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Objective@#To analyze a family with recurrent fetal copy number variations (microdeletion and microduplication, respectively) of 1p31.1 using single nucleotide polymorphism-based array (SNP-array) and G banding chromosomal karyotyping.@*Methods@#Amniocentesis and chorionic villus sampling were performed for a woman during the two pregnancies. Whole genome SNP-array was used to detect genomic imbalance of the fetus. The couple was also subjected to G-banding chromosomal analysis and SNP-array analysis.@*Results@#SNP-array showed a 1p31.1 (70 164 686-83 474 843)×1 and a 1p31.1 (70 164 686-83 479 747) × 3 in the fetuses during the two pregnancies, respectively. SNP array results of the couple appeared to be normal. The mother of the fetuses had a 46, XX, inv(1)(p31.1p32.1) karyotype.@*Conclusion@#The paracentric inversion in chromosome 1 in the gravida probably underlies the recurrent 1p31.1 copy number variations in the fetuses. SNP-array combined with G banding chromosomal analysis are suitable for prenatal diagnosis for recurrent microdeletion and microduplication in the same chromosomal region, and can provide detailed information for genetic counseling.
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Objective@#To evaluate the application value and significance of low-depth whole-genome sequencing for copy number variations (CNV-Seq) in the genetic diagnosis and prenatal diagnosis of X-linked ichthyosis (XLI) due to STS gene deletion.@*Methods@#Clinical data were collected from 3 616 subjects who received CNV-Seq, and single-gene test results were collected from 7 patients or pedigrees with ichthyosis in The First Affiliated Hospital of Zhengzhou University in 2018. The 3 616 samples included 2 891 prenatal samples from pregnant women (most were amniotic fluid samples, some fetal villus samples, very few umbilical blood samples) and 725 peripheral blood samples from other subjects. Genomic DNA was extracted from amniocytes or peripheral blood, and then subjected to CNV-Seq. Quantitative PCR (qPCR) and single nucleotide polymorphism (SNP) -comparative genomic hybridization (CGH) array were performed to verify the detected CNVs. Pathogenicity of the CNVs was analyzed according to the database of genomic variants (DGV) , database of genomic variation and phenotype in humans using ensembl resources (DECIPHER) , clinical genome resource (ClinGen) and online Mendelian inheritance in man (OMIM) .@*Results@#Of the 3 616 subjects receiving CNV-Seq, Xp22.31 deletion was identified in prenatal samples from 6 pregnant women, including 5 male and 1 female fetuses. The deleted fragment of Xp22.31 covered the XLI region containing the major gene STS. The parental CNV-Seq showed that the Xp22.31 deletion was spontaneous mutation in 2 of the 6 fetuses, and inherited from the parents in the other 4 fetuses. qPCR confirmed that the female fetus was a carrier of a complete heterozygous deletion of the STS gene, and there was a complete deletion of the STS gene in the other 5 male fetuses. SNP-CGH array also confirmed that the female fetus was heterozygous Xp22.31 deletion carrier, which was consistent with the CNV-Seq results. Ichthyosis gene panel sequencing in the 7 patients with ichthyosis showed 1 with harlequin ichthyosis, 2 with ichthyosis vulgaris, 3 with XLI, and no causative mutation in 1. CNV-Seq confirmed that Xp22.31 deletion existed in the above 2 patients with XLI due to STS gene deletion. Moreover, Xp22.31 duplication was found in 16 out of 3 616 subjects receiving CNV-Seq, but they were all individuals or fetuses with normal phenotype.@*Conclusions@#CNV-Seq is a stable and reliable method for screening whole-genome CNVs, and can be applied to genetic diagnosis and prenatal diagnosis of XLI due to STS gene deletion. The deletion of Xp22.31 fragment containing the STS gene can cause XLI, and the duplication of the same region is highly likely to be the polymorphic variation.
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Objective To evaluate the application value and significance of low-depth whole-genome sequencing for copy number variations(CNV-Seq)in the genetic diagnosis and prenatal diagnosis of X-linked ichthyosis(XLI)due to STS gene deletion. Methods Clinical data were collected from 3616 subjects who received CNV-Seq, and single-gene test results were collected from 7 patients or pedigrees with ichthyosis in The First Affiliated Hospital of Zhengzhou University in 2018. The 3616 samples included 2891 prenatal samples from pregnant women(most were amniotic fluid samples, some fetal villus samples, very few umbilical blood samples)and 725 peripheral blood samples from other subjects. Genomic DNA was extracted from amniocytes or peripheral blood, and then subjected to CNV-Seq. Quantitative PCR(qPCR)and single nucleotide polymorphism(SNP)-comparative genomic hybridization(CGH)array were performed to verify the detected CNVs. Pathogenicity of the CNVs was analyzed according to the database of genomic variants(DGV), database of genomic variation and phenotype in humans using ensembl resources (DECIPHER), clinical genome resource (ClinGen) and online Mendelian inheritance in man (OMIM). Results Of the 3616 subjects receiving CNV-Seq, Xp22.31 deletion was identified in prenatal samples from 6 pregnant women, including 5 male and 1 female fetuses. The deleted fragment of Xp22.31 covered the XLI region containing the major gene STS. The parental CNV-Seq showed that the Xp22.31 deletion was spontaneous mutation in 2 of the 6 fetuses, and inherited from the parents in the other 4 fetuses. qPCR confirmed that the female fetus was a carrier of a complete heterozygous deletion of the STS gene, and there was a complete deletion of the STS gene in the other 5 male fetuses. SNP-CGH array also confirmed that the female fetus was heterozygous Xp22.31 deletion carrier, which was consistent with the CNV-Seq results. Ichthyosis gene panel sequencing in the 7 patients with ichthyosis showed 1 with harlequin ichthyosis, 2 with ichthyosis vulgaris, 3 with XLI, and no causative mutation in 1. CNV-Seq confirmed that Xp22.31 deletion existed in the above 2 patients with XLI due to STS gene deletion. Moreover, Xp22.31 duplication was found in 16 out of 3616 subjects receiving CNV-Seq, but they were all individuals or fetuses with normal phenotype. Conclusions CNV-Seq is a stable and reliable method for screening whole-genome CNVs, and can be applied to genetic diagnosis and prenatal diagnosis of XLI due to STS gene deletion. The deletion of Xp22.31 fragment containing the STS gene can cause XLI, and the duplication of the same region is highly likely to be the polymorphic variation.
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OBJECTIVE@#To analyze a family with recurrent fetal copy number variations (microdeletion and microduplication, respectively) of 1p31.1 using single nucleotide polymorphism-based array (SNP-array) and G banding chromosomal karyotyping.@*METHODS@#Amniocentesis and chorionic villus sampling were performed for a woman during the two pregnancies. Whole genome SNP-array was used to detect genomic imbalance of the fetus. The couple was also subjected to G-banding chromosomal analysis and SNP-array analysis.@*RESULTS@#SNP-array showed a 1p31.1 (70 164 686-83 474 843) ×1 and a 1p31.1 (70 164 686-83 479 747) ×3 in the fetuses during the two pregnancies, respectively. SNP array results of the couple appeared to be normal. The mother of the fetuses had a 46,XX,inv(1)(p31.1p32.1) karyotype.@*CONCLUSION@#The paracentric inversion in chromosome 1 in the gravida probably underlies the recurrent 1p31.1 copy number variations in the fetuses. SNP-array combined with G banding chromosomal analysis are suitable for prenatal diagnosis for recurrent microdeletion and microduplication in the same chromosomal region, and can provide detailed information for genetic counseling.
Subject(s)
Female , Humans , Pregnancy , Amniocentesis , Chromosomes, Human, Pair 1 , Genetics , DNA Copy Number Variations , Fetus , Karyotyping , Polymorphism, Single Nucleotide , Prenatal DiagnosisABSTRACT
Objective To Investigate the expression of IL-21 and Blimp1 mRNA in Rheumatoid arthritis ( RA) patients and the influence on the expression of Blimp 1 in peripheral blood mononuclear cells (PBMCs) of RA patients after IL-21 stimulated; To further explore the mechanism of IL-21 and blimp1 in the pathogenesis of RA.Methods Case control study.The samples of peripheral venous blood from 50 RA patients of department of rheumatology of The First Affiliated Hospital of Zhengzhou University and 50 healthy people were collected respectively , then the plasma and PBMCs was separated.IL-21 in plasma was measured by ELISA; the correlation between patients clinical index DAS 28, anti-CCP antibody and IL-21 was analyzed.Blimp1 mRNA of patients′PBMCs was detected by qPCR; PMBCs were isolated from RA patient and then cultured in vitro.Blimp1 mRNA level was measured by qPCR and the ratio of CD 20 positive B cell and the ratio of CD138 positive cells in all groups were detected by flow cytometry after 72 h stimulated by IL-21 and CD40L.Results IL-21 content in RA patient blood plasma (130.51 ±11.35)ng/L was significantly higher than that in healthy control (25.46 ±6.05)ng/L, t=5.39,P<0.05.Besides, IL-21 level also had a close relativity with patients DAS28(r=0.658) and anti-CCP antibody (r=0.674, P=0.039 and 0.035).In addition, the expression level of Blimp1 mRNA in RA patient PMBCs (1.321 ± 0.11)was higher than that in healthy control group (1.000 ±0.000), Z=-2.48, P<0.05.While after IL-21 and/or CD40L stimulation, Blimp1 mRNA of IL-21 group and CD40L+IL-21 group(1.084 ±0.029, 1.157 ±0.028)were higher than those of control (1.000 ±0.000)(P=0.002,P=0.001), moreover the expressive level of Blimp1mRNA of CD40L+IL-21 group was higher than that of control group (t=4.862, P=0.02).Compared to negative control group , the ratio of CD20 positive B cells [2.42 ±0.35, 2.63 ± 0.33, 6.35(4.85,6.57),F=278.363,P<0.001] and the ratio of CD138 positive cells(0.474 ±0.110, 0.668 ±0.120, 0.955 ±0.170,F=49.01, P<0.001) in CD40L group, IL-21 group and CD40L+IL-21 group were much higher and the differences among CD 40L+IL-21 group with CD40L group and IL-21 group were statistically significant.Conclusion IL-21 could promote the level of Blimp 1 mRNA in peripheral blood mononuclear cells in RA patient; IL-21 and CD40L could co-promote B cell maturation though regulating Blimp1 mRNA expression and eventually participate in RA pathogenesis.
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Objective To investigate the effect of methylation of the APC gene on expression and the correlation with clinical data in pancreatic cancer.Methods Sixty postoperative tissue samples with pancreatic cancer were collected in the First Affiliated Hospital of Zhengzhou University from August 2010 to January 2011,20 benign pancreatic disease tissues were collected as control groups.APC promoter methylation and gene expression levels were detected by Methylation Specific PCR (MSP),Real Time PCR (RT-PCR) and Western blot in 60 pancreatic carcinoma,42 metastasis and 20 benign pancreatic disease tissues,then analyze the relation between methylation of the APC gene and the clinical data.Results APC promoter methlation was observed 48.53％,46.67％ and 1.16％ in pancreatic carcinoma,metastasis and benign pancreatic disease tissue,respectively.Methylation of APC in pancreatic carcinoma and metastasis increased significantly compared with control tissues (x2 =12.903,14.402; P ＜ 0.05).There were no statistically significant differences of APC expression in these tissues (P ＞ 0.05).There was a significant correlation between methylation of APC and clinicopathological stage (x2 =6.801,P ＜ 0.05),but no correlation with gender,age,tumor size,histological grade and metastasis (x2 =0.727,1.311,0.372,0.148,0.017 ; P ＞ 0.05).Conclusion The methylation of APC gene is closely related with pancreatic carcinoma inogenesis and the clinicopathological stage,but do not effect the expression of APC in tissues.