Tag: PRSice-2
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…
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 …
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 …
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 …
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…
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…
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…
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…
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….
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…
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…
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…
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…
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…
