Nature Search

Diagnosis and management of neuropsychiatric SLE

In systemic lupus erythematosus (SLE), central nervous system involvement can present as various neurological and psychiatric features, as a primary manifestation of SLE or arising from other causes. In this Review, the author discusses advances in knowledge of the immunopathogenesis, diagnosis and management of neuropsychiatric events in patients with SLE.

John G. Hanly
Reviews11 Feb 2014
Nature Reviews Rheumatology

Volume: 10, P: 338-347
cellSTAAR: incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of noncoding regions

cellSTAAR advances noncoding rare variant association analysis by integrating single-cell genomics data.

Eric Van Buren
Yi Zhang
Xihong Lin
Research31 Dec 2025
Nature Methods

Volume: 23, P: 338-349
Publisher Correction: Recent advances in the diagnosis and management of neuropsychiatric lupus

Alexandra C. Legge
John G. Hanly
Amendments and Corrections13 Nov 2024
Nature Reviews Rheumatology

Volume: 21, P: 63
High-dose vitamin D supplementation and prostate cancer progression: a phase II randomised trial in localised prostate cancer cases with intermediate risk of progression (ProsD)

Visalini Nair-Shalliker
David P. Smith
Howard Gurney
Research21 Dec 2025
British Journal of Cancer

Volume: 134, P: 735-745
A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies

MultiSTAAR provides a general and flexible statistical framework for functionally informed multi-trait rare variant analysis of biobank-scale sequencing studies by jointly analyzing multiple traits and incorporating annotation information.

Xihao Li
Han Chen
Xihong Lin
Research07 Feb 2025
Nature Computational Science

Volume: 5, P: 125-143
Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis

Using data from a single time point, passenger-approximated clonal expansion rate (PACER) estimates the fitness of common driver mutations that lead to clonal haematopoiesis and identifies TCL1A activation as a mediator of clonal expansion.

Joshua S. Weinstock
Jayakrishnan Gopakumar
Siddhartha Jaiswal
Research12 Apr 2023
Nature

Volume: 616, P: 755-763
Sequencing in over 50,000 cases identifies coding and structural variation underlying atrial fibrillation risk

Analyses of genome and exome sequencing data identify rare coding and structural variants associated with atrial fibrillation and highlight genetic links between atrial fibrillation and cardiomyopathies.

Seung Hoan Choi
Sean J. Jurgens
Patrick T. Ellinor
Research06 Mar 2025
Nature Genetics

Volume: 57, P: 548-562
Insight into SLE-related migraine using brain single-photon-emission computed tomography

John G Hanly
Claire Barber
Comments & Opinion20 Feb 2007
Nature Clinical Practice Rheumatology

Volume: 3, P: 200-201
Variant-specific inflation factors for assessing population stratification at the phenotypic variance level

Pooling participant-level genetic data into a single analysis can result in variance stratification, reducing statistical performance. Here, the authors develop variant-specific inflation factors to assess variance stratification and apply this to pooled individual-level data from whole genome sequencing.

Tamar Sofer
Xiuwen Zheng
Kenneth M. Rice
ResearchOpen Access09 Jun 2021
Nature Communications

Volume: 12, P: 1-14
A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies

STAARpipeline is a comprehensive framework for flexible and scalable rare-variant association analysis using whole-genome sequencing data and annotation information.

Zilin Li
Xihao Li
Xihong Lin
Research27 Oct 2022
Nature Methods

Volume: 19, P: 1599-1611
Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data

Analysis of whole-genome sequences of 25,465 individuals of European ancestry shows that rare variants contribute substantially to the heritability of height and body mass index.

Pierrick Wainschtein
Deepti Jain
Peter M. Visscher
Research07 Mar 2022
Nature Genetics

Volume: 54, P: 263-273
Diagnosis of cognitive impairment in adult and pediatric SLE

Systemic lupus erythematosus is frequently associated with neuropsychiatric syndromes, which can have a serious impact on the quality of a patient's life. Several methods are used to characterize cognitive impairment in these patients; however, studies have identified flaws in these assessments, highlighting the careful consideration needed when undertaking neuropsychological testing.

John G. Hanly
John D. Fisk
News & Views23 Aug 2011
Nature Reviews Rheumatology

Volume: 7, P: 564-565
Whole Genome Association Study of the Plasma Metabolome Identifies Metabolites Linked to Cardiometabolic Disease in Black Individuals

Most studies of the genetics of the metabolome have been done in individuals of European descent. Here, the authors integrate genomics and metabolomics in Black individuals, highlighting the value of whole genome sequencing in diverse populations and linking circulating metabolites to human disease.

Usman A. Tahir
Daniel H. Katz
Robert E. Gerszten
ResearchOpen Access22 Aug 2022
Nature Communications

Volume: 13, P: 1-16
Recent advances in the diagnosis and management of neuropsychiatric lupus

Neuropsychiatric manifestations of systemic lupus erythematosus (SLE) are common and negatively impact health. Diagnosing neuropsychiatric SLE is challenging owing to a lack of reliable biomarkers, and current treatments rely on clinical experience. This Review covers recent clinical advances in this area and emphasizes the need for further research.

Alexandra C. Legge
John G. Hanly
Reviews02 Oct 2024
Nature Reviews Rheumatology

Volume: 20, P: 712-728
Clonal haematopoiesis and risk of chronic liver disease

A study shows that clonal haematopoiesis of indeterminate potential is associated with an increased risk of chronic liver disease specifically through the promotion of liver inflammation and injury.

Waihay J. Wong
Connor Emdin
Pradeep Natarajan
Research12 Apr 2023
Nature

Volume: 616, P: 747-754
Genome sequencing unveils a regulatory landscape of platelet reactivity

Platelet aggregation is associated with myocardial infarction and stroke. Here, the authors have conducted a whole genome sequencing association study on platelet aggregation, discovering a locus in RGS18, where enhancer assays suggest an effect on activity of haematopoeitic lineage transcription factors.

Ali R. Keramati
Ming-Huei Chen
Andrew D. Johnson
ResearchOpen Access15 Jun 2021
Nature Communications

Volume: 12, P: 1-13
Whole genome sequence analysis of blood lipid levels in >66,000 individuals

Although the common genetic variants contributing to blood lipid levels have been studied, the contribution of rare variants is less understood. Here, the authors perform a rare coding and noncoding variant association study of blood lipid levels using whole genome sequencing data.

Margaret Sunitha Selvaraj
Xihao Li
Pradeep Natarajan
ResearchOpen Access11 Oct 2022
Nature Communications

Volume: 13, P: 1-18
Meta-analysis of genome-wide association studies discovers multiple loci for chronic lymphocytic leukemia

Chronic lymphocytic leukemia is a highly inheritable cancer. Here the authors conduct a metaanalysis of four genome-wide association studies and identify three novel loci located near EOMES, SERPINB6 and LPPassociated with risk of this disease.

Sonja I. Berndt
Nicola J. Camp
Susan L. Slager
ResearchOpen Access09 Mar 2016
Nature Communications

Volume: 7, P: 1-9
Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia

Susan Slager and colleagues report a meta-analysis of genome-wide association studies for chronic lymphocytic leukemia (CLL). They identify nine loci newly associated with CLL.

Sonja I Berndt
Christine F Skibola
Susan L Slager
Research16 Jun 2013
Nature Genetics

Volume: 45, P: 868-876
Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies

MetaSTAAR enables functionally informed rare variant association analysis in biobank-scale cohorts using an efficient, sparse matrix approach for summary statistic storage.

Xihao Li
Corbin Quick
Xihong Lin
Research23 Dec 2022
Nature Genetics

Volume: 55, P: 154-164
A genome-wide association study of marginal zone lymphoma shows association to the HLA region

Marginal zone lymphoma (MZL) is a common subtype of B-cell non-Hodgkin lymphoma. Here the authors carry out a two-stage genome-wide association study in over 8,000 Europeans and identify two new MZL risk loci at chromosome 6p, implicating the major histocompatibility complex in the disease for the first time.

Joseph Vijai
Zhaoming Wang
Alexandra Nieters
ResearchOpen Access08 Jan 2015
Nature Communications

Volume: 6, P: 1-7
A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

A high-resolution reference panel based on whole-genome sequencing data enables accurate imputation of HLA alleles across diverse populations and fine-mapping of HLA association signals for HIV-1 host response.

Yang Luo
Masahiro Kanai
Soumya Raychaudhuri
Research05 Oct 2021
Nature Genetics

Volume: 53, P: 1504-1516
Expression of the zinc transporter ZnT4 is decreased in the progression from early prostate disease to invasive prostate cancer

Susan M Henshall
Daniel E H Afar
Robert L Sutherland
Research04 Sept 2003
Oncogene

Volume: 22, P: 6005-6012
Author Correction: Clonal haematopoiesis and risk of chronic liver disease

Waihay J. Wong
Connor Emdin
Pradeep Natarajan
Amendments and Corrections03 Jul 2023
Nature

Volume: 619, P: E47
p53 nuclear accumulation as an early indicator of lethal prostate cancer

David I. Quinn
Phillip D. Stricker
Kate L. Mahon
ResearchOpen Access14 Aug 2019
British Journal of Cancer

Volume: 121, P: 578-583
The gene cortex controls mimicry and crypsis in butterflies and moths

Wing colour patterning of multiple species in the butterfly genus Heliconius is controlled by differential expression of the gene cortex, a member of a conserved family of cell cycle regulators.

Nicola J. Nadeau
Carolina Pardo-Diaz
Chris D. Jiggins
Research01 Jun 2016
Nature

Volume: 534, P: 106-110
Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling

The combination of nearly real-time genome sequencing of SARS-CoV-2 in infected patients during the first 10 weeks of COVID-19 containment in Australia and epidemiological modeling is helping in understanding the dynamics of the COVID-19 pandemic and potentially guiding public health decisions.

Rebecca J. Rockett
Alicia Arnott
Vitali Sintchenko
Research09 Jul 2020
Nature Medicine

Volume: 26, P: 1398-1404
Author Correction: A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

Yang Luo
Masahiro Kanai
Soumya Raychaudhuri
Amendments and Corrections02 Nov 2021
Nature Genetics

Volume: 53, P: 1722
Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma

James Cerhan and colleagues report genome-wide association and meta-analysis studies to identify genetic susceptibility loci for diffuse large B cell lymphoma. They identify four loci that influence genetic susceptibility to this B cell malignancy.

James R Cerhan
Sonja I Berndt
Stephen J Chanock
Research28 Sept 2014
Nature Genetics

Volume: 46, P: 1233-1238
A targeted association study in systemic lupus erythematosus identifies multiple susceptibility alleles

M L Budarf
P Goyette
J D Rioux
Research21 Oct 2010
Genes & Immunity

Volume: 12, P: 51-58
New developments in existing WHO entities and evolving molecular concepts: The Genitourinary Pathology Society (GUPS) update on renal neoplasia

Kiril Trpkov
Ondrej Hes
Anthony J. Gill
Research04 Mar 2021
Modern Pathology

Volume: 34, P: 1392-1424
Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus

Timothy Vyse and colleagues report the results of a large-scale association study of systemic lupus erythematosus (SLE). They identify ten new susceptibility loci and implicate aberrant regulation of innate and adaptive immunity genes in disease pathogenesis.

James Bentham
David L Morris
Timothy J Vyse
Research26 Oct 2015
Nature Genetics

Volume: 47, P: 1457-1464
Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes

Sonja I. Berndt
Joseph Vijai
Nathaniel Rothman
Research22 Oct 2022
Leukemia

Volume: 36, P: 2835-2844
Expanding the clinicopathological spectrum of succinate dehydrogenase-deficient renal cell carcinoma with a focus on variant morphologies: a study of 62 new tumors in 59 patients

Talia L. Fuchs
Fiona Maclean
Anthony J. Gill
Research23 Dec 2021
Modern Pathology

Volume: 35, P: 836-849
Novel, emerging and provisional renal entities: The Genitourinary Pathology Society (GUPS) update on renal neoplasia

Kiril Trpkov
Sean R. Williamson
Ondrej Hes
Research01 Feb 2021
Modern Pathology

Volume: 34, P: 1167-1184
Correction to: Novel, emerging and provisional renal entities: the Genitourinary Pathology Society (GUPS) update on renal neoplasia

Kiril Trpkov
Sean R. Williamson
Ondrej Hes
Amendments and Corrections16 Mar 2021
Modern Pathology

Volume: 34, P: 1037
Correction: Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes

Sonja I. Berndt
Joseph Vijai
Nathaniel Rothman
Amendments and Corrections04 Sept 2023
Leukemia

Volume: 37, P: 2142

Search

Diagnosis and management of neuropsychiatric SLE

cellSTAAR: incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of noncoding regions

Publisher Correction: Recent advances in the diagnosis and management of neuropsychiatric lupus

High-dose vitamin D supplementation and prostate cancer progression: a phase II randomised trial in localised prostate cancer cases with intermediate risk of progression (ProsD)

A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies

Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis

Sequencing in over 50,000 cases identifies coding and structural variation underlying atrial fibrillation risk

Insight into SLE-related migraine using brain single-photon-emission computed tomography

Variant-specific inflation factors for assessing population stratification at the phenotypic variance level

A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies

Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data

Diagnosis of cognitive impairment in adult and pediatric SLE

Whole Genome Association Study of the Plasma Metabolome Identifies Metabolites Linked to Cardiometabolic Disease in Black Individuals

Recent advances in the diagnosis and management of neuropsychiatric lupus

Clonal haematopoiesis and risk of chronic liver disease

Genome sequencing unveils a regulatory landscape of platelet reactivity

Whole genome sequence analysis of blood lipid levels in >66,000 individuals

Meta-analysis of genome-wide association studies discovers multiple loci for chronic lymphocytic leukemia

Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia

Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies

A genome-wide association study of marginal zone lymphoma shows association to the HLA region

A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

Expression of the zinc transporter ZnT4 is decreased in the progression from early prostate disease to invasive prostate cancer

Author Correction: Clonal haematopoiesis and risk of chronic liver disease

p53 nuclear accumulation as an early indicator of lethal prostate cancer

The gene cortex controls mimicry and crypsis in butterflies and moths

Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling

Author Correction: A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma

A targeted association study in systemic lupus erythematosus identifies multiple susceptibility alleles

New developments in existing WHO entities and evolving molecular concepts: The Genitourinary Pathology Society (GUPS) update on renal neoplasia

Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus

Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes

Expanding the clinicopathological spectrum of succinate dehydrogenase-deficient renal cell carcinoma with a focus on variant morphologies: a study of 62 new tumors in 59 patients

Novel, emerging and provisional renal entities: The Genitourinary Pathology Society (GUPS) update on renal neoplasia

Correction to: Novel, emerging and provisional renal entities: the Genitourinary Pathology Society (GUPS) update on renal neoplasia

Correction: Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes

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