The Wide Spectrum of Next-Generation Sequencing Assays with VarSeqGolden Helix
There is a strong motivation for labs to bring most, if not all, of their next-gen sequencing pipeline in-house. This is especially relevant for clinical applications where there is a need to validate any routine diagnostics when seeking to provide genetic results to patients. The entirety of the NGS pipeline is highly automatable and comprised of multiple stages but from the geneticist's point of view, the tertiary stage requires the lengthiest review. This stage is where the geneticist sifts through the massive collection of genetic variants to find and report on those most relevant to the patient or population. Unfortunately, the tertiary stage can be a fairly sophisticated process and there aren’t many tools on the market that handle it comprehensively and simply. Many of the tools that are available may have severe limitations on the scale of genomic data they can process or limitations on the types of NGS assays that can be designed. Moreover, their license model may be on an individual sample basis and present cost-benefit hurdles for the user, especially when sample load will inevitably increase. Fortunately, none of these assay or cost-based issues are relevant with Golden Helix products.
The goal of this webcast is to expose our viewers to the versatility that GHI VarSeq provides when constructing your dream NGS assay. This demonstration will provide examples of germline and somatic workflows for both single and multi-sample analysis for a variety of different disorders. Please join us and learn more about the analytical possibilities you can achieve when using the VarSeq software.
Organ-i World Transplant Congress Soild Organ Rejection Test (k-SORT)Kevin Jaglinski
SORT
Solid Organ Rejection Test is a gene based biomarker panel that evaluates the gene expression profile of RNA isolated from peripheral blood leukocytes. SORT is intended for diagnosis and subsequent monitoring of renal transplant recipients who have a high probability of early cellular or humoral acute rejection at the time of testing. SORT should be utilized in conjunction with standard clinical assessment.
The renal transplant community is heavily reliant on serum creatinine levels as a trigger to diagnose acute rejection. However, serum creatinine is a late indicator of renal injury and exhibits high variability and high false positivity. These inadequacies lead to delayed diagnosis and irreversible renal damage.
As such, we developed the World’s first predictive test of acute rejection. This solid organ rejection test (SORT) accurately detects acute rejection 4 months prior to biopsy or other signs of clinical graft dysfunction.
SORT is intended to be utilized in conjunction with standard clinical assessment.
In the US for 0.5 Million patients with Renal Failure, transplant is the treatment of choice, but due to a critical shortage of organs, there are 85,000 patients on the waitlist of 2.5 years. Only 21,000 receive kidney transplants annually. This costs Medicare $6.3 Billion. The absence of accurate, non-invasive monitoring tests is an unmet need reflected in the high attrition rates. Organ-I is commercializing, ‘SORT’ (Solid Organ Rejection Test) first predictive, accurate, non-invasive test available to patients, averting the need for unnecessary biopsies and saving upwards of $750M.
The Wide Spectrum of Next-Generation Sequencing Assays with VarSeqGolden Helix
There is a strong motivation for labs to bring most, if not all, of their next-gen sequencing pipeline in-house. This is especially relevant for clinical applications where there is a need to validate any routine diagnostics when seeking to provide genetic results to patients. The entirety of the NGS pipeline is highly automatable and comprised of multiple stages but from the geneticist's point of view, the tertiary stage requires the lengthiest review. This stage is where the geneticist sifts through the massive collection of genetic variants to find and report on those most relevant to the patient or population. Unfortunately, the tertiary stage can be a fairly sophisticated process and there aren’t many tools on the market that handle it comprehensively and simply. Many of the tools that are available may have severe limitations on the scale of genomic data they can process or limitations on the types of NGS assays that can be designed. Moreover, their license model may be on an individual sample basis and present cost-benefit hurdles for the user, especially when sample load will inevitably increase. Fortunately, none of these assay or cost-based issues are relevant with Golden Helix products.
The goal of this webcast is to expose our viewers to the versatility that GHI VarSeq provides when constructing your dream NGS assay. This demonstration will provide examples of germline and somatic workflows for both single and multi-sample analysis for a variety of different disorders. Please join us and learn more about the analytical possibilities you can achieve when using the VarSeq software.
Organ-i World Transplant Congress Soild Organ Rejection Test (k-SORT)Kevin Jaglinski
SORT
Solid Organ Rejection Test is a gene based biomarker panel that evaluates the gene expression profile of RNA isolated from peripheral blood leukocytes. SORT is intended for diagnosis and subsequent monitoring of renal transplant recipients who have a high probability of early cellular or humoral acute rejection at the time of testing. SORT should be utilized in conjunction with standard clinical assessment.
The renal transplant community is heavily reliant on serum creatinine levels as a trigger to diagnose acute rejection. However, serum creatinine is a late indicator of renal injury and exhibits high variability and high false positivity. These inadequacies lead to delayed diagnosis and irreversible renal damage.
As such, we developed the World’s first predictive test of acute rejection. This solid organ rejection test (SORT) accurately detects acute rejection 4 months prior to biopsy or other signs of clinical graft dysfunction.
SORT is intended to be utilized in conjunction with standard clinical assessment.
In the US for 0.5 Million patients with Renal Failure, transplant is the treatment of choice, but due to a critical shortage of organs, there are 85,000 patients on the waitlist of 2.5 years. Only 21,000 receive kidney transplants annually. This costs Medicare $6.3 Billion. The absence of accurate, non-invasive monitoring tests is an unmet need reflected in the high attrition rates. Organ-I is commercializing, ‘SORT’ (Solid Organ Rejection Test) first predictive, accurate, non-invasive test available to patients, averting the need for unnecessary biopsies and saving upwards of $750M.
Golden Helix’s SNP & Variation Suite (SVS) has been used by researchers around the world to do association testing and trait analysis on large cohorts of samples in both humans and other species. As samples size increase to do population-scale genomics, the analysis methods need to adapt to remain computable on your analysis workstation.
One of the most popular methods for determining population structure in SVS is Principal Component Analysis. In this webcast, we review the fundamentals of this methodology, as well as how we have advanced the state of the art by implementing a new “Large Data PCA” capability in SVS, handling over 10 times as many samples as previously possible at a fraction of the time. Join us as we cover:
A review of SVS association testing and trait analysis capabilities
Usage of Principle Component Analysis to discern population structure
Scaling PCA beyond the limitations of computer hardware Other SVS improvements based on ongoing feedback from the user community
SVS continues to move forward as a flexible and powerful tool to perform genotype and Large-N variant analysis. We hope you enjoy this webcast highlighting the exciting new features and select enhancements we have made.
VarSeq 2.5.0: VSClinical AMP Workflow from the User PerspectiveGolden Helix
With our recent launch of VarSeq 2.5.0, our ability to expedite somatic analysis for NGS labs is more accessible than ever before. Our recent webcasts have shown our range of updates, including our new oncogenicity classifier and carrier status workflows:
Identifying Oncogenic Variants in VarSeq
VarSeq 2.5.0: Empowering Family Planning through Carrier Screening Analysis
In this user perspective webcast, we will highlight how the combination of our new oncogenicity classifier and the updates to our CancerKB database streamline the interpretation of oncogenic variants. In addition, as NGS labs progress from gene panels to WES analysis for ideal genomic signature generation, we will demonstrate how a VarSeq somatic workflow can scale with these increased scopes of data analysis with ease.
Our user perspective webcast will cover:
Application of virtual panels to WES tumor/normal workflows.
Use of the oncogenicity classifier to streamline filter chains.
Updates to our CancerKB database to include the CancerKB gene track.
Including parallel germline secondary findings for the whole NGS workflow.
Icbme2020- Use of neural network algorithms to predict arterial blood gas ite...Mohammad Sabouri
Use of neural network algorithms to predict arterial blood gas items in trauma victims
Milad Shayan
Mohammad Sabouri
Dr. Shahram Paydar
Leila Shayan
ACRRL
Applied Control & Robotics Research Laboratory of Shiraz University
Department of Power and Control Engineering, Shiraz University, Fars, Iran.
27th National and 5th International Conference of Biomedical Engineering
https://sites.google.com/view/acrrl/
http://icbme.ir/
A weighted angiographic scoring model (W-CTO score) to
predict success of antegrade wire crossing in chronic total
occlusion: analysis from a single centre
Driving Applications on the UCSD Big Data Freeway SystemLarry Smarr
Keynote lecture by Calit2 Director Larry Smarr to the Cubic and UC San Diego Innovation Workshop on February 26, 2014 explores driving applications on the UCSD Big Data freeway system.
Golden Helix’s SNP & Variation Suite (SVS) has been used by researchers around the world to do association testing and trait analysis on large cohorts of samples in both humans and other species. As samples size increase to do population-scale genomics, the analysis methods need to adapt to remain computable on your analysis workstation.
One of the most popular methods for determining population structure in SVS is Principal Component Analysis. In this webcast, we review the fundamentals of this methodology, as well as how we have advanced the state of the art by implementing a new “Large Data PCA” capability in SVS, handling over 10 times as many samples as previously possible at a fraction of the time. Join us as we cover:
A review of SVS association testing and trait analysis capabilities
Usage of Principle Component Analysis to discern population structure
Scaling PCA beyond the limitations of computer hardware Other SVS improvements based on ongoing feedback from the user community
SVS continues to move forward as a flexible and powerful tool to perform genotype and Large-N variant analysis. We hope you enjoy this webcast highlighting the exciting new features and select enhancements we have made.
VarSeq 2.5.0: VSClinical AMP Workflow from the User PerspectiveGolden Helix
With our recent launch of VarSeq 2.5.0, our ability to expedite somatic analysis for NGS labs is more accessible than ever before. Our recent webcasts have shown our range of updates, including our new oncogenicity classifier and carrier status workflows:
Identifying Oncogenic Variants in VarSeq
VarSeq 2.5.0: Empowering Family Planning through Carrier Screening Analysis
In this user perspective webcast, we will highlight how the combination of our new oncogenicity classifier and the updates to our CancerKB database streamline the interpretation of oncogenic variants. In addition, as NGS labs progress from gene panels to WES analysis for ideal genomic signature generation, we will demonstrate how a VarSeq somatic workflow can scale with these increased scopes of data analysis with ease.
Our user perspective webcast will cover:
Application of virtual panels to WES tumor/normal workflows.
Use of the oncogenicity classifier to streamline filter chains.
Updates to our CancerKB database to include the CancerKB gene track.
Including parallel germline secondary findings for the whole NGS workflow.
Icbme2020- Use of neural network algorithms to predict arterial blood gas ite...Mohammad Sabouri
Use of neural network algorithms to predict arterial blood gas items in trauma victims
Milad Shayan
Mohammad Sabouri
Dr. Shahram Paydar
Leila Shayan
ACRRL
Applied Control & Robotics Research Laboratory of Shiraz University
Department of Power and Control Engineering, Shiraz University, Fars, Iran.
27th National and 5th International Conference of Biomedical Engineering
https://sites.google.com/view/acrrl/
http://icbme.ir/
A weighted angiographic scoring model (W-CTO score) to
predict success of antegrade wire crossing in chronic total
occlusion: analysis from a single centre
Driving Applications on the UCSD Big Data Freeway SystemLarry Smarr
Keynote lecture by Calit2 Director Larry Smarr to the Cubic and UC San Diego Innovation Workshop on February 26, 2014 explores driving applications on the UCSD Big Data freeway system.
Immunizing Image Classifiers Against Localized Adversary Attacksgerogepatton
This paper addresses the vulnerability of deep learning models, particularly convolutional neural networks
(CNN)s, to adversarial attacks and presents a proactive training technique designed to counter them. We
introduce a novel volumization algorithm, which transforms 2D images into 3D volumetric representations.
When combined with 3D convolution and deep curriculum learning optimization (CLO), itsignificantly improves
the immunity of models against localized universal attacks by up to 40%. We evaluate our proposed approach
using contemporary CNN architectures and the modified Canadian Institute for Advanced Research (CIFAR-10
and CIFAR-100) and ImageNet Large Scale Visual Recognition Challenge (ILSVRC12) datasets, showcasing
accuracy improvements over previous techniques. The results indicate that the combination of the volumetric
input and curriculum learning holds significant promise for mitigating adversarial attacks without necessitating
adversary training.
Hybrid optimization of pumped hydro system and solar- Engr. Abdul-Azeez.pdffxintegritypublishin
Advancements in technology unveil a myriad of electrical and electronic breakthroughs geared towards efficiently harnessing limited resources to meet human energy demands. The optimization of hybrid solar PV panels and pumped hydro energy supply systems plays a pivotal role in utilizing natural resources effectively. This initiative not only benefits humanity but also fosters environmental sustainability. The study investigated the design optimization of these hybrid systems, focusing on understanding solar radiation patterns, identifying geographical influences on solar radiation, formulating a mathematical model for system optimization, and determining the optimal configuration of PV panels and pumped hydro storage. Through a comparative analysis approach and eight weeks of data collection, the study addressed key research questions related to solar radiation patterns and optimal system design. The findings highlighted regions with heightened solar radiation levels, showcasing substantial potential for power generation and emphasizing the system's efficiency. Optimizing system design significantly boosted power generation, promoted renewable energy utilization, and enhanced energy storage capacity. The study underscored the benefits of optimizing hybrid solar PV panels and pumped hydro energy supply systems for sustainable energy usage. Optimizing the design of solar PV panels and pumped hydro energy supply systems as examined across diverse climatic conditions in a developing country, not only enhances power generation but also improves the integration of renewable energy sources and boosts energy storage capacities, particularly beneficial for less economically prosperous regions. Additionally, the study provides valuable insights for advancing energy research in economically viable areas. Recommendations included conducting site-specific assessments, utilizing advanced modeling tools, implementing regular maintenance protocols, and enhancing communication among system components.
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Cosmetic shop management system project report.pdfKamal Acharya
Buying new cosmetic products is difficult. It can even be scary for those who have sensitive skin and are prone to skin trouble. The information needed to alleviate this problem is on the back of each product, but it's thought to interpret those ingredient lists unless you have a background in chemistry.
Instead of buying and hoping for the best, we can use data science to help us predict which products may be good fits for us. It includes various function programs to do the above mentioned tasks.
Data file handling has been effectively used in the program.
The automated cosmetic shop management system should deal with the automation of general workflow and administration process of the shop. The main processes of the system focus on customer's request where the system is able to search the most appropriate products and deliver it to the customers. It should help the employees to quickly identify the list of cosmetic product that have reached the minimum quantity and also keep a track of expired date for each cosmetic product. It should help the employees to find the rack number in which the product is placed.It is also Faster and more efficient way.
Water scarcity is the lack of fresh water resources to meet the standard water demand. There are two type of water scarcity. One is physical. The other is economic water scarcity.
Explore the innovative world of trenchless pipe repair with our comprehensive guide, "The Benefits and Techniques of Trenchless Pipe Repair." This document delves into the modern methods of repairing underground pipes without the need for extensive excavation, highlighting the numerous advantages and the latest techniques used in the industry.
Learn about the cost savings, reduced environmental impact, and minimal disruption associated with trenchless technology. Discover detailed explanations of popular techniques such as pipe bursting, cured-in-place pipe (CIPP) lining, and directional drilling. Understand how these methods can be applied to various types of infrastructure, from residential plumbing to large-scale municipal systems.
Ideal for homeowners, contractors, engineers, and anyone interested in modern plumbing solutions, this guide provides valuable insights into why trenchless pipe repair is becoming the preferred choice for pipe rehabilitation. Stay informed about the latest advancements and best practices in the field.
Saudi Arabia stands as a titan in the global energy landscape, renowned for its abundant oil and gas resources. It's the largest exporter of petroleum and holds some of the world's most significant reserves. Let's delve into the top 10 oil and gas projects shaping Saudi Arabia's energy future in 2024.
Student information management system project report ii.pdfKamal Acharya
Our project explains about the student management. This project mainly explains the various actions related to student details. This project shows some ease in adding, editing and deleting the student details. It also provides a less time consuming process for viewing, adding, editing and deleting the marks of the students.
4. Motivation & Objective
In the United States alone, dehydration affects 30 million children annually 1 and
accounts for 400,000 pediatric emergency room visits 2.
• Intravascular volume or fluid status depends on the concentration of Chloride
and Bicarbonate ion in blood, but it takes significant amount of time to find out
the concentration in laboratory. Using PIV for an alternate method to predict
intravascular volume status.
• To identify the changes in PIV signal before and after bolus.
• To define a quantitative matric for intravascular volume status, possibly from PIV
signal.
• Predict the dehydration level of a patient; i.e. to predict the amount of fluid
needed to restore the normal fluid amount.
[1] Niescierenko M and Bachur R. Advances in Pediatric Dehydration Therapy. Curr Opin Pediatr 2013; 25: 304-309.
[2] Wathern JE, Mackenzie T, Bothner JP. Usefulness of the serum electrolyte panel in the management of pediatric patients treated with intravenously administered fluids. Pediatrics. 2004; 114: 1227-34.
4/19/2023 mahayat@uark.edu 4
5. Hypothesis
• Crosstalk between heart rate and PIV signals
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Bit Rate = 60 x Frequency = 60/T = 138
bpm
f = 2.3 Hz
6. Data
• Group 1 : Hydrated, no bolus given
• Data when they arrived at hospital
• Group 2 : Hydrated, bolus given
• Before bolus data and after bolus data
• Group 3 : Dehydrated, bolus given
• Before bolus data and after bolus data
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7. Methods of Analysis
• Time Domain
• Gram-Schmidt Orthogonalization
• Frequency Domain
• Logistic Regression
• Forward Search
• Logistic Regression with LASSO
• KL Divergence
4/19/2023 mahayat@uark.edu 7
9. Logistic Regression
• Two categories: Y = 1 or Y = 0 (the first element of x is 1)
• Log likelihood ratio (LLR )
• Decision boundary is a hyperplane defined by
• Decision
• If
• If
10. Logistic Regression
• Maximum likelihood (ML) is used to find the coefficients
• Log-likelihood function of the i-th training sample
• If
• If
• The Log-likelihood function can be written as
11. Logistic Regression
• Maximum likelihood estimation of
• Log-likelihood function of n samples
We want to find β that can maximize
• The first derivative of
This equation can be solved numerically
13. Results
4/19/2023 mahayat@uark.edu 13
(a) Cross validation in LR gave poor results in
detection.
(b) New three patients were identified correctly
(c) Relevant frequencies were identified assuming
gaussian distribution. (p-value)
(d) Submitted these results in a medical conference.
Fourier transform of a 10s window with frequencies
limited up to 20 Hz with 50 sample points.
15. Logistic Regression LASSO
• LASSO : Least Absolute Shrinkage & Selection Operator
Cost Function : Logistic Regression
Cost Function : Logistic Regression with LASSO:
16. Logistic Regression LASSO
• For no cross validation LASSO gives the exact
same result for window detection as without
LASSO.
• With cross validation LASSO, it forces some of
the β coefficients to be zero.
4/19/2023 mahayat@uark.edu 16
Data
0 1
Detection
0 88 % 29 %
1 12 % 71 %
17. Kullback-Leibler Divergence
• For comparing the probability distribution across groups before and after
bolus.
4/19/2023 mahayat@uark.edu 17
18. Possible Application
• War Zone
• Dehydration of babies
• Pyloric Stenosis
• Department of Defense
• Pig Experiments
4/19/2023 mahayat@uark.edu 18
19. Collaborators
• Dr. Jingxian Wu
• Dr. Morten Olgaard Jensen (BME, UArk)
• Dr. Hanna K. Jensen (BME, UArk)
• Dr. Kevin Sexton (UAMS)
• Dr. Patrick Bonasso (UAMS)
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