IVPN - Personalized Medicine

#Personlaized_Medicine_Bioinformatics (No.6) 🧬 File Formats 💾 In our previous post, we highlighted the importance of Quality Control (QC) in NGS data analysis. QC is the initial step that ensures your raw sequencing data is accurate, error-free, and ready for reliable downstream analysis 💻. Before proceeding with the NGS data analysis workflow, it's important to understand the key file formats used to store and represent sequencing data. These formats are the building blocks for subsequent genomic data analysis steps ✅.    1. FASTA: This is the simplest format for reporting sequences and is widely accepted by sequence analysis programs. It includes a sequence name, a description (such as sequencer info or annotations), and the sequence itself, which can represent either nucleic acids or amino acids. Each sequence has at least two lines: the first line is the header, starting with a ">" symbol. The portion from ">" to the first whitespace is the sequence identifier, while everything after it is the description (which can include the machine serial number or read orientation). Most sequence databases store sequences in FASTA format, which can also be generated from a FASTQ file. 2. FASTQ: Sequencing instruments typically produce raw read data in FASTQ format, which contains nucleotide sequences (A, T, G, C, and N for unknown bases) similar to FASTA files. In addition, FASTQ files include quality scores for each base, represented using ASCII characters, ranging from (quality score of 0) to K (quality score of 42). 3. SAM (Sequence Alignment Map): This is a text-based format for strong read alignments against reference sequences. This is generated by almost every alignment algorithm that exists. 4. BAM (Binary Alignment Map file): This is a compressed binary version of the SAM format, making it smaller and faster to read. However, it is not human-readable and requires conversion to other formats (eg: SAM) or the use of tools like Samtools, Picard Tools, and IGV.  5. CRAM (Compression Alignment/ Map): This is a newer format similar to BAM, retaining the same information as SAM while being compressed. However, it is more efficient by storing only the differences between aligned sequences and a reference, greatly reducing storage space. 6. VCF (Variant Call Format): Text file format utilized to store gene sequence variations which are typically generated as the output of a bioinformatics pipeline. 7. GFF3 (General Feature Format): Is a tab-delimited text file that holds information about gene annotation which indicates the location of all genes within the reference genome provided as FASTA file. and it is vital that the annotation file corresponds to the reference genome version. Thanks to the IVPNeer Zena Jandali for this review👏👏 #NGS #Bioinformatics #File_Formats #PersonalizedMedicine #Pharmacogenomics #FASTA #Quality_control

#Presicion_Medicine_in_Oncology (No.1) 💊 Advancements in Precision Oncology for Hepatocellular Carcinoma (HCC) with ctDNA 🧬 When talking about personalized medicine, circulating tumor DNA (ctDNA) is revolutionizing the approach to HCC treatment. This non-invasive liquid biopsy method offers a promising alternative to traditional invasive biopsies, providing insights into cancer-specific genetic and epigenetic changes 📈. 🔬Key Highlights: Early Detection & Monitoring: ctDNA enables early diagnosis and real-time monitoring of HCC, capturing tumor heterogeneity and guiding precise treatment strategies. 🧬 Technological Advances: Next-generation sequencing and PCR-based assays have significantly improved the detection and quantification of ctDNA. 💊 Clinical Applications: ctDNA is pivotal in assessing treatment response, detecting minimal residual disease, and predicting prognosis. ⚠️ Challenges & Future Directions: Despite its potential, challenges such as high costs, the need for standardized methodologies, and integration into clinical practice remain. Dive deeper into the transformative role of ctDNA in precision oncology for HCC by exploring the full study. https://lnkd.in/dHvSsz77 Thanks to the IVPNeer Ahmed Obaid for this summarization 👏👏 #PrecisionOncology #Presicion_Medicine #Oncology #ctDNA #HCC #Pharmacogenomis #NGS

As next-generation sequencing (NGS) continues to revolutionize research, understanding how we store and manage NGS data is more important than ever 💾 💡How do you store your NGS data, and what challenges do you face when selecting the right file format? Join the discussion and vote in the poll below! Let’s learn from each other’s experiences and explore best practices in data storage for NGS📊 #NGS #Data #Data_Storage #Bioinformatics #PersonalizedMedicine

📍RNPGx Guideline for the use of antidepressants in relation to CYP2C19 and CYP2D6 genetic polymorphisms🧬 French National Network of Pharmacogenetics (RNPGx) has a unique focus on recommending pharmacogenetic testing. It evaluates the evidence for the functionality of pharmacogene variants, categorizing them into three levels: demonstrated, probable, or potential functionality ⚠️ The RNPGx strongly recommends conducting CYP2D6 and CYP2C19 genotyping prior to the initiation an antidepressant treatment. This is particularly crucial for patients identified as having a high risk of toxicity associated with these medications. The article by Picard et al. [Article:28237406] highlights the compelling evidence that supports the necessity of assessing the CYP2D6 and CYP2C19 genetic polymorphisms, thereby advocating for their use in clinical practice. Kirchheiner et al. [Article:15037866] and Crews et al. [Article:22205192], publications state that due to the significant risk of adverse effects that could lead to the discontinuation of treatment, it is advisable to avoid using certain antidepressants in patients who exhibit complete CYP2D6 or CYP2C19 deficiency 🚫. For those with partial deficiencies, a dose reduction of approximately 25-50% from the standard dosage can be considered to mitigate risks while still providing therapeutic benefits↔️. Furthermore, given the current absence of robust biomarkers that predict individual responses, the implementation of these genetic tests may serve to optimize antidepressant treatment protocols. This approach can help tailor therapies to minimize adverse effects while maximizing efficacy ✅. In the section dedicated to "Interpreting test results" the article elaborates on the functional categories and phenotype classifications for CYP2C19 and CYP2D6 as published by the Clinical Pharmacogenetics Implementation Consortium (CPIC). It also discusses the guidelines for prescribing antidepressants as articulated by Leon et al. [Articles:16384813, 25200585]. These guidelines provide essential insights for clinicians on how to interpret genetic test results to inform dosing strategies for tricyclic antidepressants and other related medications. The collaborative nature of this effort underscores the importance of integrating pharmacogenetic insights into standard psychiatric care, ultimately enhancing patient safety and treatment outcomes💊↖️. Reference: https://lnkd.in/d6JjsrSX  Thank to the IVPNeer Shaimaa Ahmed Abdel-mougood, BPharm, PharmD, MSc.IPH, MSc.Biotech (MBT) 👏👏 #personalized_Medicine #CYP2D6 #CYP2C19 #Genotyping #antidepressants #CPIC #Pharmacogenomis

🔍 Exploring the Crucial Role of CYP2D6 in Pharmacogenomics: A Comprehensive Review “A Review of the Important Role of CYP2D6 in Pharmacogenomics“ published in the journal Genes by MDPI. Authored by Christopher Taylor and colleagues, this article provides a thorough examination of the cytochrome P450 2D6 (CYP2D6) enzyme, which is pivotal in the metabolism of approximately 20% of commonly prescribed drugs across various medical fields including psychiatry, pain management, oncology, and cardiology. 🧬 Key Insights from the Review: Genetic Diversity: CYP2D6 is highly polymorphic, which means it has many genetic variants that significantly influence its drug-metabolizing function. This genetic diversity can lead to varied drug responses among individuals, affecting both efficacy and safety. 💊 Clinical Implementation: Despite its significance, the integration of CYP2D6 genotyping into clinical practice has been slow. The review calls for increased efforts to overcome these challenges to fully realize the potential benefits of personalized medicine. 🔬 Advancements in Technology: The article highlights novel laboratory methods and computational approaches, including machine learning, to predict the functional impact of CYP2D6 variants. These advancements are crucial for improving the accuracy of genotype-phenotype correlations. 📝 Pharmacogenomic Guidelines: There are established guidelines by entities like the Clinical Pharmacogenetics Implementation Consortium (CPIC) and the Dutch Pharmacogenetics Working Group (DPWG), which provide recommendations based on CYP2D6 genotype. These guidelines are essential for clinicians to make informed therapeutic decisions. ✅ Future Directions: The review discusses the need for cost-effective, rapid, and reliable testing methods that can be integrated into clinical settings. It also points out the necessity for ongoing research to further elucidate the complex genotype-phenotype relationships associated with CYP2D6. 🌍 Implications for Healthcare: Understanding and implementing CYP2D6 pharmacogenomics can significantly reduce adverse drug reactions and improve drug efficacy, leading to more personalized and effective healthcare solutions. 🔗 For those interested in the detailed mechanisms of drug metabolism and the impact of genetic variability on pharmacotherapy, this article is a must-read. It not only underscores the importance of CYP2D6 in drug metabolism but also highlights the broader implications of pharmacogenomics in modern medicine. 👉 Read the full article here https://lnkd.in/d6cmaYMu Thanks to the IVPNeer Ahmed Obaid for summarizing the review paper 👏👏 #Pharmacogenomics #PersonalizedMedicine #DrugMetabolism #CYP2D6 #HealthcareInnovation

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🔍 Understanding Genetic Testing for Breast Cancer 🎗️ Breast cancer is a significant health concern, and understanding the genetic factors that contribute to its risk can be vital for prevention and early detection🌸🧬. Genetic testing has become an essential tool for females with a family history of breast cancer or those at increased risk⚠️. Here are some key genes that are commonly tested: 1- BRCA1 (Breast cancer gene 1) and BRCA2 (Breast cancer gene 2): These genes produce proteins that help repair damaged DNA. Mutations in either gene can significantly increase the risk of breast cancer. 2- PALB2 (Partner and Localizer of BRCA2): A tumor suppressor gene that works with BRCA1 and BRCA2 in the homologous recombination repair (HRR) pathway, which is essential for repairing DNA breaks. Genetic variants in PALB2 are associated with a high risk of breast cancer. 3- TP53 (Tumor Protein p53): This tumor suppressor gene encodes the p53 protein, which regulates DNA repair and cell division. Mutations in TP53 are found in nearly 30% of breast cancer cases. 4- CHEK2 (Checkpoint Kinase 2): A tumor suppressor gene encoding a serine/threonine kinase involved in DNA repair, cell cycle regulation, and apoptosis. Genetic variants in CHEK2 are linked to increased breast cancer risk. Other genes also play a role in breast cancer susceptibility, and genetic testing can provide invaluable information for individuals and families, guiding personalized screening and preventive measures💊🧬. Together, we can enhance awareness and empower females to take charge of their health 🎀. Thanks to the brilliant IVPNeer Sahar Altoum, RPh., M.Sc. for this review👏 #BreastCancer #GeneticTesting #PersonalizedMedicine #Healthcare #PatientCare #BRCA #Pink_October

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🌟 Unlock the Future of Personalized Medicine! 🌟 🔬 Join us for the exclusive webinar: The PREPARE Study – Results and Future Perspectives 🗓 Thursday, October 31, 2024 ⏰ 5:00 PM (KSA Time) We are honored to host Prof. Jesse Swen, a leading expert from Leiden University Medical Center, who will unveil breakthrough findings from the PREPARE Study! 🗣 Moderated by Prof. Nancy Hakooz, University of Jordan Why Attend? ✔️ Discover the impact of the PREPARE Study ✔️ Learn about the future of personalized medicine ✔️ Get exclusive insights from top experts Don’t miss out on shaping the future of healthcare! 🔗 Secure your spot now https://lnkd.in/dnrv7Wcz #HealthcareInnovation #Pharmacogenomics #PrecisionMedicine #IVPN #FutureofHealth

🧬 The Power of Personalized Breast Cancer Treatment with WGS and WES 🎗️ October's Breast Cancer Awareness Month shines a spotlight on the importance of early detection, research, and innovative treatments 🎀. Traditionally, treatment decisions for breast cancer were based on tumor stage, grade, and hormone receptor status. However, breast cancer is a heterogeneous disease, meaning that tumors with similar characteristics can have vastly different genetic profiles. This is where Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES) make a game-changing impact🔬 . By analyzing a patient’s entire genome or exome, these technologies can uncover unique mutations driving the tumor’s growth, which can be used to: 1. Identify patients who will respond to specific therapies: For example, patients with BRCA1/2 mutations are more likely to respond to PARP inhibitors, which target DNA repair mechanisms. 2. Avoid unnecessary treatments: WGS and WES can identify patients unlikely to benefit from certain therapies, reducing exposure to side effects and avoiding unnecessary costs. 3. Develop new targeted therapies: By identifying novel cancer-driving genes, researchers can develop new drugs that target these specific vulnerabilities. Many ongoing clinical trials are investigating how WGS and WES can guide treatment decisions such as selecting targeted therapies based on tumor mutations or identifying patients more likely to benefit from chemotherapy. As highlighted in the latest review by Ganatra et al. (2024), WGS and WES have the potential to revolutionize breast cancer treatment by shifting from a one-size-fits-all approach to one where treatment is tailored to each patient’s unique genetic makeup🧬💊. Thanks to the IVPNeer Zena Jandali for such review 🌸 #BreastCancerAwareness #NGS #WGS #WES #PersonalizedMedicine #CancerResearch #PrecisionOncology