisomy type of UPD by genome-wide single nucleotide polymorphism array. MYF5 was significantly downregulated by 69.14% (**p < 0.01) in HeLa cells transfected with mutant MYF5 containing c.191delC compared to those transfected with the wild-type MYF5, resulting in a truncated protein with a size of ∼20 kDa. In conclusion, this study identified a novel homozygous mutation in MYF5, broadening the genetic spectrum of EORVA and further deepening the understanding of this rare disease.
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Affiliation(s)
- Qianqian Li
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaofan Zhu
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chenguang Yu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Lin Shang
- Department of Foot and Ankle Surgery, Zhengzhou Orthopedic Hospital, Zhengzhou, China
| | - Ranran Li
- School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Xia Wang
- AiLife Diagnostics, Inc., Houston, TX, United States
| | - Yaping Yang
- AiLife Diagnostics, Inc., Houston, TX, United States
| | - Jingjing Meng
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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46
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Ashenhurst JR, Nhan H, Shelton JF, Wu S, Tung JY, Elson SL, Stoller JK. Prevalence of Alpha-1 Antitrypsin Deficiency, Self-Reported Behavior Change, and Health Care Engagement Among Direct-to-Consumer Recipients of a Personalized Genetic Risk Report. Chest 2022; 161:373-381. [PMID: 34656525 DOI: 10.1016/j.chest.2021.09.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/09/2021] [Accepted: 09/12/2021] [Indexed: 10/20/2022] Open
Abstract
BACKGROUND Alpha-1 antitrypsin deficiency (AATD) is an autosomal co-dominant condition that predisposes to emphysema, cirrhosis, panniculitis, and vasculitis. Underrecognition has prompted efforts to enhance early detection and testing of at-risk individuals. Direct-to-consumer (DTC) genetic testing represents an additional method of detection. RESEARCH QUESTION The study addressed three questions: (1) Does a DTC testing service identify previously undetected individuals with AATD? (2) What was the interval between initial AATD-related symptoms and initial diagnosis of AATD in such individuals? and (3) What was the behavioral impact of learning about a new diagnosis of AATD through a DTC test? STUDY DESIGN AND METHODS In this cross-sectional study, 195,014 individuals responded to a survey within the 23andMe, Inc. research platform. RESULTS Among 195,014 study participants, the allele frequency for the PI∗S and PI∗Z AATD variants was 21.6% (6.5% for PI∗Z and 15.1% for PI∗S); 0.63% were PI∗ZZ, half of whom reported having a physician confirm the diagnosis. Approximately 27% of those with physician-diagnosed AATD reported first becoming aware of AATD through the DTC test. Among those newly aware participants, the diagnostic delay interval was 22.3 years. Participants frequently shared their DTC test results with health care providers (HCPs) and the reported impact of learning a diagnosis of AATD was high. For example, 51.1% of PI∗ZZ individuals shared their DTC result with an HCP. The OR for PI∗ZZ smokers to report smoking reduction as a result of receiving the DTC result was 1.7 (95% CI = 1.4-2.2) compared with those without a Z allele and for reduced alcohol consumption this was 4.0 (95% CI = 2.6-5.9). INTERPRETATION In this largest available report on DTC testing for AATD, this test, in combination with clinical follow-up, can help to identify previously undiagnosed AATD patients. Moreover, receipt of the DTC AATD report was associated with positive behavior change, especially among those with risk variants.
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Affiliation(s)
| | | | | | | | | | | | - James K Stoller
- Education Institute and Respiratory Institute, Cleveland Clinic, Cleveland, OH
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Yoon CJ, Kim SY, Nam CH, Lee J, Park JW, Mun J, Park S, Lee S, Yi B, Min KI, Wiley B, Bolton KL, Lee JH, Kim E, Yoo HJ, Jun JK, Choi JS, Griffith M, Griffith OL, Ju YS. Estimation of intrafamilial DNA contamination in family trio genome sequencing using deviation from Mendelian inheritance. Genome Res 2022; 32:2134-2144. [PMID: 36617634 PMCID: PMC9808622 DOI: 10.1101/gr.276794.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 10/31/2022] [Indexed: 12/12/2022]
Abstract
With the increasing number of sequencing projects involving families, quality control tools optimized for family genome sequencing are needed. However, accurately quantifying contamination in a DNA mixture is particularly difficult when genetically related family members are the sources. We developed TrioMix, a maximum likelihood estimation (MLE) framework based on Mendel's law of inheritance, to quantify DNA mixture between family members in genome sequencing data of parent-offspring trios. TrioMix can accurately deconvolute any intrafamilial DNA contamination, including parent-offspring, sibling-sibling, parent-parent, and even multiple familial sources. In addition, TrioMix can be applied to detect genomic abnormalities that deviate from Mendelian inheritance patterns, such as uniparental disomy (UPD) and chimerism. A genome-wide depth and variant allele frequency plot generated by TrioMix facilitates tracing the origin of Mendelian inheritance deviations. We showed that TrioMix could accurately deconvolute genomes in both simulated and real data sets.
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Affiliation(s)
- Christopher J. Yoon
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,Research Center for Natural Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea;,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea;,McDonnell Genome Institute, St. Louis, Missouri 63108, USA
| | - Su Yeon Kim
- Research Center for Natural Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Chang Hyun Nam
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Junehawk Lee
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon 34141, Korea
| | - Jung Woo Park
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon 34141, Korea
| | - Jihyeob Mun
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon 34141, Korea
| | | | - Soyoung Lee
- GENOME INSIGHT Incorporated, Daejeon 34051, Korea
| | - Boram Yi
- GENOME INSIGHT Incorporated, Daejeon 34051, Korea
| | - Kyoung Il Min
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Brian Wiley
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Kelly L. Bolton
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Eunjoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea;,Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon 34141, Korea
| | - Hee Jeong Yoo
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam 13620, Korea;,Department of Psychiatry, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jong Kwan Jun
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Ji Seon Choi
- Department of Laboratory Medicine, International St. Mary's Hospital, Catholic Kwandong University College of Medicine, Incheon 22711, Korea
| | - Malachi Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,McDonnell Genome Institute, St. Louis, Missouri 63108, USA
| | - Obi L. Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,McDonnell Genome Institute, St. Louis, Missouri 63108, USA
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea;,GENOME INSIGHT Incorporated, Daejeon 34051, Korea
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Bu X, Li X, Zhou S, Shi L, Jiang X, Peng C, Li H, He J. Prenatal diagnosis of complete paternal uniparental isodisomy for chromosome 3: a case report. Mol Cytogenet 2021; 14:50. [PMID: 34742342 PMCID: PMC8572431 DOI: 10.1186/s13039-021-00569-8] [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: 08/02/2021] [Accepted: 10/09/2021] [Indexed: 11/17/2022] Open
Abstract
Background Uniparental disomy (UPD) is defined as an inheritance of two chromosomes from only one of the parents with no representative copy from the other. Paternal-origin UPD of chromosome 3 is a very rare condition, with only five cases of paternal UPD(3) reported. Case presentation Here, we report a prenatal case that is only the second confirmed paternal UPD(3) reported with no apparent disease phenotype. The fetus had a normal karyotype and normal ultrasound features throughout gestation. Copy neutral regions of homozygosity on chromosome 3 were identified by single nucleotide polymorphism (SNP) array. Subsequent SNP array data of parent–child trios showed that the fetus carried complete paternal uniparental isodisomy (isoUPD) of chromosome 3. The parents decided to continue with the pregnancy after genetic counseling, and the neonate had normal physical findings at birth and showed normal development after 1.5 years. Conclusions These findings provided further evidence to confirm that there were no important imprinted genes on paternal chromosome 3 that caused serious diseases and a reference for the prenatal diagnosis and genetic counseling of UPD(3) in the future.
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Affiliation(s)
- Xiufen Bu
- Department of Genetics and Eugenics, Changsha Hospital for Maternal and Child Health Care, Changsha, 410007, Hunan, China
| | - Xu Li
- Department of Basic Medicine, Yiyang Medical College, Yiyang, 413000, Hunan, China
| | - Shihao Zhou
- Department of Genetics and Eugenics, Changsha Hospital for Maternal and Child Health Care, Changsha, 410007, Hunan, China
| | - Liangcheng Shi
- Department of Genetics and Eugenics, Changsha Hospital for Maternal and Child Health Care, Changsha, 410007, Hunan, China
| | - Xuanyu Jiang
- Department of Genetics and Eugenics, Changsha Hospital for Maternal and Child Health Care, Changsha, 410007, Hunan, China
| | - Can Peng
- Department of Genetics and Eugenics, Changsha Hospital for Maternal and Child Health Care, Changsha, 410007, Hunan, China
| | - Hongyu Li
- Department of Genetics and Eugenics, Changsha Hospital for Maternal and Child Health Care, Changsha, 410007, Hunan, China
| | - Jun He
- Department of Genetics and Eugenics, Changsha Hospital for Maternal and Child Health Care, Changsha, 410007, Hunan, China.
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Berland S, Rustad CF, Bentsen MHL, Wollen EJ, Turowski G, Johansson S, Houge G, Haukanes BI. Double paternal uniparental isodisomy 7 and 15 presenting with Beckwith-Wiedemann spectrum features. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006113. [PMID: 34615670 PMCID: PMC8751407 DOI: 10.1101/mcs.a006113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/31/2021] [Indexed: 12/16/2022] Open
Abstract
Here we describe for the first time double paternal uniparental isodisomy (iUPD) 7 and 15 in a baby boy with features in the Beckwith–Wiedemann syndrome spectrum (BWSp) (placentomegaly, hyperinsulinism, enlarged viscera, hemangiomas, and earlobe creases) in addition to conjugated hyperbilirubinemia. His phenotype was also reminiscent of genome-wide paternal uniparental isodisomy. We discuss the most likely origin of the UPDs: a maternal double monosomy 7 and 15 rescued by duplication of the paternal chromosomes after fertilization. So far, paternal UPD7 is not associated with an abnormal phenotype, whereas paternal UPD15 causes Angelman syndrome. Methylation analysis for other clinically relevant imprinting disorders, including BWSp, was normal. Therefore, we hypothesized that the double UPD affected other imprinted genes. To look for such effects, patient fibroblast RNA was isolated and analyzed for differential expression compared to six controls. We did not find apparent transcription differences in imprinted genes outside Chromosomes 7 and 15 in patient fibroblast. PEG10 (7q21.3) was the only paternally imprinted gene on these chromosomes up-regulated beyond double-dose expectation (sixfold). We speculate that a high PEG10 level could have a growth-promoting effect as his phenotype was not related to aberrations in BWS locus on 11p15.5 after DNA, RNA, and methylation testing. However, many genes in gene sets associated with growth were up-regulated. This case broadens the phenotypic spectrum of UPDs but does not show evidence of involvement of an imprinted gene network.
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Affiliation(s)
- Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Cecilie F Rustad
- Department of Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway
| | - Mariann H L Bentsen
- Department of Pediatric and Adolescent Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Embjørg J Wollen
- Department of Pediatric Hepatology, Division of Pediatric and Adolescent Medicine, University of Oslo, Oslo University Hospital HF, 0424 Oslo, Norway
| | - Gitta Turowski
- Department of Pathology, Center for Perinatal and Pregnancy-Related Pathology, Oslo University Hospital-Ullevål, 0424 Oslo, Norway
| | - Stefan Johansson
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway.,Department of Clinical Science, University of Bergen, 5007 Bergen, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Bjørn I Haukanes
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway
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50
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Tao Y, Han D, Wei Y, Wang L, Song W, Li X. Case Report: Complete Maternal Uniparental Disomy of Chromosome 2 With a Novel UNC80 Splicing Variant c.5609-4G> A in a Chinese Patient With Infantile Hypotonia With Psychomotor Retardation and Characteristic Facies 2. Front Genet 2021; 12:747422. [PMID: 34594366 PMCID: PMC8476880 DOI: 10.3389/fgene.2021.747422] [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: 07/26/2021] [Accepted: 09/02/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Infantile hypotonia with psychomotor retardation and characteristic facies 2 (IHPRF2) is a rare autosomal recessive neurodevelopmental disorder caused by mutations in the UNC80 gene. It is characterized by severe global developmental delay, poor or absent speech and absent or limited walking abilities. The current study explored a case of a Chinese patient with IHPRF2 caused by a novel splicing variant of UNC80. Case Report: The proband is a 8-year-old Chinese male manifested with global developmental delay, severe truncal hypotonia, absent speech and intellectual disability. SNP array analysis revealed a uniparental isodisomy of the entire chromosome 2 [UPD(2)] in the proband. Whole exome sequencing (WES) subsequently identified a novel mutation c.5609-4G>A in the UNC80 gene, which was inherited from his mother and was confirmed by Sanger sequencing, indicating that UPD(2) was of maternal origin. Conclusion: A novel UNC80 homozygous splicing variant c.5609-4G>A associated with maternal UPD(2) was identified. These findings indicate that UPD poses a high risk of autosomal recessive diseases, and provides information on the variant spectrum for UNC80. Our findings elucidate on understanding of the genotype-phenotype associations that occur in IHPRF2 patients.
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Affiliation(s)
- Yilun Tao
- Medical Genetic Center, Changzhi Maternal and Child Health Care Hospital, Changzhi, China
| | - Dong Han
- Medical Genetic Center, Changzhi Maternal and Child Health Care Hospital, Changzhi, China
| | - Yiju Wei
- Department of Pediatrics, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, United States
| | - Lihong Wang
- Department of Pediatrics, Changzhi Maternal and Child Health Care Hospital, Changzhi, China
| | - Wenxia Song
- Obstetrics Department, Changzhi Maternal and Child Health Care Hospital, Changzhi, China
| | - Xiaoze Li
- Medical Genetic Center, Changzhi Maternal and Child Health Care Hospital, Changzhi, China
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