Detection of fetal epigenetic biomarkers through genome-wide DNA methylation study for non-invasive prenatal diagnosis.

The discovery of cell-free DNA fetal (cff DNA) in maternal plasma during pregnancy provides a novel perspective for the development of non­invasive prenatal diagnosis (NIPD). Against the background of maternal DNA, the use of the relatively low concentration of cff DNA is limited in NIPD. Therefore, in order to overcome the complication of the background of maternal DNA and expand the scope of cff DNA application in clinical practice, it is necessary to identify novel universal fetal­specific DNA markers. The GeneChip Human Promoter 1.0R Array set was used in the present study to analyze the methylation status of 12 placental tissue and maternal peripheral blood whole­genome DNA samples. In total, 5 fetus differential hypermethylation regions and 6 fetus differential hypomethylation regions were identified. In order to verify the 11 selected methylation regions and detect the differential CpG sites in these regions, a bisulfate direct sequencing strategy was used. In total, 87 fetal differential methylation CpG sites were identified from 123 CpG sites. The detection of fetal differential methylation DNA regions and CpG sites may be instrumental in the development of efficient NIPD and in the expansion of its application in other disorders.

Integrated miRNA and mRNA expression profiling in fetal hippocampus with Down syndrome.

BACKGROUNDS: Down syndrome (DS), caused by triplication of human chromosome 21, is the most common aneuploidies. The main characteristic of DS patients is intellectual disability. MicroRNAs (miRNAs) play important regulatory roles in various biological processes, such as embryonic development, cell differentiation, proliferation and apoptosis. Several miRNAs have shown association with DS. However, the role of miRNAs in DS patients has not been well elaborated. METHODS: In this research, total RNA extracted from fetal hippocampal tissues was used to analyze miRNA and mRNA expression via Affymetrix miRNA 4.0 and PrimeView Human Gene Expression Array, respectively. Then miRNA and gene expression profiles were integrated by correlation analysis to identify dysregulated miRNAs with their predicted target mRNAs. Microarray data were further validated by real-time PCR. Regulation of zeste homolog 2 (EZH2) expression by hsa-miR-138 was determined by luciferase reporter assay. RESULTS: We analyzed microRNA expression profile in hippocampal tissues from DS fetal using miRNA microarray. Further with the use of mRNA microarray data, we integrate miRNA expression and mRNA expression in hippocampus of trisomy 21 fetus to elucidate the mechanism that underlying DS abnormalities. We characterized the repertoire of specific miRNAs involved in hippocampus in trisomy 21 patients, highlighting hsa-miR-138 and hsa-miR-409, in particular the importance of hsa-miR-138, especially the -5p strand. Furthermore, the expression level of predicted target genes of hsa-miR-138-5p in trisomy 21 fetus, including zeste homolog 2 (EZH2) were further confirmed. In addition, luciferase assay indicated that EZH2 was a direct target of hsa-miR-138 in HEK293T cells. CONCLUSION: The function of hsa-miR-138-5p and its target EZH2 was involved in hippocampus in DS patients. Our findings provide a clue to study the underlying molecular mechanisms in DS patients, and its potential contribution in improving understanding of intellectual disability development in DS patients.

Clinical findings and molecular cytogenetic study of de novo pure chromosome 9p deletion: Pre- and postnatal diagnosis.

OBJECTIVE: The aim of this report is to describe the phenotype-genotype correlation of chromosome 9p deletion syndrome cases, particularly the prenatal cases. MATERIALS AND METHODS: A 30-year-old woman was referred to a hospital at 19+1 weeks of gestation because of omphalocele detected in the fetus. The conventional karyotyping analysis and array comparative genomic hybridization (aCGH) were utilized for the prenatal diagnosis and genetic counseling in the fetus. The prenatal abnormality and cytogenetic findings in the fetus were compared with other patients with 9p deletion. RESULTS: Karyotype analysis of the fetus cell showed a karyotype of 46,XX,del(9)(p22). aCGH analysis detected a deletion as arr[hg19] 9p24.2p22.2(226,7812-1,7466,907)×1. Individuals with 9p deletions tend to have features with widely variable expressivity. The common clinical manifestations of the 9p deletion include development delay, learning difficulties, hypotonia and trigonocephaly. CONCLUSION: Phenotypes of 9p deletion cases are broadly in line. The prenatal diagnosis of the omphalocele provides evidence for a correlation with distal 9q deletion.

DNA methylation study of fetus genome through a genome-wide analysis.

BACKGROUND: DNA methylation is a crucial epigenetic modification of the genome which is involved in embryonic development, transcription, chromatin structure, X chromosome inactivation, genomic imprinting and chromosome stability. Consistent with these important roles, DNA methylation has been demonstrated to be required for vertebrate early embryogenesis and essential for regulating temporal and spatial expression of genes controlling cell fate and differentiation. Further studies have shown that abnormal DNA methylation is associated with human diseases including the embryonic development diseases. We attempt to study the DNA methylation status of CpG islands in fetus related to fetus growth and development. METHODS: GeneChip® Human Tiling 2.0R Array set is used for analysis of methylated DNA in a whole-genome wide in 8 pairs amniotic fluid and maternal blood DNA samples. RESULTS: We found 1 fetus hypermethylation DNA markers and 4 fetus hypomethylation DNA markers though a Genome-wide analysis. These DNA markers all found to be associated with the critical genes for fetus growth and development (SH2D3C gene, EML3 gene, TRIM71 gene, HOXA3 gene and HOXA5 gene). CONCLUSIONS: These genes can be used as a biomarker for association studying of embryonic development, pathological pregnancy and so on. The present study has provided new and fundamental insights into the roles that DNA methylation has in embryonic development and in the pathological pregnancy.

[Analysis of CYP17A1 gene mutation in a child patient with 17 alpha-hydroxylase/17, 20-lyase deficiency].

OBJECTIVE: To analyze CYP17A1 gene mutations in a child patient with 17 alpha-hydroxylase/17, 20-lyase deficiency (17OHD), and to review characteristics of CYP17A1 gene mutations in Chinese patients with 17OHD. METHODS: Clinical data were collected. PCR and DNA sequencing were performed to detect mutations in the patient. RESULTS: The patient has presented classical features of 17OHD including hypertension, hypokalemia, decreased sex hormones and plasma cortisol, and elevated blood adrenocorticotrophic hormone. A compound heterozygous mutation c.987C>A and c.985del was detected in the CYP17A1 gene, which resulted in two premature stop codons at positions 328 and 417. CONCLUSION: A compound mutation, c.987C>A and c.985del, has been identified in a patient with 17OHD. Among CYP17A1 gene mutations identified in Chinese patients, missence mutations have been most common, and exons 5 and 8 have been the mutation hotspots.

[Maternal cell contamination of prenatal samples and the potential effects on prenatal diagnosis results].

OBJECTIVE: To assess the frequency and significance of maternal cell contamination (MCC) in the invasive prenatal diagnosis, and to analysis the MCC effect on prenatal diagnosis results. METHODS: Totally 519 amniotic fluid samples from second trimester pregnancy, 57 chorionic villus samples from first trimester pregnancy, and 576 blood samples from corresponded pregnant women were collected and genotyped by Promega PowerPlex 16 system. MCC was determined according to the genotyping results. Karyotypic and molecular diagnosis results were contrasted between MCC and non-MCC specimen of the same fetal. RESULTS: MCC presented in 3.1% (16/519) uncultured amniotic fluid, 1.3% (7/519) cultured amniotic fluid and 5% (3/57) villi specimens. In the study of fetal karyotype, MCC had no significant effect on normal female fetus; but for male fetus and abnormal female fetus, there were risk of erroneous results of mosaics. As to molecular diagnosis, MCC resulted in more complex effects for the different diagnostic methods. And 10%MCC had led to misdiagnosis. CONCLUSIONS: For the prenatal cytogenetic tests, MCC should be excluded when there were mosaicism karyotype results or suspicious MCC of chorionic villi samples. The effects of MCC had more seriously impact on prenatal molecular testing, which suggesting the recommend regular identity test for MCC should be carried out.

[Detection and prenatal diagnosis for RS1 gene mutations in two Chinese families with X-linked juvenile retinoschisis].

OBJECTIVE: To identify potential mutations of retinoschisis 1 (RS1) gene responsible for X-linked retinoschisis (XLRS) in two Chinese families. METHODS: The 6 exons and flanking intronic regions were analyzed with PCR and direct sequencing. RESULTS: Two RS1 mutations were identified in the two families, which included 1 frameshift mutation (c.573delG, p.Pro192fs) and 1 missense mutation (c.626G>A, p.Arg209His). CONCLUSION: Two RS1 mutations have been identified, among which Pro192fs mutation is discovered for the first time in Chinese population. Above results may enrich our understanding of the clinical manifestations of XLRS and facilitated early diagnosis and genetic counseling for the disease.

[Efficiency of multiplex ligation-dependent probe amplification combined with short tandem repeat linkage analysis for the prenatal diagnosis for Duchenne muscular dystrophy].

OBJECTIVE: To investigate the efficiency of multiplex ligation-dependent probe amplification (MLPA) combined with short tandem repeat (STR) linkage analysis for the prenatal diagnosis for Duchenne muscular dystrophy (DMD). METHODS: Gender of the fetus was first determined by the presence of Y chromosome sex-determining gene (SRY). Subsequently, combined MLPA and STR linkage analysis were applied for the probands, pregnant women and fetuses in 45 affected families. RESULTS: Among the 45 families, 31 SRY-positive fetuses were identified, among whom six were diagnosed with DMD. For 14 SRY-negative fetuses, four were diagnosed as carriers. The remainders were normal. CONCLUSION: MLPA can detect mutations in the exons of dystrophin gene, whilst STR linkage analysis can determine whether the fetus has inherited the maternal X chromosome bearing the mutant gene. As the result, the method can detect affected fetuses in which no exonic mutations are detected with MLPA. By combining the two methods, the diagnostic rate for DMD can be greatly improved.

[Clinical application of noninvasive prenatal diagnosis using cell free fetal DNA in maternal plasma].

OBJECTIVE: To investigate the clinical value of non-invasive prenatal diagnosis using cell free fetal DNA (cff-DNA) in maternal blood. METHODS: From Sep. 2010 to Mar. 2012, 103 pregnant women who came to Henan Province People's Hospital in the first trimester for prenatal diagnosis of sex-linked inherited diseases were included in the first trimester group. From Oct. 2010 to Jan. 2012, 205 pregnant women undergoing amniotic fluid sampling for fetal karyotype analysis in the same hospital were included in the second trimester group. Real time quantitative PCR and fluorescent PCR were used to detect sex determining region of Y chromosome gene (SRY) and amelogenin gene (AML) on cff-DNA of the first trimester group. Moreover, 12 Y chromosome STR loci analysis were performed for 33 male fetuses and their fathers. Massively Parallel Signature Sequencing (MPSS) was used for aneuploidy analysis in cff-DNA of the second trimester group. RESULTS: (1) In the first trimester group, there were 53 SRY positive and 50 SRY negative. Compared with the results of cff-DNA of chorionic villus samples, there was one SRY false positive and one false negative results, with a sensitivity of 98% and specificity of 98%. For the AML gene test, there were two PCR products of male fetuses:102 bp fragment originating from X chromosome (AML X) and 108 bp fragment from Y chromosome (AML Y); but only AML X was found in products from female fetuses. In the first trimester group, 102 bp and 108 bp fragments were detected in 52 cases, and only 102 bp fragment was found in the other cases. Compared to AML results from chorionic villus samples, there were 2 false negative results, with a sensitivity of 96% and specificity of 100%. (2) For cff-DNA with plasma SRY over 30 copy/ml, Y STR loci were analyzed on cff-DNA of 33 fetuses and their fathers. The Y STR loci less then 200 bp were successfully detected, while Y STR loci with PCR products between 200-300 bp showed low signal or could not be amplicated; and no PCR products more than 300 bp were detected from cff-DNA. Comparing the detected Y STR loci of cff-DNA to the fathers, 32 fetuses were concordant with their fathers'. Exogenous contamination was found in the rest one sample. (3) In the second trimester group, 6 fetuses with abnormal karyotype (two trisomy 21, three trisomy 18 and one 45, XO) were detected by cff-DNA and were proved by karyotype analysis. Moreover, the MPSS results of cff-DNA revealed one 45, Y and one trisomy 16 whose karyotype analysis showed normal results. And in one case, MPSS suggested less chrX or chrY, that was proved to be 47, XYY by karyotype analysis. CONCLUSIONS: (1) Cff-DNA in maternal blood can be used to determine fetal gender in early prenancy with considerable sensitivity and specificity. But the trace cff-DNA and the high maternal DNA background might have impact on the result. (2) Analysis of cff-DNA in maternal blood of the second trimester women showed that MPSS could be used for prenatal screening of trisomy 21 and trisomy 18. However, further research should be done for other chromosomes aneuploidy detection.

Potential association of DRD2 and DAT1 genetic variation with heroin dependence.

The aim of our study was to investigate the potential association of dopamine receptor D2 gene (DRD2) TaqI RFLP A (rs1800497) and dopamine transporter gene (DAT) 3'untranslated region VNTR genetic variations with heroin addiction. Genotyping was performed using PCR-based techniques in 530 heroin abusers and 500 controls. Our results showed that DRD2 TaqI A1 allele carriers (genotypes A1A1 and A1A2) were prone to heroin abuse in models of dominance or co-dominance. We detected a 12 repeat allele and 6/6, 7/9, 9/11, 10/12 genotype in a Chinese/eastern Asian population for the first time. However, no significant differences in the DAT1 VNTR were found between the two groups in either genotypic or allelic distributions and there was no gene interaction between the two genetic loci.

[Genetic variation of 9 X-linked short tandem repeat loci among four populations of Inner Mongolian].

OBJECTIVE: To investigate the genetic structure of X chromosome in Mongolia, Ewenki, Elunchun and Dawoer in Inner Mongolia. METHODS: Nine short tandem repeat (STR) markers on the X chromosome (DXS6789, DXS101, DXS8378, DXS7132, DXS7133, DXS7423, DXS6804, DXS6799 and HPRTB) were analyzed in the four populations from Inner Mongolian (Mongol, Ewenki,Oroqen and Daur) for their genetic diversity, forensic suitability and possible genetic affinities of the populations. Frequencies and other parameters of forensic interest were computed. RESULTS: The results revealed that the nine markers described here have a moderate degree of variability in the population groups. And there are significant differences in the genetic variability among the populations. Genetic distance and cluster analyses show very low genetic distance between Mongol and Han (Xi'an) communities. The results based on genetic distance analyses are consistent with earlier studies based on linguistic as well as immigration history and origin of these populations. CONCLUSION: The nine STR loci studied here were found not only useful in studying genetic variations between populations but also suitable for human identity testing.

Genetic polymorphisms of nine X-STR loci in four population groups from Inner Mongolia, China.

Nine short tandem repeat (STR) markers on the X chromosome (DXS101, DXS6789, DXS6799, DXS6804, DXS7132, DXS7133, DXS7423, DXS8378, and HPRTB) were analyzed in four population groups (Mongol, Ewenki, Oroqen, and Daur) from Inner Mongolia, China, in order to learn about the genetic diversity, forensic suitability, and possible genetic affinities of the populations. Frequency estimates, Hardy-Weinberg equilibrium, and other parameters of forensic interest were computed. The results revealed that the nine markers have a moderate degree of variability in the population groups. Most heterozygosity values for the nine loci range from 0.480 to 0.891, and there are evident differences of genetic variability among the populations. A UPGMA tree constructed on the basis of the generated data shows very low genetic distance between Mongol and Han (Xi'an) populations. Our results based on genetic distance analysis are consistent with the results of earlier studies based on linguistics and the immigration history and origin of these populations. The minisatellite loci on the X chromosome studied here are not only useful in showing significant genetic variation between the populations, but also are suitable for human identity testing among Inner Mongolian populations.

[Genetic structure of X-STR loci of Ewenki nationality and its affinity with other nationalities].

OBJECTIVE: To determine the genetic diversity of X-TR loci, and to evaluate the genetic structure X chromosome's of Ewenki nationality and its affinity with other nationalities. METHODS: We chose 9 X-TR (DXS6804, DXS7133, DXS101, DXS6789, DXS6799, DXS7423, HPRTB, DXS8378, DXS7132) as genetic markers from 99 irrelative individules to determine the genetic diversity of Ewenki in Inner Mongolian. Cluster analysis and phylogenic trees was applied to show the genetic distance among the nationalities. RESULTS: We got 51 alleles in the studied population, with the frequency diverse between 0.0109 and 0.6863. Genotype frequency was from 0.0217 to 0.3778. Heterozygosity(H),the power of discrimination(PD) and the polymorphism information conten (PIC) were consistent with the forensic application. Cluster analysis and phylogenic trees revealed that Ewenki nationality had estrangement genetic affinity with the other 3 major nationalities in inner mongolia and Han nationality in Xi'an. CONCLUSION: The genetic information demonstrates that the 9 chosen gene makers were highly informative loci and are suitable for population genetics research and forensic application.