Tag: PRSice
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…
Rare coding variants as risk modifiers of the 22q11.2 deletion implicate postnatal cortical development in syndromic schizophrenia
Edelmann L, Pandita RK, Morrow BE. Low-copy repeats mediate the common 3-Mb deletion in patients with velo-cardio-facial syndrome. Am J Hum Genet. 1999;64:1076–86. Article CAS PubMed PubMed Central Google Scholar Shaikh TH, Kurahashi H, Saitta SC, O’Hare AM, Hu P, Roe BA, et al. Chromosome 22-specific low copy repeats and…
Full-Time Research Assistant Professor
Position Description The Cruchaga Lab, member of the Neurogenomics and Informatics Center (NGI) at Washington University School of Medicine, invites applications for a faculty position at the rank of Research Assistant Professor to develop a project to identify novel genes and pathways in Alzheimer’s Disease utilizing Whole Genome Sequencing. The…
Bioinformatics Programmer II – Hybrid/Remote
#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….
A sex-specific genome-wide association study of depression phenotypes in UK Biobank
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….
Bioinformatics Programmer II – Hybrid/Remote – 119126 at UC San Diego Health System
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…
How can I calculate PRS for all samples by using PRSice-2.
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…
PRSice-2 Documentation
PRSice-2 Documentation 1 Hi, Does anyone has detailed documentation of PRSice-2 software? The official website has been down for several weeks. Thank you! Mengna PRSice-2 • 69 views We lost the domain name because we forgot the login password… You can now revert to the repo doc (which is the…
Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations
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),…
Alternatives and detailed information of Prsice
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…
Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing
** Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing ** The NeuroGenomics and Informatics (NGI) Center lead by Dr. Carlos Cruchaga at Washington University School of Medicine is recruiting a Bioinformatics Scientist to work on Whole Genome and Whole Exome Sequencing. We are seeking an experienced, self-motivated, self-driven scientist…
How to find out why PRSice-2 excludes ambiguous SNPs
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…
Do we need to apply the same p-value threshold on all 22 chromsomes?
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…
How can I make sure certain SNPs are not removed during the clumping stage of PRS calculation using PRSice
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…
PRS from a dataset on which the GWAS is based on
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
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
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
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…
PRSice-2 without Ref SNP ID
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
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…
PRSice “command not found”
PRSice “command not found” 0 Hi all, When running PRSice (version 2.3.3), I got the “command not found” for the commands: –perm –thread –binary-target T How to make these commands working. Best regards, Redha Command • 17 views • link updated 1 hour ago by Sam ★ 3.7k • written…
