Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms

Rao, Junhua; Peng, Lihua; Liang, Xinming; Jiang, Hui; Geng, Chunyu; Zhao, Xing‐Ming; Liu, Xin; Fan, Guangyi; Chen, Fang; Mu, Feng

doi:10.1186/s12859-020-03859-x

Cited by 14 publications

(7 citation statements)

References 30 publications

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“…We performed WGS to detect the missing variants in four patients (A2018, A3537, A3742, and A4170) who had only one pathogenic variant detected using MGI, as previously described. 17 , 18 In brief, the WGS libraries were sequenced on the DNBSEQ-T7 platform (MGI Tech) using a 100 bp paired-end mode with a 30-fold minimal median coverage per genome. The data were mapped to the human genome GRCh37/hg19 with the Burrows–Wheeler Aligner.…”

Section: Methodsmentioning

confidence: 99%

Comprehensive Genetic Analysis Unraveled the Missing Heritability in a Chinese Cohort With Wolfram Syndrome 1: Clinical and Genetic Findings

Zhang

Xie

et al. 2022

Invest. Ophthalmol. Vis. Sci.

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Purpose To identify the missing heritability of patients with Wolfram syndrome 1 (WFS1) in a Chinese cohort and to report their clinical and genetic features. Methods We recruited 24 unrelated patients with suspected WFS1 who carried at least one variant in WFS1 . All patients underwent ophthalmic examinations and comprehensive molecular genetic analyses, including Sanger-DNA sequencing of WFS1 and next-generation sequencing of the whole WFS1 sequence. Results We identified 38 distinct pathogenic variants of WFS1 in the 24 probands, comprising 23 patients with biallelic variants and one patient with a monoallelic variant. Sanger-DNA sequencing of WFS1 initially detected 35 variants, and subsequent whole genome sequencing revealed three missing variants: one novel deep intronic variant (DIV), one copy number variant (CNV), and one variant in the promoter region. Minigene assays showed that the DIV activated cryptic splice sites, leading to the insertion of pseudoexons. Optic atrophy was observed in all patients, and diabetes mellitus (DM) was revealed in 21 patients (91.3%), hearing loss in nine patients (39.1%), renal tract abnormalities in nine patients (39.1%), and diabetes insipidus in five patients (21.7%). The mean onset age for DM was significantly younger in the patients with biallelic null variants than in the patients with biallelic missense variants. Conclusions Our results extend the pathogenic variant spectrum of WFS1 . DIVs and CNVs explained rare unresolved Chinese cases with WFS1. The patients showed a wide and variable clinical spectrum, supporting the importance of genetic analysis for patients with atypical WFS1.

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Section: Methodsmentioning

confidence: 99%

Comprehensive Genetic Analysis Unraveled the Missing Heritability in a Chinese Cohort With Wolfram Syndrome 1: Clinical and Genetic Findings

Zhang

Xie

et al. 2022

Invest. Ophthalmol. Vis. Sci.

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“…TRIzol (Rio et al 2010;Zhang et al 2010) was used for RNA extraction. The mRNA from three organs (three replicates) was purified from the total RNA using oligo (dT) magnetic beads for sequencing (Young et al 2010;Patterson et al 2019;Rao et al 2020). A DNA probe was digested with DNase I after hybridisation with rRNA to obtain purified RNA.…”

Section: Preparation and Treatment Of Plant Materialsmentioning

confidence: 99%

A preliminary study on the root-knot nematode resistance of a cherry plum cultivar Mirabolano 29C

Liu¹,

Zhu²,

Li³

et al. 2023

CZECH J GENET PLANT

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Grafting is the most important means of breeding peach, plum, apricot, and other fruit trees, and the selection of the rootstock is crucial to the quality of the grafting and the yield of the products. The traditional commonly used peach rootstock is susceptible to root-knot nematode infections, resulting in a decreased yield, while a variety of cherry plum rootstocks, Mirabolano 29C, is resistant to root-knot nematode. In this study, root-knot nematode infection experiments on seedlings of traditional peach rootstocks and Mirabolano 29C confirmed that Mirabolano 29C was indeed more resistant to root-knot nematodes. At the same time, we compared the roots of the root-knot nematode uninfected and infected Mirabolano 29C by transcriptome sequencing and found 3 176 differentially expressed genes. A further functional enrichment analysis of these genes found that the secondary metabolites, phenylpropane and flavonoids, may be responsible for the high resistance of Mirabolano 29C to root-knot nematodes. These results can provide a reference value for the disease resistance breeding of rootstocks.

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“…The integrity of RNA and the library was examined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). For sequencing, mRNA with Poly (A) of livers (six samples) was enriched from total RNA using oligo (dT) magnetic beads [13,14]. First-strand cDNA was synthesized using random N6 primers, followed by second-strand cDNA synthesis.…”

Section: Rna Extraction Library Preparation and Sequencingmentioning

confidence: 99%

Transcriptome Comparison Reveals the Difference in Liver Fat Metabolism between Different Sheep Breeds

Jin

Fei

et al. 2022

Animals

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Hu sheep and Tibetan sheep are two commonly raised local sheep breeds in China, and they have different morphological characteristics, such as tail type and adaptability to extreme environments. A fat tail in sheep is the main adipose depot in sheep, whereas the liver is an important organ for fat metabolism, with the uptake, esterification, oxidation, and secretion of fatty acids (FAs). Meanwhile, adaptations to high-altitude and arid environments also affect liver metabolism. Therefore, in this study, RNA-sequencing (RNA-seq) technology was used to characterize the difference in liver fat metabolism between Hu sheep and Tibetan sheep. We identified 1179 differentially expressed genes (DEGs) (Q-value < 0.05) between the two sheep breeds, including 25 fat-metabolism-related genes. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, 16 pathways were significantly enriched (Q-value < 0.05), such as the proteasome, glutamatergic synapse, and oxidative phosphorylation pathways. In particular, one of these pathways was enriched to be associated with fat metabolism, namely the thermogenesis pathway, to which fat-metabolism-related genes such as ACSL1, ACSL4, ACSL5, CPT1A, CPT1C, SLC25A20, and FGF21 were enriched. Then, the expression levels of ACSL1, CPT1A, and FGF21 were verified in mRNA and protein levels via qRT-PCR and Western blot analysis between the two sheep breeds. The results showed that the mRNA and protein expression levels of these three genes were higher in the livers of Tibetan sheep than those of Hu sheep. The above genes are mainly related to FAs oxidation, involved in regulating the oxidation of liver FAs. So, this study suggested that Tibetan sheep liver has a greater FAs oxidation level than Hu sheep liver. In addition, the significant enrichment of fat-metabolism-related genes in the thermogenesis pathway appears to be related to plateau-adaptive thermogenesis in Tibetan sheep, which may indicate that liver- and fat-metabolism-related genes have an impact on adaptive thermogenesis.

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Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms

Cited by 14 publications

References 30 publications

Comprehensive Genetic Analysis Unraveled the Missing Heritability in a Chinese Cohort With Wolfram Syndrome 1: Clinical and Genetic Findings

Comprehensive Genetic Analysis Unraveled the Missing Heritability in a Chinese Cohort With Wolfram Syndrome 1: Clinical and Genetic Findings

A preliminary study on the root-knot nematode resistance of a cherry plum cultivar Mirabolano 29C

Transcriptome Comparison Reveals the Difference in Liver Fat Metabolism between Different Sheep Breeds

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