Tag: PRSice

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….

Continue Reading PRSice and R lm() show different association analysis output (coefficient, SE and P)

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…

Continue Reading There are 1 region(s)/phenotype(s) with p-value > 0.1 (not significant).

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…

Continue Reading Effect allele flipping

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…

Continue Reading Bgen file not being opened by PRSice

Genome-wide analyses identify NEAT1 as genetic modifier of age at onset of amyotrophic lateral sclerosis | Molecular Neurodegeneration

van Es MA, Hardiman O, Chio A, Al-Chalabi A, Pasterkamp RJ, Veldink JH, van den Berg LH. Amyotrophic Lateral Sclerosis. Lancet (London England). 2017;390:2084–98. Article  PubMed  Google Scholar  Liu MS, Cui LY, Fan DS. Age at onset of Amyotrophic Lateral Sclerosis in China. Acta Neurol Scand. 2014;129:163–7. Article  CAS  PubMed …

Continue Reading Genome-wide analyses identify NEAT1 as genetic modifier of age at onset of amyotrophic lateral sclerosis | Molecular Neurodegeneration

Genome-wide association study in 404,302 individuals identifies 7 significant loci for reaction time variability

MacDonald SW, Li SC, Bäckman L. Neural underpinnings of within-person variability in cognitive functioning. Psychol Aging. 2009;24:792–808. Article  PubMed  Google Scholar  Haynes BI, Bunce D, Kochan NA, Wen W, Brodaty H, Sachdev PS. Associations between reaction time measures and white matter hyperintensities in very old age. Neuropsychologia. 2017;96:249–55. Article  PubMed …

Continue Reading Genome-wide association study in 404,302 individuals identifies 7 significant loci for reaction time variability

Functional characterization of Alzheimer’s disease genetic variants in microglia

Nott, A. et al. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Science 366, 1134–1139 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  Neuner, S. M., Tcw, J. & Goate, A. M. Genetic architecture of Alzheimer’s disease. Neurobiol. Dis. 143, 104976 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar …

Continue Reading Functional characterization of Alzheimer’s disease genetic variants in microglia

Phenotype File Not Read Correctly

PRSice – Phenotype File Not Read Correctly 0 I am using PRSice2 on the UKBB dataset. The phenotype is generated for a subset of patients, and it is absent for the remainder of the cohort. In total, there are over 400k absent phenotypes, so there are over 400k NaN values…

Continue Reading Phenotype File Not Read Correctly

Transcriptomic risk scores for attention deficit/hyperactivity disorder

Song P, Zha M, Yang Q, Zhang Y, Li X, Rudan I. The prevalence of adult attention-deficit hyperactivity disorder: A global systematic review and meta-analysis. J Glob Health. 2021;11:1–9. Article  Google Scholar  Faraone SV, Asherson P, Banaschewski T, Biederman J, Buitelaar JK, Ramos-Quiroga JA, et al. Attention-deficit/hyperactivity disorder. Nat Rev…

Continue Reading Transcriptomic risk scores for attention deficit/hyperactivity disorder

Cross-phenotype relationship between opioid use disorder and suicide attempts: new evidence from polygenic association and Mendelian randomization analyses

Degenhardt L, Grebely J, Stone J, Hickman M, Vickerman P, Marshall BDL, et al. Global patterns of opioid use and dependence: harms to populations, interventions, and future action. Lancet. 2019;394:1560–79. Article  CAS  PubMed  PubMed Central  Google Scholar  Patten DK, Schultz BG, Berlau DJ. The Safety and Efficacy of Low-Dose Naltrexone…

Continue Reading Cross-phenotype relationship between opioid use disorder and suicide attempts: new evidence from polygenic association and Mendelian randomization analyses

Cross-ancestry genome-wide association meta-analyses of hippocampal and subfield volumes

Scoville, W. B. & Milner, B. Loss of recent memory after bilateral hippocampal lesions. J. Neurol. Neurosurg. Psychiatry 20, 11–21 (1957). Article  CAS  PubMed  PubMed Central  Google Scholar  Morris, R. G., Garrud, P., Rawlins, J. N. & O’Keefe, J. Place navigation impaired in rats with hippocampal lesions. Nature 297, 681–683…

Continue Reading Cross-ancestry genome-wide association meta-analyses of hippocampal and subfield volumes

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…

Continue Reading PRSice-2 using SNPs with extremely low P-value

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…

Continue Reading Rare coding variants as risk modifiers of the 22q11.2 deletion implicate postnatal cortical development in syndromic schizophrenia

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…

Continue Reading Full-Time Research Assistant Professor

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….

Continue Reading Bioinformatics Programmer II – Hybrid/Remote

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….

Continue Reading A sex-specific genome-wide association study of depression phenotypes in UK Biobank

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…

Continue Reading Bioinformatics Programmer II – Hybrid/Remote – 119126 at UC San Diego Health System

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…

Continue Reading How can I calculate PRS for all samples by using PRSice-2.

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…

Continue Reading PRSice-2 Documentation

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),…

Continue Reading Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations

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…

Continue Reading Alternatives and detailed information of Prsice

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…

Continue Reading Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing

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…

Continue Reading How to find out why PRSice-2 excludes ambiguous SNPs

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…

Continue Reading Do we need to apply the same p-value threshold on all 22 chromsomes?

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…

Continue Reading How can I make sure certain SNPs are not removed during the clumping stage of PRS calculation using PRSice

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…

Continue Reading PRS from a dataset on which the GWAS is based on

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…

Continue Reading PRS using PGS Catalog

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…

Continue Reading PRS in UK Biobank – no covariate file and no phenotype file

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…

Continue Reading Validation in new sample

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…

Continue Reading PRSice-2 without Ref SNP ID

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…

Continue Reading Polygenic Risk Score Plot

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…

Continue Reading PRSice “command not found”