Implementation of YAML-based models for PGx and PRS genomic analysis
Application of long-read sequencing to improve genotyping of complex pharmacogenetic regions Pharmacogenomics (PGx) is a critical field in personalized medicine, focusing on how an individual’s genetic makeup influences their response to drugs. By analyzing genetic variants that affect drug metabolism, efficacy, and toxicity, PGx can guide tailored treatments, ensuring optimal drug selection and dosing. This […]
From Phenotype to Clinical Practice: Implementing Pharmacogenetic (PGx) Recommendations
Pharmacogenomics, the study of how genes affect a person’s response to drugs, is crucial in the realm of personalized medicine. Pharmacogenes, the genes encoding factors directly involved in drug actions, can be broadly classified into two functional groups: metabolic enzymes and transporters/receptors. Enzyme pharmacogenes are responsible for converting substrates, such as drugs, into smaller molecules, […]
Empowering Precision Medicine: Can Long-Read Sequencing Deliver Enhanced Genetic Insights?
A typical single read using current short-read sequencing technology spans approximately 150 nucleotides. Alignment of these reads becomes difficult when a sequence lacks specificity, such as when it contains repetitive motifs. Consequently, such reads often receive lower mapping quality scores since they can potentially align to multiple regions within a genome. For example, the read […]
Unique Molecular Identifiers (UMIs) in low-frequency somatic variant detection
Unique Molecular Identifiers (UMIs), also known as Molecular Barcodes or Random Barcodes, are short random nucleotide sequences used to label each DNA or RNA molecule in a sample for high-throughput sequencing. These unique identifiers serve as molecular tags, allowing the distinction of true variants that are present in the original sample from errors introduced during […]
Case study: Diagnosis of a rare coexistence of two independent primary pediatric tumors using HPO-based gene panel in WES analysis.
The specification of the list of genes to be analyzed is of high importance in the NGS data analysis pipeline, as it determines the scope of the analysis. This is especially significant in the case of WES and WGS data, where multiple variants within the analyzed sample are expected to differ from the reference genome. […]
Quality control during NGS data analysis in Intelliseq workflows
Implementation of Quality Control (QC) steps in the Next-Generation Sequencing (NGS) data analysis pipelines ensures the reliability of the generated genomic information. NGS technologies produce vast amounts of data, making it crucial to identify and address potential issues early in the analysis workflow. QC involves a series of systematic tests and filtering steps aimed at […]
From genetic data to accurate diagnosis: case study on practical use of NGS data analysis by Intelliseq
Precision medicine revolutionizes healthcare by customizing medical decisions and treatments according to an individual’s unique genetic makeup and other relevant factors like lifestyle and family disease history. This patient-centered approach empowers healthcare providers to utilize targeted therapies that specifically address the molecular and genetic characteristics of a patient’s condition. By doing so, precision medicine reduces […]
Inheritance patterns in NGS-based Disease Diagnosis
Understanding the inheritance patterns of genes is particularly significant in the context of genetic diseases. The identification and classification of these patterns provide valuable insights into the likelihood of a genetic variant causing a disease. By incorporating zygosity and gene inheritance information, IntelliseqFlow workflows assign specific inheritance pattern matches to identified variants. This comprehensive approach […]
Identification of SNVs (Single Nucleotide Variants) and small indels (insertion-deletion) by iFlow
Ten most common types of genetic variations in the human genome are variations of a single nucleotide (SNV, Single Nucleotide Variant). These include a single nucleotide substitution (transition and transversion), insertion, or deletion within a DNA sequence. All of us inherit multiple single nucleotide variants (SNVs) from our parents. Additionally, during our lifetime, de novo […]
Structural Variants (SVs) – Large-scale genome rearrangements
The Structural Variants (SVs) are large-scale genetic alterations that affect the structure of the genome. They can involve deletions, insertions, inversions, duplications, and translocations of DNA segments that are at least 50 base pairs long. SCHEME ILLUSTRATING THE SV: Structural variants (SVs) can be found in both coding and non-coding regions of the genome. Some […]