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CMS specifications


Unique identifier OMICS_09815
Name CMS
Alternative name Composite of Multiple Signals
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Ilya Shlyakhter

Publications for Composite of Multiple Signals

CMS citations


Deep whole genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

Nat Commun
PMCID: 5915442
PMID: 29691385
DOI: 10.1038/s41467-018-03274-0

[…] array and whole-genome sequencing (WGS), a variety of analytical methods, such as F-statistics (FST), integrated haplotype score (iHS), cross-population extended haplotype homozygosity (XP-EHH), and composite of multiple signals (CMS), have been developed to fine-map natural selection signatures embedded in the human genome sequences. These methods have successfully detected genetic loci under ex […]


Localization of adaptive variants in human genomes using averaged one dependence estimation

Nat Commun
PMCID: 5818606
PMID: 29459739
DOI: 10.1038/s41467-018-03100-7

[…] ation in order to identify genomic windows containing selective sweeps. These windows vary in size from 20 to 200 kb, often identifying candidate sweep regions containing many genes,. One method, the Composite of Multiple Signals or “CMS”,, uses component statistics that can be computed site by site in pursuit of localizing adaptive variants within genomic windows, but the output from this method […]


Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu

Front Genet
PMCID: 5462927
PMID: 28642786
DOI: 10.3389/fgene.2017.00068

[…] Grossman et al., ). Most importantly, coalescent simulations and accurate calibrated demographic models, which are lacking in African cattle, are not required by meta-SS in comparison to the original Composite of Multiple Signals (CMS) method proposed by Grossman et al. (). Secondly, the reference cattle populations were pooled into a single population as in Bahbahani et al. (). As suggested by Ga […]


Evolutionary history of Tibetans inferred from whole genome sequencing

PLoS Genet
PMCID: 5407610
PMID: 28448578
DOI: 10.1371/journal.pgen.1006675

[…] ntrogressions with high resolution, we performed a comprehensive genomic analysis of WGS data in 27 Tibetans[]. We estimated the demographic history of Tibetans using MSMC and ∂a∂i, and performed the Composite of Multiple Signals test for fine-mapping loci and variants with recent selective sweep. We also estimated genome-wide levels of archaic admixture, and generated a fine-scale map of Denisova […]


Evolutionary selected Tibetan variants of HIF pathway and risk of lung cancer

PMCID: 5355300
PMID: 28036300
DOI: 10.18632/oncotarget.14340

[…] nicity, 2.39 (95%CI=1.05, 5.41) when adjusted for Hindu religion and 2.01 (95%CI=0.88, 4.59) when adjusted for smoking status.To select candidate functional SNPs in the EPAS1 region, we performed the Composite of Multiple Signals (CMS) test []. The CMS test combined five independent tests (XP-EHH, iHS, diHH, FST, and DAF) to improve the power to detect recent positive selection. Using simulations, […]


Demographically Based Evaluation of Genomic Regions under Selection in Domestic Dogs

PLoS Genet
PMCID: 4778760
PMID: 26943675
DOI: 10.1371/journal.pgen.1005851

[…] ndows are often clustered across the genome (), we collapsed windows across statistics into outlier regions if they were within 200kb of each other. As a heuristic to rank outlier regions, we took a “composite of multiple signals” (CMS) approach, similar to that employed in a recent selection scan in humans []. Specifically, we computed CMS1-FDR as (1-FDRΔπ)*(1-FDRFST)*(1-FDRΔTD), and ranked regio […]


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CMS institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA

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