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Moch J, Radtke M, Liehr T, Eggermann T, Gilissen C, Pfundt R, Astuti G, Hentschel J, Schumann I. Automatized detection of uniparental disomies in a large cohort. Hum Genet 2024; 143:955-964. [PMID: 39012485 PMCID: PMC11303498 DOI: 10.1007/s00439-024-02687-w] [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: 04/16/2024] [Accepted: 07/03/2024] [Indexed: 07/17/2024]
Abstract
Uniparental disomy (UPD) is the inheritance of both homologues of a chromosome from only one parent. The detection of UPDs in sequencing data is not well established and a common gap in genetic diagnostics. We applied our in-house UPD detection pipeline to evaluate a cohort of 9212 samples, including multigene panels as well as exome sequencing data in a single, duo or trio constellation. We used the results to inform the design of our publicly available web app altAFplotter. UPDs categorized as heterodisomy, whole chromosome or segmental isodisomy were identified and validated with microsatellites, multiplex ligation-dependent probe amplification as well as Sanger sequencing. We detected 14 previously undiagnosed UPDs including nine isodisomies, four segmental isodisomies as well as one heterodisomy on chromosome 22. We characterized eight findings as potentially causative through homozygous pathogenic variants or imprinting disorders. Overall, our study demonstrates the utility of our UPD detection pipeline with our web app, altAFplotter, to reliably identify UPDs. This not only increases the diagnostic yield of cases with growth and metabolic disturbances, as well as developmental delay, but also enhances the understanding of UPDs that may be relevant for recurrence risks and genetic counseling.
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Affiliation(s)
- Johanna Moch
- Institute of Human Genetics, Leipzig University, Leipzig, Germany
| | | | - Thomas Liehr
- Institute of Human Genetics, Jena University, Jena, Germany
| | - Thomas Eggermann
- Institute of Human Genetics and Genomic Medicine, Aachen University, Aachen, Germany
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Galuh Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Julia Hentschel
- Institute of Human Genetics, Leipzig University, Leipzig, Germany
| | - Isabell Schumann
- Institute of Human Genetics, Leipzig University, Leipzig, Germany.
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2
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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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Xue H, Yu A, Zhang L, Chen L, Guo Q, Lin M, Lin N, Chen X, Xu L, Huang H. Genetic testing for fetal loss of heterozygosity using single nucleotide polymorphism array and whole-exome sequencing. Sci Rep 2024; 14:2190. [PMID: 38273042 PMCID: PMC10810965 DOI: 10.1038/s41598-024-52812-y] [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: 07/03/2023] [Accepted: 01/23/2024] [Indexed: 01/27/2024] Open
Abstract
The study explored the clinical significance of fetal loss of heterozygosity (LOH) identified by single-nucleotide polymorphism array (SNP array). We retrospectively reviewed data from pregnant women who underwent invasive diagnostic procedures at prenatal diagnosis centers in southeastern China from December 2016 to December 2021. SNP array was performed by the Affymetrix CytoScan 750 K array platform. Fetuses with LOH were further identified by parental verification, MS-MLPA, and/or trio whole-exome sequencing (trio-WES). The genetic results, fetal clinical manifestations, and perinatal outcome were analyzed. Of 11,062 fetuses, 106 (0.96%) had LOH exhibiting a neutral copy number, 88 (83.0%) had LOH in a single chromosome, whereas 18 (17.0%) had multiple LOHs on different chromosomes. Sixty-six fetuses had ultrasound anomalies (UAs), most frequently fetal growth restriction (18/66 (27.3%)). Parental SNP array verification was performed in 21 cases and trio-WES in 21 cases. Twelve cases had clinically relevant uniparental disomy, five had pathogenic variants, four had likely pathogenic variants, six had variants of unknown significance, and eight had identity by descent. The rate of adverse pregnancy outcomes in fetuses with LOH and UAs (24/66 (36.4%)) was higher than in those without UAs (6/40 (15.0%)) (p < 0.05). LOH is not uncommon. Molecular genetic testing techniques, including parental SNP array verification, trio-WES, methylation-specific multiplex ligation-dependent probe amplification, regular and systematic ultrasonic monitoring, and placental study, can accurately assess the prognosis and guide the management of the affected pregnancy.
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Affiliation(s)
- Huili Xue
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
| | - Aili Yu
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Lin Zhang
- Fujian Medical University, No. 88 Jiaotong Road, Cangshan District, Fuzhou City, 350001, Fujian Province, China
| | - Lingji Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Qun Guo
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Min Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
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Polonis K, Lopes JL, Cabral H, Babcock HE, Kline L, Ruiz KM, Schwartz S, Hasadsri L, Rowsey RA, Hoppman NL, Grant CL. Uniparental disomy of multiple chromosomes in two cases with a complex phenotype. Am J Med Genet A 2023; 191:1978-1983. [PMID: 37134191 DOI: 10.1002/ajmg.a.63224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [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
| | - Christina L. Grant
- Division of Genetics and Metabolism, Children's National Hospital, Washington,DC, USA
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Eggermann T, Prawitt D. Further understanding of paternal uniparental disomy in Beckwith-Wiedemann syndrome. Expert Rev Endocrinol Metab 2022; 17:513-521. [PMID: 36377076 DOI: 10.1080/17446651.2022.2144228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Paternal uniparental disomy of chromosome 11 (upd(11)pat) accounts for up to 20% of molecularly confirmed Beckwith-Wiedemann spectrum (BWSp) cases. It belongs to the BWSp subgroup with the second highest tumor risk, and therefore needs particular awareness in research, diagnostics and clinical management. AREAS COVERED We overview the contribution of paternal (mosaic) uniparental disomy of chromosome 11 (UPD, upd(11)pat) and mosaic paternal uniparental diploidy in patients with Beckwith-Wiedemann features. The review comprises the current knowledge on their formation and their molecular and clinical consequences. Accordingly, the consequences for diagnostic testing and clinical monitoring are compiled. EXPERT OPINION The necessity to diagnostically identify and thus discriminate genome-wide paternal uniparental disomy, and upd(11)pat becomes obvious, due to the differences in the clinical course, disease prognosis, and treatment. In particular, monitoring of tumor development by liquid biopsy might be a promising option in the future. From the research point of view, it should be addressed why 11p is prone to mitotic recombination and thus also provide to the role of upd(11) as second hit in tumorigenesis.
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Affiliation(s)
- Thomas Eggermann
- Medical Faculty, Institute of Human Genetics, RWTH Aachen, Aachen, Germany
| | - Dirk Prawitt
- Center for Paediatrics and Adolescent Medicine, University Medical Center, Mainz, Germany
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Wang LQ, Fernandez-Boyano I, Robinson WP. Genetic variation in placental insufficiency: What have we learned over time? Front Cell Dev Biol 2022; 10:1038358. [PMID: 36313546 PMCID: PMC9613937 DOI: 10.3389/fcell.2022.1038358] [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: 09/06/2022] [Accepted: 10/03/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic variation shapes placental development and function, which has long been known to impact fetal growth and pregnancy outcomes such as miscarriage or maternal pre-eclampsia. Early epidemiology studies provided evidence of a strong heritable component to these conditions with both maternal and fetal-placental genetic factors contributing. Subsequently, cytogenetic studies of the placenta and the advent of prenatal diagnosis to detect chromosomal abnormalities provided direct evidence of the importance of spontaneously arising genetic variation in the placenta, such as trisomy and uniparental disomy, drawing inferences that remain relevant to this day. Candidate gene approaches highlighted the role of genetic variation in genes influencing immune interactions at the maternal-fetal interface and angiogenic factors. More recently, the emergence of molecular techniques and in particular high-throughput technologies such as Single-Nucleotide Polymorphism (SNP) arrays, has facilitated the discovery of copy number variation and study of SNP associations with conditions related to placental insufficiency. This review integrates past and more recent knowledge to provide important insights into the role of placental function on fetal and perinatal health, as well as into the mechanisms leading to genetic variation during development.
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Affiliation(s)
- Li Qing Wang
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Icíar Fernandez-Boyano
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Wendy P. Robinson
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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Recessive Dystrophic Epidermolysis bullosa due to Hemizygous 40 kb Deletion of COL7A1 and the Proximate PFKFB4 Gene Focusing on the Mutation c.425A>G Mimicking Homozygous Status. Diagnostics (Basel) 2022; 12:diagnostics12102460. [PMID: 36292148 PMCID: PMC9600310 DOI: 10.3390/diagnostics12102460] [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: 08/27/2022] [Revised: 09/17/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Dystrophic Epidermolysis bullosa (DEB) is a rare inherited mechanobullous disease characterised by the hyperfragility of the skin and mucous membranes. It is (typically) caused by (loss-of-function) mutations in the COL7A1 gene that impair the formation of collagen type VII, which represents the major constituent of anchoring fibrils within the basement membrane zone of epithelialised tissues. In a 4-year-old patient diagnosed with the clinical features of recessive DEB, genotyping via Next-Generation EB Panel Sequencing initially revealed the homozygosity of the maternal c.425A>G mutation, while the paternal heterozygosity in exon 3 was lacking. This genetic profile suggested incongruent gene transmission due to uniparental isodisomy (UPD) or the occurrence of a hemizygous deletion of unknown size. Methods: Thus, the EB panel sequencing of genomic DNA, followed by a paternity test and analysis of microsatellite markers, as well as multiplex ligation-dependent probe amplification (MLPA) copy number analysis using patient and parental DNA, were performed. Results: This approach revealed a paternally derived hemizygous deletion spanning from exon 3 to exon 118. Linear amplification-mediated PCR (LAM-PCR) determined the breaking points within intron 2 of the COL7A1 gene, comprising a 40kb segment within intron 1 of the adjacent PFKFB4 gene. Conclusion: This report highlights the relevance of advanced molecular profiling to determine new/exceptional/unusual genotypes and the accurate mode of genetic transmission in DEB.
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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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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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10
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Knapp A, Jagła M, Madetko-Talowska A, Szewczyk K, Książek T, Końska K, Kwinta P. Paternal uniparental disomy of chromosome 2 resulting in a concurrent presentation of Crigler-Najjar syndrome type I and long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency. Am J Med Genet A 2022; 188:1848-1852. [PMID: 35199468 DOI: 10.1002/ajmg.a.62696] [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: 09/08/2021] [Revised: 12/27/2021] [Accepted: 01/28/2022] [Indexed: 11/06/2022]
Abstract
This is the first report of the concurrent development of long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency (LCHADD) and Crigler-Najjar syndrome type 1 (CNs1) inherited via uniparental disomy of chromosome 2, which are both autosomal recessive pathologies. Through an expanded newborn metabolic panel, a male infant was identified as having an acylcarnitine pattern typical for LCHADD, later confirmed to be caused by a well-characterized pathogenic variant in the HADHA gene located at 2p23. Prolonged non-hematologic jaundice requiring repetitive phototherapy prompted further genetic analysis, leading to the identification of another genetic abnormality consistent with CNs1, which was caused by a novel pathogenic variant in the UGT1A1 gene located at 2q37. The two identified point mutations in chromosome 2 were homozygous and present on separate arms, which indicated potential uniparental disomy. Microarray analysis of the genetic material from the patient and his parents confirmed paternal isodisomy of chromosome 2. Further studies are needed to identify other possible pathogenic variants located on the same defective chromosome, evaluate the combined effect of the two metabolic abnormalities, and plan the best possible treatment and care.
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Affiliation(s)
- Anna Knapp
- Department of Pediatrics, Chair of Pediatrics Jagiellonian University Medical College, Krakow, Poland
| | - Mateusz Jagła
- Department of Pediatrics, Chair of Pediatrics Jagiellonian University Medical College, Krakow, Poland
| | - Anna Madetko-Talowska
- University Children Hospital in Krakow, Krakow, Poland.,Department of Medical Genetics, Chair of Pediatrics Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Szewczyk
- University Children Hospital in Krakow, Krakow, Poland.,Department of Medical Genetics, Chair of Pediatrics Jagiellonian University Medical College, Krakow, Poland
| | - Teofila Książek
- University Children Hospital in Krakow, Krakow, Poland.,Department of Medical Genetics, Chair of Pediatrics Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Końska
- Department of Medical Genetics, Chair of Pediatrics Jagiellonian University Medical College, Krakow, Poland
| | - Przemko Kwinta
- Department of Pediatrics, Chair of Pediatrics Jagiellonian University Medical College, Krakow, Poland
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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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12
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Cytogenetic discrepancy between uncultured amniocytes and cultured amniocytes in mosaic trisomy 15 at amniocentesis. Taiwan J Obstet Gynecol 2021; 59:728-735. [PMID: 32917326 DOI: 10.1016/j.tjog.2020.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE We present mosaic trisomy 15 at amniocentesis. MATERIALS AND METHODS A 41-year-old woman underwent amniocentesis at 16 weeks of gestation because of an abnormal non-invasive prenatal testing (NIPT) result suspicious of trisomy 15. Amniocentesis revealed a karyotype of 46,XY. Array comparative genomic hybridization (aCGH) on uncultured amniocytes revealed 26% mosaicism for trisomy 15. She was referred for repeat amniocentesis. aCGH, interphase fluorescence in situ hybridization (FISH), quantitative fluorescent polymerase chain reaction (QF-PCR) assays and/or conventional cytogenetic analysis were applied on various cells and tissues including uncultured amniocytes, cultured amniocytes, cord blood, placenta, parental bloods and/or buccal mucosal cells. RESULTS Repeat amniocentesis at 21 weeks of gestation revealed a karyotype of 46, XY in cultured amniocytes, and 30% mosaicism for trisomy 15 by aCGH and 32% mosaicism for trisomy 15 by FISH in uncultured amniocytes. Repeat amniocentesis at 29 weeks of gestation revealed a karyotype of 46, XY in cultured amniocytes, and 15% mosaicism for trisomy 15 by aCGH and 7.2% mosaicism for trisomy 15 by FISH in uncultured amniocytes. QF-PCR on cultured amniocytes excluded uniparental disomy (UPD) 15. A phenotypically normal baby was delivered subsequently with a karyotype of 46, XY in cord blood and 2% mosaicism for trisomy 15 by FISH in buccal mucosal cells. The aCGH analysis revealed trisomy 15 in placenta and no genomic imbalance in cord blood. QF-PCR assays determined a maternal origin of trisomy 15 in placenta. CONCLUSION Cytogenetic discrepancy may occur between uncultured and cultured amniocytes in mosaic trisomy 15 at amniocentesis. The cells of trisomy 15 cell line in prenatally detected mosaic trisomy 15 may decrease in number as the fetus grows. Whenever NIPT suspects trisomy 15, a confirmatory amniocentesis should include genetic analysis on both uncultured and cultured amniocytes to exclude mosaic trisomy 15 and maternal UPD 15, especially when the cultured amniocytes have a normal karyotype.
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Liu J, He Z, Lin S, Wang Y, Huang L, Huang X, Luo Y. Absence of heterozygosity detected by single-nucleotide polymorphism array in prenatal diagnosis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 57:314-323. [PMID: 31840905 DOI: 10.1002/uog.21951] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/19/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
OBJECTIVES To investigate the general occurrence and clinical significance of absence of heterozygosity (AOH), detected by single-nucleotide polymorphism (SNP) array on prenatal diagnosis. METHODS We recruited pregnancies undergoing invasive prenatal diagnosis at our fetal medicine center over a 6-year period. All fetuses underwent SNP array using the Affymetrix CytoScan HD array platform. AOH was defined as a chromosomal homozygosity segment with neutral copy number. Cases with AOH over 10 Mb in size or with suspected pathogenicity were further analyzed, and the clinical features and outcome were reviewed. RESULTS Of 10 294 recruited fetuses, 100 (0.97%) with AOH were identified; in 81 (81.0%) of these, AOH occurred in a single chromosome, while 19 (19.0%) patients had multiple AOHs in different chromosomes. AOH was observed in all chromosomes, chromosomes X, 2 and 16 being the most frequently involved. The length of AOH ranged from partial chromosome (9.002-80.222 Mb) to the entire chromosome. Similar AOH regions displayed varied clinical manifestations. In total, 55 patients presented with concomitant ultrasound abnormalities, the most common being multiple abnormalities (14/55 (25.5%)), genitourinary malformations (8/55 (14.5%)), skeletal malformations (5/55 (9.1%)) and small-for-gestational age (5/55 (9.1%)). Notably, the rate of adverse perinatal outcome (including termination of pregnancy, neonatal death, fetal death, selective reduction and miscarriage) in fetuses with AOH and ultrasound abnormalities (30/48 (62.5%)) was higher than in those without ultrasound abnormalities (6/40 (15.0%)) (P < 0.001). Further non-invasive prenatal testing using cell-free fetal DNA from maternal blood indicated chromosomal copy number abnormalities in 11 patients; however, they were confirmed as AOH by SNP array of the amniotic fluid. CONCLUSIONS Genetic counseling regarding a prenatal diagnosis of AOH remains challenging. To evaluate comprehensively its significance, we propose a management strategy involving further serial ultrasound examinations, parental verification, whole-exome sequencing, placental study and effective follow-up. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- J Liu
- Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Z He
- Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - S Lin
- Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Y Wang
- Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - L Huang
- Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - X Huang
- Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Y Luo
- Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
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Zhang X, Liu L, Liu Y, Pan X. Case Report: Paternal Uniparental Isodisomy and Heterodisomy of Chromosome 16 With a Normal Phenotype. Front Pediatr 2021; 9:732645. [PMID: 34746057 PMCID: PMC8569901 DOI: 10.3389/fped.2021.732645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/14/2021] [Indexed: 12/05/2022] Open
Abstract
Uniparental disomy (UPD) is a specific type of chromosomal variant that has been detected in both prenatal diagnosis and neonates with advances in molecular genetic testing technologies [mainly chromosome microarray analysis (CMA) technologies containing single-nucleotide polymorphism (SNP) probes]. In this case, we performed non-invasive prenatal genetic testing (NIPT) to screen fetuses for aneuploidy and detected the presence of aneuploidy chimerism and UPD by CMA, including SNP analysis and whole-exome sequencing, to detect pathogenic variants within the genome. The NIPT results suggested an increased number of fetal chromosome 16, and the CMA results indicated that it was the first case of holistic paternal UPD16 with isodisomy combined with heterodisomy, although no abnormal phenotype was seen in the newborn at postnatal follow-up. The homozygous region of the isodimer combined with the heterodimer is smaller than that of the complete isodimer, and it is less prone to recessive genetic diseases. A retrospective analysis of this case of paternally derived UPD16 was used to explore the uniparental diploid origin of chromosome 16 and to provide some reference for genetic counseling and prenatal diagnosis.
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Affiliation(s)
- Xu Zhang
- The Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Liu
- The Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yang Liu
- The Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xin Pan
- The Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Prenatal Detection of Uniparental Disomies (UPD): Intended and Incidental Finding in the Era of Next Generation Genomics. Genes (Basel) 2020; 11:genes11121454. [PMID: 33287348 PMCID: PMC7761756 DOI: 10.3390/genes11121454] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Prenatal detection of uniparental disomy (UPD) is a methodological challenge, and a positive testing result requires comprehensive considerations on the clinical consequences as well as ethical issues. Whereas prenatal testing for UPD in families which are prone to UPD formation (e.g., in case of chromosomal variants, imprinting disorders) is often embedded in genetic counselling, the incidental identification of UPD is often more difficult to manage. With the increasing application of high-resolution test systems enabling the identification of UPD, an increase in pregnancies with incidental detection of UPD can be expected. This paper will cover the current knowledge on uniparental disomies, their clinical consequences with focus on prenatal testing, genetic aspects and predispositions, genetic counselling, as well as methods (conventional tests and high-throughput assays).
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16
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A newborn screening pilot study using methylation-sensitive high resolution melting on dried blood spots to detect Prader-Willi and Angelman syndromes. Sci Rep 2020; 10:13026. [PMID: 32747801 PMCID: PMC7400512 DOI: 10.1038/s41598-020-69750-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 07/14/2020] [Indexed: 12/24/2022] Open
Abstract
Prader-Willi (PWS) and Angelman (AS) syndromes are two clinically distinct imprinted disorders characterized by genetic abnormalities at 15q11-q13. Early diagnosis of both syndromes provides improved treatment and accurate genetic counseling. Whole blood (WB) is the most common DNA source of many methodologies to detect PWS and AS, however, the need of WB makes a massive screening difficult in newborns due to economic and technical limitations. The aim of this study was to adapt a Methylation-sensitive High-Resolution Melting (MS-HRM) approach from dried blood spot (DBS) samples, assessing the different DNA isolation techniques and diagnostic performance. Over a 1-year period, we collected 125 DBS cards, of which 45 had already been diagnosed by MS-HRM (20 PWS, 1 AS, and 24 healthy individuals). We tested three different DBS-DNA extraction techniques assessing the DNA concentration and quality, followed by MS-HRM and statistical comparison. Each DBS-DNA extraction method was capable of accuracy in detecting all PWS and AS individuals. However, the efficiency to detect healthy individuals varied according to methodology. In our experience, DNA extracted from DBS analyzed by the MS-HRM methodology provides an accurate approach for genetic screening of imprinting related disorders in newborns, offering several benefits compared to traditional whole blood methods.
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Diagnostic testing for uniparental disomy: a points to consider statement from the American College of Medical Genetics and Genomics (ACMG). Genet Med 2020; 22:1133-1141. [PMID: 32296163 DOI: 10.1038/s41436-020-0782-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 11/08/2022] Open
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Matsubara K, Yanagida K, Nagai T, Kagami M, Fukami M. De Novo Small Supernumerary Marker Chromosomes Arising From Partial Trisomy Rescue. Front Genet 2020; 11:132. [PMID: 32174976 PMCID: PMC7056893 DOI: 10.3389/fgene.2020.00132] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/03/2020] [Indexed: 11/24/2022] Open
Abstract
Small supernumerary marker chromosomes (SMCs) are rare cytogenetic abnormalities. De novo small SMCs, particularly those combined with uniparental disomy (UPD), are assumed to result from incomplete trisomy rescue. Recently, a one-off cellular event designated as chromothripsis was reported as a mechanism for trisomy rescue in micronuclei. This Perspective article aims to highlight a possible association among trisomy rescue, chromothripsis, and SMCs. We propose that chromothripsis-mediated incomplete trisomy rescue in micronuclei underlies various chromosomal rearrangements including SMCs, although other mechanisms such as U-type exchange may also yield SMCs. These assumptions are primarily based on observations of previously reported patients with complex rearrangements and our patient with a small SMC. Given the high frequency of trisomic cells in human preimplantation embryos, chromothripsis-mediated trisomy rescue may be a physiologically important phenomenon. Nevertheless, trisomy rescue has a potential to produce UPD, SMCs, and other chromosomal rearrangements. The concepts of trisomy rescue, chromothripsis, and micronuclei provide novel insights into the mechanism for the maintenance and modification of human chromosomes.
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Affiliation(s)
- Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | | | | | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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Lysinuric protein intolerance with homozygous SLC7A7 mutation caused by maternal uniparental isodisomy of chromosome 14. J Hum Genet 2019; 64:1137-1140. [PMID: 31427715 DOI: 10.1038/s10038-019-0657-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/19/2019] [Accepted: 08/02/2019] [Indexed: 11/08/2022]
Abstract
Lysinuric protein intolerance (LPI) is caused by mutations in the SLC7A7 gene at 14q11.2. Its clinical presentation includes failure to thrive, protein intolerance due to a secondary urea cycle defect, interstitial lung disease, renal tubulopathy, and immune disorders. Maternal uniparental disomy 14 (UPD14mat) is the most common cause of Temple syndrome (TS14), which is characterized by severe intrauterine and postnatal growth failure. Here, we describe a severe form of LPI accompanied by TS14 in an 11-month-old girl, which presented as profound failure to thrive and delayed development. LPI was diagnosed by the detection of a homozygous mutation of c.713 C>T (p.Ser238Phe) in SLC7A7, which was eventually found to co-occur with UPD14mat. Despite receiving a protein-restricted diet with citrulline and lysine supplementation, the severe failure to thrive has persisted at follow-up of the patient at 4 years of age.
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The significance of trisomy 7 mosaicism in noninvasive prenatal screening. Hum Genomics 2019; 13:18. [PMID: 30971315 PMCID: PMC6458712 DOI: 10.1186/s40246-019-0201-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/18/2019] [Indexed: 12/18/2022] Open
Abstract
Background This study was an evaluation of the role of noninvasive prenatal testing (NIPT) in the detection of trisomy 7 in prenatal diagnosis. Method A total of 35 consecutive cases underwent screening for trisomies by cell-free DNA testing between April 2015 and November 2017 due to suspicious NIPT results; these cases represented 0.11% of patients (35/31,250) with similar frequencies of abnormal results among the laboratories performing the tests. NIPT was offered to further screen for common fetal chromosomal abnormalities. Karyotype analysis, chromosomal microarray analysis (CMA), and next-generation sequencing (NGS) were used to detect 20, 14, and 25 patients, respectively, who accepted confirmatory diagnostic testing. Results High-risk results by NIPT were recorded for trisomy 7 alone in 29 women: dual aneuploidy in 4 patients and multiple aneuploidy in 2 patients. Karyotype analysis of amniotic fluid cells was normal in all 20 pregnancies, suggesting a probability of confined placental mosaicism. Further CMA data were obtained in 14 of the cases mentioned above, and 2 fetuses were detected with positive results with copy number variation. The NGS results suggested that all these samples were placental chimerisms of chromosome 7, except for one sample that was found to be an additional chimerism of chromosome 2, which was also consistent with the NIPT result. Conclusion Our results may be useful for the counseling of pregnant women in the detection of trisomy 7 by NIPT.
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Molecular investigation of uniparental disomy (UPD) in spontaneous abortions. Eur J Obstet Gynecol Reprod Biol 2019; 236:116-120. [PMID: 30903884 DOI: 10.1016/j.ejogrb.2019.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/01/2019] [Accepted: 03/03/2019] [Indexed: 11/23/2022]
Abstract
OBJECTIVE About 10-15% of all clinically recognized pregnancies end as spontaneous abortions while at least 50% of pregnancies are lost before reaching term gestation. Genetic abnormalities are responsible for ≥50% of all early miscarriages. The aim is to indentify associations between UPD and abortions and regarding UPD as pathogenetic mechanism possibly to understand the role of imprinted genes or recessive mutations in abortions. STUDY DESIGN To determine additional factors causing spontaneous abortions we searched for uniparental disomies (UPD) which is known to be associated with distinct birth defects as per the chromosome involved and parental origin. Studies were carried on DNA of 68 cases of first trimester spontaneous abortions and DNA of their parents. We examined tissue from aborted fetuses, especially in the first trimester, with molecular techniques to detect UPD to chromosomes that contain imprinting genes.The inheritance of each region of the chromosome was determined by comparing the genotypes obtained from abortion and parental DNA. RESULTS Of the 68 cases of spontaneous abortions investigated, 324% were found to be biparental inheritance or were uninformative in locus that they were examined, 4118% were matUPD, 147% trisomy for a chromosome, 8,8% patUPD and 294% matUPD and trisomy for a certain chromosome. Most cases of UPD found on chromosomes 21 and 14. Many of those are found in combination with chromosomes 13, 20 and 22. CONCLUSIONS UPD might be a common finding among spontaneous abortuses. UPD can be a cause of miscarriage if localized to regions of chromosomes with imprinted genes which control embryogenesis and fetal development and or can activate a recessive mutation in genes which are essential for early embryogenesis.
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Cioppi F, Riera-Escamilla A, Manilall A, Guarducci E, Todisco T, Corona G, Colombo F, Bonomi M, Flanagan CA, Krausz C. Genetics of ncHH: from a peculiar inheritance of a novel GNRHR mutation to a comprehensive review of the literature. Andrology 2018; 7:88-101. [PMID: 30575316 DOI: 10.1111/andr.12563] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/21/2018] [Accepted: 10/10/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Normosmic congenital hypogonadotropic hypogonadism (ncHH) is caused by the deficient production, secretion, or action of gonadotropin-releasing hormone (GnRH). Its typical clinical manifestation is delayed puberty and azoospermia. Homozygous and compound heterozygous mutations in the GNRHR gene (4q13.2) are the most frequent genetic causes of ncHH. OBJECTIVES (i) Characterization at the molecular level (genetic origin and functional effect) of a unique homozygous mutation (p.Gly99Glu) in a ncHH man; (ii) to provide a comprehensive catalog of GNRHR mutations with genotype-phenotype correlation and comparison of in vitro studies vs. in silico prediction tools. MATERIAL AND METHODS A ncHH man and his parents, in whom we performed the following: (i) Sanger sequencing, qPCR of the GNRHR gene; (ii) chromosome 4 SNP array; and (iii) competition binding assay and inositol phosphate signaling assay. PubMed and Human Genome Mutation Database (HGMD) search for GNRHR mutations. Bioinformatic analysis of 55 reported variants. RESULTS qPCR showed two GNRHR copies in the index case. SNP array revealed the inheritance of two homologous chromosomes 4 from the mother (maternal heterodisomy; hUPD) with two loss of heterozygosity regions, one of them containing the mutated gene (maternal isodisomy; iUPD). Functional studies for the p.Gly99Glu mutation demonstrated a right-shifted GnRH-stimulated signaling response. Bioinformatic tools show that commonly used in silico tools are poor predictors of the function of ncHH-associated GNRHR variants. DISCUSSION Functional analysis of the p.Gly99Glu mutation is consistent with severely decreased GnRH binding affinity (a severe partial loss-of-function mutation). Complete LOF variants are associated with severe and severe/moderate phenotype, whereas partial LOF variants show wide range of clinical manifestations. CONCLUSION This is the first ncHH patient carrying a novel causative missense mutation of GNRHR with proven 'severe pLOF' due to maternal hUPD/iUPD of chromosome 4. Our literature review shows that functional studies remain essential both for diagnostic and potential therapeutic purposes.
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Affiliation(s)
- F Cioppi
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - A Riera-Escamilla
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Catalonia, Spain
| | - A Manilall
- School of Physiology, University of the Witwatersrand Faculty of Health Sciences, Johannesburg, South Africa
| | - E Guarducci
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - T Todisco
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - G Corona
- Endocrinology Unit, Maggiore-Bellaria Hospital Bologna, Bologna, Italy
| | - F Colombo
- Department of Urology and Gynecology, Bologna University Hospital - Policlinico S.Orsola, Bologna, Italy
| | - M Bonomi
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.,Division of Endocrinology and Metabolism, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - C A Flanagan
- School of Physiology, University of the Witwatersrand Faculty of Health Sciences, Johannesburg, South Africa
| | - C Krausz
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Florence, Florence, Italy
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Niida Y, Ozaki M, Shimizu M, Ueno K, Tanaka T. Classification of Uniparental Isodisomy Patterns That Cause Autosomal Recessive Disorders: Proposed Mechanisms of Different Proportions and Parental Origin in Each Pattern. Cytogenet Genome Res 2018; 154:137-146. [PMID: 29656286 DOI: 10.1159/000488572] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2018] [Indexed: 01/18/2023] Open
Abstract
Patients with autosomal recessive (AR) disorders are usually born to parents both of whom are heterozygous carriers of the disease. However, in some instances only one of the parents is a carrier and a mutation is segregated to the patient through uniparental isodisomy (UPiD). Recently, an increasing number of such case reports has been published, and it has become clear that there are several different UPiD patterns that cause AR disorders. In this article, we report 3 remarkable patients with different patterns of UPiD. We then review 85 cases collected in the literature. We realized that they can be classified into 3 patterns: UPiD of the whole chromosome, segmental UPiD with uniparental heterodisomy (UPhD), and segmental UPiD caused by post-zygotic mitotic recombination (MiRe). Whole chromosomal UPiD accounted for the majority of cases, with paternal origin accounting for approximately twice as many cases as maternal origin. Most cases of segmental UPiD with UPhD were of maternal origin, with a dominancy of nondisjunction in meiosis I, while segmental UPiD through MiRe is the smallest pattern with equal parental origin. These differences in proportion and parental origin in each pattern can be explained by considering nondisjunction during oogenesis as the starting point and UPiD as subsequent events.
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Bruechle NO, Steuernagel P, Zerres K, Kurth I, Eggermann T, Knopp C. Uniparental disomy as an unexpected cause of Meckel-Gruber syndrome: report of a case. Pediatr Nephrol 2017. [PMID: 28620746 DOI: 10.1007/s00467-017-3710-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Meckel-Gruber syndrome (MKS, OMIM #607361) is a rare pre- or perinatal lethal autosomal recessive ciliopathy caused by mutations in at least 12 known genes. It has a clinical and genetic overlap with other viable ciliopathies, especially Joubert syndrome and Joubert syndrome-related disorders. MKS is characterized by multicystic kidney dysplasia, central nervous system malformations (usually occipital encephalocele), ductal plate malformation of the liver, and postaxial polydactyly. CASE DIAGNOSIS We identified a homozygous mutation in TMEM67 (MKS3) in a fetus affected by MKS; however, only the mother was a carrier of the respective mutation. Genotyping with polymorphic microsatellite markers and single nucleotide polymorphism (SNP) array revealed a maternal uniparental disomy (UPD) of the entire chromosome 8 (upd(8)mat), harboring TMEM67. CONCLUSIONS This is the first reported case of UPD as a cause of MKS. The possible underlying mechanisms for uniparental disomy (UPD) are reviewed. Even if rare, awareness of UPD and comprehensive work-up in the case of unexpected homozygosity for a recessive mutation is essential for accurate genetic counseling and assessment of the risk of recurrence.
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Affiliation(s)
- Nadia Ortiz Bruechle
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.,Institute of Pathology, Medical Faculty, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Peter Steuernagel
- Institute of Human Genetics, Hospital Oldenburg, Rahel-Straus-Straße 10, 26133, Oldenburg, Germany
| | - Klaus Zerres
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Cordula Knopp
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
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Griffin NG, Cronin KD, Walley NM, Hulette CM, Grant GA, Mikati MA, LaBreche HG, Rehder CW, Allen AS, Crino PB, Heinzen EL. Somatic uniparental disomy of Chromosome 16p in hemimegalencephaly. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a001735. [PMID: 28864461 PMCID: PMC5593155 DOI: 10.1101/mcs.a001735] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 04/24/2017] [Indexed: 02/05/2023] Open
Abstract
Hemimegalencephaly (HME) is a heterogeneous cortical malformation characterized by enlargement of one cerebral hemisphere. Somatic variants in mammalian target of rapamycin (mTOR) regulatory genes have been implicated in some HME cases; however, ∼70% have no identified genetic etiology. Here, we screened two HME patients to identify disease-causing somatic variants. DNA from leukocytes, buccal swabs, and surgically resected brain tissue from two HME patients were screened for somatic variants using genome-wide genotyping arrays or sequencing of the protein-coding regions of the genome. Functional studies were performed to evaluate the molecular consequences of candidate disease-causing variants. Both HME patients evaluated were found to have likely disease-causing variants in DNA extracted from brain tissue but not in buccal swab or leukocyte DNA, consistent with a somatic mutational mechanism. In the first case, a previously identified disease-causing somatic single nucleotide in MTOR was identified. In the second case, we detected an overrepresentation of the alleles inherited from the mother on Chromosome 16 in brain tissue DNA only, indicative of somatic uniparental disomy (UPD) of the p-arm of Chromosome 16. Using methylation analyses, an imprinted locus on 16p spanning ZNF597 was identified, which results in increased expression of ZNF597 mRNA and protein in the brain tissue of the second case. Enhanced mTOR signaling was observed in tissue specimens from both patients. We speculate that overexpression of maternally expressed ZNF597 led to aberrant hemispheric development in the patient with somatic UPD of Chromosome 16p possibly through modulation of mTOR signaling.
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Affiliation(s)
- Nicole G Griffin
- Institute for Genomic Medicine, Columbia University, New York, New York 10032, USA
| | - Kenneth D Cronin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Nicole M Walley
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Christine M Hulette
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Gerald A Grant
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Mohamad A Mikati
- Division of Pediatric Neurology, Duke University Medical Center, Durham, North Carolina 27710, USA.,Department of Neurobiology, Duke University, Durham, North Carolina 27708, USA
| | | | | | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina 27710, USA
| | - Peter B Crino
- Department of Neurology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, USA
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University, New York, New York 10032, USA.,Department of Pathology and Cell Biology, Columbia University, New York, New York 10032, USA
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26
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Chantot-Bastaraud S, Stratmann S, Brioude F, Begemann M, Elbracht M, Graul-Neumann L, Harbison M, Netchine I, Eggermann T. Formation of upd(7)mat by trisomic rescue: SNP array typing provides new insights in chromosomal nondisjunction. Mol Cytogenet 2017; 10:28. [PMID: 28770003 PMCID: PMC5526280 DOI: 10.1186/s13039-017-0329-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/11/2017] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Maternal uniparental disomy (UPD) of chromosome 7 (upd(7)mat) accounts for approximately 10% of patients with Silver-Russell syndrome (SRS). For upd(7)mat and trisomy 7, a significant number of mechanisms have been proposed to explain the postzygotic formation of these chromosomal compositions, but all have been based on as small number of cases. To obtain the ratio of isodisomy and heterodisomy in UPDs (hUPD, iUPD) and to determine the underlying formation mechanisms, we analysed a large cohort of upd(7)mat patients (n = 73) by SNP array typing. Based on these data, we discuss the UPDs and their underlying trisomy 7 formation mechanisms. RESULTS A whole chromosome 7 maternal iUPD was confirmed in 28.8%, a mixture or complete maternal hUPD in 71.2% of patients. CONCLUSIONS We could demonstrate that nondisjunction mechanism affecting chromosome 7 are similar to that of the chromosomes more frequently involved in trisomy (and/or UPD), and that mechanisms other than trisomic rescue have a lower significance than previously suspected. Furthermore, we suggest SNP array typing for future parent- and cell-stage-of origin studies in human aneuploidies as they allow the definite classification of trisomies and UPDs, and provide information on recombinational events and their suggested association with aneuploidy formation.
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Affiliation(s)
- Sandra Chantot-Bastaraud
- INSERM, UMR_S 938, CDR Saint-Antoine, F-75012 Paris, France
- UMR_S 938, CDR Saint-Antoine, Sorbonne Universities, UPMC Univ Paris, 06 Paris, France
- APHP, Armand Trousseau Hospital, Pediatric Endocrinology, Paris, France
- APHP, Hôpital Armand-Trousseau, Département de Génétique, UF de Génétique Chromosomique, Paris, France
| | - Svea Stratmann
- Institute of Human Genetics, RWTH University Hospital Aachen, Pauwelsstr 30, D-52074 Aachen, Germany
| | - Frédéric Brioude
- INSERM, UMR_S 938, CDR Saint-Antoine, F-75012 Paris, France
- UMR_S 938, CDR Saint-Antoine, Sorbonne Universities, UPMC Univ Paris, 06 Paris, France
- APHP, Armand Trousseau Hospital, Pediatric Endocrinology, Paris, France
| | - Matthias Begemann
- Institute of Human Genetics, RWTH University Hospital Aachen, Pauwelsstr 30, D-52074 Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, RWTH University Hospital Aachen, Pauwelsstr 30, D-52074 Aachen, Germany
| | | | - Madeleine Harbison
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Irène Netchine
- INSERM, UMR_S 938, CDR Saint-Antoine, F-75012 Paris, France
- UMR_S 938, CDR Saint-Antoine, Sorbonne Universities, UPMC Univ Paris, 06 Paris, France
- APHP, Armand Trousseau Hospital, Pediatric Endocrinology, Paris, France
| | - Thomas Eggermann
- Institute of Human Genetics, RWTH University Hospital Aachen, Pauwelsstr 30, D-52074 Aachen, Germany
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Yingjun X, Zhiyang H, Linhua L, Fangming S, Linhuan H, Jinfeng T, Qianying P, Xiaofang S. Chromosomal uniparental disomy 16 and fetal intrauterine growth restriction. Eur J Obstet Gynecol Reprod Biol 2017; 211:1-7. [DOI: 10.1016/j.ejogrb.2016.12.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/18/2016] [Indexed: 11/28/2022]
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28
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Scheuvens R, Begemann M, Soellner L, Meschede D, Raabe-Meyer G, Elbracht M, Schubert R, Eggermann T. Maternal uniparental disomy of chromosome 16 [upd(16)mat]: clinical features are rather caused by (hidden) trisomy 16 mosaicism than by upd(16)mat itself. Clin Genet 2017; 92:45-51. [DOI: 10.1111/cge.12958] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/21/2016] [Accepted: 12/23/2016] [Indexed: 02/04/2023]
Affiliation(s)
- R. Scheuvens
- Institute of Human Genetics; University Hospital, Technical University (RWTH) Aachen; Aachen Germany
| | - M. Begemann
- Institute of Human Genetics; University Hospital, Technical University (RWTH) Aachen; Aachen Germany
| | - L. Soellner
- Institute of Human Genetics; University Hospital, Technical University (RWTH) Aachen; Aachen Germany
| | | | | | - M. Elbracht
- Institute of Human Genetics; University Hospital, Technical University (RWTH) Aachen; Aachen Germany
| | | | - T. Eggermann
- Institute of Human Genetics; University Hospital, Technical University (RWTH) Aachen; Aachen Germany
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29
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Niida Y, Yokoi A, Kuroda M, Mitani Y, Nakagawa H, Ozaki M. Reply to: Uniparental disomy of chromosome 1 unmasks recessive mutations of PPT1 in a boy with neuronal ceroid lipofuscinosis type 1. Brain Dev 2017; 39:184-185. [PMID: 27616753 DOI: 10.1016/j.braindev.2016.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
Affiliation(s)
- Yo Niida
- Center for Medical Genetics, Kanazawa Medical University Hospital, Ishikawa, Japan.
| | - Ayano Yokoi
- Department of Pediatrics, Institute of Medical, Pharmaceutical and Health Sciences, School of Medicine, Kanazawa University, Ishikawa, Japan
| | - Mondo Kuroda
- Department of Pediatrics, Institute of Medical, Pharmaceutical and Health Sciences, School of Medicine, Kanazawa University, Ishikawa, Japan
| | - Yusuke Mitani
- Department of Pediatrics, Institute of Medical, Pharmaceutical and Health Sciences, School of Medicine, Kanazawa University, Ishikawa, Japan
| | - Hiroyasu Nakagawa
- Department of Pediatrics, Institute of Medical, Pharmaceutical and Health Sciences, School of Medicine, Kanazawa University, Ishikawa, Japan
| | - Mamoru Ozaki
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Ishikawa, Japan
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30
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HMSN Lom in 12 Czech patients, with one unusual case due to uniparental isodisomy of chromosome 8. J Hum Genet 2016; 62:431-435. [PMID: 28003645 DOI: 10.1038/jhg.2016.148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 10/21/2016] [Accepted: 11/01/2016] [Indexed: 11/08/2022]
Abstract
Hereditary motor and sensory neuropathy-type Lom (HMSNL), also known as CMT4D, a demyelinating neuropathy with late-onset deafness is an autosomal recessive disorder threatening Roma population worldwide. The clinical phenotype was reported in several case reports before the gene discovery. HMSNL is caused by a homozygous founder mutation p.Arg148* in the N-Myc downstream-regulated gene 1. Here, we report findings from the Czech Republic, where HMSNL was found in 12 Czech patients from eight families. In these 12 patients, 11 of the causes were due to p.Arg148* mutation inherited from both parents by the autosomal recessive mechanism. But in one case, the recessive mutation was inherited only from one parent (father) and unmasked owing to an uniparental isodisomy of the entire chromosome eight. The inherited peripheral neuropathy owing to an isodisomy of the whole chromosome pointed to an interesting, less frequent possibility of recessive disease and complications with genetic counseling.
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31
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Joshi RS, Garg P, Zaitlen N, Lappalainen T, Watson CT, Azam N, Ho D, Li X, Antonarakis SE, Brunner HG, Buiting K, Cheung SW, Coffee B, Eggermann T, Francis D, Geraedts JP, Gimelli G, Jacobson SG, Le Caignec C, de Leeuw N, Liehr T, Mackay DJ, Montgomery SB, Pagnamenta AT, Papenhausen P, Robinson DO, Ruivenkamp C, Schwartz C, Steiner B, Stevenson DA, Surti U, Wassink T, Sharp AJ. DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome. Am J Hum Genet 2016; 99:555-566. [PMID: 27569549 DOI: 10.1016/j.ajhg.2016.06.032] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/30/2016] [Indexed: 02/07/2023] Open
Abstract
Genomic imprinting is a mechanism in which gene expression varies depending on parental origin. Imprinting occurs through differential epigenetic marks on the two parental alleles, with most imprinted loci marked by the presence of differentially methylated regions (DMRs). To identify sites of parental epigenetic bias, here we have profiled DNA methylation patterns in a cohort of 57 individuals with uniparental disomy (UPD) for 19 different chromosomes, defining imprinted DMRs as sites where the maternal and paternal methylation levels diverge significantly from the biparental mean. Using this approach we identified 77 DMRs, including nearly all those described in previous studies, in addition to 34 DMRs not previously reported. These include a DMR at TUBGCP5 within the recurrent 15q11.2 microdeletion region, suggesting potential parent-of-origin effects associated with this genomic disorder. We also observed a modest parental bias in DNA methylation levels at every CpG analyzed across ∼1.9 Mb of the 15q11-q13 Prader-Willi/Angelman syndrome region, demonstrating that the influence of imprinting is not limited to individual regulatory elements such as CpG islands, but can extend across entire chromosomal domains. Using RNA-seq data, we detected signatures consistent with imprinted expression associated with nine novel DMRs. Finally, using a population sample of 4,004 blood methylomes, we define patterns of epigenetic variation at DMRs, identifying rare individuals with global gain or loss of methylation across multiple imprinted loci. Our data provide a detailed map of parental epigenetic bias in the human genome, providing insights into potential parent-of-origin effects.
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Affiliation(s)
- Ricky S Joshi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paras Garg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Noah Zaitlen
- Department of Medicine, UCSF MC2552, 1700 4th Street, Byers Hall Suite 503C, San Francisco, CA 94158, USA
| | - Tuuli Lappalainen
- New York Genome Center, 101 Avenue of the Americas, 7th Floor, New York, NY 10013, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Corey T Watson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nidha Azam
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel Ho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xin Li
- Departments of Pathology, Genetics and Computer Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 9th Floor, 1 rue Michel-Servet, 1211 Geneva, Switzerland
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Karin Buiting
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, Germany
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bradford Coffee
- Emory Genetics Laboratory, Emory University, Atlanta, GA 30033, USA
| | - Thomas Eggermann
- Institute of Human Genetics, University Hospital, RWTH, 52074 Aachen, Germany
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Joep P Geraedts
- Department of Genetics and Cell Biology, Research Institute GROW, Faculty of Health, Medicine and Life Sciences, Maastricht University, PO Box 5800, Maastricht AZ 6202, the Netherlands
| | - Giorgio Gimelli
- Laboratorio di Citogenetica, Istituto G. Gaslini, 16148 Genova, Italy
| | - Samuel G Jacobson
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA 19104, USA
| | - Cedric Le Caignec
- CHU Nantes, Service de Génétique Médicale, Institut de Biologie, 9 quai Moncousu, 44093 Nantes, France; INSERM, UMR 957, Nantes 44035, France; Université de Nantes, Nantes atlantique universités, Pathophysiology of Bone Resorption and Therapy of Primary Bone Tumours, Nantes 44035, France
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Deborah J Mackay
- Wessex Regional Genetics Laboratory Salisbury District Hospital, Salisbury, Wiltshire SO2 8BJ, UK
| | - Stephen B Montgomery
- Departments of Pathology, Genetics and Computer Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alistair T Pagnamenta
- National Institute for Health Research Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Peter Papenhausen
- Division of Cytogenetics, LabCorp, Center for Molecular Biology and Pathology, Research Triangle Park, NC 27709, USA
| | - David O Robinson
- Wessex Regional Genetics Laboratory Salisbury District Hospital, Salisbury, Wiltshire SO2 8BJ, UK
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Charles Schwartz
- J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Bernhard Steiner
- Institute of Medical Genetics, University of Zurich, 8603 Schwerzenbach, Switzerland
| | - David A Stevenson
- Division of Medical Genetics, Lucile Salter Packard Children's Hospital, 300 Pasteur Drive, Boswell Building A097, Stanford, CA 94304, USA
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Thomas Wassink
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Li N, Ding YU, Yu T, Li J, Shen Y, Wang X, Fu Q, Shen Y, Huang X, Wang J. Causal variants screened by whole exome sequencing in a patient with maternal uniparental isodisomy of chromosome 10 and a complicated phenotype. Exp Ther Med 2016; 11:2247-2253. [PMID: 27284308 PMCID: PMC4887894 DOI: 10.3892/etm.2016.3241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 02/11/2016] [Indexed: 11/18/2022] Open
Abstract
Uniparental disomy (UPD), which is the abnormal situation in which both copies of a chromosomal pair have been inherited from one parent, may cause clinical abnormalities by affecting genomic imprinting or causing autosomal recessive variation. Whole Exome Sequencing (WES) and chromosomal microarray analysis (CMA) are powerful technologies used to search for underlying causal variants. In the present study, WES was used to screen for candidate causal variants in the genome of a Chinese pediatric patient, who had been shown by CMA to have maternal uniparental isodisomy of chromosome 10. This was associated with numerous severe medical problems, including bilateral deafness, binocular blindness, stunted growth and leukoderma. A total of 13 rare homozygous variants of these genes were identified on chromosome 10. These included a classical splice variant in the HPS1 gene (c.398+5G>A), which causes Hermansky-Pudlak syndrome type 1 and may explain the patient's ocular and dermal disorders. In addition, six likely pathogenic genes on other chromosomes were found to be associated with the subject's ocular and aural disorders by phenotypic analysis. The results of the present study demonstrated that WES and CMA may be successfully combined in order to identify candidate causal genes. Furthermore, a connection between phenotype and genotype was established in this patient.
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Affiliation(s)
- Niu Li
- Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Y U Ding
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Tingting Yu
- Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Juan Li
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Yongnian Shen
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Xiumin Wang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Qihua Fu
- Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China; Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Yiping Shen
- Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China; Boston Children's Hospital, Boston, MA 02115, USA
| | - Xiaodong Huang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Jian Wang
- Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China; Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
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Sachwitz J, Strobl-Wildemann G, Fekete G, Ambrozaitytė L, Kučinskas V, Soellner L, Begemann M, Eggermann T. Examinations of maternal uniparental disomy and epimutations for chromosomes 6, 14, 16 and 20 in Silver-Russell syndrome-like phenotypes. BMC MEDICAL GENETICS 2016; 17:20. [PMID: 26969265 PMCID: PMC4787016 DOI: 10.1186/s12881-016-0280-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/26/2016] [Indexed: 12/19/2022]
Abstract
Background Silver-Russell syndrome (SRS) is a growth retardation disorder with a very broad molecular and clinical spectrum. Whereas the association of SRS with imprinting disturbances of chromosomes 11p15.5 and 7 is generally accepted, there are controversial discussions on the involvement of other molecular changes. The recent reports on the occurrence of maternal uniparental disomies of chromosomes 6, 16 and 20 (upd(6, 16, 20)mat), as well as 14q32 imprint alterations in patients with SRS phenotypes raise the question on the involvement of these mutations in the etiology of SRS. Methods A cohort of 54 growth retarded patients with SRS features was screened for aberrant methylation patterns of chromsomes 6, 14, 16 and 20. Results One carrier of a 14q32 epimutation was identified whereas epimutations and maternal UPD for chromosomes 6, 16 and 20 were excluded. Conclusions Our data and those from the literature confirm that 14q32 disturbances significantly contribute to the mutation spectrum in this cohort. Furthermore, maternal uniparental disomy of chromosomes 6, 16 and 20 can be observed, but are rare. In case they occur they can be regarded as causative for clinical features.
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Affiliation(s)
- Jana Sachwitz
- Institute of Human Genetics, RWTH Aachen, Pauwelsstr. 30, Aachen, Germany
| | | | - György Fekete
- II. Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Laima Ambrozaitytė
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Lukas Soellner
- Institute of Human Genetics, RWTH Aachen, Pauwelsstr. 30, Aachen, Germany
| | - Matthias Begemann
- Institute of Human Genetics, RWTH Aachen, Pauwelsstr. 30, Aachen, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, RWTH Aachen, Pauwelsstr. 30, Aachen, Germany.
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Lee M, Xu G, Wang K, Wang H, Zhang J, Tang Z, Lin Z, Yang Y. Recessive dystrophic epidermolysis bullosa caused by a de novo interstitial deletion spanning COL7A1 and a hemizygous splicing mutation in trans. Clin Exp Dermatol 2016; 41:372-8. [PMID: 26940370 DOI: 10.1111/ced.12809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2015] [Indexed: 12/18/2022]
Abstract
BACKGROUND Recessive dystrophic epidermolysis bullosa (RDEB) is a rare heritable blistering skin condition caused by loss-of-function mutations in the COL7A1 gene. Incongruent gene transmission is occasionally reported in recessive diseases, and its underlying mechanism is often uniparental disomy (UPD). AIM To understand the genetic basis of incongruent gene transmission in a Chinese family with RDEB, in which a discrepancy of COL7A1 genotyping was encountered during our mutation analysis. METHODS We used a pCAS2 minigene-based in vitro splicing assay to confirm the pathogenicity of the splicing variant we identified in the proband. Next, a combination of genetic tools, including whole-genome SNP array analysis and multiplex ligation-dependent probe amplification copy number analysis, was used to unravel the cause of the discrepancy in the COL7A1 genotyping. RESULTS Sanger sequencing identified a novel, single-peak mutation, c.4980+5G>C, in COL7A1 in the proband, which was heterozygous in his father and wild type in his mother. In vitro splicing assay showed that c.4980+5G>C was pathogenic and led to skipping of COL7A1 exon 53. SNP array analysis and multiplex ligation-dependent probe amplification of the proband's DNA revealed a maternally derived, de novo, interstitial deletion on chromosome 3p21.31, which removed COL7A1 and 15 flanking genes, excluding the possibility of UPD. CONCLUSION Our findings favour an exceptionally rare event, namely a de novo COL7A1 microdeletion in concurrence with an inherited mutation in trans. This study should aid molecular diagnosis and genetic counselling of RDEB and possibly other recessive diseases in which genotyping discrepancy is encountered.
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Affiliation(s)
- M Lee
- Department of Dermatology, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - G Xu
- Department of Dermatology, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China.,Department of Dermatology, The Affiliated Hospital of Qingdao University, Qingdao Shandong, China
| | - K Wang
- Department of Dermatology, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - H Wang
- Department of Dermatology, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - J Zhang
- Department of Dermatology, Qilu Hospital of Shandong University (Qingdao), Qingdao, China
| | - Z Tang
- Department of Dermatology, Qilu Hospital of Shandong University, Jinan, China
| | - Z Lin
- Department of Dermatology, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - Y Yang
- Department of Dermatology, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Beijing, China
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Furutani K, Kodera Y, Hiruma M, Ishii H, Baba H. Difficult tracheal intubation in a patient with maternal uniparental disomy 14. JA Clin Rep 2016; 2:25. [PMID: 29497680 PMCID: PMC5818854 DOI: 10.1186/s40981-016-0051-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 09/16/2016] [Indexed: 12/03/2022] Open
Abstract
Background Maternal uniparental disomy 14 (UPD(14)mat) is an imprinting disorder. It is a rare disease, but there is the possibility that more undiagnosed patients might exist because the clinical features of UPD(14)mat resemble those of the Prader-Willi syndrome or other congenital diseases. We performed anesthetic management for an 8-year-old girl with UPD(14)mat. Case presentations She was admitted to undergo correction surgery due to symptomatic scoliosis. Preoperative examination revealed that she had a restricted mouth opening and retrognathia, as well as some typical characteristics of UPD(14)mat, such as small hands, growth retardation, and precocious puberty. We induced general anesthesia using sevoflurane without any problems. However, the tracheal intubation was difficult because of the restricted mouth opening. We used the McGRATHR MAC videolaryngoscope to overcome this problem. Conclusions We speculate that the craniofacial deformity in case of UPD(14)mat patients may lead to difficulty in tracheal intubation.
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Affiliation(s)
- Kenta Furutani
- Division of Anesthesiology, Niigata University Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-ku, Niigata 951-8510 Japan
| | - Yoshie Kodera
- Division of Anesthesiology, Niigata University Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-ku, Niigata 951-8510 Japan
| | - Masataka Hiruma
- Division of Anesthesiology, Niigata University Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-ku, Niigata 951-8510 Japan
| | - Hideaki Ishii
- Division of Anesthesiology, Niigata University Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-ku, Niigata 951-8510 Japan
| | - Hiroshi Baba
- Division of Anesthesiology, Niigata University Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-ku, Niigata 951-8510 Japan
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Chen CP, Chern SR, Chen YN, Wu PS, Yang CW, Chen LF, Wang W. Mosaic trisomy 15 at amniocentesis: Prenatal diagnosis, molecular genetic analysis and literature review. Taiwan J Obstet Gynecol 2015; 54:426-31. [DOI: 10.1016/j.tjog.2015.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2015] [Indexed: 10/23/2022] Open
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Wallerstein R, Misra S, Dugar RB, Alem M, Mazzoni R, Garabedian MJ. Current knowledge of prenatal diagnosis of mosaic autosomal trisomy in amniocytes: karyotype/phenotype correlations. Prenat Diagn 2015; 35:841-7. [DOI: 10.1002/pd.4620] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 05/01/2015] [Accepted: 05/07/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Robert Wallerstein
- Departments of Pediatrics; Santa Clara Valley Medical Center; San Jose CA USA
| | - Sonya Misra
- Departments of Pediatrics; Santa Clara Valley Medical Center; San Jose CA USA
| | - R. Bryce Dugar
- Departments of Pediatrics; Santa Clara Valley Medical Center; San Jose CA USA
| | - Monika Alem
- Obstetrics and Gynecology; Santa Clara Valley Medical Center; San Jose CA USA
| | - Ronit Mazzoni
- Obstetrics and Gynecology; Santa Clara Valley Medical Center; San Jose CA USA
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Palumbo P, Palumbo O, Leone MP, Stallone R, Palladino T, Zelante L, Carella M. Maternal uniparental isodisomy (iUPD) of chromosome 4 in a subject with mild intellectual disability and speech delay. Am J Med Genet A 2015; 167A:2219-22. [DOI: 10.1002/ajmg.a.37142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 04/19/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Pietro Palumbo
- Medical Genetics Unit; IRCCS Casa Sollievo della Sofferenza; San Giovanni Rotondo (FG) Italy
| | - Orazio Palumbo
- Medical Genetics Unit; IRCCS Casa Sollievo della Sofferenza; San Giovanni Rotondo (FG) Italy
| | - Maria Pia Leone
- Medical Genetics Unit; IRCCS Casa Sollievo della Sofferenza; San Giovanni Rotondo (FG) Italy
| | - Raffaella Stallone
- Medical Genetics Unit; IRCCS Casa Sollievo della Sofferenza; San Giovanni Rotondo (FG) Italy
| | - Teresa Palladino
- Medical Genetics Unit; IRCCS Casa Sollievo della Sofferenza; San Giovanni Rotondo (FG) Italy
| | - Leopoldo Zelante
- Medical Genetics Unit; IRCCS Casa Sollievo della Sofferenza; San Giovanni Rotondo (FG) Italy
| | - Massimo Carella
- Medical Genetics Unit; IRCCS Casa Sollievo della Sofferenza; San Giovanni Rotondo (FG) Italy
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Azzi S, Salem J, Thibaud N, Chantot-Bastaraud S, Lieber E, Netchine I, Harbison MD. A prospective study validating a clinical scoring system and demonstrating phenotypical-genotypical correlations in Silver-Russell syndrome. J Med Genet 2015; 52:446-53. [PMID: 25951829 PMCID: PMC4501172 DOI: 10.1136/jmedgenet-2014-102979] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/10/2015] [Indexed: 12/28/2022]
Abstract
Background Multiple clinical scoring systems have been proposed for Silver-Russell syndrome (SRS). Here we aimed to test a clinical scoring system for SRS and to analyse the correlation between (epi)genotype and phenotype. Subjects and methods Sixty-nine patients were examined by two physicians. Clinical scores were generated for all patients, with a new, six-item scoring system: (1) small for gestational age, birth length and/or weight ≤−2SDS, (2) postnatal growth retardation (height ≤−2SDS), (3) relative macrocephaly at birth, (4) body asymmetry, (5) feeding difficulties and/or body mass index (BMI) ≤−2SDS in toddlers; (6) protruding forehead at the age of 1–3 years. Subjects were considered to have likely SRS if they met at least four of these six criteria. Molecular investigations were performed blind to the clinical data. Results The 69 patients were classified into two groups (Likely-SRS (n=60), Unlikely-SRS (n=9)). Forty-six Likely-SRS patients (76.7%) displayed either 11p15 ICR1 hypomethylation (n=35; 58.3%) or maternal UPD of chromosome 7 (mUPD7) (n=11; 18.3%). Eight Unlikely-SRS patients had neither ICR1 hypomethylation nor mUPD7, whereas one patient had mUPD7. The clinical score and molecular results yielded four groups that differed significantly overall and for individual scoring system factors. Further molecular screening led identifying chromosomal abnormalities in Likely-SRS-double-negative and Unlikely-SRS groups. Four Likely-SRS-double negative patients carried a DLK1/GTL2 IG-DMR hypomethylation, a mUPD16; a mUPD20 and a de novo 1q21 microdeletion. Conclusions This new scoring system is very sensitive (98%) for the detection of patients with SRS with demonstrated molecular abnormalities. Given its clinical and molecular heterogeneity, SRS could be considered as a spectrum.
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Affiliation(s)
- Salah Azzi
- INSERM, UMR_S 938, CDR Saint-Antoine, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris, France Department of Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Jennifer Salem
- MAGIC Foundation, RSS/SGA Research & Education Fund, Oak Park, Illinois, USA
| | - Nathalie Thibaud
- INSERM, UMR_S 938, CDR Saint-Antoine, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris, France Department of Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France
| | | | - Eli Lieber
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, University of California, Los Angeles, California, USA
| | - Irène Netchine
- INSERM, UMR_S 938, CDR Saint-Antoine, Paris, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, Paris, France Department of Pediatric Endocrinology, APHP, Armand Trousseau Hospital, Paris, France
| | - Madeleine D Harbison
- Department of Pediatrics, Ichan School of Medicine at Mount Sinai, New York, New York, USA
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Eggermann T, Soellner L, Buiting K, Kotzot D. Mosaicism and uniparental disomy in prenatal diagnosis. Trends Mol Med 2015; 21:77-87. [DOI: 10.1016/j.molmed.2014.11.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/18/2014] [Accepted: 11/26/2014] [Indexed: 01/21/2023]
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Eggermann T, Kotzot D. Uniparentale Disomien und Mosaike. MED GENET-BERLIN 2014. [DOI: 10.1007/s11825-014-0004-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Zusammenfassung
Für die Entstehung von uniparentalen Disomien (UPD) sind verschiedene Mechanismen bekannt, von denen insbesondere der häufigste, der „trisomy rescue“, mit Mosaiken aus einer trisomen Zelllinie und einer disomen 46,XN-Zelllinie mit UPD einhergehen kann. Daher wird diskutiert, ob ein Großteil der UPD schwache oder nichterkannte Mosaike sein könnten. Inwieweit eine trisome Zelllinie den Phänotyp beeinflusst, hängt wahrscheinlich vom Chromosom und v. a. vom prozentualen Anteil im jeweiligen Gewebe ab. Möglicherweise haben die trisomen Zellen mancher UPD-Mosaike sogar einen Selektionsnachteil, sodass sie zumindest postnatal in der Routineanalytik aus Lymphozyten nicht darstellbar sind. Bei Beteiligung eines Chromosoms, für das „Imprinting“-Phänomene bekannt sind, muss die entsprechende Erkrankung berücksichtigt werden. Während die postnatale molekulare Abklärung einer UPD bei Vorliegen einer entsprechenden klinischen Symptomatik und/oder chromosomaler bzw. molekularer Vorbefunde indiziert ist, sind im Rahmen der pränatalen Testung auf UPD und Imprinting-Erkrankungen die Konsequenzen eines positiven Befunds vor der Diagnostik im Rahmen einer genetischen Beratung mit den Eltern zu diskutieren. Die Bedeutung von Mosaiken für die UPD-Diagnostik muss vor dem Hintergrund des beteiligten Chromosoms bzw. der assoziierten Erkrankung, des zugrunde liegenden Entstehungsmechanismus und der verwendeten Methode bewertet werden.
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Affiliation(s)
- Thomas Eggermann
- Aff1 grid.412301.5 0000000086531507 Institut für Humangenetik Universitätsklinikum der RWTH Aachen Pauwelsstr. 30 52074 Aachen Deutschland
| | - Dieter Kotzot
- Aff2 grid.5361.1 0000000088532677 Sektion Humangenetik, Department für Medizinische Genetik, Molekulare und Klinische Pharmakologie Medizinische Universität Innsbruck Innsbruck Österreich
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Genomic imbalance in products of conception: single-nucleotide polymorphism chromosomal microarray analysis. Obstet Gynecol 2014; 124:202-209. [PMID: 25004334 DOI: 10.1097/aog.0000000000000325] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To report the full cohort of identifiable anomalies, regardless of known clinical significance, in a large-scale cohort of postmiscarriage products-of-conception samples analyzed using a high-resolution single-nucleotide polymorphism (SNP)-based microarray platform. High-resolution chromosomal microarray analysis allows for the identification of visible and submicroscopic cytogenomic imbalances; the specific use of SNPs permits detection of maternal cell contamination, triploidy, and uniparental disomy. METHODS Miscarriage specimens were sent to a single laboratory for cytogenomic analysis. Chromosomal microarray analysis was performed using a SNP-based genotyping microarray platform. Results were evaluated at the cytogenetic and microscopic (greater than 10 Mb) and submicroscopic (less than 10 Mb) levels. Maternal cell contamination was assessed using information derived from fetal and maternal SNPs. RESULTS Results were obtained on 2,389 of 2,392 specimens (99.9%) that were less than 20 weeks of gestation. Maternal cell contamination was identified in 528 (22.0%) specimens. The remaining 1,861 specimens were considered to be of true fetal origin. Of these, 1,106 (59.4%) showed classical cytogenetic abnormalities: aneuploidy accounted for 945 (85.4%), triploidy for 114 (10.3%), and structural anomalies or tetraploidy for the remaining 47 (4.2%). Of the 755 (40.6%) cases considered normal at the cytogenetic level, SNP chromosomal microarray analysis revealed a clinically significant copy number change or whole-genome uniparental disomy in 12 (1.6%) and three (0.4%) cases, respectively. CONCLUSION Chromosomal microarray analysis of products-of-conception specimens yields a high diagnostic return. Using SNPs extends the scope of detectable genomic abnormalities and facilitates reporting "true" fetal results. This supports the use of SNP chromosomal microarray analysis for cytogenomic evaluation of miscarriage specimens when clinically indicated. LEVEL OF EVIDENCE III.
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Laverdure N, Dabadie A, Alex-Cordier MP, Odent S, Lachaux A. Maternal uniparental disomy 14 revealed by alpha 1 antitrypsin deficiency. Clin Res Hepatol Gastroenterol 2014; 38:604-6. [PMID: 24636467 DOI: 10.1016/j.clinre.2014.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 01/02/2014] [Accepted: 01/19/2014] [Indexed: 02/04/2023]
Abstract
UNLABELLED Alpha 1 antitrypsin deficiency (AATD) is an autosomal co-dominant disease linked to a mutation of the SERPINA1 gene localized to chromosome 14q32. Uniparental disomy (UPD) is known to be a genetic mechanism that causes various syndromes. Maternal UPD14 presents with a Prader-Willi syndrome-like phenotype. No publications to date have dealt with the association of these two syndromes. In this article, we report on two cases of AATD (from different families), which lead to the diagnosis of maternal UPD14. AATD was diagnosed early in both children. Their clinical presentations were typical (chronic cytolysis in patient 1 and neonatal cholestasis in patient 2); serum alpha 1 antitrypsin levels were low (P1 0.33g/L and P2 0.35g/L), and both patients had a Z phenotype. A pedigree study of both families showed that the father had an M phenotype and the mother an MZ phenotype, which was unexpected. On the other hand, both children were born before term and presented with symmetrical growth retardation, early eating difficulties, moderate hypotonia, understated dysmorphic features and moderate psychomotor retardation, suggestive of a Prader-Willi syndrome-like phenotype. Genotyping was performed to explain gene transmission inconsistencies, and highlighted maternal UPD 14 in both families. CONCLUSION Logically, maternal UPD 14 can induce AATD. In light of these observations, it seems appropriate to search for AATD in patients with maternal UPD 14 in order to prevent a progression of the disease. These cases also underline the significance of maternal UPD 14, which should be suspected in AATD in view of the discordance with Mendel's allelic transmission law.
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Affiliation(s)
- Noémie Laverdure
- Service de gastroentérologie, hépatologie et nutrition pédiatrique, hôpital Femme-Mère-Enfant, hospices civils de Lyon, université Lyon 1, CHU de Lyon, 59, boulevard Pinel, 69500 Bron, France.
| | - Alain Dabadie
- Service de pédiatrie, hôpital Sud, université Rennes 1, CHU de Rennes, 16, boulevard de Bulgarie, BP 90347, 35203 Rennes cedex, France
| | - Marie Pierre Alex-Cordier
- Service de génétique clinique, hôpital Femme-Mère-Enfant, hospices civils de Lyon, université Lyon 1, CHU de Lyon, 59, boulevard Pinel, 69500 Bron, France
| | - Sylvie Odent
- Service de génétique clinique, hôpital Sud, université Rennes 1, CHU de Rennes, 16, boulevard de Bulgarie, BP 90347, 35203 Rennes cedex, France
| | - Alain Lachaux
- Service de gastroentérologie, hépatologie et nutrition pédiatrique, hôpital Femme-Mère-Enfant, hospices civils de Lyon, université Lyon 1, CHU de Lyon, 59, boulevard Pinel, 69500 Bron, France
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Bug S, Solfrank B, Schmitz F, Pricelius J, Stecher M, Craig A, Botcherby M, Nevinny-Stickel-Hinzpeter C. Diagnostic utility of novel combined arrays for genome-wide simultaneous detection of aneuploidy and uniparental isodisomy in losses of pregnancy. Mol Cytogenet 2014; 7:43. [PMID: 25013457 PMCID: PMC4090657 DOI: 10.1186/1755-8166-7-43] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 05/27/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND This proof-of-principle study demonstrates the usefulness and robustness of a novel array based method for the elucidation of genetic causes underlying early pregnancy loss. A combined microarray utilizing comparative genomic hybridization and single nucleotide polymorphism detection (CGH + SNP) was used for parallel genome-wide identification of copy number and heterozygosity status of 70 products of conception. Results of samples with previously determined aneuploidies were juxtaposed to those of a second cohort appearing normal after routine genetic diagnostics. RESULTS All chromosomal imbalances were confirmed, in one sample of the aneuploid panel additional monosomy X was discovered. Genome-wide uniparental disomy causing a complete hydatidiform mole was identified in another sample. No specimen featured microaberrations of obvious clinical relevance. Among cases with presumable euploidy, one microdeletion and a single region of homozygosity were assigned unclear clinical significance. CONCLUSIONS The results prove the utility of combined imbalance and homozygosity mapping for routine workup of these challenging specimens. Moreover parallel screening at submicroscopic resolution facilitates the detection of novel genetic alterations underlying spontaneous abortion.
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Affiliation(s)
- Stefanie Bug
- synlab Medizinisches Versorgungszentrum Humane Genetik München, Lindwurmstraße 23, D-80337 Munich, Germany
| | - Beate Solfrank
- synlab Medizinisches Versorgungszentrum Humane Genetik München, Lindwurmstraße 23, D-80337 Munich, Germany
| | - Felizitas Schmitz
- synlab Medizinisches Versorgungszentrum Humane Genetik München, Lindwurmstraße 23, D-80337 Munich, Germany
| | - Jana Pricelius
- synlab Medizinisches Versorgungszentrum Humane Genetik München, Lindwurmstraße 23, D-80337 Munich, Germany
| | - Mona Stecher
- synlab Medizinisches Versorgungszentrum Humane Genetik München, Lindwurmstraße 23, D-80337 Munich, Germany
| | - Andrew Craig
- BlueGnome Ltd, An Illumina Company, Cambridge, UK
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Intrauterine growth retardation fetus with trisomy 16 mosaicism. Case Rep Genet 2014; 2014:739513. [PMID: 24955263 PMCID: PMC4052622 DOI: 10.1155/2014/739513] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 05/05/2014] [Accepted: 05/06/2014] [Indexed: 11/21/2022] Open
Abstract
Fetal trisomy 16 is considered uniformly lethal early in gestation. It has been reported to be associated with the variability of clinical features
and outcomes. Mosaic trisomy 16 leads to a high risk of abnormality in prenatal cases. Intrauterine growth retardation (IUGR) is a common outcome of mosaic trisomy 16. Herein, we report on the case of Thai male IUGR fetus with trisomy 16 mosaicism. The fetal body was too small. Postmortem investigation of placenta revealed the abnormality including small placenta with furcated cord insertion and single umbilical cord artery. Cytogenetic study demonstrated trisomy 16 that was found 100% in placenta and only 16% in the fetal heart while other organs had normal karyotype. In addition, cardiac and other internal organs examination revealed normal morphology.
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Abstract
Robertsonian translocations (ROBs) are whole arm rearrangements involving the acrocentric chromosomes 13-15 and 21-22 and carriers are at increased risk for aneuploidy and thus uniparental disomy (UPD). Chromosomes 14 and 15 are imprinted with expression of genes dependent on the parental origin of the chromosome. Correction of a trisomic or monosomic conceptus for chromosomes 14 or 15 would lead to one of the established UPD 14mat/pat or UPD 15 (Prader-Willi/Angelman) syndromes (PWS/AS). In view of this, prenatal UPD testing should be considered for balanced carriers of a ROB, fetuses with a familial or de novo balanced ROB that contains chromosome 14 or 15 or with a normal karyotype when a parent is a carrier of a balanced ROB with a 14 or 15. Individuals with congenital anomalies and an abnormal phenotype and carry a ROB involving the two imprinted chromosomes should also be UPD tested.
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Affiliation(s)
- Moh-Ying Yip
- SEALS Genetics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Randwick (Sydney), NSW 2031, Australia
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Complete Maternal Isodisomy of Chromosome 5 in a Japanese Patient with Netherton Syndrome. J Invest Dermatol 2014; 134:849-852. [DOI: 10.1038/jid.2013.398] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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García MM, Velez C, Fenollar-Cortés M, Bustamante A, Lorda-Sanchez I, Soriano-Guillén L, Trujillo-Tiebas MJ. Paternal isodisomy of chromosome 5 in a patient with recessive multiple epiphyseal dysplasia. Am J Med Genet A 2014; 164A:1075-8. [PMID: 24458706 DOI: 10.1002/ajmg.a.36378] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/06/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Mónica Martínez García
- Servicio de Genética del Hospital Fundación Jiménez Díaz de Madrid, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
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Bhatt AD, Liehr T, Bakshi SR. Phenotypic spectrum in uniparental disomy: Low incidence or lack of study? INDIAN JOURNAL OF HUMAN GENETICS 2013; 19:311-4. [PMID: 24339543 PMCID: PMC3841555 DOI: 10.4103/0971-6866.120819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
CONTEXT Alterations in the human chromosomal complement are expressed phenotypically ranging from (i) normal, via (ii) frequent fetal loss in otherwise normal person, to (iii) sub-clinical to severe mental retardation and dysmorphism in live births. A subtle and microscopically undetectable chromosomal alteration is uniparental disomy (UPD), which is known to be associated with distinct birth defects as per the chromosome involved and parental origin. UPD can be evident due to imprinted genes and/or activation of recessive mutations. AIMS The present study comprises of data mining of published UPD cases with a focus on associated phenotypes. The goal was to identify non-random and recurrent associations between UPD and various genetic conditions, which can possibly indicate the presence of new imprinted genes. SETTINGS AND DESIGN Data mining was carried out using the homepage "http://www.fish.uniklinikum-jena.de/UPD.html.", an online catalog of published cases with UPD. MATERIALS AND METHODS The UPD cases having normal karyotype and with or without clinical findings were selected to analyze the associated phenotypes for each chromosome, maternal or paternal involved in UPD. RESULTS Our results revealed many genetic conditions (other than the known UPD syndromes) to be associated with UPD. Even in cases of bad obstetric history as well as normal individuals chance detection of UPD has been reported. CONCLUSIONS The role of UPD in human genetic disorders needs to be studied by involving larger cohorts of individuals with birth defects as well as normal population. The genetic conditions were scrutinized in terms of inheritance patterns; majority of these were autosomal recessive indicating the role of UPD as an underlying mechanism.
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Affiliation(s)
- Arpan D Bhatt
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
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Uniparental disomy analysis in trios using genome-wide SNP array and whole-genome sequencing data imply segmental uniparental isodisomy in general populations. Gene 2013; 512:267-74. [PMID: 23111162 DOI: 10.1016/j.gene.2012.10.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Revised: 10/04/2012] [Accepted: 10/19/2012] [Indexed: 11/24/2022]
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