Structural variation and its potential impact on genome instability: Novel discoveries in the EGFR landscape by long-read sequencing

Abstract

Structural variation (SV) is typically defined as variation within the human genome that exceeds 50 base pairs (bp). SV may be copy number neutral or it may involve duplications, deletions, and complex rearrangements. Recent studies have shown SV to be associated with many human diseases. However, studies of SV have been challenging due to technological constraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examine SV in the EGFR landscape of four haplotypes derived from two human samples. We analyzed the EGFR gene and its landscape (+/-500,000 base pairs) using this approach and were able to identify a region of non-coding DNA with over 90% similarity to the most common activating EGFR mutation in non-small cell lung cancer. Based on previously published Alu-element genome instability algorithms, we propose a molecular mechanism to explain how this non-coding region of DNA may be interacting with and impacting the stability of the EGFR gene and potentially generating this cancer-driver gene. By these techniques, we were also able to identify previously hidden structural variation in the four haplotypes and in the human reference genome (hg38). We applied previously published algorithms to compare the relative stabilities of these five different EGFR gene landscape haplotypes to estimate their relative potentials to generate the EGFR exon 19, 15 bp canonical deletion. To our knowledge, the present study is the first to use the differences in genomic architecture between targeted cancer-linked phased haplotypes to estimate their relative potentials to form a common cancer-linked driver mutation.

PI3K Inhibitors in Cancer: Clinical Implications and Adverse Effects

“…Although the mechanism of action of this subunit is not well known, some reports still indicate that it works via GPCR signaling [ 34 ]. E633K is a p110ß helical mutation first reported in HER2+ breast cancer [ 35 , 36 ]. PIK3CA D1067V is another recurrent somatic mutation in the p110β subunit which induced in vitro and in vivo cancer cell growth via the activated PI3K signaling pathway.…”

Novel Diagnostic and Therapeutic Techniques Reveal Changed Metabolic Profiles in Recurrent Focal Segmental Glomerulosclerosis 

“…Concentrations of 163 metabolites including 13 amino acid/ biogenic amines, sum hexoses, 41 acylcarnitines, 15 lysophosphatidylcholines, 77 phospho-and sphingolipids, and 15 sphingomyelines from serum samples were determined using a targeted metabolomics approach using the Absolute IDQ p150 Kit (Biocrates LIFE Science AG) 75 . Brie y, the liquid chromatography with tandem liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis carried out by means of multiplereaction monitoring (MRM) acquisition using a Waters Acquity UPLC System coupled with QTRAP 5500 (AB Sciex, Darmstadt, Germany).…”

Application of long-read sequencing to the detection of structural variants in human cancer genomes

“…An SNV located in the regulatory region of the NFATC1 gene in the RERC-LC-Ad1 lung cancer cell line and allele-specific transcription with the mutation was detected. In 2020, Cook et al focused on two deletions in exon 19 of the EGFR gene [85] , which is the most important driver gene of lung adenocarcinoma, being responsible for the disease in 50% of Japanese patients with lung adenocarcinoma [86] . The authors conducted PacBio CCS sequencing of the samples from two patients with lung adenocarcinoma, and conducted haplotype phasing using WhatsHap [87] .…”