Validation and depth evaluation of low-pass genome sequencing in prenatal diagnosis using 387 amniotic fluid samples.

BACKGROUND: Low-pass genome sequencing (LP GS) is an alternative to chromosomal microarray analysis (CMA). However, validations of LP GS as a prenatal diagnostic test for amniotic fluid are rare. Moreover, sequencing depth of LP GS in prenatal diagnosis has not been evaluated. OBJECTIVE: The diagnostic performance of LP GS was compared with CMA using 375 amniotic fluid samples. Then, sequencing depth was evaluated by downsampling. RESULTS: CMA and LP GS had the same diagnostic yield (8.3%, 31/375). LP GS showed all copy number variations (CNVs) detected by CMA and six additional variant of uncertain significance CNVs (>100 kb) in samples with negative CMA results; CNV size influenced LP GS detection sensitivity. CNV detection was greatly influenced by sequencing depth when the CNV size was small or the CNV was located in the azoospermia factor c (AZFc) region of the Y chromosome. Large CNVs were less affected by sequencing depth and more stably detected. There were 155 CNVs detected by LP GS with at least a 50% reciprocal overlap with CNVs detected by CMA. With 25 M uniquely aligned high-quality reads (UAHRs), the detection sensitivity for the 155 CNVs was 99.14%. LP GS using samples with 25 M UAHRs showed the same performance as LP GS using total UAHRs. Considering the detection sensitivity, cost and interpretation workload, 25 M UAHRs are optimal for detecting most aneuploidies and microdeletions/microduplications. CONCLUSION: LP GS is a promising, robust alternative to CMA in clinical settings. A total of 25 M UAHRs are sufficient for detecting aneuploidies and most microdeletions/microduplications.

Noninvasive Prenatal Screening for Common Fetal Aneuploidies Using Single-Molecule Sequencing.

Amplification biases caused by next-generation sequencing (NGS) for noninvasive prenatal screening (NIPS) may be reduced using single-molecule sequencing (SMS), during which PCR is omitted. Therefore, the performance of SMS-based NIPS was evaluated. We used SMS-based NIPS to screen for common fetal aneuploidies in 477 pregnant women. The sensitivity, specificity, positive predictive value, and negative predictive value were estimated. The GC-induced bias was compared between the SMS- and NGS-based NIPS methods. Notably, a sensitivity of 100% was achieved for fetal trisomy 13 (T13), trisomy 18 (T18), and trisomy 21 (T21). The positive predictive value was 46.15% for T13, 96.77% for T18, and 99.07% for T21. The overall specificity was 100% (334/334). Compared with NGS, SMS (without PCR) had less GC bias, a better distinction between T21 or T18 and euploidies, and better diagnostic performance. Overall, our results suggest that SMS improves the performance of NIPS for common fetal aneuploidies by reducing the GC bias introduced during library preparation and sequencing.

Lack of MECP2 gene transcription on the duplicated alleles of two related asymptomatic females with Xq28 duplications and opposite X-chromosome inactivation skewing.

Xq28 duplication syndrome (MIM# 300815) is a severe neurodevelopmental disorder in males due to MeCP2 overexpression. Most females with MECP2 duplication are asymptomatic carriers, but there are phenotypic heterogeneities. Skewed X-chromosome inactivation (XCI) can protect females from exhibiting clinical phenotypes. Herein we reported two asymptomatic females (mother and grandmother) with interstitial Xq28 duplication. AR and RP2 assays showed that both had extremely skewed XCI, the Xq28 duplicated chromosome was inactivated in the mother, but was surprisingly activated in the grandmother. Interestingly, by combining RNA sequencing and whole-exome sequencing, we confirmed that XIST only expressed in the Xq28 duplication chromosomes of the two females, indicating that the Xq28 duplication chromosomes were inactive. Meanwhile, MECP2 and most XCI genes in the duplicated X-chromosomes were not transcriptionally expressed or upregulated, precluding major clinical phenotypes in the two females, especially the grandmother. We showed that XCI status detected using RNA sequencing was more relevant for establishing the clinical phenotype of MECP2 duplication in females. It suggested that there were other factors maintaining the XCI status in addition to DNA methylation, a possible additional inhibition mechanism occurred at the transcriptional level in the unmethylated X-chromosome, counter balancing the MECP2 duplication's detrimental phenotype effects.

Preimplantation genetic diagnosis and screening (PGD/S) using a semiconductor sequencing platform.

BACKGROUND: Recent advances in semiconductor sequencing platform (SSP) have provided new methods for preimplantation genetic diagnosis/screening (PGD/S). The present study aimed to evaluate the applicability and efficiency of SSP in PGD/S. METHODS: The artificial positive single-cell-like DNAs and normal single-cell samples were chosen to test our semiconductor sequencing platform for preimplantation genetic diagnosis/screening (SSP-PGD/S) method with two widely used whole-genome amplification (WGA) kits. A total of 557 single blastomeres were collected from in vitro fertilization (IVF) couples, and their WGA products were processed and analyzed by our SSP-PGD/S method in comparison with array comparative genomic hybridization (array-CGH). RESULTS: Our SSP-PGD/S method indicated high compatibilities with two commercial WGA kits. For 557 single blastomeres, our method with four million reads in average could detect 24-chromosome aneuploidies as well as microdeletion/microduplication of the size over 4 Mb, providing 100% consistent conclusion with array-CGH method in the classification of whether it was transplantable. CONCLUSIONS: Our studies suggested that SSP-PGD/S represents a valuable alternative to array-CGH and brought PGD/S into a new era of more rapid, accurate, and economic.

[Genetic analysis of a child with Sotos syndrome].

OBJECTIVE: To explore the genetic basis for a child with mentally retardation. METHODS: G-banding karyotyping, single nucleotide polymorphism array (SNP-array) and fluorescence in situ hybridization (FISH) were performed for the child. Karyotyping and FISH were also carried out for her parents. RESULTS: SNP-array has detected a 5077 kb microdeletion at 5q35.2q35.3 and a 4964 kb microduplication at 7q36.2q36.3 in the child. The results were confirmed by FISH. Based on above results, the father was subsequently found to carry a cryptic t(5;7) (q35.2; q36.2) translocation. The child was verified to have inherited a der(5) t(5;7)(q35.2; q36.2) from her father. CONCLUSION: The 5077 kb microdeletion at 5q35.2q35.3 may have predisposed to the Sotos syndrome in the child. SNP-array combined with G-banding karyotyping and FISH can help to detect cryptic chromosomal translocations among patients.

[Genetic diagnosis of a fetus with Dandy-Walker syndrome].

OBJECTIVE: To explore the genetic basis for a fetus with Dandy-Walker malformation. METHODS: G-banding chromosomal karotyping, single nucleotide polymorphism microarray (SNP array) and fluorescence in situ hybridization (FISH) were carried out for the fetus. Chromosomal karyotyping and FISH assay were also carried out for both parents. RESULTS: SNP array has detected a 4266 kb microdeletion at 6p25.3p25.1 in the fetus, which was confirmed by FISH. FISH analysis of the parents demonstrated that the father has carried a cryptic t(6;14) (p25.1;p13) translocation, while the fetus has a der(6)t(6;14)(p25.1;p13) derived the paternal translocation. CONCLUSION: The der(6)t(6;14)(p25.1;p13) probably underlies the Dandy-Walker malformation in the fetus. The 6p25.3p25.1 microdeletion is due to unbalanced gametes produced by the father's cryptic balanced translocation.

[Prenatal diagnosis of a fetus with Phelan-McDermid syndrome].

OBJECTIVE: To diagnose a fetus with Phelan-McDermid syndrome (PMS) using various techniques. METHODS: Single nucleotide polymorphism array (SNP Array), multiplex ligation-dependent probe amplification (MLPA), fluorescence in situ hybridization (FISH) were applied in conjunction for the prenatal diagnosis of the fetus. RESULTS: SNP Array detected a 4.03 Mb microdeletion at 22q13.31q13.33 in the fetus, which was confirmed by FISH and MLPA. FISH analysis of the parents suggested that the 22q13.31q13.33 deletion has a de novo origin. CONCLUSION: Combined use of various techniques can enable accurate prenatal diagnosis and genetic counseling.

[Single nucleotide polymorphism microarray in prenatal diagnosis of fetuses with absent nasal bone].

OBJECTIVE: To assess the clinical application of single nucleotide polymorphism microarray (SNP array) in prenatal genetic diagnosis for fetuses with absent nasal bone. METHODS: Seventy four fetuses with absent nasal bone detected by prenatal ultrasound scanning were recruited from Women's Hospital, Zhejiang University School of Medicine during June 2015 and October 2018. The chromosome karyotypes analysis and SNP array were performed. The correlation between absent fetal nasal bone and chromosome copy number variants was analyzed. RESULTS: Among 74 fetuses, 19 were detected to have chromosomal abnormalities, including 16 cases of trisomy-21, 1 case of trisomy-18 and two cases of micro-deletion/duplication. Among 46 cases with isolated absence of nasal bone, 3 had trisomy-21, and 1 had a micro-duplication. Absence of nasal bone in association with nuchal translucency thickening had a higher rate of abnormal karyotypes compared with isolated absence of nasal bone (χ2=32.27,P<0.01). CONCLUSIONS: Fetuses with absent nasal bone and nuchal translucency thickening are likely to have chromosome abnormalities, and SNP array testing is recommended to exclude the chromosome abnormalities.

[Application of single nucleotide polymorphism microarray in clinical diagnosis of intellectual disability or retardation].

OBJECTIVE: To assess the clinical application of single nucleotide polymorphism microarray (SNP array) in patients with intellectual disability/developmental delay(ID/DD). METHODS: SNP array was performed to detect genome-wide DNA copy number variants (CNVs) for 145 patients with ID/DD in Women's Hospital, Zhejiang University School of Medicine from January 2013 to June 2018. The CNVs were analyzed by CHAS software and related databases. RESULTS: Among 145 patients, pathogenic chromosomal abnormalities were detected in 32 cases, including 26 cases of pathogenic CNVs and 6 cases of likely pathogenic CNVs. Meanwhile, 18 cases of uncertain clinical significance and 14 cases of likely benign were identified, no significant abnormalities were found in 81 cases (including benign). CONCLUSIONS: SNP array is effective for detecting chromosomal abnormalities in patients with ID/DD with high efficiency and resolution.

[Genetic analysis of a fetus with multiple malformations caused by complex translocations of four chromosomes].

OBJECTIVE: To conduct genetic analysis in a fetus with complex translocation of four chromosomes. METHODS: G-banded chromosome karyotype analysis, single nucleotide polymorphism array (SNP array) and fluorescence in situ hybridization (FISH) were performed in a fetus with multiple malformations. Peripheral blood chromosome karyotype and FISH were also carried out for the parents. RESULTS: The fetal amniotic fluid karyotype was 46, XY, t(12; 13)(q22; q32). SNP array analysis showed that there were 20 192 kb duplication at 1q42.13q44 and 13 293 kb deletion at 15q26.1q26.3 in the fetus. The results of karyotype and SNP array were inconsistent. FISH analyses on the parental peripheral blood samples demonstrated that the mother was a cryptic 46, XX, t(1; 15)(q42.1; q26.1) translocation. The fetus had inherited 46, XY, t(12; 13)(q22; q32) from his father and der(15)t(1; 15)(q42.1; q26.1) from his mother. CONCLUSIONS: The 1q42.13q44 duplication and 15q26.1q26.3 deletion may have contributed to the abnormal sonographic features of the fetus. The combination of cytogenetic, SNP array and FISH techniques was beneficial for providing an accurate genetic counseling.

XCI-escaping gene KDM5C contributes to ovarian development via downregulating miR-320a.

Mechanisms underlying female gonadal dysgenesis remain unclarified and relatively unstudied. Whether X-chromosome inactivation (XCI)-escaping genes and microRNAs (miRNAs) contribute to this condition is currently unknown. We compared 45,X Turner Syndrome women with 46,XX normal women, and investigated differentially expressed miRNAs in Turner Syndrome through plasma miRNA sequencing. We found that miR-320a was consistently upregulated not only in 45,X plasma and peripheral blood mononuclear cells (PBMCs), but also in 45,X fetal gonadal tissues. The levels of miR-320a in PBMCs from 45,X, 46,XX, 46,XY, and 47,XXY human subjects were inversely related to the expression levels of XCI-escaping gene KDM5C in PBMCs. In vitro models indicated that KDM5C suppressed miR-320a transcription by directly binding to the promoter of miR-320a to prevent histone methylation. In addition, we demonstrated that KITLG, an essential gene for ovarian development and primordial germ cell survival, was a direct target of miR-320a and that it was downregulated in 45,X fetal gonadal tissues. In conclusion, we demonstrated that downregulation of miR-320a by the XCI-escaping gene KDM5C contributed to ovarian development by targeting KITLG.

[Single nucleotide polymorphism-array in genetic analysis of chorionic villi from early spontaneous miscarriages].

OBJECTIVE: To assess the clinical application of single nucleotide polymorphism (SNP)-array in detecting abnormal chromosome karyotypes of chorionic villi from early spontaneous abortuses. METHODS: A total of 861 chorionic villus samples from unexplained early spontaneous abortion were collected from Women's Hospital, Zhejiang University School of Medicine during October 2013 and June 2016, and SNP-array was performed to detect genome-wide DNA copy number variants. RESULTS: All samples were successfully tested by SNP-array and 440 cases (51.10%) were found to have abnormal chromosome constitutions. Aneuploidy was identified in 358 (41.58%) cases, distributing in all chromosomes except chromosome 1. Triploidy and haploidy were found in 21 (2.44%) and one case (0.12%), respectively. Thirty-seven cases (4.30%) were identified as single chromosomal segment deletion or duplication, 25 of which were less than 10 Mb in size. For 6 of 25 cases with unclear pathogenesis, family studies were carried out to identify origin of deletion or duplication, showing that 4 cases were de novo and 2 were inherited from one of the parents. Twenty-three cases (2.67%) showed two chromosomal deletion/duplication segments. Combining with karyotyping and fluorescence in situ hybridization, 6 cases were identified as de novo aberration and 11 carried small-size segmental balanced abnormality. CONCLUSIONS: SNP-array can provide a relatively comprehensive genetic analysis of chorionic villi and can detect various kinds of chromosome abnormalities in spontaneous miscarriages.

An efficient molecular genetic testing strategy for incontinentia pigmenti based on single-tube long fragment read sequencing.

Incontinentia pigmenti (IP) is a rare X-linked dominant neuroectodermal dysplasia that primarily affects females. The only known causative gene is IKBKG, and the most common genetic cause is the recurrent IKBKG△4-10 deletion resulting from recombination between two MER67B repeats. Detection of variants in IKBKG is challenging due to the presence of a highly homologous non-pathogenic pseudogene IKBKGP1. In this study, we successfully identified four pathogenic variants in four IP patients using a strategy based on single-tube long fragment read (stLFR) sequencing with a specialized analysis pipeline. Three frameshift variants (c.519-3_519dupCAGG, c.1167dupC, and c.700dupT) were identified and subsequently validated by Sanger sequencing. Notably, c.519-3_519dupCAGG was found in both IKBKG and IKBKGP1, whereas the other two variants were only detected in the functional gene. The IKBKG△4-10 deletion was identified and confirmed in one patient. These results demonstrate that the proposed strategy can identify potential pathogenic variants and distinguish whether they are derived from IKBKG or its pseudogene. Thus, this strategy can be an efficient genetic testing method for IKBKG. By providing a comprehensive understanding of the whole genome, it may also enable the exploration of other genes potentially associated with IP. Furthermore, the strategy may also provide insights into other diseases with detection challenges due to pseudogenes.

A novel F8 variant in a Chinese hemophilia A family and involvement of X-chromosome inactivation: A case report.

RATIONALE: Hemophilia A (HA) is an X-linked recessive bleeding disorder, which shows factor VIII (FVIII) deficiency caused by genetic variant in F8 gene. PATIENT CONCERNS: Males with F8 variants are affected, whereas female carriers with a wide range of FVIII levels are usually asymptomatic, it is possible that different X-chromosome inactivation (XCI) may effect the FVIII activity. DIAGNOSES: We identified a novel variant F8: c.6193T > G in a Chinese HA proband, it was inherited from the mother and grandmother with different FVIII levels. INTERVENTIONS: We performed Androgen receptor gene (AR) assays and RT-PCR. OUTCOMES: AR assays revealed that the X chromosome with the F8 variant was severely skewed inactivated in the grandmother with higher FVIII levels, but not in the mother with lower FVIII levels. Further, RT-PCR of mRNA confirmed that only the wild allele of F8 was expressed in the grandmother, with lower expression in the wild allele of the mother. LESSONS: Our findings suggest that F8: c.6193T > G could be the cause of HA and that XCI affected the FVIII plasma levels in female carriers.

Case report: A compound heterozygous mutations in ASNS broadens the spectrum of asparagine synthetase deficiency in the prenatal diagnosis.

Asparagine synthetase deficiency (ASNSD) is a rare congenital disorder characterized by severe progressive microcephaly, global developmental delay, spastic quadriplegia, and refractory seizures. ASNSD is caused by variations of the ASNS gene. The present study showed a Chinese family with a fetus suffering microcephaly. Whole-exome sequencing and Sanger sequencing were used to identify the disease-associated genetic variants. Compound heterozygous variants c.97C>T p. (R33C) and c.1031-2_1033del were identified in the ASNS gene and the variants were inherited from the parents. The mutation site c.97C>T was highly conserved across a wide range of species and predicted to alter the local electrostatic potential. The variant c.1031-2_1033del was classified pathogenic. However, there is no case report of prenatal diagnosis of ASNSD. This is the first description of fetal compound mutations in the ASNS gene leading to ASNSD, which expanded the spectrum of ASNSD.

Efficient removal of tetracycline hydrochloride by high entropy oxides in visible photo-Fenton catalytic process.

A novel type of oxide material, high entropy oxide (Mn0.2Fe0.2Co0.2Ni0.2Cu0.2)3O4 (MFO) composites with spinel structure were successfully synthesized by a simple solution combustion in this paper, and it was first applied to the degradation of antibiotic organic pollutants in water by photo-Fenton. SEM and BET characterization showed that the composite was porous and had a large specific surface area. XPS results showed that Fe, Mn, Cu, Co and Ni all participated in the redox reaction of the catalytic process. The redox pairs of Mn2+/Mn3+, Cu+/Cu2+, Co2+/Co3+, Ni2+/Ni3+ can accelerate the Fe2+/Fe3+ redox cycling in MFO to activate H2O2 and produce more reactive oxygen species. The catalytic performance of MFO composite was investigated using tetracycline hydrochloride (TC-HCl) as a model pollutant. The results displayed that the degradation rate of TC-HCl by MFO was 92.9% when the initial pH was 4, the dose of H2O2 was 50 mM, and the irradiation time was 60 min. The high entropy oxide MFO composites could build up an internal electric field, which restrains electron-hole recombination, improves the transfer of photogenerated charge carriers and maximize photocatalytic property. In addition, the free radical capture experiment determined that the main active species of the degradation reaction were e-, •O2- and •OH. The synergistic effect of the five components in the high entropy oxide strengthens lattice distortion and defects, increases oxygen vacancies, and thus has enhanced catalytic effect for TC-HCl degradation. This work shows that high entropy oxides have excellent catalytic performance for tetracycline organic pollutants, and it is speculated that high entropy oxides have good application prospects in the field of advanced oxidation technology for the degradation of organic pollutants.

Single-cell landscape analysis reveals systematic senescence in mammalian Down syndrome.

BACKGROUND: Down syndrome (DS), which is characterized by various malfunctions, is the most common chromosomal disorder. As the DS population continues to grow and most of those with DS live beyond puberty, early-onset health problems have become apparent. However, the cellular landscape and molecular alterations have not been thoroughly studied. METHODS: This study utilized single-cell resolution techniques to examine DS in humans and mice, spanning seven distinct organs. A total of 71 934 mouse and 98 207 human cells were analyzed to uncover the molecular alterations occurring in different cell types and organs related to DS, specifically starting from the fetal stage. Additionally, SA-ß-Gal staining, western blot, and histological study were employed to verify the alterations. RESULTS: In this study, we firstly established the transcriptomic profile of the mammalian DS, deciphering the cellular map and molecular mechanism. Our analysis indicated that DS cells across various types and organs experienced senescence stresses from as early as the fetal stage. This was marked by elevated SA-ß-Gal activity, overexpression of cell cycle inhibitors, augmented inflammatory responses, and a loss of cellular identity. Furthermore, we found evidence of mitochondrial disturbance, an increase in ribosomal protein transcription, and heightened apoptosis in fetal DS cells. This investigation also unearthed a regulatory network driven by an HSA21 gene, which leads to genome-wide expression changes. CONCLUSION: The findings from this study offer significant insights into the molecular alterations that occur in DS, shedding light on the pathological processes underlying this disorder. These results can potentially guide future research and treatment development for DS.

Case Report: Identification Pathogenic Abnormal Splicing of BBS1 Causing Bardet-Biedl Syndrome Type I (BBS1) due to Missense Mutation.

Conventionally, protein features affected by missense mutation was attributed to destroy an important domain with amino acid alternation, and it was difficult to clearly specify the pathogenicity of a novel missense mutation. Nevertheless, the associations between missense mutations and abnormal splicing are nowadays increasingly reported. Rarely, some missense mutations, locating at the non-canonical splicing sites, are observed to damage the splicing process. In this study, a couple has three adverse pregnancy history that the affected fetus presented typical polydactyly, renal abnormalities, and cerebral ventriculomegaly. To identify its genetic etiology, whole-exome sequencing (WES) was performed and a missense mutation c.1339G > A was identified, which was located at the non-canonical splicing sites of the BBS1 gene. Then, reverse transcription polymerase chain reaction was carried out and demonstrated extra 115bp originating from intron 13 cut into cDNA, which generated a predicted premature termination codon (PTC) in the BBS1 protein. Further expression analysis by using real-time reverse-transcribed PCR confirmed the occurrence of nonsense-mediated decay (NMD). Therefore, the pathogenicity of the missense mutation c.1339G > A was explicit and our study helped to extend the spectrum of pathogenic mutations in Bardet-Biedl syndrome type I.

Corrigendum: Case Report: Prenatal Diagnosis for a Rett Syndrome Family Caused by a Novel MECP2 Deletion With Heteroduplexes of PCR Product.

[This corrects the article DOI: 10.3389/fped.2021.748641.].

Enhanced catalytic performance of Cu-doped MnFe2O4 magnetic ferrites: Tetracycline hydrochloride attacked by superoxide radicals efficiently in a strong alkaline environment.

It is important to develop a catalyst that can maintain good activity in alkaline environment for Fenton or Fenton-like reactions. In order to achieve stable Fenton catalytic degradation in a wide pH range, this study reports Cu-doped MnFe2O4 heterogeneous catalysts still has excellent effect when the pH is extended to 11 for removing organic pollutants, such as tetracycline hydrochloride (TC-HCl). The synergistic effect among Fe, Mn and Cu ions has been proved to enhanced the catalytic activity in this work. When the molar ratio of Cu/Mn = 4:1, the porous Cu0·8Mn0·2Fe2O4 materials had the highest photo-Fenton catalytic activity compared with pure MnFe2O4, CuFe2O4 and other CuxMn1-xFe2O4. The XPS showed that Cu0·8Mn0·2Fe2O4 formed oxygen vacancies, which exposed more active sites to attract more H2O2 for TC-HCl degradation. Results indicated 94.3% of TC-HCl was efficiently degraded by 0.1 g/L Cu0·8Mn0·2Fe2O4 with 50 mM H2O2 at pH = 11 under 30 min visible light irradiation, and the corresponding apparent rate constant was 0.08286 min-1. With free radicals quenching experiment, O2- was responsible for the high catalytic degradation and OH was participated in the photo-Fenton reaction. To sum up, Cu0·8Mn0·2Fe2O4 exhibited high activity, great stability and easily recyclable, which eliminated the pH limitation of the Fenton reaction and provided practical application performance for water purification.