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Improving the informativeness of Mendelian disease-derived pathogenicity scores for common disease

Pathogenicity scores are instrumental in prioritizing variants for Mendelian disease, yet their application to common disease is largely unexplored. Here, the authors assess the utility of pathogenicity scores for 41 complex traits and develop a framework to improve their informativeness for common disease.

Samuel S. Kim
Kushal K. Dey
Alkes L. Price
ResearchOpen Access07 Dec 2020
Nature Communications

Volume: 11, P: 1-15
Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores

PolyPred and PolyPred⁺ methods that leverage fine-mapping and non-European training data significantly improve cross-population polygenic prediction accuracy when applied to diseases and complex traits in UK Biobank populations.

Omer Weissbrod
Masahiro Kanai
Alkes L. Price
Research07 Apr 2022
Nature Genetics

Volume: 54, P: 450-458
Environment dominates over host genetics in shaping human gut microbiota

Statistical analyses of a metagenomics-sequenced human cohort identify a relatively minor role for genetics in determining microbiome composition and show that several human phenotypes are as strongly associated with the gut microbiome as with host genetics.

Daphna Rothschild
Omer Weissbrod
Eran Segal
Research28 Feb 2018
Nature

Volume: 555, P: 210-215
Accurate liability estimation improves power in ascertained case-control studies

LEAP (liability estimator as a phenotype) corrects for confounding factors in case-control GWAS with increased power.

Omer Weissbrod
Christoph Lippert
David Heckerman
Research09 Feb 2015
Nature Methods

Volume: 12, P: 332-334
Bacterial SNPs in the human gut microbiome associate with host BMI

A new framework for linking metagenomic data on the gut microbiome to human traits uncovers bacterial SNPs that associate with BMI in geographically independent cohorts.

Liron Zahavi
Amit Lavon
Eran Segal
Research02 Nov 2023
Nature Medicine

Volume: 29, P: 2785-2792
Improving fine-mapping by modeling infinitesimal effects

A downsampling approach to assess causal variant fine-mapping, replication failure rate, finds that commonly used methods may be miscalibrated. Simulations suggest this is probably due to a nonsparse genetic architecture model misspecification. Incorporating infinitesimal effects in the SuSiE and FINEMAP frameworks improves performance.

Ran Cui
Roy A. Elzur
Hilary K. Finucane
Research30 Nov 2023
Nature Genetics

Volume: 56, P: 162-169
Whole-genome sequencing reveals that variants in the Interleukin 18 Receptor Accessory Protein 3′UTR protect against ALS

Eitan et al. discovered genetic variants in the 3′UTR for the gene encoding IL-18 receptor that protect against ALS. The variant 3′UTR destabilizes the mRNA and dampens microglia NF-κB signaling and neurotoxicity, thus emphasizing the value of noncoding genetic association studies.

Chen Eitan
Aviad Siany
Eran Hornstein
Research31 Mar 2022
Nature Neuroscience

Volume: 25, P: 433-445
A reference map of potential determinants for the human serum metabolome

The levels of 1,251 metabolites are measured in 475 phenotyped individuals, and machine-learning algorithms reveal that diet and the microbiome are the determinants with the strongest predictive power for the levels of these metabolites.

Noam Bar
Tal Korem
Eran Segal
Research11 Nov 2020
Nature

Volume: 588, P: 135-140
Functional disease architectures reveal unique biological role of transposable elements

Transposable elements (TE) make up a large component of the human genome and have been shown to contribute to human diseases. Here, Hormozdiari et al. estimate the contribution of TEs to the heritability of 41 complex traits and diseases and find enrichment of SINEs in blood traits.

Farhad Hormozdiari
Bryce van de Geijn
Alkes L. Price
ResearchOpen Access06 Sept 2019
Nature Communications

Volume: 10, P: 1-8
Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity

A heritability-based framework for evaluation of SNP-to-gene linking methods is used to construct an optimal, combined approach and applied to 49 traits. Analysis of trait omnigenicity suggests gene-level architecture varies depending on variant frequency.

Steven Gazal
Omer Weissbrod
Alkes L. Price
Research06 Jun 2022
Nature Genetics

Volume: 54, P: 827-836
Large-scale association analyses identify host factors influencing human gut microbiome composition

Analysis of human genotypes and 16S microbiome data of 18,473 individuals from 25 cohorts through a genome-wide association study, a phenome-wide association study and Mendelian randomization identifies host genetic and microbial trait associations.

Alexander Kurilshikov
Carolina Medina-Gomez
Alexandra Zhernakova
Research18 Jan 2021
Nature Genetics

Volume: 53, P: 156-165
Functionally informed fine-mapping and polygenic localization of complex trait heritability

PolyFun is a computationally scalable framework for functionally informed fine-mapping that makes full use of genome-wide data. It prioritizes more variants than previous methods when applied to 49 complex traits from UK Biobank.

Omer Weissbrod
Farhad Hormozdiari
Alkes L. Price
Research16 Nov 2020
Nature Genetics

Volume: 52, P: 1355-1363
Detecting heritable phenotypes without a model using fast permutation testing for heritability and set-tests

Standard approaches for heritability and set testing in statistical genetics rely on parametric models that might not hold in reality and give inflated p-values. Here, the authors develop a fast method for permutation-based testing of marker sets and of heritability that does not suffer from model misspecification.

Regev Schweiger
Eyal Fisher
Eran Halperin
ResearchOpen Access21 Nov 2018
Nature Communications

Volume: 9, P: 1-9
From a genome-wide screen of RNAi molecules against SARS-CoV-2 to a validated broad-spectrum and potent prophylaxis

A genome-wide screen of 16,471 RNAi triggers targeting SARS-CoV-2 genome by Sens.AI. identifies hyper-potent RNAi candidates against SARS-CoV-2 that are further validated in vitro and in vivo.

Ohad Yogev
Omer Weissbrod
Yaniv Erlich
ResearchOpen Access16 Mar 2023
Communications Biology

Volume: 6, P: 1-12
Prediction of acute myeloid leukaemia risk in healthy individuals

Individuals who are at high risk of developing acute myeloid leukaemia can be identified years before diagnosis using genetic information from blood samples.

Sagi Abelson
Grace Collord
Liran I. Shlush
Research09 Jul 2018
Nature

Volume: 559, P: 400-404
Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins

Zeev Waks
Omer Weissbrod
Yaara Goldschmidt
ResearchOpen Access23 Dec 2016
Scientific Reports

Volume: 6, P: 1-12
Further Improvements to Linear Mixed Models for Genome-Wide Association Studies

Christian Widmer
Christoph Lippert
David Heckerman
ResearchOpen Access12 Nov 2014
Scientific Reports

Volume: 4, P: 1-13

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