Categories
Tag: PRS
PRSice and R lm() show different association analysis output (coefficient, SE and P)
PRSice and R lm() show different association analysis output (coefficient, SE and P) 0 Hey, I am struggling to understand Why am I getting different association analysis output (coefficient, SE and P) between PRSice and lm() function in R. Not only the values, even the direction of association is different….
Achievements, accolades highlight past year at VUMC | VUMC Reporter
Editor’s note — the following is a roundup of the news that made headlines at Vanderbilt University Medical Center in 2023. Whole-genome sequencing agreement Nashville Biosciences LLC, a wholly owned subsidiary of Vanderbilt University Medical Center, and Illumina Inc., a global leader in DNA sequencing and array-based technologies,…
Understanding GPU Memory 2: Finding and Removing Reference Cycles
by Aaron Shi, Zachary DeVito This is part 2 of the Understanding GPU Memory blog series. Our first post Understanding GPU Memory 1: Visualizing All Allocations over Time shows how to use the memory snapshot tool. In this part, we will use the Memory Snapshot to visualize a GPU memory…
Diving into PyTorch: A Beginner’s Tale of Contribution | by Weinheimergracia | Dec, 2023
Hey there, fellow code wranglers and AI enthusiasts! I’m Cami, your friendly neighborhood tech explorer, and I’m about to take you on a wild ride through my latest adventure: contributing to PyTorch without being an expert in it. Yes, you read that right! My Unexpected Journey into PyTorch So, I…
automatic tests keep failling
On Tue, Dec 19, 2023 at 1:54 PM John Cremona <john.c…@gmail.com> wrote: > > I am finding it impossible to get simple PRs to get past the automatic testing workflow system, which are repeatedly failing for reasons which have noting to do with any code I have changed. > > Two…
Surgical Management and Long-Term Outcomes of BIA-ALCL: A Multidisciplinary Approach
Kaartinen I, Sunela K, Alanko J, Hukkinen K, Karjalainen-Lindsberg ML, Svarvar C. Breast implant-associated anaplastic large cell lymphoma—from diagnosis to treatment. Eur J Surg Oncol. 2017;43(8):1385–92. doi.org/10.1016/j.ejso.2017.05.021. Article CAS PubMed Google Scholar Leberfinger AN, Behar BJ, Williams NC, et al. Breast implant-associated anaplastic large cell lymphoma: a systematic review. JAMA…
Understanding GPU Memory 1: Visualizing All Allocations over Time
by Aaron Shi, Zachary DeVito During your time with PyTorch on GPUs, you may be familiar with this common error message: torch.cuda.OutOfMemoryError: CUDA out of memory. Tried to allocate 512.00 MiB. GPU 0 has a total capacity of 79.32 GiB of which 401.56 MiB is free. In this series, we…
Nurix Therapeutics Presents Positive Clinical Data from Its Novel Bruton’s Tyrosine Kinase (BTK) Degrader Programs, NX-5948 and NX-2127, at the 65th American Society of Hematology (ASH) Annual Meeting | Vaccines
Nurix Therapeutics Presents Positive Clinical Data from Its Novel Bruton’s Tyrosine Kinase (BTK) Degrader Programs, NX-5948 and NX-2127, at the 65th American Society of Hematology (ASH) Annual Meeting Details Category: Vaccines Published on Tuesday, 12 December 2023 14:30 Hits: 227 Positive preliminary efficacy data with a favorable safety profile support…
Northumbria University Research Fellowship Health & Life Science
–Must See– Northumbria University Research Fellowship Research Fellow in Health and Life Sciences Northumbria University, Newcastle City Campus, United Kingdom ABOUT THE ROLE We are seeking to appoint a highly committed, motivated, and creative scientist to join the Northumbria University bioinformatics research group. The research will develop new data science…
Research Fellow in Health and Life Sciences job with NORTHUMBRIA UNIVERSITY
ABOUT THE ROLE We are seeking to appoint a highly committed, motivated, and creative scientist to join the Northumbria University bioinformatics research group. The research will develop new data science methods that leverage the large amounts of public data from UKBiobank, dbGAP, and internal Whole Sequence data and use state-of-the-art…
Acd Rat shRNA Plasmid (Locus ID 307798) Clinisciences
Product Data Locus ID 307798 Synonyms MGC116400 Vector pRS E. coli Selection Ampicillin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components Acd – Rat, 4 unique 29mer shRNA constructs in retroviral untagged vector(Gene ID = 307798). 5µg purified plasmid DNA per construct29-mer scrambled shRNA cassette in pRS Vector, TR30012,…
Automating API Documentation: A Journey from TypeScript to OpenAPI and Schema Governence with Optic
In the previous blog post Documenting and Testing Schemas of Serverless Stacks with Optic & Cypress, we focused on the benefits of schema testing and governance. Briefly, some of the core problems addressed were: Effortless API Documentation: Automating the API documentation creation and update, ensuring that our API documentation evolves…
East Asian-specific and cross-ancestry genome-wide meta-analyses provide mechanistic insights into peptic ulcer disease
We conducted a three-stage genome-wide analysis of PUD and its subtypes. An overview of the workflow is provided in Fig. 1 and Supplementary Fig. 1. PUD cases in the east Asian populations were obtained by combining individuals with any of the two major PUD subtypes (DU and GU), which were…
There are 1 region(s)/phenotype(s) with p-value > 0.1 (not significant).
I’m trying to get a PRS for a very small subset of samples (~400 training, ~200 testing). Firstly I C+T the training data previous to PRSice. My .log is PRSice 2.3.3 (2020-08-05) github.com/choishingwan/PRSice(C) 2016-2020 Shing Wan (Sam) Choi and Paul F. O’ReillyGNU General Public License v3If you use PRSice in…
Effect allele flipping
Dear Sam and all, I used PRSice for calculating PRS based on the well-known 30 SNP list that is specific for type 1 diabets. I found that PRSice version 2.6.1 considered only SNPs whose effect allele are alternative alleles in the target file for PRS calculation. All SNPs that thier…
OAS2 Human shRNA Plasmid Kit (Locus ID 4939) Clinisciences
Product Data Locus ID 4939 Vector pRS E. coli Selection Ampicillin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components OAS2 – Human, 4 unique 29mer shRNA constructs in retroviral untagged vector(Gene ID = 4939). 5µg purified plasmid DNA per construct29-mer scrambled shRNA cassette in pRS Vector, TR30012, included for…
OpenAPI & AsyncAPI $ref: Advanced Guide
After using OpenAPI or AsyncAPI for a while, you might notice your description documents have become a rather unwieldy mess of YAML and JSON. You end up with a whole lot of repetition, and this huge mess just loves to trigger merge conflicts as multiple developers change different things but…
Phenotype integration improves power and preserves specificity in biobank-based genetic studies of major depressive disorder
Phenotype imputation increases effective sample size We focused on the deepest available measure of MDD in UK Biobank11, LifetimeMDD, which we derived by applying clinical diagnostic criteria in silico to MDD symptom data from the Patient Health Questionnaire 9 (PHQ9) and the Composite International Diagnostic Interview Short Form (CIDI-SF) in…
Navigating the Road Ahead with Genomics and Polygenic Risk Scores, ET HealthWorld
by Dr Firoz Ahmad Cardiovascular diseases (CVD) as a result of coronary artery diseases (CAD) are a group of health issues that affect the heart and the blood vessels which are essential for optimal heart functioning. It is a leading cause of death worldwide, particularly in India, where it accounts…
Chemo Plus Tecentriq Shows Improvements in Endometrial Carcinoma
A phase 3 trial demonstrated progression-free survival improvements with Tecentriq-chemotherapy combination in patients with endometrial carcinoma. The treatment combination of Tecentriq (atezolizumab) and platinum-based chemotherapy demonstrated benefits for patients with frontline advanced or recurrent endometrial carcinoma, specifically patients with deficient mismatch repair (dMMR) status, according to data from a phase…
IL6 Human shRNA Plasmid Kit (Locus ID 3569) Clinisciences
Product Data Locus ID 3569 Synonyms BSF-2; BSF2; CDF; HGF; HSF; IFN-beta-2; IFNB2; IL-6 Vector pRS E. coli Selection Ampicillin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components IL6 – Human, 4 unique 29mer shRNA constructs in retroviral untagged vector(Gene ID = 3569). 5µg purified plasmid DNA per construct29-mer…
Preliminary Data of MK-1084 +/- Pembrolizumab in Solid Tumors and NSCLC
Carlos Rojas, MD, medical oncology, Centro de Investigacion Clinica, Bradford Hill, discusses preliminary findings from a phase 1 trial (NCT05067283) which evaluated MK-1084, a selective KRAS G12C inhibitor, alone in patients with advanced solid tumors, as well as in combination with pembrolizumab (Keytruda) for the first-line treatment of metastatic non–small…
AMH Human shRNA Plasmid Kit (Locus ID 268) Clinisciences
Product Data Locus ID 268 Synonyms MIF; MIS Vector pRS E. coli Selection Ampicillin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components AMH – Human, 4 unique 29mer shRNA constructs in retroviral untagged vector(Gene ID = 268). 5µg purified plasmid DNA per construct29-mer scrambled shRNA cassette in pRS Vector,…
Bgen file not being opened by PRSice
Bgen file not being opened by PRSice 0 I used the following command to calculate PRS of a sequenced file coming from a collaborator. I imputed the vcf file which gave me separate vcf files for each chromosome. I then converted them to bgen and generated bgi and sample files…
Sage 10.0 released
Congratulations to Volker and to all Sage contributors on the new release. 2023-05-21 01:00 UTC, Matthias Köppe: Thanks. > Some notes: > > – The list of “New Contributors” was also automatically generated > by GitHub. It did not know the contributors of previous versions. > I’ve manually removed many…
IGF1 Receptor (IGF1R) Human shRNA Plasmid Kit (Locus ID)
Product Data Locus ID 3480 Synonyms CD221; IGFIR; IGFR; JTK13 Vector pRS E. coli Selection Ampicillin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components IGF1R – Human, 4 unique 29mer shRNA constructs in retroviral untagged vector(Gene ID = 3480). 5µg purified plasmid DNA per construct29-mer scrambled shRNA cassette in…
CHRNA2 Human shRNA Plasmid Kit (Locus ID 1135) Quimigen
Product Data Locus ID 1135 Vector pRS E. coli Selection Ampicillin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components CHRNA2 – Human, 4 unique 29mer shRNA constructs in retroviral untagged vector(Gene ID = 1135). 5µg purified plasmid DNA per construct29-mer scrambled shRNA cassette in pRS Vector, TR30012, included for…
BioAtla Reports Third Quarter 2023 Financial Results and Highlights Recent Progress
BioAtla, Inc. Observed additional clinical responses and FDA feedback supports path forward for CAB-AXL-ADC (BA3011) non-small cell lung cancer (NSCLC) registrational study; detailed interim Phase 2 data to be presented at upcoming IASLC conference in early December and discussed at KOL event on December 4, 2023 Observed new PRs with…
Relay Therapeutics Reports Third Quarter 2023 Financial Results and Corporate Highlights
Relay Therapeutics, Inc. Reported initial RLY-4008 (lirafugratinib) data demonstrating durable responses across multiple FGFR2-altered solid tumors Announced plans to initiate RLY-2608 + fulvestrant + CDK4/6 triplet combinations in HR+/HER2- breast cancer by YE 2023 Updated pipeline to extend cash runway by approximately 1 year Approximately $811 million in cash, cash…
HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases
HLA allele calling from WES HLA-HD was used to call HLA alleles for 454,824 participants at 3-field resolution (representing the allele’s serological specificity, HLA protein, and synonymous variants). We used the UKB whole-genome genotyping (unavailable in 1283 participants) projected on the 1000 Genome reference to estimate genetic ancestry. We found…
Allelica launches the Allelica Precision Server, an on-premises solution for clinical bioinformatics analyses
Allelica announces the release of the Allelica Precision Server for CLIA-compliant, on-premises analysis and clinical reporting of polygenic risk score, pharmacogenomics and carrier screening NEW YORK, Nov. 3, 2023 /PRNewswire/ — Allelica, the leading provider of software tools for clinical bioinformatics, announced the launch of its latest innovation, the Allelica…
Accelerating Inference on x86-64 Machines with oneDNN Graph
by Intel Supported in PyTorch 2.0 as a beta feature, oneDNN Graph leverages aggressive fusion patterns to accelerate inference on x86-64 machines, especially Intel® Xeon® Scalable processors. oneDNN Graph API extends oneDNN with a flexible graph API to maximize the optimization opportunity for generating efficient code on AI hardware. It…
No valid entries in –score file
PLINK Error: No valid entries in –score file 0 Hi, I ran this command on plink1.9 to calculate the poligenic score. plink –vcf sample –score output.txt 1 2 3 –out poligenic_results – output.txt: ID ALT UKB-b-15541 rs10399793 C 0.000345793 rs2462492 T -0.00027716 – sample.vcf: #CHROM POS ID REF ALT QUAL…
Cannot proceed with –glm regression on phenotype ‘platelet_count’, since covariate correlation matrix could not be inverted (VIF_INFINITE)
Hi, I am trying to run GWAS on the Platelet Count phenotype.I am using sex, age, assessment center, genotype measurement, and 40 PCs as a covariance matrix. I removed NA from the phenotype file, and I fitted it to the covariance matrix so it contains the same IDs.I calculated the…
Multiple courses for one instructor/grader in one single user server in JupyterHub on Kuberentes
Hi, I’m trying to set up nbgrader with JupyterHub with KubeSpawner. I want to achieve following: – one instructor is able to work with multiple courses in one notebook instance – several graders are able to access relevant formgraders – students are able to subscribe to multiple courses = see assignments…
PyTorch Conference: Full Schedule
Integrating an NPU with PyTorch 2.0 Compile – Sol Kim & Juho Ha, FuriosaAIWe would share our experiences of integrating NPU and its compiler, written in Rust, with ‘PyTorch 2.0 Compile’ through the following subjects: 1. Leveraging PyTorch 2.0 Features for NPU Accelerable Model Compilation: We will elaborate on how…
Does Pain When I Run Mean I Need Days Off?
Runners are a persistent bunch with goals to conquer and PRs to smash. That could explain why so many runners have stories of when they experienced an ache, kept running through it, and then ended up with an injury that put them on the sidelines for months. A better approach…
B cell polygenic risk scores associate with anti-dsDNA antibodies and nephritis in systemic lupus erythematosus
Objective: B cell function and autoantibodies are important in SLE pathogenesis. In this work, we aimed to investigate the impact of cumulative SLE B cell genetics on SLE subphenotype and autoantibody profile. Methods: Female patients with SLE (n=1248) and healthy controls (n=400) were genotyped using Illumina’s Global Screening Array. Two…
How Do Genetic Factors Play a Role in Chronic Pain and Opioid Use Disorder?
Published 36 minutes ago Submitted by Illumina Photo: Washington University collaborators Simon Haroutounian, PhD and Emma Johnson, PhD Originally published on Illumina News Center Emma Johnson, PhD, assistant professor of Psychiatry at Washington University School of Medicine in St. Louis, was thrilled to win Illumina’s Polygenic Risk Scores Research Grant…
public databases – Converting VCF format to text for use with PLINK and understanding column mapping
I successfully completed Nature PRS tutorial, which is based on PLINK. Turning to my real data, I downloaded ukb-d-20544_1.vcf.gz. Now I’m facing the problem that I seem to be unable to use it in PLINK or find the correct data format to download at all, and I am a bit…
Relay Therapeutics Announces Initial RLY-4008
35% ORR in patients with FGFR2 fusions (excluding CCA) & 40% ORR in patients with FGFR2-altered HR+/HER2- breast cancer RLY-4008 commercialization plans to focus on broader tumor agnostic opportunities Clinical focus on PI3Kα mutant selective programs, with plans to initiate RLY-2608 triplet combinations in HR+/HER2- breast cancer by YE 2023…
How Generative AI Can Increase Developer Productivity Now
You can’t walk into a developer Discord without a chat about generative AI. After all, software development teams are trying to do more with less, while the tech stack is increasingly complex — making the search for developer productivity feel more urgent than ever. Add to this the 27 million…
Bridging RT Before CAR T-Cell Therapy Can Benefit Patients With R/R DLBCL
Patients with relapsed/refractory (R/R) diffuse large B-cell lymphoma (DLBCL) may benefit from bridging radiation therapy (bRT) ahead of receiving chimeric antigen receptor (CAR) T-cell therapy, according to an abstract presented at the 2023 American Society for Radiation Oncology (ASTRO) Annual Meeting and published in the International Journal of Radiation Oncology,…
Viracta Therapeutics (VIRX) to host R&D day highlighting Nana-val in Epstein-Barr virus (EBV)-related cancers
Viracta Therapeutics, Inc. (Nasdaq: VIRX), a clinical-stage precision oncology company focused on treating and preventing virus-related cancers affecting patients worldwide, today announced plans to highlight new data from studies Preliminary clinical and preclinical data for naatinostat and valganciclovir (Nana-val), its all-oral investigational therapy for Epstein-Barr virus (EBV)-related cancers, today (Wednesday,…
OBM Genetics | Whole Genome Sequencing in Era of Newborn Screening
Abstract After the completion of the human genome project, there have been many advances in the field of genetics. With next generation sequencing, patients can undergo genomic analysis through whole exome or whole genome testing. These comprehensive tests can shorten the diagnostic odyssey and guide medical management and thereby potentially…
[OpenAPI Hub] Service teams should be guided to create a feature branch for new versions
When creating new service features in OpenAPI Hub, service teams should be guided to create a feature branch. Personally, as a “code owner” for many services, I prefer seeing PR validation on each PR targeting the feature branch, but 1) appreciate not every service team might want to work this…
How To Interpret Raw Dna Data
Source: Towardsdatascience.com Raw DNA data refers to the uninterpreted genetic information obtained from DNA sequencing. It contains the complete genetic code of an individual, providing valuable insights into ancestry, health, and other genetic traits. For those who have taken a DNA test, understanding how to interpret raw DNA data can…
Genome-Wide Association Study of Alopecia Areata in Taiwan
Introduction Alopecia areata (AA) is one of Taiwan’s most common autoimmune hair diseases and incidence rate of AA is 0.22%.1–3 The main symptoms of AA are rapid, non-scarring hair loss that affects body hair, facial hair, eyelashes, and brows.1,2 In the United States, the prevalence of AA is estimated to…
Is this commit not very strange? – JupyterHub
ajpikul September 20, 2023, 3:42pm 1 73aa219ebe5fdf7600f4fde38f6568c3aafb5706 Isn’t that commit message strange? Isn’t there a standard for accepting commits? It would be better with a proper message, or if it the PR was squashed but I guess its a bit late to correct this. The associated PR is Use {base_url}/api…
Reviewing Options After CAR T-Cell Therapy Progression in R/R DLBCL
Mehdi H. Hamadani, MD (Moderator) Professor of Internal Medicine Division of Hematology & Oncology Medical College of Wisconsin Milwaukee, WI DISCUSSION QUESTIONS If a patient relapses after or refractory to chimeric antigen receptor (CAR) T-cell therapy for diffuse large B-cell lymphoma (DLBCL), do you have a preferred regimen? What factors influence…
Why and how to address this?
Dear All, I’m preparing data for Mendelian randomization (MR) analysis to assess causal effect of telomere length on kidney phenotype in UK Biobank (UKB) data. The following steps were what I have done: 1. I started to search for prior research summary data and found close to 800 SNPs for…
Plink codes showed GWAS results with effect size (beta) and SE as NA: Why and How?
Plink codes showed GWAS results with effect size (beta) and SE as NA: Why and How? 0 Dear All, I’m preparing data for Mendelian randomization (MR) analysis to assess causal effect of telomere length on kidney phenotype using UK Biobank (UKB) data. The following steps were what I have done:…
Babel CLI vulnerability in Javascript ES6 generator
Description The babel upgrades done to the Javascript Flowtyped generator are needed in the Javascript ES6 generator as well. The 6.26.0 version of babel-cli causes a lot of npm audit vulnerabilities openapi-generator version Using the latest 4.0.3 release, ES6 Javascript generator OpenAPI declaration file content or url Command line used…
A journey to enable generative AI on a new hardware platform with PyTorch 2.0 for PyTorch Conference 2023
Abstract This talk explains our journey in enabling generative AI applications on a new hardware (HW) platform. We are working on running generative AI applications on IBM z from correctness and runtime performance perspectives. We share experiences for developers to write PyTorch and its ecosystem for a new HW. IBM…
Lab Testing Volume, Spend to Rise
Clinical lab testing and the associated costs are tracking a path that will see them become an even more significant and expensive part of healthcare. The rise in the volume, variety and complexity of tests holds promise for improving healthcare for patients, but also poses challenges for providers and health…
Polygenic Risk Score Identifies Individuals at Higher Risk of POAG
A polygenic risk score (PRS) was able to identify individuals who had the highest risk of primary open-angle glaucoma (POAG) in a study aimed at finding the prevalence of POAG based on structural coding and self-reports. The study, published in JAMA Ophthalmology, suggests that PRS stratification may help identify those…
Intel Announces Joining PyTorch Foundation to Help Advance AI
Intel issued a press release on its official website a few days ago, announcing that it has joined the PyTorch Foundation as a Premier member. Intel said that it has been actively involved in the development of PyTorch for five years, helping to optimize PyTorch’s CPU inference performance, and using…
Lebanon: Lebanon’s food insecurity persists as economic crisis continues (May – October 2023) Published on August 7, 2023 – Lebanon
Attachments Overview The second IPC Acute Food Insecurity Analysis conducted in Lebanon in May 2023 estimated that, in the current analysis period between May and October 2023, about 1.4 million Lebanese, Syrian and Palestine refugees in Lebanon (PRL) and Palestine Refugees from Syria (PRS) are experiencing high levels of acute…
Experts Call for Better FDA Policing of Direct-to-Consumer Polygenic Risk Scores
NEW YORK—Experts have called for US Food and Drug Administration regulation of direct-to-consumer (DTC) tests that use a polygenic risk score (PRS) to estimate an individual’s disease risk. PRS are genome-wide measures of individuals’ genetic propensities for diseases that, combined with other lifestyle factors, can give a better idea of…
Multiomics Helps Identify Potential Drug Targets for Dyslipidemia
NEW YORK — Using a multiomics and multi-trait approach, an international team of researchers has prioritized 30 potential therapeutic targets for dyslipidemia, which they believe are more likely to succeed in clinical trials than other drug targets. In a study published in Cell Reports Medicine on Wednesday, scientists at the…
[Solved] pUC19FrgA is the pUC19 2686 bp plasmid carrying fragment A with a – Molecular biology for neuroscientists (NEUR0006)
pUC19-FrgA is the pUC19 (2686 bp) plasmid carrying fragment A with a length of 2 kb in the the SalI site. This fragment shall be isolated and cloned into the SalI site of yeast shuttle vector pRS (8.5 kb). You must show your calculations to obtain credit. Reagents: Plasmids are…
NKX019 Showcases Manageable Safety, Early Activity in R/R B-cell Non-Hodgkin Lymphoma
Michael Dickinson, MBBS, DMedSc, FRACP, FRCPA The allogeneic natural killer (NK) cell therapy NKX019 was found to have an acceptable toxicity profile and to induce deep and durable responses in patients with relapsed or refractory B-cell non-Hodgkin lymphomas, according to preliminary data from a phase 1 trial (NCT05020678).1 Data presented…
[BUG][PYTHON] Client response is not respecting capital letters
Bug Report Checklist Description Python response containing keys in capital letters are being converted to lowercase. Therefore, schema is not being respect. I’m not sure if attribute map should be done at response time. openapi-generator version 3.0.3 OpenAPI declaration file content or url openapi: 3.0.3 info: title: Sample service version:…
Lenvatinib/Pembrolizumab Elicits High, Durable Responses in Advanced RCC
Lenvatinib (Lenvima) with pembrolizumab (Keytruda) elicited higher, more durable responses and improved survival outcomes compared with sunitinib (Sutent) in the treatment of patients with advanced renal cell carcinoma (RCC), according to findings from the phase 3 CLEAR study (NCT02811861). In data presented at the 2023 Kidney Cancer Research Summit, the…
Polygenic Risk Score Methods
Polygenic Risk Score Methods 0 Dear all, “I have a general question regarding the statistical methods behind PRS. Am I understanding correctly that many of the older PRS models (especially for breast cancer, for example jmg.bmj.com/content/56/9/581.long) simply sum up the GWAS-identified SNPs with their respective GWAS effect sizes without considering…
PLINK1.9 check sex problem
PLINK1.9 check sex problem 0 Hello! I use plink1.9 with –check-sex option to check sex in data with only one sample. I use –read-freq with a file contained frequencies of variants from chrX of 1000G (obtained by –freq). My problem is that for all samples I have F=-1 and SNPSEX=2….
Rail Corridor VIII, Phase 3
Project Description Provision of a sovereign loan of up to EUR 175 million to the Republic of North Macedonia (the “Borrower”) for the benefit of the Public Enterprise for Railways Infrastructure (“PERI”) for completion of the last section of rail infrastructure on the…
Inventory managment with automatic unit conversion, address management, tags and OpenAPI support – InvenTree 0.12.0
InvenTree 25 2,790 9.8 Python Open Source Inventory Management System This one is huge – 175 PRs huge. We have an extensive blog post out too. My personal highlights: kom2 1 2 10.0 Go Interface KiCad database libraries with non-ODBC systems using magic Want to get involved? We appreciate any…
How to merge BLE_UART and Aes_ctr project file – Nordic Q&A – Nordic DevZone
Hello, I have two project one is Ble UART and second AES_ctr, i want to combine AES_ctr project and sdk_config.h file into BLE_UART ,so i can use AES API in BLE UART code can you guide me how to start it. <!DOCTYPE CrossStudio_Project_File> <solution Name=”nrf_crypto_aes_ctr_pca10056″ target=”8″ version=”2″> <project Name=”nrf_crypto_aes_ctr_pca10056″> <configuration …
Novel ADC Delivers Responses and a Manageable Safety Profile in R/R Non-Hodgkin Lymphoma
Zilovertamab vedotin (MK-2140) was tolerable and generated early efficacy signals in patients with relapsed/refractory non-Hodgkin lymphoma (NHL), according to findings from the phase 1, first-in-human waveLINE-001 trial (NCT03833180) that were presented at the 17th Annual International Conference on Malignant Lymphoma. At a median follow-up of 14.3 months (range, 0.5-48.5), 96%…
Transcriptomic and in vivo approaches introduced human iPSC-derived microvesicles for skin rejuvenation
Boer, M., Duchnik, E., Maleszka, R. & Marchlewicz, M. Structural and biophysical characteristics of human skin in maintaining proper epidermal barrier function. Postepy Dermatol. Alergol. 33, 1–5 (2016). PubMed PubMed Central Google Scholar Watt, F. M. & Fujiwara, H. Cell-extracellular matrix interactions in normal and diseased skin. Cold Spring Harb….
Duvelisib Demonstrates Higher Activity in Angioimmunoblastic Peripheral T-Cell Lymphoma
Neha Mehta-Shah, MD, MSCI Treatment with duvelisib (Copiktra) led to a high response rate in patients with peripheral T-cell lymphoma (PTCL), with activity favoring patients with PTCL not otherwise specified (NOS) and angioimmunoblastic T-cell lymphoma (AITL), according to histology-specific outcomes from the phase 2 PRIMO trial (NCT03372057) presented at the…
Colorectal Cancer Polygenic Risk Score Could Impact Timing of Cancer Screening
Credit: Mohammed Haneefa Nizamudeen/Getty Images Researchers from the Institute for Molecular Medicine Finland (FIMM) have demonstrated that a colorectal cancer (CRC) polygenic risk score (PRS) they have developed has the potential to inform the timing of when patients should begin screening for the disease. Use of the PRS could help…
Genome-wide association study of thoracic aortic aneurysm and dissection in the Million Veteran Program
Common variants associated with TAAD We designed a two-phased GWAS. The initial MVP discovery analysis was composed of 8,626 individuals (7,050 European, 1,266 African and 310 Hispanic ancestry participants) with TAAD and 453,043 disease-free individuals from the same ancestral groups (Supplementary Fig. 1); their baseline characteristics are presented in Supplementary…
How Kaggle Teams Can Help You Find Good Candidates
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….
Using Deep Neural Networks to Predict Protein Structures
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…
How to Optimize a Model in PyTorch
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…
5min snip from Changelog Master Feed
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….
NALIRIFOX Delivers Substantial Survival Advantage to Patients With mPDAC
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…
The power of predictive genomics
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:…
Whole-genome sequencing of Listeria monocytogenes isolated from the first listeriosis foodborne outbreak in South Korea
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
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…
A score file with chr & positions instead of SNP IDs
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…
Frequency/count too large on line XXX of –read-freq file with multiallelics?
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 impact of rare protein coding genetic variation on adult cognitive function
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…
FDA Clears IND for AFM13/AB-101 in R/R Classical Hodgkin Lymphoma
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…
Kinnate Bio: Novel Approach To BRAF Class II And III, But Uninspiring Data (NASDAQ:KNTE)
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…
–score returns PRS/2
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…
mbedtls-platform-support 0.1.0 on Cargo – Libraries.io
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…
Research Assistant, Theranostics Centre for Excellence – Diagnostic Radiology job with NATIONAL UNIVERSITY OF SINGAPORE
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/Chemo May Prolong Survival in Classic Hodgkin Lymphoma
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…
ctDNA Genomic Profiling Can Guide Targeted Therapy in Advanced Cancer
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
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…
Introducing WebRIDEr: The WebR “IDE”-ish REPL You Didn’t Know You Needed
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…
Applying Precision Medicine at Scale
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
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…
PD-1 inhibitors in the treatment of gastric carcinoma
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…
Expert Charts the Changing Treatment Landscape in CRPC
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…
Can genes expose more glaucoma in the population?
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…
microRNA-182-5p inhibits hypertrophic scar formation
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…