OBJECTIVE: To explore the genetic basis for a patient with autism. METHODS: High-throughput sequencing was carried out to detect copy number variations in the patient. RESULTS: DNA sequencing found that the patient has carried a 0.11 Mb deletion in distal 2p16.3 spanning from genomic position 50 820 001 to 50 922 000, which resulted removal of exon 6 and part of intron 7 of the NRXN1 gene. The same deletion was not found his parents and brother. CONCLUSION Partial deletion of the NRXN1 gene may underlie the disease in this patient.
Autistic Disorder ; genetics ; Cell Adhesion Molecules, Neuronal ; genetics ; DNA Copy Number Variations ; Gene Deletion ; Humans ; Male ; Nerve Tissue Proteins ; genetics

OBJECTIVE: To explore the genetic basis for a couple who had developed polyhydramnios during three pregnancies and given birth to two liveborns featuring limb contracture, dyspnea and neonatal death. METHODS: Whole-exome sequencing (WES) was carried out on fetal tissue and peripheral blood samples from the couple. Suspected variants were verified by Sanger sequencing. RESULTS: The fetus was found to harbor homozygous nonsense c.3718C>T (p.Arg1240Ter) variants of the CNTNAP1 gene, which were respectively inherited from its mother and father. The variant was unreported previously. According to the guidelines of the American College of Medical Genetics and Genomics, the variant was predicted to be pathogenic (PVS1+PM2+PP4). CONCLUSION The novel homozygous nonsense variants of the CNTNAP1 gene probably underlay the lethal congenital contracture syndrome type 7 (LCCS7) in this pedigree. Above finding has enabled genetic counseling and prenatal diagnosis for the family.
Cell Adhesion Molecules, Neuronal ; China ; Contracture/genetics* ; Female ; Humans ; Infant, Newborn ; Mutation ; Pedigree ; Pregnancy ; Whole Exome Sequencing

OBJECTIVE: To summarize the genetic diagnosis, low-depth copy number variation sequencing (CNV-seq) and prenatal finding in 7 fetuses with 2p16.3 deletions only involving the NRXN1 gene. METHODS: The 7 fetuses have all been found to have loss of heterozygosity at 2p16.3 by CNV-seq, which were verified by quantitative real-time PCR (qPCR). Specific regions of NRXN1 gene deletions were identified, and the CNVs were verified in their parents. Outcome of the pregnancies were followed up. RESULTS: Among 16 502 prenatal samples, 7 fetuses were found to harbor a 120 kb ~ 900 kb microdeletion in the 2p16.3 region, which yielded a prevalence of 0.424‰. The deleted region mainly involved 50 200 000-51 880 000 positions of chromosome 2 and involved only the NRXN1 gene. All of the 7 fetal CNVs were confirmed by qPCR, including 2 cases with heterozygous deletion of exons 1 to 6, 1 with heterozygous deletion of exons 1 to 19, 1 with heterozygous deletion of exons 19 to 22, and 3 with heterozygous deletion of introns 6 to 7 of the NRXN1 gene. Verification in the parents had found that one deletion was inherited from the father, 1 was from the mother, 2 cases were de novo in origin, whilst the remaining 3 had refused parental verification. After genetic counseling, one couple had elected induced abortion, 1 case has not been born yet, whilst the other 5 cases were born healthy. Follow up had identified no mental abnormalities among the children. CONCLUSION Seven fetuses with heterozygous 2p16.3 deletions only involving the NRXN1 gene were detected by CNV-seq. The specific deletion of the NRXN1 gene was verified by qPCR. Prenatal genetic counseling and fertility guidance has been provided to the particular family by combining the results of CNV testing, pedigree analysis and pregnancy outcome.
Female ; Humans ; Pregnancy ; Calcium-Binding Proteins/genetics* ; Cell Adhesion Molecules, Neuronal/genetics* ; DNA Copy Number Variations ; Nerve Tissue Proteins/genetics* ; Neural Cell Adhesion Molecules/genetics* ; Prenatal Diagnosis ; Real-Time Polymerase Chain Reaction ; Infant, Newborn

Background: The pathogenicity of cleft lip (CL) is pretty complicated since it is influenced by the interaction of environment and genetic factors. The purpose of this study was to conduct a genome-wide screening of aberrant methylation loci in partial lesion tissues of patients with nonsyndromic CL (NSCL) and preliminarily validate candidate dysmethylated genes associated with NSCL. Methods: Fifteen healthy and sixteen NSCL fetal lip tissue samples were collected. The Infinium HumanMethylation450 BeadChip was used to screen aberrant methylation loci in three NSCL and three healthy lip tissues. The differential methylation sites and functions of the annotated genes between NSCL and healthy lip tissues were analyzed using minfi package of R software, cluster analysis, Gene Ontology (GO) annotation, and metabolic pathway annotation. Gene expression was assessed in nine differentially methylated genes by real-time polymerase chain reaction (PCR). The transcriptions mRNA levels of three out of nine candidate genes were downregulated remarkably in NSCL lip tissues, and these three genes' abnormal methylation loci were validated by pyrosequencing in 16 NSCL cases and 15 healthy cases. Results: In total, 4879 sites in the genes of NSCL odinopoeia fetuses showed aberrant methylation when compared with normal lip tissue genome. Among these, 3661 sites were hypermethylated and 1218 sites were hypomethylated as compared to methylation levels in healthy specimens. These aberrant methylation sites involved 2849 genes and were widely distributed among the chromosomes. Most differentially methylated sites were located in cytosine-phosphoric acid-guanine islands. Based on GO analysis, aberrantly methylated genes were involved in 11 cellular components, 13 molecular functions, and a variety of biological processes. Notably, the transcription of DAB1, REELIN, and FYN was significantly downregulated in lesion tissues of NSCL fetus (P < 0.05). Pyrosequencing results validated that there were two loci in DAB1 with high methylation status in patient tissues (P < 0.05). Conclusions We detected numerous aberrantly methylated loci in lesion tissues of NSCL fetus. Aberrant gene expression in the REELIN signaling pathway might be related with NSCL. Decreased transcription of DAB1, a member of REELIN signal pathway, resulted from its abnormal high methylation, which might be one of the factors underlying the occurrence of NSCL.
Case-Control Studies ; Cell Adhesion Molecules, Neuronal ; genetics ; Cleft Lip ; genetics ; DNA Methylation ; Extracellular Matrix Proteins ; genetics ; Humans ; Methylation ; Nerve Tissue Proteins ; genetics ; Polymorphism, Single Nucleotide ; Serine Endopeptidases ; genetics ; Signal Transduction

Granular corneal dystrophy, type II (CGD2; Avellino corneal dystrophy) is the most common corneal dystrophy among Koreans, but its pathophysiology is still poorly understood. Many reports showed that even though the causative mutation is the same TGFBI R124H mutation, there are severe and mild phenotypes of the corneal dystrophy. We also observed the phenotype differences in our samples. For this reason, we focused our effort on the identification of unknown genetic factor related to phenotype variation. A total 551 individuals from 59 families were genotyped with SNP chip and used in genome-wide linkage analysis. From single-point linkage analyses, we confirmed the known 5q31 region for TGFBI gene, and selected novel nine candidate loci for CGD2. In simulation analysis, the only 3q26.3 region including neuroligin 1 gene (NLGN1) was supported by empirical statistic significance. To investigate the effect of genetic heterogeneity in linkage analysis, we classified CGD2 families into two subgroups. Although we could not find a significant evidence for correlation between the 3q26.3 region and CGD2 phenotypes, this first genome-wide analysis with CGD2 families in Korea has a very important value for offering insights in genetics of CGD2. In addition, the co-segregating loci with CGD2 including 3q26.3 would be a good target for further study to understand the pathophysiology of CGD2.
Cell Adhesion Molecules, Neuronal/genetics ; Chromosomes, Human, Pair 3/*genetics ; Chromosomes, Human, Pair 5/*genetics ; Computer Simulation ; Corneal Dystrophies, Hereditary/*genetics ; Female ; Genetic Linkage ; *Genetic Loci ; *Genome-Wide Association Study ; Genotype ; Humans ; Male ; Models, Genetic ; Polymorphism, Single Nucleotide ; Transforming Growth Factor beta1/genetics

Lung cancer in never-smokers ranks as the seventh most common cause of cancer death worldwide, and the incidence of lung cancer in non-smoking Korean women appears to be steadily increasing. To identify the effect of genetic polymorphisms on lung cancer risk in non-smoking Korean women, we conducted a genome-wide association study of Korean female non-smokers with lung cancer. We analyzed 440,794 genotype data of 285 cases and 1,455 controls, and nineteen SNPs were associated with lung cancer development (P < 0.001). For external validation, nineteen SNPs were replicated in another sample set composed of 293 cases and 495 controls, and only rs10187911 on 2p16.3 was significantly associated with lung cancer development (dominant model, OR of TG or GG, 1.58, P = 0.025). We confirmed this SNP again in another replication set composed of 546 cases and 744 controls (recessive model, OR of GG, 1.32, P = 0.027). OR and P value in combined set were 1.37 and < 0.001 in additive model, 1.51 and < 0.001 in dominant model, and 1.54 and < 0.001 in recessive model. The effect of this SNP was found to be consistent only in adenocarcinoma patients (1.36 and < 0.001 in additive model, 1.49 and < 0.001 in dominant model, and 1.54 and < 0.001 in recessive model). Furthermore, after imputation with HapMap data, we found regional significance near rs10187911, and five SNPs showed P value less than that of rs10187911 (rs12478012, rs4377361, rs13005521, rs12475464, and rs7564130). Therefore, we concluded that a region on chromosome 2 is significantly associated with lung cancer risk in Korean non-smoking women.
Adenocarcinoma/*genetics/pathology ; Adult ; Aged ; Asian Continental Ancestry Group/*genetics ; Cell Adhesion Molecules, Neuronal/*genetics ; Chromosomes, Human, Pair 2 ; Female ; *Genome-Wide Association Study ; Genotype ; Humans ; Logistic Models ; Lung Neoplasms/*genetics/pathology ; Models, Genetic ; Nerve Tissue Proteins/*genetics ; Odds Ratio ; Polymorphism, Single Nucleotide ; Republic of Korea

OBJECTIVETo study the role of cell adhesion molecules Necl1 in synaptogenesis in primary cultured neurons.

METHODSSemi-quantitive reverse transcription polymerase chain reaction (RT-PCR) was used to detect the expression pattern of Necl1 in the neuronal differentiation cell model in vitro. Western blot was performed to detect the expression pattern of Necl1 in primary cultured rat neurons and in purified synaptosome. Immunofluoresence was used to detect the synapse formation in primary neurons and in 293 cells co-culture and to detect the density of synapses in primary neuron with ectopic expression of Necl1.

RESULTSNecl1 expression increased after retinoic acid (RA) induction in SH-SY5Y and P19 cells. The increase of Necl1 expression was consistent with the days of primary neurons culture in vitro, and Necl1 partly localized in synaptosome. The overexpression of Necl1 in 293 cells induced the synapse formation between cocultured 293 cells and neurons. Ectopic expression of Necl1 in primary neurons increased the density of synapses.

CONCLUSIONNecl1 plays an important role in neuronal synapse formation.

Animals ; Blotting, Western ; Cell Adhesion Molecules, Neuronal ; genetics ; metabolism ; Cell Differentiation ; drug effects ; genetics ; Cell Line ; Cells, Cultured ; Fluorescent Antibody Technique ; Humans ; Neurons ; cytology ; drug effects ; metabolism ; Rats ; Reverse Transcriptase Polymerase Chain Reaction ; Synapses ; drug effects ; metabolism ; physiology ; Synaptosomes ; drug effects ; metabolism ; Tretinoin ; pharmacology