Benchmarking germline CNV calling tools from exome sequencing …
WebJul 13, 2021 · 2 Altmetric. Metrics. Whole-exome sequencing is an attractive alternative to microarray analysis because of the low cost and potential ability to detect copy number variations (CNV) of various ...
Atlas-CNV: a validated approach to call single-exon CNVs in the ...
WebMar 20, 2019 · 14 Citations. 18 Altmetric. Metrics. Abstract. Purpose. To provide a validated method to confidently identify exon-containing copy-number variants (CNVs), with a low false discovery rate (FDR),...
Evaluation of CNV detection tools for NGS panel data in …
WebJun 19, 2020 · Datasets and tools. Four datasets were included in this benchmark (ICR96 exon CNV validation series [], panelcnDataset [], In-house MiSeq and In-House HiSeq) (Table 1) with data from two ...
DeviCNV: detection and visualization of exon-level copy …
WebOct 16, 2018 · We propose a new pragmatic method for detecting CNVs in targeted NGS data with an intuitive visualization and a systematic method to assign confidence scores for candidate CNVs. Since DeviCNV was developed for use in clinical diagnosis, sensitivity is increased by the detection of exon-level CNVs.
CYP2D6 allele frequencies, copy number variants, and tandems in …
WebAug 1, 2018 · To assess the CYP2D6 copy number, two TaqMan ® Copy Number Assays (assay ID: Hs00010001_cn (Exon 9) and Hs04502391_cn (Intron 6); Life Technologies Corporation) are used. CYP2D6*36 contains gene conversion to CYP2D7 in exon 9 and the sequence of *10 and *36 are homologous in other regions.
Eukaryotic pre-mRNA processing | RNA splicing (article) - Khan Academy
WebA sequence of DNA encodes a pre-mRNA transcript that contains five regions that may potentially be used as exons: Exon 1, Exon 2, Exon 3, Exon 4, and Exon 5. The exons are arranged in linear order along the pre-mRNA and have introns in between them.
Targeting PRMT1-mediated SRSF1 methylation to suppress oncogenic exon ...
WebNov 8, 2023 · PRMT1 promotes exon inclusion for a large set of oncogenic targets through SRSF1 arginine methylation. In breast cancer, PRMT1, PRMT1-mediated SRSF1 arginine methylation, and PRMT1-regulated exon inclusion events are over-presented, which drive cancer cell growth.
WES Project | Jocelyn's Blog
WebMar 30, 2021 · normal_cn: The copy number of the locus in non-malignant cells. This should generally be 2 except for sex chromosomes in males. （以上四列在VEP注释后得到的.maf文件里） minor_cn: The copy number of the minor allele in the malignant cells. This must be less than equal the value in the major_cn column.
RNA-seq转录组数据分析丨一套完整的案例流程 - 知乎
Web将生成的RNA-Seq_Practice_countstable保存到本地，然后计算FPKM和TPM值，在R语言中进行相关计算。. FPKM（Fragments Per Kilobase of exon model per Million mapped fragments）表示每千个碱基的转录每百万映射读取的fragments，该方法是利用每个样本的总fragments数进行校正。优点是消除样本间和基因间的差异，但是该方法主要 ...
Agronomy | Free Full-Text | Genome-Wide Identification of ... - MDPI
Web2 days ago · The phytochrome-interacting factor (PIF) proteins are part of a subfamily of basic helix–loop–helix (bHLH) transcription factors that integrate with phytochromes (PHYs) and are known to play important roles in adaptive changes in plant architecture. However, the characterization and function of PIFs in potatoes are currently poorly understood. In this study, we identified seven PIF members ...
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