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A method for noninvasive detection of fetal large deletions/duplications by low coverage massively parallel sequencing

Chen, Shengpei ; Lau, Tze Kin ; Zhang, Chunlei ; [et al.]

Wiley ; 2013

In: Prenatal Diagnosis Vol. 33, No. 6 ( 2013-06), p. 584-590

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In: Prenatal Diagnosis, Wiley, Vol. 33, No. 6 ( 2013-06), p. 584-590

Abstract: What's already known about this topic? Sequencing‐based noninvasive prenatal detection of fetal aneuploidy has been proven to be highly accurate. However, it is still a challenge to detect fetal deletion/duplication syndrome because of the interference from maternal DNA in maternal plasma. What does this study add? Here, we developed a practical bioinformatic methodology to detect fetal chromosomal deletions/duplications of 〉 10 Mb using low coverage whole genome sequencing of maternal plasma.

Type of Medium: Online Resource

ISSN: 0197-3851 , 1097-0223

URL: Issue

URL: Article

DOI: 10.1002/pd.v33.6

DOI: 10.1002/pd.4110

RVK:

XA 10000

Language: English

Publisher: Wiley

Publication Date: 2013

detail.hit.zdb_id: 1491217-X

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DataSheet9.ZIP

Wu, Zuoxing ; Li, Chen ; Chen, Yu ; [et al.]

Frontiers Media SA ; 2022

In: Frontiers in Pharmacology Vol. 13 ( 2022-3-23)

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In: Frontiers in Pharmacology, Frontiers Media SA, Vol. 13 ( 2022-3-23)

Abstract: Bone homeostasis only exists when the physical function of osteoblast and osteoclast stays in the balance between bone formation and resorption. Bone resorption occurs when the two processes are uncoupled, shifting the balance in favour of bone resorption. Excessive activation of osteoclasts leads to a range of osteolytic bone diseases including osteoporosis, aseptic prosthesis loosening, rheumatoid arthritis, and osteoarthritis. Receptor activator of nuclear factor kappa-B ligand (RANKL) and its downstream signaling pathways are recognized as key mediators that drive the formation and activation of osteoclastic function. Hence, osteoclast formation and/or its function remain as dominant targets for research and development of agents reaching the treatment towards osteolytic diseases. Chrysin (CHR) is a flavonoid with a wide range of anti-inflammatory and anti-tumor effects. However, its effect on osteoclasts remains unknown. In this study, we found the effects of CHR on inhibiting osteoclast differentiation which were assessed in terms of the number and size of TRAcP positive multinucleated osteoclasts (OCs). Further, the inhibitory effects of CHR on bone resorption and osteoclast fusion of pre-OC were assessed by hydroxyapatite resorption pit assay and F-actin belts staining; respectively. Western blotting analysis of RANKL-induced signaling pathways and immunofluorescence analysis for p65 nuclear translocation in response to RANKL-induced osteoclasts were used to analyze the mechanism of action of CHR affecting osteoclasts. Lastly, the murine calvarial osteolysis model revealed that CHR could protect against particle-induced bone destruction in vivo . Collectively, our data strongly suggested that CHR with its promising anti-tumor effects would also be a potential therapeutic agent for osteolytic diseases.

Type of Medium: Online Resource

ISSN: 1663-9812

URL: Article

DOI: 10.3389/fphar.2022.793087

DOI: 10.3389/fphar.2022.793087.s001

DOI: 10.3389/fphar.2022.793087.s002

DOI: 10.3389/fphar.2022.793087.s003

DOI: 10.3389/fphar.2022.793087.s004

DOI: 10.3389/fphar.2022.793087.s005

DOI: 10.3389/fphar.2022.793087.s006

DOI: 10.3389/fphar.2022.793087.s007

DOI: 10.3389/fphar.2022.793087.s008

DOI: 10.3389/fphar.2022.793087.s009

Language: Unknown

Publisher: Frontiers Media SA

Publication Date: 2022

detail.hit.zdb_id: 2587355-6

SSG: 15,3

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Dummy-template Pickering emulsion imprinted microspheres online pretreatment and analysis for the estrogens in cosmetics

Guo, Pengqi ; Liu, Chenming ; Zhong, Fanru ; [et al.]

Elsevier BV ; 2023

In: Journal of Chromatography A Vol. 1691 ( 2023-02), p. 463815-

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In: Journal of Chromatography A, Elsevier BV, Vol. 1691 ( 2023-02), p. 463815-

Type of Medium: Online Resource

ISSN: 0021-9673

URL: Article

DOI: 10.1016/j.chroma.2023.463815

RVK:

VA 5050.A

RVK:

VG 7204

RVK:

IE 1100

RVK:

VA 1120

Language: English

Publisher: Elsevier BV

Publication Date: 2023

detail.hit.zdb_id: 1491247-8

detail.hit.zdb_id: 1171488-8

SSG: 11

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A Heterozygous Truncating Mutation in BNC1 Causes Male Subfertility: BNC1 Cooperates with TAF7L to Regulate Spermatogenesis

Li, Jingyi ; Liu, Yifeng ; Xu, Haiyan ; [et al.]

Elsevier BV ; 2018

In: SSRN Electronic Journal

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In: SSRN Electronic Journal, Elsevier BV

Type of Medium: Online Resource

ISSN: 1556-5068

URL: Article

DOI: 10.2139/ssrn.3244812

Language: English

Publisher: Elsevier BV

Publication Date: 2018

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Genetic deconvolution of fetal and maternal cell-free DNA in maternal plasma enables next-generation non-invasive prenatal screening

Xu, Chenming ; Li, Jianli ; Chen, Songchang ; [et al.]

Springer Science and Business Media LLC ; 2022

In: Cell Discovery Vol. 8, No. 1 ( 2022-10-13)

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In: Cell Discovery, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2022-10-13)

Abstract: Current non-invasive prenatal screening (NIPS) analyzes circulating fetal cell-free DNA (cfDNA) in maternal peripheral blood for selected aneuploidies or microdeletion/duplication syndromes. Many genetic disorders are refractory to NIPS largely because the maternal genetic material constitutes most of the total cfDNA present in the maternal plasma, which hinders the detection of fetus-specific genetic variants. Here, we developed an innovative sequencing method, termed co ordinative a llele-aware t arget e nrichment seq uencing (COATE-seq), followed by multidimensional genomic analyses of sequencing read depth, allelic fraction, and linked single nucleotide polymorphisms, to accurately separate the fetal genome from the maternal background. Analytical confounders including multiple gestations, maternal copy number variations, and absence of heterozygosity were successfully recognized and precluded for fetal variant analyses. In addition, fetus-specific genomic characteristics, including the cfDNA fragment length, meiotic error origins, meiotic recombination, and recombination breakpoints were identified which reinforced the fetal variant assessment. In 1129 qualified pregnancies tested, 54 fetal aneuploidies, 8 microdeletions/microduplications, and 8 monogenic variants were detected with 100% sensitivity and 99.3% specificity. Using the comprehensive cfDNA genomic analysis tools developed, we found that 60.3% of aneuploidy samples had aberrant meiotic recombination providing important insights into the mechanism underlying meiotic nondisjunctions. Altogether, we show that the genetic deconvolution of the fetal and maternal cfDNA enables thorough and accurate delineation of fetal genome which paves the way for the next-generation prenatal screening of essentially all types of human genetic disorders.

Type of Medium: Online Resource

ISSN: 2056-5968

URL: Article

DOI: 10.1038/s41421-022-00457-4

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2022

detail.hit.zdb_id: 2842548-0

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Clinical application of noninvasive prenatal testing for the detection of trisomies 21, 18, and 13: a hospital experience

Zhou, Qiyin ; Pan, Ling ; Chen, Songchang ; [et al.]

Wiley ; 2014

In: Prenatal Diagnosis Vol. 34, No. 11 ( 2014-11), p. 1061-1065

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In: Prenatal Diagnosis, Wiley, Vol. 34, No. 11 ( 2014-11), p. 1061-1065

Abstract: What's already known about this topic? Noninvasive prenatal testing (NIPT) has been adopted by many clinical settings to detect trisomies 21, 18, and 13. What does this study add? In our hospital setting, NIPT solved the problem of limited medical resources for invasive diagnostic testing in high‐risk women. NIPT coupled with other prenatal screening methods helped more women access prenatal diagnosis. In our clinical practice, NIPT provided a more suitable and efficient prenatal screening‐diagnosis workflow.

Type of Medium: Online Resource

ISSN: 0197-3851 , 1097-0223

URL: Issue

URL: Article

DOI: 10.1002/pd.v34.11

DOI: 10.1002/pd.4428

RVK:

XA 10000

Language: English

Publisher: Wiley

Publication Date: 2014

detail.hit.zdb_id: 1491217-X

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Detection of cryptic balanced chromosomal rearrangements using high-resolution optical genome mapping

Zhang, Shuo ; Pei, Zhenle ; Lei, Caixia ; [et al.]

BMJ ; 2023

In: Journal of Medical Genetics Vol. 60, No. 3 ( 2023-03), p. 274-284

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In: Journal of Medical Genetics, BMJ, Vol. 60, No. 3 ( 2023-03), p. 274-284

Abstract: Chromosomal rearrangements have profound consequences in diverse human genetic diseases. Currently, the detection of balanced chromosomal rearrangements (BCRs) mainly relies on routine cytogenetic G-banded karyotyping. However, cryptic BCRs are hard to detect by karyotyping, and the risk of miscarriage or delivering abnormal offspring with congenital malformations in carrier couples is significantly increased. In the present study, we aimed to investigate the potential of single-molecule optical genome mapping (OGM) in unravelling cryptic chromosomal rearrangements. Methods Eleven couples with normal karyotypes that had abortions/affected offspring with unbalanced rearrangements were enrolled. Ultra-high-molecular-weight DNA was isolated from peripheral blood cells and processed via OGM. The genome assembly was performed followed by variant calling and annotation. Meanwhile, multiple detection strategies, including FISH, long-range-PCR amplicon-based next-generation sequencing and Sanger sequencing were implemented to confirm the results obtained from OGM. Results High-resolution OGM successfully detected cryptic reciprocal translocation in all recruited couples, which was consistent with the results of FISH and sequencing. All high-confidence cryptic chromosomal translocations detected by OGM were confirmed by sequencing analysis of rearrangement breakpoints. Moreover, OGM revealed additional complex rearrangement events such as inverted aberrations, further refining potential genetic interpretation. Conclusion To the best of our knowledge, this is the first study wherein OGM facilitate the rapid and robust detection of cryptic chromosomal reciprocal translocations in clinical practice. With the excellent performance, our findings suggest that OGM is well qualified as an accurate, comprehensive and first-line method for detecting cryptic BCRs in routine clinical testing.

Type of Medium: Online Resource

ISSN: 0022-2593 , 1468-6244

URL: Article

DOI: 10.1136/jmedgenet-2022-108553

RVK:

WA 15000

Language: English

Publisher: BMJ

Publication Date: 2023

detail.hit.zdb_id: 2009590-9

SSG: 12

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Parental mosaicism detection and preimplantation genetic testing in families with multiple transmissions of de novo mutations

Xu, Naixin ; Shi, Weihui ; Cao, Xianling ; [et al.]

BMJ ; 2023

In: Journal of Medical Genetics Vol. 60, No. 9 ( 2023-09), p. 910-917

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In: Journal of Medical Genetics, BMJ, Vol. 60, No. 9 ( 2023-09), p. 910-917

Abstract: De novo mutations (DNMs) are linked with many severe early-onset disorders ranging from rare congenital malformation to intellectual disability. Conventionally, DNMs are considered to have an estimated recurrence rate of 1%. Recently, studies have revealed a higher prevalence of parental mosaicism, leading to a greater recurrence risk, resulting in a second child harbouring the same DNM as a previous child. Methods In this study, we included 10 families with DNMs leading to adverse pregnancy outcomes. DNA was extracted from tissue samples, including parental peripheral blood, parental saliva and paternal sperm. High-throughput sequencing was used to screen for parental mosaicism with a depth of more than 5000× on average and a variant allele fraction (VAF) detection limit of 0.5%. Results The presence of mosaicism was detected in sperms in two families, with VAFs of 2.8% and 2.5%, respectively. Both families have a history of multiple adverse pregnancies and DNMs shared by siblings. Preimplantation genetic testing (PGT) and prenatal diagnosis were performed in one family, thereby preventing the reoccurrence of DNMs. Conclusion This study is the first to report the successful implementation of PGT for monogenic/single gene defects in the parental mosaicism family. Our study suggests that mosaic detection of paternal sperm is warranted in families with recurrent DNMs leading to adverse pregnancy outcomes, and PGT can effectively block the transmission of the pathogenic mutation.

Type of Medium: Online Resource

ISSN: 0022-2593 , 1468-6244

URL: Article

DOI: 10.1136/jmg-2022-108920

RVK:

WA 15000

Language: English

Publisher: BMJ

Publication Date: 2023

detail.hit.zdb_id: 2009590-9

SSG: 12

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Table3.XLSX

Xu, Naixin ; Zhou, Xuanyou ; Shi, Weihui ; [et al.]

Frontiers Media SA ; 2022

In: Frontiers in Physiology Vol. 13 ( 2022-8-5)

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In: Frontiers in Physiology, Frontiers Media SA, Vol. 13 ( 2022-8-5)

Abstract: Recurrent pregnancy loss (RPL) is a major type of pathological pregnancy that still lacks reliable early diagnosis and effective treatment. The placenta is critical to fetal development and pregnancy success because it participates in critical processes such as early embryo implantation, vascular remodeling, and immunological tolerance. RPL is associated with abnormalities in the biological behavior of placental villous trophoblasts, resulting in aberrant placental function. MicroRNAs (miRNAs) are increasingly being recognized as essential regulators of placental development, as well as potential biomarkers. In this study, plasma miRNAs and placental messenger RNAs (mRNAs) from RPL patients and normal pregnant (NP) controls were sequenced and analyzed. Compared to those in NP controls, 108 circulating miRNAs and 1199 placental mRNAs were differentially expressed in RPL samples. A total of 140 overlapping genes (overlapping between plasma miRNA target genes and actual placental disorder genes) were identified, and functional enrichment analysis showed that these genes were mainly related to cell proliferation, angiogenesis, and cell migration. The regulatory network among miRNAs, overlapping genes, and downstream biological processes was analyzed by protein–protein interactions and Cytoscape. Moreover, enriched mRNAs, which were predictive targets of the differentially expressed plasma miRNAs miR-766-5p, miR-1285-3p, and miR-520a-3p, were accordingly altered in the placenta. These results suggest that circulating miRNAs may be involved in the pathogenesis of RPL and are potential noninvasive biomarkers for RPL.

Type of Medium: Online Resource

ISSN: 1664-042X

URL: Article

DOI: 10.3389/fphys.2022.893744

DOI: 10.3389/fphys.2022.893744.s001

DOI: 10.3389/fphys.2022.893744.s002

DOI: 10.3389/fphys.2022.893744.s003

Language: Unknown

Publisher: Frontiers Media SA

Publication Date: 2022

detail.hit.zdb_id: 2564217-0

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Mitochondrial Dysfunctions Contribute to Hypertrophic Cardiomyopathy in Patient iPSC-Derived Cardiomyocytes with MT-RNR2 Mutation

Li, Shishi ; Pan, Huaye ; Tan, Chao ; [et al.]

Elsevier BV ; 2018

In: Stem Cell Reports Vol. 10, No. 3 ( 2018-03), p. 808-821

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In: Stem Cell Reports, Elsevier BV, Vol. 10, No. 3 ( 2018-03), p. 808-821

Type of Medium: Online Resource

ISSN: 2213-6711

URL: Article

DOI: 10.1016/j.stemcr.2018.01.013

Language: English

Publisher: Elsevier BV

Publication Date: 2018

detail.hit.zdb_id: 2720528-9

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