Large regions of homozygosity in prenatal diagnosis.

Chromosomal microarrays (CMA) incorporate single nucleotide polymorphisms to enable the detection of regions of homozygosity (ROH). Here, we retrospectively analyzed 6288 prenatal cases who performed CMA to explored the clinical implications of large ROH in prenatal diagnosis. We analyzed cases with ROH larger than 10 megabases and reviewed the ultrasound findings; karyotype results and pregnancy follow-up data. Cases with possible imprinting disorders were assessed by methylation-specific multiplex ligation-dependent probe amplification. In total, we identified 50 cases with large ROH and chromosomes 1 and 2 were the most affected. About 59.18% of the ROH cases had ultrasound abnormalities, with the most common findings being ultrasound soft-marker abnormalities. There were seven fetuses had ROH which covered almost the entire chromosome and four had terminal ROH that involved almost the entire long arm of the chromosomes, which indicated uniparental disomy (UPD), of which 70% showed abnormal ultrasound findings. Ten cases with multiple ROH on different chromosomes indicated the third to fifth degree of consanguinity. In this study, we highlighted the clinical relevance of large ROH related to UPD. The analysis of ROH allowed us to gain further understanding of complex cytogenetic and disease mechanisms in prenatal diagnosis.

AMGDTI: drug-target interaction prediction based on adaptive meta-graph learning in heterogeneous network.

Prediction of drug-target interactions (DTIs) is essential in medicine field, since it benefits the identification of molecular structures potentially interacting with drugs and facilitates the discovery and reposition of drugs. Recently, much attention has been attracted to network representation learning to learn rich information from heterogeneous data. Although network representation learning algorithms have achieved success in predicting DTI, several manually designed meta-graphs limit the capability of extracting complex semantic information. To address the problem, we introduce an adaptive meta-graph-based method, termed AMGDTI, for DTI prediction. In the proposed AMGDTI, the semantic information is automatically aggregated from a heterogeneous network by training an adaptive meta-graph, thereby achieving efficient information integration without requiring domain knowledge. The effectiveness of the proposed AMGDTI is verified on two benchmark datasets. Experimental results demonstrate that the AMGDTI method overall outperforms eight state-of-the-art methods in predicting DTI and achieves the accurate identification of novel DTIs. It is also verified that the adaptive meta-graph exhibits flexibility and effectively captures complex fine-grained semantic information, enabling the learning of intricate heterogeneous network topology and the inference of potential drug-target relationship.

Comprehensive analysis on subchondral bone marrow lesions of human osteoarthritis by integrating bulk and single-cell transcriptomes.

OBJECTIVE: This study aims to demonstrate the cellular composition and underlying mechanisms in subchondral bone marrow lesions (BMLs) of knee osteoarthritis (OA). METHODS: BMLs were assessed by MRI Osteoarthritis Knee Score (MOAKS)≥2. Bulk RNA-sequencing (bulk-seq) and BML-specific differentially expressed genes (DEGs) analysis were performed among subchondral bone samples (including OA-BML=3, paired OA-NBML=3; non-OA=3). The hub genes of BMLs were identified by verifying in independent datasets and multiple bioinformatic analyses. To further estimate cell-type composition of subchondral bone, we utilized two newly developed deconvolution algorithms (MuSiC, MCP-counter) in transcriptomic datasets, based on signatures from open-accessed single-cell RNA sequencing (scRNA-seq). Finally, competing endogenous RNA (ceRNA) and transcription factor (TF) networks were constructed through multiple predictive databases, and validated by public non-coding RNA profiles. RESULTS: A total of 86 BML-specific DEGs (up 79, down 7) were identified. IL11 and VCAN were identified as core hub genes. The "has-miR-424-5p/lncRNA PVT1" was determined as crucial network, targeting IL11 and VCAN, respectively. More importantly, two deconvolution algorithms produced approximate estimations of cell-type composition, and the cluster of heterotopic-chondrocyte was discovered abundant in BMLs, and positively correlated with the expression of hub genes. CONCLUSION: IL11 and VCAN were identified as the core hub genes of BMLs, and their molecular networks were determined as well. We profiled the characteristics of subchondral bone at single-cell level and determined that the heterotopic-chondrocyte was abundant in BMLs and was closely linked to IL11 and VCAN. Our study may provide new insights into the microenvironment and pathological molecular mechanism of BMLs, and could lead to novel therapeutic strategies.

Minimizing the Anticodon-Recognized Loop of Methanococcus jannaschii Tyrosyl-tRNA Synthetase to Improve the Efficiency of Incorporating Noncanonical Amino Acids.

In the field of genetic code expansion (GCE), improvements in the efficiency of noncanonical amino acid (ncAA) incorporation have received continuous attention. By analyzing the reported gene sequences of giant virus species, we noticed some sequence differences at the tRNA binding interface. On the basis of the structural and activity differences between Methanococcus jannaschii Tyrosyl-tRNA Synthetase (MjTyrRS) and mimivirus Tyrosyl-tRNA Synthetase (MVTyrRS), we found that the size of the anticodon-recognized loop of MjTyrRS influences its suppression activity regarding triplet and specific quadruplet codons. Therefore, three MjTyrRS mutants with loop minimization were designed. The suppression of wild-type MjTyrRS loop-minimized mutants increased by 1.8-4.3-fold, and the MjTyrRS variants enhanced the activity of the incorporation of ncAAs by 15-150% through loop minimization. In addition, for specific quadruplet codons, the loop minimization of MjTyrRS also improves the suppression efficiency. These results suggest that loop minimization of MjTyrRS may provide a general strategy for the efficient synthesis of ncAAs-containing proteins.

[Prenatal diagnosis and genetic analysis of a fetus with partial deletion of Yq and mosaicism of 45,X].

OBJECTIVE: To carry out prenatal diagnosis and genetic analysis for a fetus with disorders of sex development (DSDs). METHODS: A fetus with DSDs who was identified at the Shenzhen People's Hospital in September 2021 was selected as the study subject. Combined molecular genetic techniques including quantitative fluorescence PCR (QF-PCR), multiplex ligation-dependent probe amplification (MLPA), chromosomal microarray analysis (CMA), quantitative real-time PCR (qPCR), as well as cytogenetic techniques such as karyotyping analysis and fluorescence in situ hybridization (FISH) were applied. Ultrasonography was used to observe the phenotype of sex development. RESULTS: Molecular genetic testing suggested that the fetus had mosaicism of Yq11.222qter deletion and X monosomy. Combined with the result of cytogenetic testing, its karyotype was determined as mos 45,X[34]/46,X,del(Y)(q11.222)[61]/47,X,del(Y)(q11.222),del(Y)(q11.222)[5]. Ultrasound examination suggested hypospadia, which was confirmed after elective abortion. Combined the results of genetic testing and phenotypic analysis, the fetus was ultimately diagnosed with DSDs. CONCLUSION: This study has applied a variety of genetic techniques and ultrasonography to diagnose a fetus with DSDs with a complex karyotype.

Prenatal diagnosis of Pfeiffer syndrome type 2 with increased nuchal translucency.

Pfeiffer syndrome (PS) is a rare autosomal dominant genetic disorder characterized by craniosynostosis, broad thumbs / toes. Here, we report a case of PS type 2 with increased nuchal translucency in early trimester.

[Genetic analysis of a family with 9q34.3 microdeletion and microduplication caused by abnormal chromosome balance structure].

OBJECTIVE: To perform prenatal diagnosis, pedigree analysis, and genetic counseling of a pregnant woman who gave birth to a child with Kleefstra syndrome. METHODS: Karyotype analysis, chromosomal microarray analysis (CMA), multiplex ligation-dependent probe amplification (MLPA) and fluorescence in situ hybridization (FISH) were used of peripheral blood and amniotic fluid to find causes. Recurrence risk assessment was performed later. RESULTS: The amniotic fluid sample showed a 9q34.3 microduplication of arr (hg19) 9q34.3 (140 168 806-141 020 389)× 3, which overlapped the 9q34.3 microdeletion region of proband. The pregnant woman was detected with a balanced translocation of ish, t(9;17)(9q34.3; qter) (9p+; 17p+,9q+, 17q+). No other abnormal results were found in the family. CONCLUSION: Offspring who share the same chromosome segment deletion or duplication are always from parent who carries balanced chromosomal structural aberration.

Single-cell chromatin accessibility landscape of human umbilical cord blood in trisomy 18 syndrome.

BACKGROUND: Trisomy 18 syndrome (Edwards syndrome, ES) is a type of aneuploidy caused by the presence of an extra chromosome 18. Aneuploidy is the leading cause of early pregnancy loss, intellectual disability, and multiple congenital anomalies. The research of trisomy 18 is progressing slowly, and the molecular characteristics of the disease mechanism and phenotype are still largely unclear. RESULTS: In this study, we used the commercial Chromium platform (10× Genomics) to perform sc-ATAC-seq to measure chromatin accessibility in 11,611 single umbilical cord blood cells derived from one trisomy 18 syndrome patient and one healthy donor. We obtained 13 distinct major clusters of cells and identified them as 6 human umbilical cord blood mononuclear cell types using analysis tool. Compared with the NC group, the ES group had a lower ratio of T cells to NK cells, the ratio of monocytes/DC cell population did not change significantly, and the ratio of B cell nuclear progenitor and megakaryocyte erythroid cells was higher. The differential genes of ME-0 are enriched in Human T cell leukemia virus 1 infection pathway, and the differential peak genes of ME-1 are enriched in apopotosis pathway. We found that CCNB2 and MCM3 may be vital to the development of trisomy 18. CCNB2 and MCM3, which have been reported to be essential components of the cell cycle and chromatin. CONCLUSIONS: We have identified 6 cell populations in cord blood. Disorder in megakaryocyte erythroid cells implicates trisomy 18 in perturbing fetal hematopoiesis. We identified a pathway in which the master differential regulatory pathway in the ME-0 cell population involves human T cell leukemia virus 1 infection, a pathway that is dysregulated in patients with trisomy 18 and which may increase the risk of leukemia in patients with trisomy 18. CCNB2 and MCM3 in progenitor may be vital to the development of trisomy 18. CCNB2 and MCM3, which have been reported to be essential components of the cell cycle and chromatin, may be related to chromosomal abnormalities in trisomy 18.

Simultaneous detection of fetal aneuploidy, de novo FGFR3 mutations and paternally derived ß-thalassemia by a novel method of noninvasive prenatal testing.

OBJECTIVE: The aim is to develop a novel noninvasive prenatal testing (NIPT) method that simultaneously performs fetal aneuploidy screening and the detection of de novo and paternally derived mutations. METHODS: A total of 68 pregnancies, including 26 normal pregnancies, 7 cases with fetal aneuploidies, 7 cases with fetal achondroplasia or thanatophoric dysplasia, 18 cases with fetal skeletal abnormalities, and 10 cases with ß-thalassemia high risk were recruited. Plasma cell-free DNA was amplified by Targeted And Genome-wide simultaneous sequencing (TAGs-seq) to generate around 99% of total reads covering the whole-genome region and around 1%  covering the target genes. The reads on the whole-genome region were analyzed for fetal aneuploidy using a binary hypothesis T-score and the reads on target genes were analyzed for point mutations by calculating the minor allelic frequency of loci on FGFR3 and HBB. TAGs-seq results were compared with conventional NIPT and diagnostic results. RESULTS: In each sample, TAGs-seq generated 44.7-54 million sequencing reads covering the whole-genome region of 0.1-3× and the target genes of >1000×depth. All cases of fetal aneuploidy and de novo mutations of achondroplasia/thanatophoric dysplasia were identified with high sensitivities and specificities except for one false-negative paternal mutation of ß-thalassemia. CONCLUSIONS: TAGs-seq is a novel NIPT method that combines the fetal aneuploidy screening and the detection of de novo FGFR3 mutations and paternal HBB mutations.

Prenatal Diagnosis of Fetus With Transaldolase Deficiency Identifies Compound Heterozygous Variants: A Case Report.

Transaldolase (TALDO) deficiency is a rare autosomal recessive disorder caused by variants in the TALDO1 gene that commonly results in multisystem dysfunction. Herein, we reported compound heterozygous variants in a Chinese prenatal case with TALDO deficiency using whole-exome sequencing (WES) for trios and Sanger sequencing. The heterozygous variants were located on the TALDO1 gene: NM_006755.2:c.574C > T(Chr11:g.763456C > T), a missense variant in exon 5 paternally inherited; NM_006755.2:c.462-2A > G(Chr11:g.763342A > G), a splicing aberration in intron 4 maternally inherited. The qualitative analysis of urinary polyols in neonatal urine indicated that xylitol + arabitol and ribitol in the proband's urine were significantly increased. These findings expand the variation spectrum of the TALDO1 gene, provide solid evidence for the counseling of the family in regard to future pregnancies, strongly support the application of WES in prenatal diagnosis, and further prove that effective postpartum treatments could improve prognosis.

[Analysis for 6-methyladenine modification of DNA in chorionic tissue from aborted fetuses with monosomy 21].

OBJECTIVE: To study the correlation of genome-wide distribution of 6-methyladenine (6mA) of DNA in chorionic tissues from abortuses with monosomy 21. METHODS: Genomic DNA was extracted from chorionic samples from four abortuses with monosomy 21 and four without. After quality and purity test, partial DNA was subjected to chromatin immunoprecipitation with anti-6mA antibody, and then identified by sequencing. The sequencing data was analyzed by using bioinformatic software for the difference in 6mA between the two groups. RESULTS: Analysis of read peaks suggested that the control group have much more 6mA genes (n=4607) compared with the experiment group (n=1059). For chromosome 21, this difference is even more pronounced (8032 vs. 1769). Above results suggested that the level of 6mA modification in monosomy 21 is low. Gene ontology enrichment analysis and KEGG pathway enrichment analysis indicated that the absence of 6mA genes in monosomy 21 is closely related to the growth and development of embryo. CONCLUSION: The 6mA modification of human genes may play a similar role to 5-methylcytosine (5mC) modification during the growth and development of embryos.

Performance Evaluation of NIPT in Detection of Chromosomal Copy Number Variants Using Low-Coverage Whole-Genome Sequencing of Plasma DNA.

OBJECTIVES: The aim of this study was to assess the performance of noninvasively prenatal testing (NIPT) for fetal copy number variants (CNVs) in clinical samples, using a whole-genome sequencing method. METHOD: A total of 919 archived maternal plasma samples with karyotyping/microarray results, including 33 CNVs samples and 886 normal samples from September 1, 2011 to May 31, 2013, were enrolled in this study. The samples were randomly rearranged and blindly sequenced by low-coverage (about 7M reads) whole-genome sequencing of plasma DNA. Fetal CNVs were detected by Fetal Copy-number Analysis through Maternal Plasma Sequencing (FCAPS) to compare to the karyotyping/microarray results. Sensitivity, specificity and were evaluated. RESULTS: 33 samples with deletions/duplications ranging from 1 to 129 Mb were detected with the consistent CNV size and location to karyotyping/microarray results in the study. Ten false positive results and two false negative results were obtained. The sensitivity and specificity of detection deletions/duplications were 84.21% and 98.42%, respectively. CONCLUSION: Whole-genome sequencing-based NIPT has high performance in detecting genome-wide CNVs, in particular >10Mb CNVs using the current FCAPS algorithm. It is possible to implement the current method in NIPT to prenatally screening for fetal CNVs.

Co-doping of Ag into Mn:ZnSe Quantum Dots: Giving Optical Filtering effect with Improved Monochromaticity.

In optics, when polychromatic light is filtered by an optical filter, the monochromaticity of the light can be improved. In this work, we reported that Ag dopant atoms could be used as an optical filter for nanosized Mn:ZnSe quantum dots (QDs). If no Ag doping, aqueous Mn:ZnSe QDs have low monochromaticity due to coexisting of strong ZnSe band gap emission, ZnSe trap emission, and Mn dopant emission. After doping of Ag into QDs, ZnSe band gap and ZnSe trap emissions can be filtered, leaving only Mn dopant emission with improved monochromaticity. The mechanism for the optical filtering effect of Ag was investigated. The results indicate that the doping of Ag will introduce a new faster deactivation process from ZnSe conduction band to Ag energy level, leading to less electrons deactived via ZnSe band gap emission and ZnSe trap emission. As a result, only Mn dopant emission is left.

Tuning the emission of aqueous Cu:ZnSe quantum dots to yellow light window.

Synthesis of internally doped Cu:ZnSe QDs in an aqueous solution still suffers from narrow tunable emissions from the blue to green light window. In this work, we extended the emission window of aqueous Cu:ZnSe QDs to the yellow light window. Our results show that high solution pH, multiple injections of Zn precursors, and nucleation doping strategy are three key factors for preparing yellow emitted Cu:ZnSe QDs. All these factors can depress the reactivity of CuSe nuclei and Zn monomers, promoting ZnSe growth outside CuSe nuclei rather than form ZnSe nuclei separately. With increased ZnSe QD size, the conduction band and nearby trap state energy levels shift to higher energy sites, causing Cu:ZnSe QDs to have a much longer emission.

Caution for monitoring the surface modification of dually emitted ZnSe quantum dots by time-resolved photoluminescence.

This work wants to give a caution for monitoring the surface modification of dually emitted ZnSe quantum dots (QDs) by using time-resolved photoluminescence (PL). Aqueous ZnSe QDs have two emission bands: namely ZnSe band gap emission centered at 395 nm and ZnSe trap emission centered at 470 nm. By fitting the measured PL spectra by two peaks, serious overlapping of two emission bands can be found in the range of 360-430 nm. As a result, the measured PL lifetimes at 395 nm (the peak position of ZnSe band gap emission) is just an apparent value, composing of both ZnSe band emission (contribution proportion about 80%) and ZnSe trap emission (contribution proportion about 20%). Due to the much smaller PL lifetime of ZnSe band gap emission (less than 20 ns) than that of ZnSe trap emission (about 50-70 ns), the elevated contribution proportion of ZnSe band gap emission at improved QD surface modification will lead to the decreased average PL lifetime at 395 nm. This result is completely opposite to the traditional result where improved QD surface modification leads to increased PL lifetimes on the basis of single emitted QDs. Hence, when time-resolved PL is used for monitoring the surface modification of dually emitted QDs, the emission bands overlapping should be taken into consideration with caution.

[Clinical study on efficacy and safety of labor analgesia with inhalation of nitrous oxide in oxygen].

OBJECTIVE: To investigate the efficacy and safety of labor analgesia with inhalation of 50% nitrous oxide in oxygen. METHODS: A total of 1300 cases of term primiparous women in labor were divided into two groups. Study group (n = 658) 50% nitrous oxide in oxygen was inhaled during labor for relieving labor pain. Control group (n = 642) intermittent inhalation of 50% oxygen was carried out during labor. Two groups were compared with following indices: duration of the labor, delivery mode, meconium stained of amniotic fluid, postpartum bleeding volume, neonatal Apgar score, side effect of nitrous oxide, and blood gas analysis of samples from maternal radius artery and fetal umbilical blood. RESULTS: The efficiency of relieving labor pain in study group was much better than that of control group (80.9% vs 0.9%, P < 0.001). Rate of cesarean section in study group was lower than control group (11.6% vs 19.3%, P < 0.05). The active phase of labor in study group was shorter than control group (153 min vs 187 min, P < 0.05). There was side effect of dizziness in 39.4% cases of study group but there were no any complaint in the control group cases. There were no significantly differences in duration of the labor, meconium stained amniotic fluid, postpartum bleeding volume, neonatal Apgar score, and blood gas analysis between two groups (P > 0.05). CONCLUSION: Inhalation of 50% nitrous oxide in oxygen was safe and effective labor analgesia. It is acceptable. The measure of relieving labor pain may increase the vaginal birth rate. There is no severe side effect on mother and baby.