OBJECTIVE: To report on the phenotype of an adult patient with 2p23.2p22.1 duplication and explore its genotype-phenotype correlation. METHODS: A pregnant woman who had presented at the Affiliated Drum Tower Hospital of Nanjing University Medical School on January 12, 2024 for a high risk signaled by NIPT was selected as the study subject. Amniotic fluid and peripheral blood samples were collected and subjected to chromosomal microarray analysis (CMA). The phenotype of the patient was observed, the medical history was taken, combined with the result of CMA assay, relevant database was searched for similar cases reported in the literature, and the correlation between genotype and phenotype was analyzed. RESULTS: The CMA result of the patient was arr[GRCh38]2p23.2p22.1(27961669_39280633)×3, which indicated a 11.31 Mb duplication. The woman was found to have short stature, learning disability, visual deficit, sleep disorder and other disorders. CONCLUSION The duplication of PPP1CB and SOS1 genes within the 2p23.2p22.1 region can result in Noonan syndrome-like clinical manifestations such as short stature and reduced visual acuity. The duplication of the PPP1CB gene may be associated with the abnormal visual phenotype.
Humans ; Female ; Chromosomes, Human, Pair 2/genetics* ; Adult ; Pregnancy ; Chromosome Duplication ; Phenotype

OBJECTIVE: To carry out genetic analysis for a fetus with confined placental mosaicism (CPM) for trisomy 2 (T2) in conjunct with fetal uniparental disomy (UPD). METHODS: Amniocentesis and chromosomal karyotyping was carried out for a pregnant woman with a high risk for chromosome 2 anomalies indicated by non-invasive prenatal testing (NIPT). Single nucleotide polymorphism array (SNP-array) and trio-whole exome sequencing (Trio-WES) were carried out. Ultrasonography was used to closely monitor the fetal growth. Multifocal sampling of the placenta was performed after delivery for copy number variation sequencing (CNV-seq). RESULTS: The fetus was found to have a normal chromosomal karyotype. SNP-array has revealed multiple regions with loss of heterozygosity (LOH) on chromosome 2. Trio-WES confirmed the presence of maternal UPD for chromosome 2. Ultrasonography has revealed intrauterine growth restriction and oligohydramnios. Intrauterine fetal demise had occurred at 23⁺⁴ weeks of gestation. Pathological examination had failed to find salient visceral abnormality. The placenta was proved to contain complete T2 by CNV-seq. CONCLUSION T2 CPM can cause false positive result for NIPT and may be complicated with fetal UPD, leading to adverse obstetric outcomes such as intrauterine growth restriction, oligohydramnios and intrauterine fetal demise.
Female ; Humans ; Pregnancy ; Amniocentesis ; Chromosomes, Human, Pair 2/genetics* ; DNA Copy Number Variations ; Fetal Death ; Fetal Growth Retardation/genetics* ; Fetus ; Mosaicism ; Oligohydramnios ; Placenta ; Trisomy/genetics* ; Uniparental Disomy/genetics*

Objective: To summarize the genetics and clinical phenotypes of epilepsy children with 2q24.3 microdeletion. Methods: All the patients with 2q24.3 microdeletion were retrospectively collected at the Pediatric Department of Peking University First Hospital from March 2017 to July 2022. The features of clinical manifestations, electroencephalogram (EEG), and neuroimaging were analyzed. Results: There were 13 patients with 2q24.3 microdeletion were included. All 13 patients had de novo copy number variation (CNV) with a deletion size ranged 0.18-7.31 Mb. The main pathogenic genes in the region were SCN3A, SCN2A, TTC21B, SCN1A and SCN9A genes. Among the 13 patients, 7 were boys, and 6 were girls. The onset age of epilepsy was 3.3(2.5, 6.0) months. Multiple seizure types were observed, including focal seizures in 13 patients, generalized tonic-clonic seizures (GTCS) in 6 patients, myoclonic seizures in 3 patients, epileptic spasm in 2 patients, and tonic seizures in 2 patients. Seizures were fever sensitivity in 9 patients. Status epilepticus was observed in 6 patients. One case had normal mental motor development and 12 cases had different degrees of developmental delay. Six patients had craniofacial abnormality, 1 had six-finger deformity of the right thumb, and 1 had multiple system abnormalities. EEG showed focal discharge in 3 cases, multifocal discharges in 5 cases, multifocal and generalized discharges in 1 case. Brain magnetic resonance imaging (MRI) showed enlargement of subarachnoid spaces in the frontal and temporal region in 4 patients, enlargement of lateral ventricle in 4 patients and delayed myelination of white matter in 1 patient. Dravet syndrome was diagnosed in 5 cases. The age at the last follow-up were 2.5(1.4,5.5) years, 1 patient was seizure free longer than 1 year, and 12 patients still had seizures. Conclusions: The epilepsy associated with 2q24.3 microdeletion is mainly induced by the deletion of SCN3A, SCN2A and SCN1A genes. The seizure onset age of 2q24.3 microdeletion related epilepsy was in infancy. Multiple seizure types are observed and the common seizure types include focal seizures and GTCS. Most patients have fever sensitivity and status epilepticus. Most patients have developmental delay. The phenotype of patients with deletion of SCN3A and SCN2A gene is more severe than that of patients with deletion of SCN1A gene only.
Humans ; Abnormalities, Multiple ; Chromosomes ; DNA Copy Number Variations ; Epilepsies, Myoclonic ; Epilepsy ; Fever ; NAV1.7 Voltage-Gated Sodium Channel ; Phenotype ; Retrospective Studies ; Seizures ; Status Epilepticus ; Chromosomes, Human, Pair 2

OBJECTIVE: To explore the genetic basis for a fetus with lissencephaly. METHODS: Genomic DNA was extracted from amniotic fluid sample and subjected to copy number variation (CNV) analysis. RESULTS: The fetus was found to harbor a heterozygous 5.2 Mb deletion at 17p13.3p13.2, which encompassed the whole critical region of Miller-Dieker syndrome (MDS) (chr17: 1-2 588 909). CONCLUSION The fetus was diagnosed with MDS. Deletion of the PAFAH1B1 gene may account for the lissencephaly found in the fetus.
1-Alkyl-2-acetylglycerophosphocholine Esterase/genetics* ; Chromosome Deletion ; Chromosomes, Human, Pair 17/genetics* ; Classical Lissencephalies and Subcortical Band Heterotopias/genetics* ; Female ; Fetus ; Genetic Testing ; Humans ; Microtubule-Associated Proteins/genetics* ; Pregnancy ; Prenatal Diagnosis

OBJECTIVE: To explore the genetic etiology for a newborn with corneal opacity. METHODS: The neonate and her parents were subjected to routine G-banding chromosomal karyotyping analysis. Copy number variation (CNV) was analyzed with low-coverage whole-genome sequencing (WGS) and single nucleotide polymorphism microarray (SNP array). RESULTS: No karyotypic abnormality was found in the newborn and her parents. Low-coverage WGS has identified a de novo 5.5 Mb microdeletion at chromosome 8q21.11-q21.13 in the neonate, which encompassed the ZFHX4 and PEX2 genes. The result was confirmed by SNP array-based CNV analysis. CONCLUSION The newborn was diagnosed with chromosome 8q21.11 deletion syndrome. ZFHX4 may be one of the key genes underlying this syndrome.
Chromosome Banding ; Chromosomes, Human, Pair 8/genetics* ; DNA Copy Number Variations ; Female ; Genetic Testing ; Homeodomain Proteins/genetics* ; Humans ; Infant, Newborn ; Karyotyping ; Monosomy/genetics* ; Peroxisomal Biogenesis Factor 2/genetics* ; Polymorphism, Single Nucleotide ; Transcription Factors/genetics*

OBJECTIVE: To carry out cyto- and molecular genetic testing for a child featuring facial dysmorphism and attention deficit and hyperactive disorder. METHODS: The child was subjected to routine peripheral blood lymphocyte chromosomal karyotyping, fluorescence in situ hybridization (FISH) and single nucleotide polymorphism array (SNP-array) analyses. RESULTS: The child's facial dysmorphism included low-set ears, curly ear auricle, protuberance of eyebrow arch, nostril notch, short and flat philtrum and thin upper lip. SNP-array revealed that he has carried a 4.883 Mb deletion at 2q37. His chromosomal karyotype was ultimately determined as 45, XY, der(2;21) (2pter→ 2q37.3::21p13→ 21p10::20p10→ 20pter), der(20) (21qter→ 21q10::20q10→ 20qter). CONCLUSION A rare case of 2q37 deletion syndrome involving three chromosomes was discovered. Combined use of various cyto- and molecular genetic techniques is crucial for the diagnosis of chromosomal abnormalities with complex structures.
Child ; Chromosome Deletion ; Chromosomes ; Chromosomes, Human, Pair 2 ; Humans ; In Situ Hybridization, Fluorescence ; Karyotyping ; Male ; Translocation, Genetic

OBJECTIVE: To explore the influence of uniparental disomy (UPD) on bipartite and tripartite paternity testing. METHODS: Two cases of paternity testing were analyzed by multiplex amplification and capillary electrophoresis typing. Suspected UPD was verified by using single nucleotide polymorphism array (SNP array). Parental power index was calculated by using a bipartite or tripartite model. RESULTS: The two cases were found to harbor respectively three short tandem repeats on chromosome 2 and two short tandem repeats on chromosome 15. SNP array verified that both cases were of UPD. Case 1 had a parental power index of 122274987565.23 by a tripartite model, while case 2 had a parental power index of 13500.8463 by a bipartite model. Based on the technical specification, the conclusions supported a biological parent-child relationship in both cases. CONCLUSION UPD may lead to misjudgment of paternity testing. The possibility of UPD should be considered when certain loci which do not conform to Mendelian inheritance have aggregated to one chromosome.
Chromosomes, Human, Pair 2 ; genetics ; Humans ; Microsatellite Repeats ; Paternity ; Polymorphism, Single Nucleotide ; Uniparental Disomy ; genetics

OBJECTIVE: To analyze the clinical characteristics and genetic basis of a child affected with Glass syndrome. METHODS: Clinical manifestations and auxiliary examination results of the child were analyzed. Potential mutation was detected with next generation sequencing and validated by Sanger sequencing. RESULTS: The child has featured growth and mental retardation, delayed speech, cleft palate, crowding of teeth, and downslanting palpebral fissures. DNA sequencing revealed a de novo heterozygous missense mutation c.1166G>A (p.R389H) in exon 8 of the SATB2 gene in the child. CONCLUSION The heterozygous mutation c.1166G>A (p.R389H) of the SATB2 gene probably account for the Glass syndrome in the patient.
Abnormalities, Multiple ; genetics ; Child ; Chromosome Deletion ; Chromosomes, Human, Pair 2 ; Humans ; Intellectual Disability ; genetics ; Matrix Attachment Region Binding Proteins ; genetics ; Mutation ; Transcription Factors ; genetics

OBJECTIVE: To analyze the genotype and phenotype of a sibpair with partial deletion of SATB2 gene caused by 2q33.1 microdeletion. METHODS: Both children have featured mental retardation and development delay, and were subjected to karyotyping, single nucleotide microarray (SNP array) and real-time fluorescence quantitative PCR analysis. Karyotyping and SNP Array analysis were also carried out on their parents to verify the origin of mutation. RESULTS: Both sibs had a normal karyotype. SNP array showed that sib 1 had arr[hg19]2q33.1(200 192 328 - 200 197 269)×1 (4.9 kb), 2q35 (218 105 663 - 218 816 675)×3 (711 kb), while sib 2 had arr[hg19]2q33.1(200 192 328 - 200 197 269)×1 (4.9 kb), 2q35 (218 105 663-218 810 908)×3 (705.2 kb). The deletion has partially overlapped with that of 2q33.1 microdeletion syndrome and involved part of the SATB2 gene. The result of real-time fluorescence quantitative PCR assay was consistent with that of SNP assay. The duplication has originated from their father and has not been associated with any disease phenotypen. CONCLUSION Both sibs have carried partial deletion of SATB2 gene and had similar clinical phenotypes. Haploinsufficiency of such gene probably underlies the clinical manifestations in both patients.
Child ; Chromosome Deletion ; Chromosome Disorders ; Chromosomes, Human, Pair 2 ; Genetic Testing ; Humans ; Karyotyping ; Matrix Attachment Region Binding Proteins ; genetics ; Phenotype ; Transcription Factors ; genetics

OBJECTIVE: To carry out single nucleotide polymorphism (SNP)-based chromosome microarray analysis (CMA) for a boy featuring global developmental delay. METHODS: The SNP array was conducted for the child, and real-time PCR was used to validate its result and identify the origin of pathological copy number variants. RESULTS: SNP array revealed that the patient has carried a de novo 2.5 Mb duplication at 2q22.3q23.3, which encompassed ACVR2A, KIF5C, MBD5, EPC2, LYPD6, LYPD6, MMADHC and ORC4 genes. Literature review suggested that the MBD5 gene from the duplicated region may have predisposed to the global developmental delay shown by the girl. CONCLUSION The patient's clinical phenotype was consistent to that of 2q23 duplication, for which the MBD5 gene may play a key role. CMA has provided an important tool for the diagnosis of patients with global developmental delay.
Child ; Chromosome Deletion ; Chromosomes, Human, Pair 2 ; DNA Copy Number Variations ; DNA-Binding Proteins ; genetics ; Female ; Genotype ; Humans ; Kinesin ; Phenotype