LDSC statistics

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Protocols

LDSC specifications

Information


Unique identifier OMICS_14187
Name LDSC
Alternative names LD SCore regression, LDSCore
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, Python, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.0
Stability Stable
Requirements
Python, argparse, bitarray, numpy, pandas, scipy
Maintained Yes

Subtool


  • LDSC-SEG

Download


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Versioning


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Documentation


Maintainers


  • person_outline Alkes Price
  • person_outline Hilary Finucane

Publications for LD SCore regression

LDSC citations

 (122)
call_split

GWAS on family history of Alzheimer’s disease

2018
PMCID: 5959890
PMID: 29777097
DOI: 10.1038/s41398-018-0150-6
call_split See protocol

[…] th the stage 2 summary output from the International Genomics of Alzheimer’s Project (IGAP) study and the stage 1 output for the SNPs that did not contribute to stage 2. Linkage disequilibrium score (LDSC) regression was used to estimate the genetic correlation between the maternal and paternal AD GWAS results and to test for residual confounding in the meta-analysis by examining the LDSC intercep […]

call_split

Elucidating the genetic architecture of reproductive ageing in the Japanese population

2018
Nat Commun
PMCID: 5958096
PMID: 29773799
DOI: 10.1038/s41467-018-04398-z
call_split See protocol

[…] Tissue enrichment analyses were performed using MAGMA (implemented through FUMA) and LDSC-SEG. Software supplied default parameters were used for both approaches, and East-Asian specific LD scores and LD information were used where appropriate. Tissue enrichment was performed on tissu […]

library_books

Genome wide association study in 176,678 Europeans reveals genetic loci for tanning response to sun exposure

2018
Nat Commun
PMCID: 5940788
PMID: 29739929
DOI: 10.1038/s41467-018-04086-y

[…] The genomic inflation factor (λGC) was calculated as the ratio between the observed and expected median χ2 statistics. We used the LD score regression (LDSC) software (version 1.0.0) to quantify the proportion of such inflation that was due to the presence of polygenic inheritance and to other confounding biases, such as populati […]

library_books

Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies

2018
Nat Commun
PMCID: 5916929
PMID: 29695774
DOI: 10.1038/s41467-018-03766-z

[…] essed sets and gene.pathway set to all promoters overlapping LD clumps for a GWAS disease. No trend based on an additional covariate was used.Partitioned heritability analysis was performed using the ldsc tool from (https://github.com/bulik/ldsc),. The two analyses below were done based on recommended practice by the creators of the tool: https://github.com/bulik/ldsc/wiki/LD-Score-Estimation-Tuto […]

library_books

Biological Insights Into Muscular Strength: Genetic Findings in the UK Biobank

2018
Sci Rep
PMCID: 5915424
PMID: 29691431
DOI: 10.1038/s41598-018-24735-y

[…] By leveraging genome-wide information from our meta-analysis, we used LD-score regression– to estimate heritability of grip strength, to evaluate partitioned heritability by functional categories and to identify genetic correlation with other traits. LD-score regression […]

library_books

Genetic validation of bipolar disorder identified by automated phenotyping using electronic health records

2018
PMCID: 5904248
PMID: 29666432
DOI: 10.1038/s41398-018-0133-7

[…] To assess whether our EHR-based phenotypes capture heritable components of BD, we used LD score regression (LDSC),, to estimate SNP-based heritability (h2g) for each EHR-based BD cohort. We then examined the degree to which heritable influences on our BD phenotypes overlap with those tr […]

Citations

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LDSC institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Computer Science, Harvard University, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA; Medical Research Council (MRC) Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK; Harvard Society of Fellows, Harvard University, Cambridge, MA, USA; Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA; Division of Rheumatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA; Partners Center for Personalized Genetic Medicine, Boston, MA, USA; Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
LDSC funding source(s)
Supported by NIH grants R01 MH107649, R01 MH109978 and U01 CA194393 and by the Fannie and John Hertz Foundation.

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