Evaluating Splice Site Variants in VarSeq

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To adequately assess a variant's pathogenicity it is crucial to take into account the variant's effect on splicing. While mutations that disrupt the pairs of bases at the beginning of a splice site are straightforward to identify, detection of disrupted splice sites caused by changes to the splice motif is more difficult. In this webcast, we will discuss VarSeq's capabilities for detecting both disrupted and novel splice sites. This will include a deep dive into several splice site variants to examine their effect and assess their pathogenicity.

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Evaluating Splice Site Variants in VarSeq
Nathan Fortier, Ph.D. – Director of Research
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NIH Grant Funding Acknowledgments
▪ Research reported in this publication was supported by the National Institute Of
General Medical Sciences of the National Institutes of Health under:
- Award Number R43GM128485
- Award Number 2R44 GM125432-01
- Award Number 2R44 GM125432-02
- Montana SMIR/STTR Matching Funds Program Grant Agreement Number 19-51-RCSBIR-005
▪ PI is Dr. Andreas Scherer, CEO Golden Helix.
▪ The content is solely the responsibility of the authors and does not necessarily
represent the official views of the National Institutes of Health.

Golden Helix – Who We Are
Golden Helix is a global bioinformatics
company founded in 1998.
GWAS
Genomic Prediction
Large-N Population Studies
RNA-Seq
CNV-Analysis
Variant Warehouse
Centralized Annotations
Hosted Reports
Sharing and Integration
Variant Calling
Filtering and Annotation
Clinical Reports
CNV Analysis
Pipeline: Run Workflows

Cited in over 1,300 peer-reviewed publications

Golden Helix – Who We Are
When you choose a Golden Helix solution, you get more than
just software
▪ REPUTATION
▪ TRUST
▪ EXPERIENCE
▪ INDUSTRY FOCUS
▪ THOUGHT
LEADERSHIP
▪ COMMUNITY
▪ TRAINING
▪ SUPPORT
▪ RESPONSIVENESS
▪ INNOVATION and
SPEED

VSClinical
▪ Complete Support for ACMG Guideline
Workflow:
- Implements a guided workflow for following the ACMG guideline
scoring and classifying
- Place criteria into conceptually related groups, paired with their
opposites, and formatted as answerable question.
▪ Aggregate and Automate:
- Questions have supporting evidence presented with rich and
interactive visuals
- Automatically computed recommendations for questions that have
explicit bioinformatic evidence, with supporting reasons for each
answer.
▪ Expert and Beginner Friendly:
- Start with descriptive summaries and recommendations for a
variant
- Deep dive into Population Catalogs, Gene Impact, Published
Studies and Clinical tabs
- Integrated documentation, readings on scoring criteria and
citations

Splice Sites
▪ Understanding a variant’s impact on
splicing is crucial
▪ Synonymous variants can disrupt
existing splice sites or introduce
novel splice sites
▪ Such variants can cause exon
skipping or truncation

Splice Sites
▪ Introns have distinct nucleotide
pairs at each end
- GT at the 5’ end (Donor Site)
- AG at the 3’ end (Acceptor Site)
▪ Area surrounding nucleotide pair is
defined by a splice motif
▪ Sequences around splice sites are
highly variable
▪ Machine learning and probabilistic
methods are used to identify sites

Algorithms
▪ VSClinical supports four splice site prediction algorithms
- PWM: Uses position weight matrix similar to SpliceSiteFinder and
Human Splice Finder
- MaxEntScan: Approximates sequence motifs using Maximum
Entropy Distribution
- NNSplice: Identifies splice sites using neural networks
- GeneSplicer: Uses Markov models combined with maximal
dependence decomposition

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NGS tests in the clinic cover more use cases than ever and are increasingly complex to implement. This leads to an increase in time to validate and bring tests to production, impacting a lab’s ability to be economically viable and serve the needs of patients. Core to the complexity is the expansion of tests to include multiple types of biomarkers and variants, including CNVs, gene fusions, and genomic signatures. The bioinformatics demands of these pipelines require powerful tools with built-in capabilities to handle the diverse needs of modern NGS tests and to integrate and automate the disparate steps leading to clinical insight. Join us in this webinar as we explore the VarSeq suites’ capabilities as a fast, modular, and highly configurable solution for variant analysis and interpretation. We will cover: The bioinformatic diversity of comprehensive genetic tests with NGS Automation of FASTQ to clinical reports without losing control over the results of a test Leverage built-in and custom automation capabilities in the VSClinical cancer guideline workflow to reduce work and improve accuracy Reporting the relevant diagnostic and therapeutic findings for a patient based on the raw genomic data of modern NGS tests requires both human experience and advanced analysis software. We hope you can join us as we unpack how automation is a critical part of implementing NGS tests and furthering the application of precision medicine.

Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solution

Golden Helix

Comprehensive genomic testing via next generation sequencing (NGS) is being increasingly adapted as part of cancer care in conjunction with molecular and immunohistochemical tests. Comprehensive genomic profiling potentially expands the number of targeted therapies that are available to patients, improves patient diagnosis and prognosis, and increases the number of clinical trials that are relevant to patients. However, with these advancements come challenges such as gaps in expertise resulting in inadequate efforts to interpret genomic data accurately and efficiently, poorly coordinated efforts to implement precision care, patients being diagnosed and treated despite inadequate access to relevant information and subsequent lack of patient exposure to all available treatment options. Golden Helix CancerKB v2.0 provides a means of closing the gap, whether you're a beginner who is trying to capture the vast amount of knowledge in the cancer field or an expert who has high sample volume AND needs to keep up with the ever-evolving knowledge of Tier II and III variants. In this webcast, we will discuss and apply Golden Helix CancerKB in the context of cancer precision medicine. Golden Helix CancerKB is systematically curated and reviewed by experts in the field and contains information about cancer genes, biomarkers, and treatments generated from several trusted cancer resources. With VarSeq 2.3.0’s added support for comprehensive cancer genomic profiling tests, Golden Helix CancerKB has expanded to include interpretations for genomic signatures, combination biomarkers, and more investigational (tier II) biomarkers, among several other additions that will be discussed. With the Golden Helix CancerKB database, users will experience a streamlined automatic matching of biomarkers to available drugs and trials which ultimately saves users massive amounts of time and effort while reducing the possibility for errors.

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VarSeq 2.3.0 facilitates the evaluation of a multitude of somatic genomic variations with a more refined user interface to streamline variant evaluation. Our recent webcasts have shown the full range of these newly developed upgrades: VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation VarSeq 2.3.0: New TSO-500 and Genomic Signature Support in VSClinical AMP Now, we are showing it all in action from the user’s perspective. This webcast will provide a comprehensive demonstration of performing somatic variation analysis and reporting. We will review how to use workflow automation to expedite the NGS project creation process and report rendering. We will also demonstrate the streamlined capture of knowledge during variant evaluation by leveraging our clinical expert-curated interpretations with the Golden Helix Cancer Knowledge Base (CancerKB). We hope you will join us to see VarSeq 2.3.0 from a user’s perspective, covering: -Somatic variant workflows: necessary algorithms and filtering strategies -Import of all relevant biomarker and genomic signatures data from TSO-500 -Review content and value of clinically curated interpretations and treatments with CancerKB -Interpretation of structural variants in the VSClinical AMP Guidelines workflow -Workflow automation with VSPipeline

A User’s Perspective: Somatic Variant Analysis in VarSeq 2.3.0

Golden Helix

Next Generation Sequencing allows for the detection of a wide variety of genomic alterations. This includes small mutations, copy number variants and complex rearrangements. However, it can be difficult to annotate, filter, and interpret these alterations. As part of our VarSeq 2.3.0 release, we have greatly simplified this process by allowing you to import, annotate, and filter mutations across all spectrums of genomic variation. This supports concurrent importation of small variants and CNVs as well as complex rearrangements. This release also includes strong support for structural variant annotation, filtering, and interpretation, including structural variant effect prediction. After filtering is complete, any clinically relevant structural variants can be interpreted with the VSClinical AMP Guidelines workflow and included in the final clinical report. Come join us for this webcast to discuss VarSeq’s enhanced import and annotation capabilities, including: Concurrent importation of variants CNVs and complex rearrangements Improved multi-threaded import which dramatically speeds up the importation of large VCFs Annotation of structural variants and prediction of effect Interpretation of structural variants in the VSClinical AMP Guidelines workflow Support for visualization and use of CRAM files as input for computing coverage statistics

VarSeq 2.3.0: Supporting the Full Spectrum of Genomic Variation

Golden Helix

Precision medicine for cancer is rapidly accelerating because of the development and approval of targeted molecular therapies. These therapies require new genomic biomarkers as an indication for use, and require evaluating additional mutation types that are available in comprehensive genomic profiling assays as well as the small variants detected by Next-Generation Sequencing gene panels. We are excited to announce VarSeq 2.3.0 which will update the VSClinical AMP workflow to meet the growing needs of labs conducting comprehensive genomic profiling (CGP) of tumors. This includes built-in support for the Illumina TruSight Oncology 500 (TSO-500) kit as well as similar kits from other vendors. The VSClinical AMP workflow has also gained native support for the bioinformatic outputs of CGP kits. Join us to learn about comprehensive genomic profiling in cancer, specifically: Evaluation and clinical reporting of genomic signatures such as Microsatellite (MSI), Tumor mutation burden (TMB), PD-L1, Homologous recombination deficiency (HRD) statuses, and more. Built-in TSO-500 import and expandable import capabilities for new genomic data types through the new advanced workflow scripting system. Golden Helix CancerKB updates with report-ready genomic-signature interpretations written for approved therapies as well as gene interpretations for all 500 genes of the TSO-500 panel. In addition, CancerKB scopes have been extended to reference multiple relevant biomarkers in a single interpretation, capture approved therapies at the tumor type level, and include interpretations for clinically relevant negative findings. Expanded clinical trial support to include international trials and the ability to search within proximity of European postal codes. VSClinical is accessing all active studies in AACT/ClinicalTrials.gov wherein users can search and select trials based on relevant drugs, biomarkers, and the geographic distance to the patient or testing site. VarSeq 2.3.0 will deliver powerful capabilities for genomic profiling in cancer, enabling a new level of personalized and effective care for your patients. We look forward to demonstrating these updates and Golden Helix’s continued innovation making the VarSeq Clinical Suite the NGS analysis platform of choice for germline and cancer testing.

VarSeq 2.3.0: New TSO-500 and Genomic Signature Support in VSClinical AMP

Golden Helix

One major hurdle facing medicine is the need to quickly identify and assess the genetic components contributing to rare diseases. It has been estimated that nearly 350 million people suffer from rare diseases, 140 million of which are children, of whom ~30% do not live past their fifth birthday1,2. The specific issue to overcome is reducing morbidity by facilitating rapid diagnosis and treatment. Fortunately, the cost of whole genome sequencing has dropped below the $1000 mark, which not only makes the NGS approach more affordable but has become the status quo method of comprehensive diagnosis for these rare disorders. Currently, there are limited options in the market when it comes to quality software that can scale to this size of data and handle variant processing and evaluation in a timely fashion. Fortunately, Golden Helix has sought to set the market standard for top-quality NGS analysis with our bioinformatic software VarSeq. The focus of this webcast will be to explore example workflows tailored for rare disorders and elaborate on how best to expedite the NGS pipeline process with our command-line tool VSPipeline. During the webcast, we will address the following: Customizing clinically validated NGS workflows with VarSeq for both single sample and trios Demonstrating the automation of ACMG-based guideline review in the VSClinical variant interpretation hub and rendering of customized clinical reports Expediting the NGS workflow via Golden Helix command-line tool VSPipeline We look forward to you joining us for our presentation, where we can demonstrate the value of our products when building your next-gen workflows. Ultimately, we wish to diminish the intimidation of genome workflow design and leave our future customers feeling confident that there is capable software to suit their needs. Bick D, Jones M, Taylor SL, et al. Case for genome sequencing in infants and children with rare, undiagnosed or genetic disease. J Med Genet 2019; 56:783-791. Owen M, Lefebvre S, Hansen C, et al. An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. Nat Commun 2022; 13: 4057. https://doi.org/10.1038/s41467-022-31446-6

Single Sample and Family Based Genome Analysis With VarSeq

Golden Helix

Somatic analysis is a complex and precise process that is constantly evolving. As the volume of available data and the accessibility of sequencing technology increase, so too does the value of a versatile, well-vetted, and efficient workflow solution. In this webcast, we will take a deep dive into the current state of our AMP interpretation software and explore various ways to optimize workflows. For anyone from grizzled VarSeq veterans to those seeing our software for the first time and labs of any size, we will provide a practical overview of our somatic analysis capabilities and how those capabilities scale with improving technology. Throughout this webcast we will be discussing the following: - Universal principles of somatic workflows, providing baseline recommendations - Specific tumor-normal and somatic-only use cases - VSClinical AMP interpretation hub and some variants of interest - Opportunities for automation and how to decrease time to report for increased throughput Join us as we show off the versatility and scalability of our AMP interpretation capabilities!

User perspective for somatic variant analysis in VSClinical AMP

Golden Helix

The automation of clinical NGS workflows provides a number of important benefits for labs. Automation reduces the time required to produce a clinical report, mitigates the possibility of human error, and improves the precision of clinical results. In turn, these benefits create higher profitability from a P&L perspective. Golden Helix software is designed to meet these needs by automating the full analysis workflow from sequencer to clinical report on a fixed annual subscription model. We are looking forward to discussing the best practices of maximizing profitability in your NGS testing lab and how Golden Helix supports these efforts. Join us in this webinar as we cover how to develop repeatable cancer and germline interpretation workflows that scale from panels to whole exomes and genomes.

Maximizing Profitability in your NGS Testing Lab

Golden Helix

VarSeq has become renowned for the accuracy of its CNV Caller, and the ease with which VSClinical takes the user through CNV evaluation. Cited in many publications, this well-validated tool brings our customers the ability to run both variant and CNV interpretations in one program, on data ranging from Gene Panels to whole genomes. What is less well known about CNV analysis through VarSeq, is that our users are not only limited to CNVs called through our software. VarSeq CNV is able to import CNVs in several file formats (VCFs, text, or tsv) generated by a wide variety of secondary callers, allowing the user to analyze their externally derived data. In this webcast, we will take you through the basics of CNV analysis with both the VarSeq CNV caller and from several common external CNV callers. Join us in this webinar as we cover: Leveraging the Copy Number Probability and Segregation Algorithm to add power to a CNV Trio workflow. Importing externally called CNVs. Expediting the path to analysis with CNV specific templates. Utilizing the auto-recommendations to efficiently analyze the pathogenicity of several CNV calls and generate clinical reports.

Handling a Variety of CNV Caller Inputs with VarSeq

Golden Helix

In the era where cloud-based solutions are the default for the modern office, it may not be obvious why many laboratories and testing centers choose to host their data and analysis pipelines on-premises or on self-managed cloud services. Next-generation sequencing enables a precision medicine approach to rare disease diagnostic and cancer therapeutics through its power to detect unique variants in individuals. This data is generated quickly and cheaply but requires a lot of disk space and processing power to arrive at clinically useful insights. When providing a clinical lab service under a regulated environment: data security, long-term affordable storage, and versioning through locked-down pipelines are all factors that must go into the choice of whether to choose a hosted analytics platform versus on-premises solutions or self-managed cloud infrastructure. Join us in this webinar as we cover: The validation and regulatory requirements that inform infrastructure and hosting decisions for NGS labs The cost structure of scaling NGS labs to exomes and genomes Deployment and security architecture for on-premises and self-managed cloud infrastructure Validating and versioning analysis pipelines with clinical tests through self-managed software lifecycles and versioned annotation sources Cybersecurity, patient data privacy, and scalable unit economics play a bigger role than ever before in the planning of NGS lab’s infrastructure choices. We look forward to you joining us as we tackle the trade-offs and choices around these topics and how deployment flexibility is a core feature of the Golden Helix VarSeq Suite.

Evaluating Cloud vs On-Premises for NGS Clinical Workflows

Golden Helix

As our users have come to know, VarSeq serves as a hub for variant annotation and the full interpretation/classification of germline (ACMG) and somatic (AMP) variants. Whether direct annotation or backend variant evidence is being presented to the user via VSClinical for the interpretation process, users greatly benefit from the hosted variant databases being available directly from VarSeq. Our team has automated much of the curation process and hosts the ongoing updates to these tracks so that users no longer suffer manual review of each database via the web or manual curation efforts. Useful databases include ClinVar and ClinGen for classification submissions, gnomAD exomes/genomes for filtering out common variants in the population, RefSeq for gene impact and sequence ontology assessment, and OMIM for phenotypic information. Obviously, there is a large collection of databases out there, and not all of them make it into our automated queue. However, GHI supports the utilization of custom databases in our software. This webcast will expose features of custom database curation/utilization in VarSeq to optimize your NGS workflows even further. During the presentation, we will discuss many different approaches with custom annotations, including: Interval Tracks: Bed files defining target regions for coverage calculations and CNV detection. Assessment catalogs: record keeping of variant classification/interpretations in VSClinical. Frequency catalogs: approaches to capture all variant allele frequencies at a project level and cohort level with VSWarehouse.

VarSeq Custom Database Curation Capabilities.pdf

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M Capital Group (“MCG”) predicts that with, against, despite, and even without the global pandemic, the medical technology (MedTech) industry shows signs of continuous healthy growth, driven by smaller, faster, and cheaper devices, growing demand for home-based applications, technological innovation, strategic acquisitions, investments, and SPAC listings. MCG predicts that this should reflects itself in annual growth of over 6%, well beyond 2028. According to Chris Mouchabhani, Managing Partner at M Capital Group, “Despite all economic scenarios that one may consider, beyond overall economic shocks, medical technology should remain one of the most promising and robust sectors over the short to medium term and well beyond 2028.” There is a movement towards home-based care for the elderly, next generation scanning and MRI devices, wearable technology, artificial intelligence incorporation, and online connectivity. Experts also see a focus on predictive, preventive, personalized, participatory, and precision medicine, with rising levels of integration of home care and technological innovation. The average cost of treatment has been rising across the board, creating additional financial burdens to governments, healthcare providers and insurance companies. According to MCG, cost-per-inpatient-stay in the United States alone rose on average annually by over 13% between 2014 to 2021, leading MedTech to focus research efforts on optimized medical equipment at lower price points, whilst emphasizing portability and ease of use. Namely, 46% of the 1,008 medical technology companies in the 2021 MedTech Innovator (“MTI”) database are focusing on prevention, wellness, detection, or diagnosis, signaling a clear push for preventive care to also tackle costs. In addition, there has also been a lasting impact on consumer and medical demand for home care, supported by the pandemic. Lockdowns, closure of care facilities, and healthcare systems subjected to capacity pressure, accelerated demand away from traditional inpatient care. Now, outpatient care solutions are driving industry production, with nearly 70% of recent diagnostics start-up companies producing products in areas such as ambulatory clinics, at-home care, and self-administered diagnostics.

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This presentation focuses on the management of alopecia through ayurveda treatment. It begins with the description of hair in classical ayurveda and conventional medicine textbooks. The common hair related problems like khalitya, indralupta, palitya, hariloma and darunaka are mentioned in Ayurveda. Next is the causes of hairfall like Asthi dhatu kshaya, sveda kshaya, conditions like darunaka or dandruff, fungal infestation, excessive use of lavana-kshara, etc. Few evidences from the researched done previously on Indralupta or alopecia and above mentioned causes are also mentioned.

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Advanced Gum Health Prebiotic: A Breakthrough in Oral Care Maintaining oral health is crucial for overall well-being. Beyond traditional methods like brushing, flossing, and regular dental check-ups, recent advancements in dental science have introduced the concept of prebiotics for enhancing gum health. Advanced gum health prebiotics represent a promising frontier in oral care, offering a novel approach to preventing gum disease and promoting a healthy oral microbiome. Understanding the Oral Microbiome The oral cavity hosts a complex ecosystem of microorganisms, collectively known as the oral microbiome. This community includes bacteria, fungi, viruses, and protozoa, which coexist in a delicate balance. A healthy oral microbiome plays a crucial role in maintaining oral health, aiding in digestion, and protecting against pathogens. However, disruptions to this balance can lead to oral health issues such as gum disease, tooth decay, and bad breath. The Role of Prebiotics in Oral Health Prebiotics are non-digestible food components that selectively stimulate the growth and activity of beneficial microorganisms in the gut. Unlike probiotics, which introduce live beneficial bacteria into the system, prebiotics serve as nourishment for the existing beneficial bacteria, promoting their growth and activity. This concept is now being applied to oral health. How Advanced Gum Health Prebiotics Work Advanced gum health prebiotics are designed to support the beneficial bacteria in the oral microbiome, creating an environment that discourages the growth of harmful bacteria. By promoting a balanced microbiome, these prebiotics help prevent gum inflammation, reduce the risk of periodontal disease, and enhance overall oral health. Reduction of Gum Inflammation: By fostering a healthy oral microbiome, prebiotics can reduce inflammation and irritation in the gums, preventing conditions like gingivitis. Prevention of Periodontal Disease: A balanced microbiome can help prevent the progression of gum disease, which, if left untreated, can lead to tooth loss. Enhanced Oral Hygiene: Regular use of prebiotics can complement traditional oral hygiene practices, leading to fresher breath and healthier gums. Natural and Safe: Prebiotics are naturally occurring substances found in various foods, making them a safe and natural addition to oral care routines. The Science Behind Prebiotics Prebiotics work by providing a food source for beneficial bacteria. These substances, often dietary fibers, are not digested by human enzymes but are fermented by the gut microbiota. In the context of oral health, prebiotics promote the growth of beneficial bacteria in the mouth, which can outcompete harmful bacteria for resources and adhesion sites on the teeth and gums. Studies have shown that prebiotics can help reduce levels of harmful bacteria, such as those responsible for periodontal disease and dental caries.

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Struggling with intense fears that disrupt your life? At Renew Life Hypnosis, we offer specialized hypnosis to overcome fear. Phobias are exaggerated fears, often stemming from past traumas or learned behaviors. Hypnotherapy addresses these deep-seated fears by accessing the subconscious mind, helping you change your reactions to phobic triggers. Our expert therapists guide you into a state of deep relaxation, allowing you to transform your responses and reduce anxiety. Experience increased confidence and freedom from phobias with our personalized approach. Ready to live a fear-free life? Visit us at Renew Life Hypnosis..

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Dive into the intricate world of cells with our detailed Slideshare presentation. This educational resource is designed to provide a thorough understanding of cells, the fundamental building blocks of all living organisms. Ideal for students, educators, and biology enthusiasts, this presentation covers: Introduction to Cell Theory: Discover the historical development of cell theory and its significance in modern biology. Types of Cells: Compare and contrast prokaryotic and eukaryotic cells, highlighting their unique features and functions. Cell Organelles and Their Functions: Explore the various organelles within a cell, such as the nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, lysosomes, and more, each described with their specific roles. Cell Membrane Structure and Function: Learn about the composition and function of the cell membrane, including its role in regulating the movement of substances in and out of the cell. Cell Division and Reproduction: Understand the processes of mitosis and meiosis, key to cellular replication and genetic diversity. Specialized Cells: Investigate the diversity of cell types, including muscle cells, nerve cells, and blood cells, and their specialized functions in multicellular organisms. Interactive Diagrams and Visual Aids: Engage with detailed diagrams and illustrations that clarify complex concepts and enhance learning.Introduction to Cell Theory: Discover the historical development of cell theory and its significance in modern biology. Types of Cells: Compare and contrast prokaryotic and eukaryotic cells, highlighting their unique features and functions. Cell Organelles and Their Functions: Explore the various organelles within a cell, such as the nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, lysosomes, and more, each described with their specific roles. Cell Membrane Structure and Function: Learn about the composition and function of the cell membrane, including its role in regulating the movement of substances in and out of the cell. Cell Division and Reproduction: Understand the processes of mitosis and meiosis, key to cellular replication and genetic diversity. Specialized Cells: Investigate the diversity of cell types, including muscle cells, nerve cells, and blood cells, and their specialized functions in multicellular organisms. Interactive Diagrams and Visual Aids: Engage with detailed diagrams and illustrations that clarify complex concepts and enhance learning. This Slideshare presentation is a valuable educational tool, offering clear explanations and engaging visuals to help you grasp the essential concepts of cellular biology. Whether preparing for exams, teaching a class, or simply exploring the microscopic foundations of life, this resource provides a comprehensive overview of the fascinating world of cells. Explore the fascinating world of cells with our comprehensive SlideShare presentation. This educational resource delves into the fundamental unit of life,

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Male patients confined to bed usually prefer to use the urinal for voiding. The use of a urinal in the standing position facilitates emptying of the bladder If the patient is unable to stand, the urinal may be used in bed. Patients may also use a urinal in the bathroom to facilitate measurement of urinary output. Provide skin care and perineal hygiene after urinal use and maintain a professional manner EQUIPMENT Urinal with end cover (usually attached) Toilet tissue Clean gloves Additional PPE, as indicated ASSESSMENT Assess the patient’s normal elimination habits. Determine why the patient needs to use a urinal, such as a physician’s order for strict bed rest or immobilization. Assess the patient’s degree of limitation and ability to help with activity Assess for activity limitations, such as hip surgery or spinal injury, which would contraindicate certain actions by the patient. Check for the presence of drains, dressings, intravenous fluid infusion sites/equipment, traction, or any other devices that could interfere with the patient’s ability to help with the procedure or that could become dislodged. Assess the characteristics of the urine and the patient’s skin. Document the patient’s tolerance of the activity. Record the amount of urine voided on the intake and output record, if appropriate. Document any other assessments, such as unusual urine characteristics or alterations in the patient’s skin. SPECIAL CONSIDERATION Urinal should not be left in place for extended periods because pressure and irritation to the patient’s skin can result. If patient is unable to use alone or with assistance, consider other interventions, such as commode or external condom catheter. It may be necessary to assist patients who have difficulty holding the urinal in place, such as those with limited upper extremity movement or alteration in mentation, to prevent spillage of urine. The urinal may also be used standing or sitting at the bedside or in the patient’s bathroom, if patient is able to do so.

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A home-based pelvic floor muscle training and bladder training in women with urinary incontinence showed that combined pelvic floor muscle training and bladder training decreased the symptoms and improved the quality of life To strengthen your pelvic floor muscles, squeeze the muscles up to 10 times while standing, sitting or lying down. Do not hold your breath or tighten stomach, bottom or thigh muscles at the same time. When you get used to doing pelvic floor exercises, you can try holding each squeeze for one second

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When a patient uses a bedpan, promote comfort and normalcy and respect the patient’s privacy as much as possible. Be sure to maintain a professional manner. In addition, provide skin care and perineal hygiene after bedpan use Regular bedpans have a rounded, smooth upper end and a tapered, open lower end. The upper end fits under the patient’s buttocks toward the sacrum, with the open end toward the foot of the bed . A special bedpan called a fracture bedpan is frequently used for patients with fractures of the femur or lower spine Fracture bedpan - used for patients with fractures of the femur or lower spine. The fracture pan has a shallow, narrow upper end with a flat wide rim, and a deeper, open lower end. The upper end fits under the patient’s buttocks toward the sacrum, with the deeper, open lower end toward the foot of the bed. Ordinary Bedpan EQUIPMENTS Bedpan (regular or fracture) Toilet tissue Disposable clean gloves Additional PPE, as indicated Cover for bedpan or urinal (disposable waterproof pad or cover) ASSESSMENT Assess the patient’s normal elimination habits. Determine why the patient needs to use a bedpan (e.g., a medical order for strict bed rest or immobilization). Assess the patient’s degree of limitation and ability to help with activity. Assess for activity limitations, such as hip surgery or spinal injury, which would contraindicate certain actions by the patient. Check for the presence of drains, dressings, intravenous fluid infusion sites/equipment, traction, or any other devices that could interfere with the patient’s ability to help with the procedure or that could become dislodged. Assess the characteristics of the urine and the patient’s skin Assisting With Use of a Bedpan When the Patient Has Limited Movement Patients who are unable to lift themselves onto the bedpan or who have activity limitations that prohibit the required actions can be assisted onto the bedpan in an alternate manner using these actions

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Benefits of Salivary Testing with Dentulu Salivary Test Kit Salivary testing has revolutionized diagnostics, offering non-invasive and highly informative insights into oral and systemic health. The Dentulu saliva test kit exemplifies these advancements. Early Detection of Diseases Periodontal Disease: Saliva testing for periodontal disease detects pathogenic bacteria before symptoms appear, allowing for timely intervention and preventing severe complications. Oral Cancer: Salivary tests identify biomarkers for oral cancer at an early stage, improving treatment success rates and patient prognosis. Non-Invasive and Comfortable Comfort: Collecting a saliva sample is painless, reducing patient anxiety and making it ideal for all ages. Convenience: Dentulu’s saliva testing kit allows at-home sample collection, facilitating regular monitoring without clinic visits. Comprehensive Analysis Microbial Profiling: The saliva test for bacteria identifies specific pathogens, enabling targeted treatment plans. Genetic Markers: The DNA saliva test kit identifies genetic predispositions, aiding in personalized preventive measures. Conclusion Dentulu’s saliva test kit offers early disease detection, comprehensive health analysis, and enhanced patient compliance, making it a valuable tool in modern healthcare. <a href="https://www.dentulu.com/blog/how-salivary-testing-is-revolutionizing-early-disease-detection/"></a> <a href="https://www.dentulu.com/saliva-testing.html></a> <a href ="https://www.dentulu.com/"></a>

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Evaluating Splice Site Variants in VarSeq

1. Evaluating Splice Site Variants in VarSeq Nathan Fortier, Ph.D. – Director of Research 20 most promising Biotech Technology Providers Top 10 Analytics Solution Providers Hype Cycle for Life sciences

2. Q & A Please enter your questions into your GoToWebinar Panel

3. NIH Grant Funding Acknowledgments ▪ Research reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under: - Award Number R43GM128485 - Award Number 2R44 GM125432-01 - Award Number 2R44 GM125432-02 - Montana SMIR/STTR Matching Funds Program Grant Agreement Number 19-51-RCSBIR-005 ▪ PI is Dr. Andreas Scherer, CEO Golden Helix. ▪ The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

4. Golden Helix – Who We Are Golden Helix is a global bioinformatics company founded in 1998. GWAS Genomic Prediction Large-N Population Studies RNA-Seq CNV-Analysis Variant Warehouse Centralized Annotations Hosted Reports Sharing and Integration Variant Calling Filtering and Annotation Clinical Reports CNV Analysis Pipeline: Run Workflows

5. Cited in over 1,300 peer-reviewed publications

6. Over 400 customers globally

7. Golden Helix – Who We Are When you choose a Golden Helix solution, you get more than just software ▪ REPUTATION ▪ TRUST ▪ EXPERIENCE ▪ INDUSTRY FOCUS ▪ THOUGHT LEADERSHIP ▪ COMMUNITY ▪ TRAINING ▪ SUPPORT ▪ RESPONSIVENESS ▪ INNOVATION and SPEED

8. VarSeq Clinical Workflows Stack

9. VSClinical ▪ Complete Support for ACMG Guideline Workflow: - Implements a guided workflow for following the ACMG guideline scoring and classifying - Place criteria into conceptually related groups, paired with their opposites, and formatted as answerable question. ▪ Aggregate and Automate: - Questions have supporting evidence presented with rich and interactive visuals - Automatically computed recommendations for questions that have explicit bioinformatic evidence, with supporting reasons for each answer. ▪ Expert and Beginner Friendly: - Start with descriptive summaries and recommendations for a variant - Deep dive into Population Catalogs, Gene Impact, Published Studies and Clinical tabs - Integrated documentation, readings on scoring criteria and citations

10. Splice Sites ▪ Understanding a variant’s impact on splicing is crucial ▪ Synonymous variants can disrupt existing splice sites or introduce novel splice sites ▪ Such variants can cause exon skipping or truncation

11. Splice Sites ▪ Introns have distinct nucleotide pairs at each end - GT at the 5’ end (Donor Site) - AG at the 3’ end (Acceptor Site) ▪ Area surrounding nucleotide pair is defined by a splice motif ▪ Sequences around splice sites are highly variable ▪ Machine learning and probabilistic methods are used to identify sites

12. Algorithms ▪ VSClinical supports four splice site prediction algorithms - PWM: Uses position weight matrix similar to SpliceSiteFinder and Human Splice Finder - MaxEntScan: Approximates sequence motifs using Maximum Entropy Distribution - NNSplice: Identifies splice sites using neural networks - GeneSplicer: Uses Markov models combined with maximal dependence decomposition

13. [Demo in VarSeq]

14. NIH Grant Funding Acknowledgments ▪ Research reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under: - Award Number R43GM128485 - Award Number 2R44 GM125432-01 - Award Number 2R44 GM125432-02 - Montana SMIR/STTR Matching Funds Program Grant Agreement Number 19-51-RCSBIR-005 ▪ PI is Dr. Andreas Scherer, CEO Golden Helix. ▪ The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

15. Q & A

Evaluating Splice Site Variants in VarSeq

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