Tag: PRS

Daniel and Chris explore the intersection of Kaggle and real-world data science in this illuminating conversation with Christof Henkel, Senior Deep Learning Data Scientist at NVIDIA and Kaggle Grandmaster. Christof offers a very lucid explanation into how participation in Kaggle can positively impact a data scientist’s skill and career aspirations….

AlphaFold is an AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence. It regularly achieves accuracy competitive with experiment, and is accelerating research in nearly every field of biology. Daniel and Chris delve into protein folding, and explore the implications of this revolutionary…

Model sizes are crazy these days with billions and billions of parameters. As Mark Kurtz explains in this episode, this makes inference slow and expensive despite the fact that up to 90%+ of the parameters don’t influence the outputs at all. Mark helps us understand all of the practicalities and…

Daniel and Chris explore the intersection of Kaggle and real-world data science in this illuminating conversation with Christof Henkel, Senior Deep Learning Data Scientist at NVIDIA and Kaggle Grandmaster. Christof offers a very lucid explanation into how participation in Kaggle can positively impact a data scientist’s skill and career aspirations….

Statistically significant and clinically meaningful improvement in overall survival (OS) and progression-free survival (PFS) has been achieved with liposomal irinotecan (Onivyde) plus 5-fluorouracil/leucovorin (5-FU) and oxaliplatin (NALIRIFOX) over gemcitabine plus nab-paclitaxel in patients with treatment-naïve metastatic pancreatic ductal adenocarcinoma (PDAC), results from the phase 3 NAPOLI 3 study (NCT04083235) show.1…

Predictive genomics provides the power to transform healthcare globally, explains Kim Caple The year 2023 marks the 70th anniversary of the discovery of the DNA double helix and the 20th anniversary of the completion of the Human Genome Project. These scientific moments in history mark progress toward a lofty goal:…

Introduction Although globalization has provided opportunities for consumers to enjoy a wide range of products and expanded global food trade, the complexity of the international food supply has contributed to an increase in foodborne outbreaks (Quested et al., 2010; Hussain and Dawson, 2013). Worldwide efforts have ensured food safety by…

PRSice-2 using SNPs with extremely low P-value 0 I would like to construct a Polygenic risk score using PRSice-2. However, our summary statistics contains a very small P-value, such as P-value=5.0×10^-1200. Perhaps that is why we cannot use this summary statistics to construct the PRS. How can I solve this…

Hello, I am calculating PRSs using the command:  plink2 \–bfile plink_file \–score score_file 1 2 3 header cols=+scoresums,-scoreavgs \–out PRS_sum Currently,  the columns in my score_file are: SNP IDs, effect allele, beta weights. I was wondering if possible to give instead of SNP IDs in the first column, chrs and…

I am encountering “Error: Frequency/count too large on line XXX of –read-freq file” when applying a score using plink2.  As far as I can tell, this seems to be happening where the site is multiallelic in the cohort that I’m applying the score in. (The derivation cohort data where the…

The UKB is approved by the North West Multi-centre Research Ethics Committee (www.ukbiobank.ac.uk/learn-more-about-uk-biobank/about-us/ethics). The current study was conducted under UKB application no. 26041. The data in the UKB were collected after written informed consent was obtained from all participants. The Human Research Committee of the MGB approved the Biobank research…

The FDA has cleared an investigational new drug application (IND) for AFM13 plus AB-101 in the treatment of patients with relapsed/refractory classical Hodgkin lymphoma, according to a press release from Affimed N.V. Investigators of the phase 2 AFM13-203 trial plan to enroll up to 134 patients with relapsed/refractory classical Hodgkin…

naphtalina/iStock via Getty Images Kinnate Biopharma (NASDAQ:KNTE) develops small molecule kinase inhibitors to treat genomically defined cancers. The company has two molecules in the clinic, exarafenib and KIN-3248. Exarafenib is an oral, small molecule pan-RAF inhibitor. It is in a phase 1 trial in patients with advanced solid tumors harboring…

Hi all, I’m working on PRS analysis using plink2 –score. To validate plink2 PRS, I calculated PRS manually (using plink2 –export A and product sum) and found that plink2 –score returns PRS/2. To make it clear, I tested with just one variant having effect_weight 0.6631986. The following table is a first…

This is an idiomatic Rust wrapper for MbedTLS, allowing you to use MbedTLS with only safe code while being able to use such great Rust features like error handling and closures. Additionally, building on MbedTLS’s focus on embedded use, this crate can be used in a no_std environment. Building This…

Job Description The National University of Singapore invites applications for multiple Research Assistant positions for the Theranostics Centre for Excellence (TCE) in the Department of Diagnostic Radiology, Yong Loo Lin School of Medicine.  The TCE is committed to developing various forms of cancer theranostics (therapeutics and diagnostics) that are clinically translatable. The center…

Pembrolizumab (Keytruda) appeared to prolong survival in combination with conventional ifosfamide, carboplatin, and etoposide (ICE) chemotherapy among patients with relapsed/refractory Hodgkin lymphoma planning to undergo autologous hematopoietic stem cell transplant (AHSCT), according to data from a phase 2 nonrandomized clinical trial (NCT03077828) published in JAMA Oncology. “The addition of checkpoint…

Genomic profiling of circulating tumor DNA (ctDNA) with a large panel appeared feasible in a routine setting and helped to obtain relevant molecular information that could inform strategies with targeted therapies for patients with metastatic solid tumors, according to findings from the prospective PRISM study published in Annals of Oncology….

Strand non-specific bam file 0 If I map a bed (annotation) file onto a Strand non-specific bam file (RNA-Seq), how is it going to know the strand? I changed the strand column of bed file as in two rows with same info and different strand. But, I got the same…

The official example WebR REPL is definitely cool and useful to get the feel for WebR. But, it is far from an ideal way to deal with it interactively, even as just a REPL. As y’all know, I’ve been conducing numerous experiments with WebR and various web technologies. I started…

Credit: HowLettery / iStock / Getty Images Plus More than 20 years ago, the announcement of the completion of the first human genome was heralded, often breathlessly, as the dawn of a new age of medicine. But how far have we actually come in using an individual’s unique molecular make…

Circos plot 0 Could anyone help me in creating sense and antisense strands in circos plot. How to create text file for it and how to represent it? circos • 38 views • link updated 3 hours ago by Ram 38k • written 3 hours ago by prs • 0…

Introduction Though prevalence and mortality have been declining over the last 50 years, stomach cancer remains the fifth–most frequently diagnosed and fourth-leading cause of cancer-related death globally, accounting for over 1 million new cases and 769,000 deaths globally in 2020.1 Esophageal cancer follows closely behind, ranking seventh in terms of…

Matthew Dallos, MD, established therapies that are beginning to move into earlier lines of treatment, emerging antibody-drug conjugates (ADCs), and the potential of third generation anti-androgen agents in advanced castration-resistant prostate cancer (CRPC) in a presentation during the 16th Annual Interdisciplinary Prostate Cancer Congress® and Other Genitourinary Malignancies, hosted by…

Glaucoma specialist and medical geneticist DR JANEY WIGGS revealed two new genes in juvenile early-onset glaucoma and dissected the value of polygenic risk scores when she delivered the Glaucoma Update Lecture at RANZCO’s 53rd Congress. Contemporary glaucoma researchers are using a genetic approach to understand the mechanisms of glaucoma. This…

Backgrounds Secondary to war wounds, surgery, trauma, etc., wound healing depends on the continuous proliferation of fibroblasts and collagen synthesis in the dermis.1,2 Skin scarring is considered as a natural outcome of the wound repair process. The incidence of scars after skin burns, trauma, and operations can be as high…

Abstract Background Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is a rare primary malignancy of the breast that has garnered significant attention in recent years. The disease was recognized as a distinct entity in 2016, and evidence-based guidelines for diagnosis and management have since been established. The classic presentation of…

GWAS-level and post-GWAS analyses GWAS of PD have nominated 90 independent risk signals in individuals of European ancestry, explaining ~16–36% of the heritable risk7, as well as two additional risk signals in Asian populations8. Typically, published GWAS are accompanied by various follow-up analyses, but performing these analyses is not always…

Software dependencies, or a piece of software that an application requires to function, are notoriously difficult to manage and constitute a major software supply chain risk. If you’re not aware of what’s in your software supply chain, an upstream vulnerability in one of your dependencies can be fatal. A simple…

Non-Coding RNA 2023, 9(2), 17; doi.org/10.3390/ncrna9020017 (registering DOI) Non-Coding RNA 2023, 9(2), 17; doi.org/10.3390/ncrna9020017 (registering DOI) Received: 30 January 2023 / Revised: 21 February 2023 / Accepted: 21 February 2023 / Published: 28 February 2023 Round 1 Reviewer 1 Report In this manuscript, the authors analyze miRNA signatures in the partial remission…

BridgePRS 1 Hi there, I am reading the new method of PRS – BridgePRS (www.biorxiv.org/content/10.1101/2023.02.17.528938v1), this is a very interesting paper regarding the transferability of PRS. I am trying to study about the methods (my statistics and mathematics background is quite weak), but one thing I don’t understand is that…

Bam to bedgraph 1 I have strand specific bam files of Riboseq data. I wish to convert it into bedgraph files – 1) Elongating coverage ; 2) Elongating A-sites. Can anyone help please! Bedtools Bam • 73 views • link updated 2 hours ago by jv ▴ 870 • written…

If anybody could help me, your help is greatly appreciated. I have been pondering this question for days now and I still cannot figure out what is the right solution! My research is to generate a polygenic risk score (PRS) for Africans, South Asians and Europeans to see if the…

NEW YORK – Bioinformatics company Allelica said on Wednesday that it is collaborating with Taiwanese precision medicine firm SP BioMed on a polygenic risk score (PRS) study of breast cancer. The goal of the study is to determine the best genotyping technology for genome-wide data generation for future applications such…

domoyega/E+ via Getty Images Investment Overview – Cash Intensive But Cash Rich – At Current Price Relay Offers The Patient Investor Value I have covered Relay Therapeutics (NASDAQ:RLAY) several times for Seeking Alpha since the company completed what was, at the time, the third largest biotech IPO in history, raising…

Zamtocabtagene autoleucel produced “promising responses” in a phase 2 trial of patients with relapsed/refractory diffuse large B-cell lymphoma (DLBCL), according to a presentation at the Tandem Meetings 2023. Zamtocabtagene autoleucel is a chimeric antigen receptor (CAR) T-cell therapy targeting both CD19 and CD20. Fresh, not cryopreserved, zamtocabtagene autoleucel produced an…

Performing gene enrichment analysis using FUMA 0 Dear all, This is the first time I have used FUMA and I find it quite hard to use, I am a undergraduate student and my final year project involves generating and validating a Polygenic Risk Score for COVID-19 susceptibility and severity. I…

#119126 Bioinformatics Programmer II – Hybrid/Remote Extended Deadline: Tue 2/21/2023 This position will remain open until a successful candidate has been identified. UCSD Layoff from Career Appointment: Apply by 10/03/2022 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 10/13/2022….

Samples This study was based on the Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH) sample37, a population-based case-cohort design to study the genetic and environmental factors associated with severe mental disorders. The iPSYCH2012 sample is nested within the entire Danish population born between 1981 and 2005 (N = 1,472,762). In total,…

Free access European cohort study 0 I’m wondering if there’s a free access cohort type study (of European ancestry) out there, like the UK BioBank. I tried accessing several ones mentioned in PRS papers since that’s what i’m working on and would like to test some scores, but all of…

Vos T, Barber RM, Bell B, Bertozzi-Villa A, Biryukov S, Bolliger I, et al. Global, regional, and national incidence, prevalence, and years lived with disability for 301 acute and chronic diseases and injuries in 188 countries, 1990-2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet. 2015;386:743–800….

Library sizes of miRNA sequencing data and TMM normalization with Edge-R 1 @tleona3-13813 Last seen 1 hour ago United States I have miRNA sequencing data from miRNA isolated from cells (PrS, PrE), miRNA isolated from cultured tissue slices (TSC), miRNA extracted from extracellular vesicles isolated from the media of the…

This position will remain open until a successful candidate has been identified. UCSD Layoff from Career Appointment: Apply by 10/03/2022 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 10/13/2022. Eligible Special Selection clients should contact their Disability Counselor for…

Manual Polygenic Risk Score calculation 1 Hi all, I am attempted to calculate PRS manually, and I’m very close to to obtaining a score. To recap what has been done, I have a patients individual in which I annotated their VCF with RSIDs. From there, I went to PGS catalog…

Bug Report Checklist Have you provided a full/minimal spec to reproduce the issue? Have you validated the input using an OpenAPI validator (example)? What’s the version of OpenAPI Generator used? Have you search for related issues/PRs? What’s the actual output vs expected output? Description Trying to generate a quite large…

How can I calculate PRS for all samples by using PRSice-2. 0 Hi. I am trying to calculate PRS by using PRSice-2. I’d like to know how to handle the model. When I provide same gwas results to PRSice-2’s –base option, is the model always same? I have several thousands…

new module: bbmap/filterbyname – PullAnswer Is there an existing module for this? [X] I have searched for the existing module Is there an open PR for this? [X] I have searched for existing PRs Is there an open issue for this? [X] I have searched for existing issues Are you…

Study cohort description We used data on a total of 172,270 individuals of Japanese and East Asian ancestry. Of these, data on 165,098 individuals were obtained from BBJ, which has enrolled ≥200,000 participants to date. BBJ is a multi-institutional hospital-based genome cohort that collected participants affected with at least one…

Study population The study sample included 34,072 unrelated (3rd degree or less) TOPMed participants from eight U.S. based cohort studies: Jackson Heart Study (JHS; n = 2504), Framingham Heart Study (FHS; n = 3520), Hispanic Community Health Study/Study of Latinos (HCHS/SOL; n = 6,408), Atherosclerosis Risk in Communities study (ARIC; n = 6197), Cardiovascular Health Study (CHS; n = 2835),…

PRSice (pronounced ‘precise’) is a software package for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS). PRSice can run at high-resolution to provide the best-fit PRS as well as provide results calculated at broad P-value thresholds, illustrating results corresponding to either, can thin SNPs according to…

Araco A, Gravante G, Araco F, Delogu D, Cervelli V, Walgenbach K. A retrospective analysis of 3,000 primary aesthetic breast augmentations: postoperative complications and associated factors. Aesthet Plast Surg. 2007;31(5):532–9. doi.org/10.1007/s00266-007-0162-8. CAS  CrossRef  Google Scholar  Nahabedian MY, Patel K. Management of common and uncommon problems after primary breast augmentation. Clin…

NEW YORK – A team from Stanford University and other centers in the US and China have demonstrated that polygenic risk scores (PRS) based on common variants can be bolstered by incorporating clues from rare variants linked to significant gene expression shifts, dubbed expression outliers. “As individual PRS estimates are…

Advances in genomic technologies continue to expand the possibilities of PGT. In a preclinical research study recently published in Nature Medicine, scientists from Silicon Valley-based genetic testing companies have examined the potential of using PGT to predict complex polygenically inherited conditions in human embryos. While the authors present interesting data,…

NEW YORK — Polygenic transcriptome risk scores may be better at gauging chronic obstructive pulmonary disease susceptibility across human ancestry groups than polygenic risk scores, a new study has found. COPD affects about 16 million people in the US and is typically diagnosed through two measures of lung function: forced…

During a Targeted Oncology case-based roundtable event, Ajay K. Gopal, MD, discussed the options for second-line and subsequent treatment of a patient with relapsed/refractory diffuse large B-cell lymphoma who refuses CAR T-cell therapy. Targeted OncologyTM: What are the recommended approaches for relapsed/refractory DLBCL in the second-line and subsequent therapies settings?…

Introduction Hair graying is one of the representative signs of aging. It has been considered to be triggered by a decreased number of follicular melanocyte stem cells (MeSCs; Nishimura et al., 2005; Iida et al., 2020) or dysfunction of MeSCs such as decreased oxidation resistance capacity with aging (Shi et…

How to find out why PRSice-2 excludes ambiguous SNPs 0 When I use PRSice to calculate PRS，it alerts it excludes 25 SNPs from the base data. But how could I know the reason why they are ambiguous? Could I explore more why they are ambiguous? Question2: If I use PRSice…

Polygenic Risk Score Calculation: Do we need to apply the same p-value threshold on all 22 chromsomes? 1 Hi there, I am using PRSice-2 to calculate the polygenic risk score for 22 chromosomes one by one. To my understanding, since the 22 chromosomes are independent of each other, and our…

Now Tin is a subclass of torch.nn.Module and it can have learnable parameters in the form of values in Taichi fields. However, now these values cannot be optimized by PyTorch optimizers, since they are not PyTorch-compatible. One way to make them to be PyTorch-compatible is to use a proxy torch.nn.Parameter…

Live webpage Auto updating website that tracks closed & open issues/PRs on scikit-learn/scikit-learn. Running locally Setup a virtual environment. Install requirements pip install -r requirements Create a personal access token and set it to GITHUB_TOKEN. Run the following to call the GitHub API for repo information and cache the results…

How can I make sure certain SNPs are not removed during the clumping stage of PRS calculation using PRSice 1 This is a two part question. First, when implementing PRSice, is there a way to make sure certain SNPs are retained for the PRS calculation? I basically want to avoid…

Real-world data on tisagenlecleucel in patients with relapsed/refractory B-cell lymphoma was consistent with the phase 2 JULIET trial, demonstrating favorable efficacy and safety. Real-world data on the use of tisagenlecleucel (Kymriah) showed greater efficacy and a favorable safety profile, according to updated findings from a study of the Center for…

Bug Report Checklist Description For oneOf fields, the python-fastapi server generator creates a function that returns a OneOf* class, but that class itself is not generated. For example, for an API like /status: get: summary: Get the status of the upstream server responses: 200: description: successful operation content: application/json: schema:…

I have a schema like so: openapi: 3.0.3 info: title: java codegen BUG description: oneOf generates incorrect model for primitive types version: 1.0.0 paths: /openapi/example/path: post: requestBody: content: application/json: schema: $ref: ‘#/components/schemas/Request’ responses: 200: description: OK content: application/json: schema: $ref: ‘#/components/schemas/Response’ components: schemas: MyString: type: string MySpecialString: anyOf: – $ref:…

Polygenetic Risk Score Calculation 1 Hello all, My company has Whole exome sequencing (WES) data for individuals lying around and was wondering if this can be used to generate Polygenetic Risk Scores (PRS)? From what I researched online, it seems to be more so used for GWAS and not WES….

ImageNet (Deng et al. 2009) is a picture database organized in keeping with the WordNet (Miller 1995) hierarchy which, traditionally, has been utilized in pc imaginative and prescient benchmarks and analysis. Nonetheless, it was not till AlexNet (Krizhevsky, Sutskever, and Hinton 2012) demonstrated the effectivity of deep studying utilizing convolutional…

Why some SNP’s are not assigned to any gene? 0 Hi everyone, I am doing polygenic risk analysis (PRS) ; As you may know PRS is done based on SNP’s. On the other hand, I would like to do some visualizations at gene level. Thus, I used rsnps library (ncbi_snp_query…

PRS from a dataset on which the GWAS is based on 0 I am using the PRSice tool to calculate PRS scores for a dataset (d1) using a set of weights from the PGS catalog. Although the weights were generated from a different cohort (d2), it appears that the original…

PRS using PGS Catalog 1 When using PRSice for PRS calculation of target data using a file of variants from the PGS catalog, does the variant file from the PGS catalog replace the GWAS summary statistics (referred to as “base data” in the tutorial)? I had previously found this similar…

PRS in UK Biobank – no covariate file and no phenotype file 1 Hi there, I am trying to undertake a PRS using UK Biobank plink data. I am trying to generate a PRS using PRSice-2. However, the issue I am having is that I do not have a covariate…

Validation in new sample 0 Hi Sam, I am trying to validate in a new sample a PRS I conceived by PRSice. I would like to ask if using snp_prs function (bigsnpr package in R) is a good way for that or should I use another tool or method. Best…

How to estimate polygenic risk score (PRSs) using the scoring files from PGSCatalog for one individual? 2 Hi all, I have an annotated vcf file for one individual which I want to estimate his polygenic risk score (PRS) for a certain trait, using the scoring files from the PGSCatalog. The…

PRSice-2 without Ref SNP ID 1 Does PRSice-2 support a base tile that has chromosome number/name and chromosome position instead of reference SNP ID in the base file? I’m trying to calculate PRS scores using a weights file from the PGS catalog with ~6 million variants. The file has only…

Polygenic Risk Score Plot 0 I have a dataset of about 6000 people, Chromosome 21. I calculated PRS using plink and PRSice. The plot is shown above. I have two questions regarding this. R2 on the y-axis explains the phenotype variation, but I want another measure like AUC (area under…