a-robust-polymerase-chain-reaction-based-assay-for-quantifying

A Robust Polymerase Chain Reaction-based Assay for Quantifying Cytosine-guanine-guanine Trinucleotide Repeats in Fragile X Mental Retardation-1 Gene

Fragile X syndrome (FXS) and associated disorders are caused by expansion of the cytosine-guanine-guanine (CGG) trinucleotide repeat in the 5&#8217; ...

jinan university

Recent studies demonstrate that whole-genome sequencing enables detection of cryptic rearrangements in apparently balanced chromosomal rearrangements (also known as balanced chromosomal abnormalities, BCAs) previously identified by conventional cytogenetic methods. We aimed to assess our analytical tool for detecting BCAs in the 1000 Genomes Project without knowing which bands were affected.

Identification of balanced chromosomal rearrangements previously unknown among participants in the 1000 Genomes Project: implications for interpretation of structural variation in genomes and the future of clinical cytogenetics.

Balanced chromosomal rearrangements (or balanced chromosome abnormalities, BCAs) are common chromosomal structural variants. Emerging studies have demonstrated the feasibility of using whole-genome sequencing (WGS) for detection of BCA-associated breakpoints, but the requirement for a priori knowledge of the rearranged regions from G-banded chromosome analysis limits its application. The protocols described here are based on low-pass WGS for detecting BCA events independent from chromosome analysis, and has been validated using genomic data from the 1000 Genomes Project. This approach adopts non-size-selected mate-pair library (3∼8 kb) with 2∼3 μg DNA as input, and requires only 30 million read-pairs (50 bp, equivalent to 1-fold base-coverage) for each sample. The complete procedure takes 13 days and the total cost is estimated to be less than $600 (USD) per sample. © 2018 by John Wiley & Sons, Inc.

Balanced Chromosomal Rearrangement Detection by Low-Pass Whole-Genome Sequencing.

Drug-loaded phase-transformation lipid nanoparticles (NPs) combined with low-intensity focused ultrasound (LIFU) for ultrasound molecular imaging and therapy, which is a very promising drug carrier and can provide both physical and chemical therapeutics, simultaneously. We successfully prepared the paclitaxel (PTX) loaded anti-LHRHR targeted phase-transformation lipid nanoparticles (PTX-anti-LHRHR-PTNPs) for ovarian cancer in this study combined with LIFU has the following characteristics: On the one hand, it showed smaller size and greater stability than blood cells, which significantly prolonged its half-life in the body, and can actively target ovarian cancer OVCAR-3 cells, and smoothly penetrate the endothelial gap into the tumor site for specifically killing the ovarian cancer cells. Thereby, the special drug carrier improved the therapeutic effect and reduced toxic and side effects, maximized the protection of normal tissues and minimized adverse reactions. On the other hand, PTX-anti-LHRHR-PTNPs can be targeted to focus after being injected intravenously and remain in the tumor target tissue for a long time. At the same time, liquid-gas phase-transformation can occur under LIFU triggering, resulting in more ideal and sustained ultrasound imaging effects. Then acoustic contrast agent is used to develop the molecular level of ultrasound scattering, so as to evaluate the diseased tissue from the molecular level.

An experimental study of ovarian cancer imaging and therapy by paclitaxel-loaded phase-transformation lipid nanoparticles combined with low-intensity focused ultrasound.

Microdeletions and microduplications can occur in any pregnancy independent of maternal age. The spectrum and features of pathogenic copy number variants including the size, genomic distribution and mode of inheritance are not well studied. These characteristics have important clinical implications regarding expanding noninvasive prenatal screening for microdeletions and microduplications.

Characteristics and mode of inheritance of pathogenic copy number variants in prenatal diagnosis.

Early life microflora is an important determinant of immune and metabolic development and may have lasting consequences. However, the mode of delivery and the effect of povidone iodine disinfection on neonatal oral microflora colonization are still unclear. The objective of the study was to understand the effects of the use of polyvidone iodine on infant's oral microflora after transvaginal examination during delivery, provided data support for the establishment of neonatal oral microflora health.

The effects of perineal disinfection on infant's oral microflora after transvaginal examination during delivery.

Emerging studies suggest that low-pass genome sequencing (GS) provides additional diagnostic yield of clinically significant copy-number variants (CNVs) compared with chromosomal microarray analysis (CMA). However, a prospective back-to-back comparison evaluating accuracy, efficacy, and incremental yield of low-pass GS compared with CMA is warranted.

Low-pass genome sequencing versus chromosomal microarray analysis: implementation in prenatal diagnosis.

 Increased nuchal translucency (NT) is an important biomarker associated with increased risk of fetal structural anomalies. It is known to be contributed by a wide range of genetic etiologies from single-nucleotide variants to those affecting millions of base pairs. Currently, prenatal diagnosis is routinely performed by karyotyping and chromosomal microarray analysis (CMA); however, both of them have limited resolution. The diversity of the genetic etiologies warrants an integrated assay such as genome sequencing (GS) for comprehensive detection of genomic variants. Herein, we aim to evaluate the feasibility of applying GS in prenatal diagnosis for the fetuses with increased NT.  We retrospectively applied GS (> 30-fold) for fetuses with increased NT (≥3.5 mm) who underwent routine prenatal diagnosis. Detection of single-nucleotide variants, copy number variants, and structural rearrangements was performed simultaneously, and the results were integrated for interpretation in accordance with the guidelines of the American College of Medical Genetics and Genomics. Pathogenic or likely pathogenic (P/LP) variants were selected for validation and parental confirmation, when available.  Overall, 50 fetuses were enrolled, including 34 cases with isolated increased NT and 16 cases with other fetal structural malformations. Routine CMA and karyotyping reported eight P/LP CNVs, yielding a diagnostic rate of 16.0% (8/50). In comparison, GS provided a twofold increase in diagnostic yield (32.0%, 16/50), including one mosaic turner syndrome, eight cases with microdeletions/microduplications, and seven cases with P/LP point mutations. Moreover, GS identified two cryptic insertions and two inversions. Follow-up study further demonstrated the potential pathogenicity of an apparently balanced insertion that disrupted an OMIM autosomal dominant disease-causing gene at the insertion site.  Our study demonstrates that applying GS in fetuses with increased NT can comprehensively detect and delineate the various genomic variants that are causative to the diseases. Importantly, prenatal diagnosis by GS doubled the diagnostic yield compared with routine protocols. Given a comparable turnaround time and less DNA required, our study provides strong evidence to facilitate GS in prenatal diagnosis, particularly in fetuses with increased NT.

Article	Year
Identification of balanced chromosomal rearrangements previously unknown among participants in the 1000 Genomes Project: implications for interpretation of structural variation in genomes an... Genetics in medicine : official journal of the American College of Medical Genetics\| PubMed ID: 29095815	2018
Balanced Chromosomal Rearrangement Detection by Low-Pass Whole-Genome Sequencing. Current protocols in human genetics\| PubMed ID: 29364520	2018
An experimental study of ovarian cancer imaging and therapy by paclitaxel-loaded phase-transformation lipid nanoparticles combined with low-intensity focused ultrasound. Biochemical and biophysical research communications\| PubMed ID: 30180951	2018
Characteristics and mode of inheritance of pathogenic copy number variants in prenatal diagnosis. American journal of obstetrics and gynecology\| PubMed ID: 31207233	2019
The effects of perineal disinfection on infant's oral microflora after transvaginal examination during delivery. BMC pregnancy and childbirth\| PubMed ID: 31234808	2019
Low-pass genome sequencing versus chromosomal microarray analysis: implementation in prenatal diagnosis. Genetics in medicine : official journal of the American College of Medical Genetics\| PubMed ID: 31447483	2019
Prenatal Diagnosis of Fetuses With Increased Nuchal Translucency by Genome Sequencing Analysis. Frontiers in genetics\| PubMed ID: 31475041	2019

Huilin Wang

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