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Article ; Online: From black and white to fifty shades of grey.

Paterson, Andrew D

2023 Volume 142, Issue 24, Page(s) 2037–2038

MeSH term(s)	Humans ; Biological Specimen Banks
Language	English
Publishing date	2023-12-14
Publishing country	United States
Document type	Editorial ; Comment
ZDB-ID	80069-7
ISSN	1528-0020 ; 0006-4971
ISSN (online)	1528-0020
ISSN	0006-4971
DOI	10.1182/blood.2023022171
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Article ; Online: Better together against genetic heterogeneity: A sex-combined joint main and interaction analysis of 290 quantitative traits in the UK Biobank.

Lin, Boxi / Paterson, Andrew D / Sun, Lei

PLoS genetics

2024 Volume 20, Issue 4, Page(s) e1011221

Abstract: Genetic effects can be sex-specific, particularly for traits such as testosterone, a sex hormone. While sex-stratified analysis provides easily interpretable sex-specific effect size estimates, the presence of sex-differences in SNP effect implies a SNP× ... ...

Abstract	Genetic effects can be sex-specific, particularly for traits such as testosterone, a sex hormone. While sex-stratified analysis provides easily interpretable sex-specific effect size estimates, the presence of sex-differences in SNP effect implies a SNP×sex interaction. This suggests the usage of the often overlooked joint test, testing for an SNP's main and SNP×sex interaction effects simultaneously. Notably, even without individual-level data, the joint test statistic can be derived from sex-stratified summary statistics through an omnibus meta-analysis. Utilizing the available sex-stratified summary statistics of the UK Biobank, we performed such omnibus meta-analyses for 290 quantitative traits. Results revealed that this approach is robust to genetic effect heterogeneity and can outperform the traditional sex-stratified or sex-combined main effect-only tests. Therefore, we advocate using the omnibus meta-analysis that captures both the main and interaction effects. Subsequent sex-stratified analysis should be conducted for sex-specific effect size estimation and interpretation.
Language	English
Publishing date	2024-04-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1011221
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Article ; Online: The effect of ascertainment on penetrance estimates for rare variants: Implications for establishing pathogenicity and for genetic counselling.

Paterson, Andrew D / Seok, Sang-Cheol / Vieland, Veronica J

PloS one

2023 Volume 18, Issue 9, Page(s) e0290336

Abstract: Next-generation sequencing has led to an explosion of genetic findings for many rare diseases. However, most of the variants identified are very rare and were also identified in small pedigrees, which creates challenges in terms of penetrance estimation ... ...

Abstract	Next-generation sequencing has led to an explosion of genetic findings for many rare diseases. However, most of the variants identified are very rare and were also identified in small pedigrees, which creates challenges in terms of penetrance estimation and translation into genetic counselling in the setting of cascade testing. We use simulations to show that for a rare (dominant) disorder where a variant is identified in a small number of small pedigrees, the penetrance estimate can both have large uncertainty and be drastically inflated, due to underlying ascertainment bias. We have developed PenEst, an app that allows users to investigate the phenomenon across ranges of parameter settings. We also illustrate robust ascertainment corrections via the LOD (logarithm of the odds) score, and recommend a LOD-based approach to assessing pathogenicity of rare variants in the presence of reduced penetrance.
MeSH term(s)	Genetic Counseling ; Penetrance ; Virulence ; High-Throughput Nucleotide Sequencing ; Lod Score
Language	English
Publishing date	2023-09-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0290336
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Article ; Online: Erythritol as a Potential Causal Contributor to Cardiometabolic Disease: A Mendelian Randomization Study.

Khafagy, Rana / Paterson, Andrew D / Dash, Satya

Diabetes

2023 Volume 73, Issue 2, Page(s) 325–331

MeSH term(s)	Humans ; Diabetes Mellitus, Type 2/genetics ; Risk Factors ; Mendelian Randomization Analysis ; Prospective Studies ; Coronary Artery Disease ; Body Mass Index ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study
Language	English
Publishing date	2023-11-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	80085-5
ISSN	1939-327X ; 0012-1797
ISSN (online)	1939-327X
ISSN	0012-1797
DOI	10.2337/db23-0330
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Article ; Online: Population-based studies reveal an additive role of type IV collagen variants in hematuria and albuminuria.

Barua, Moumita / Paterson, Andrew D

Pediatric nephrology (Berlin, Germany)

2021 Volume 37, Issue 2, Page(s) 253–262

Abstract: Specific variants in genes that encode the α3α4α5 chains of type IV collagen cause Alport syndrome (AS), which encompass a clinical spectrum from isolated hematuria to multisystem disease affecting sight, hearing and kidney function. The commonest form ... ...

Abstract	Specific variants in genes that encode the α3α4α5 chains of type IV collagen cause Alport syndrome (AS), which encompass a clinical spectrum from isolated hematuria to multisystem disease affecting sight, hearing and kidney function. The commonest form is X-linked Alport syndrome (XLAS; COL4A5) with autosomal AS (COL4A3 and COL4A4) comprising a minority of cases. While historic data estimates the frequency of AS at 1:5000-10,000, recent population-based genetic studies suggest the prevalence is considerably higher. Genome-wide association studies (GWAS) have been performed in the Icelandic (deCODE) and UK (UK Biobank) populations, demonstrating an association of type IV collagen gene variants with AS relevant kidney traits. In the Icelandic population, 1 in 600 carries a 2.5-kb COL4A3 coding deletion or a COL4A3 missense variant (rs200287952[A], Gly695Arg), both of which are strongly associated with hematuria and albuminuria (P values = 1.9 × 10
MeSH term(s)	Albuminuria/genetics ; Autoantigens/genetics ; Collagen Type IV/genetics ; Genome-Wide Association Study ; Hematuria/genetics ; Humans ; Mutation ; Nephritis, Hereditary/genetics ; Pedigree
Chemical Substances	Autoantigens ; COL4A4 protein, human ; Collagen Type IV
Language	English
Publishing date	2021-02-26
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	631932-4
ISSN	1432-198X ; 0931-041X
ISSN (online)	1432-198X
ISSN	0931-041X
DOI	10.1007/s00467-021-04934-y
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Article ; Online: Analyses of potential causal contributors to increased waist/hip ratio-associated cardiometabolic disease: A combined and sex-stratified Mendelian randomization study.

Hashemy, Habiba / Nguyen, Anthony / Khafagy, Rana / Roshandel, Delnaz / Paterson, Andrew D / Dash, Satya

Diabetes, obesity & metabolism

2024

Abstract: Background: Increased waist/hip ratio (WHR) contributes to type 2 diabetes, fatty liver, dyslipidaemia, hypertension and coronary artery disease, with potential sex-differential effects. Postulated mediators include increased lipid flux, branched-chain ... ...

Abstract	Background: Increased waist/hip ratio (WHR) contributes to type 2 diabetes, fatty liver, dyslipidaemia, hypertension and coronary artery disease, with potential sex-differential effects. Postulated mediators include increased lipid flux, branched-chain amino acids, glycine and glycoprotein acetyl, but their relative contributions and sex-specific impact on WHR-associated cardiometabolic disease (CMD) are not established. Methods: We therefore undertook combined and sex-stratified Mendelian randomization (MR) to assess the relative causal contributions of these mediators to WHR-associated CMD using summary statistics from the largest genome-wide association studies in European ancestries. Results: In sex-combined MR analyses, increased WHR significantly reduces high-density lipoprotein (beta = -0.416, SE = 0.029, p = 2.87E-47), increases triglyceride (beta = 0.431, SE = 0.029, p = 1.87E-50), type 2 diabetes (odds ratio = 2.747, SE = 0.09, p = 26E-23), coronary artery disease (odds ratio = 1.478, SE = 0.045, p = 6.96E-18), alanine transaminase (beta = 0.062, SE = 0.004, p = 6.88E-67), and systolic (beta = 0.134, SE = 0.022, p = 7.81E-10) and diastolic blood pressure (beta = 0.162, SE = 0.026, p = 5.38E-10). Adjustment for the mediators attenuated WHR's effects, but the associations remained significant with concordant results in females. In males, a similar pattern was seen, except after adjusting for the effect of the ratio of monounsaturated fatty acid to total free fatty acid, the potential causal effect of WHR was no longer significant: high-density lipoprotein (beta = -0.117, SE = 0.069, p = .09) and triglyceride (beta = 0.051, SE = 0.068, p = .459). Conclusions: MR suggests WHR increases the risk of CMD independent of these mediators, with the exception of dyslipidaemia in males, which is largely driven by the monounsaturated fatty acid to total free fatty acid ratio.
Language	English
Publishing date	2024-03-15
Publishing country	England
Document type	Journal Article
ZDB-ID	1454944-x
ISSN	1463-1326 ; 1462-8902
ISSN (online)	1463-1326
ISSN	1462-8902
DOI	10.1111/dom.15542
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Article: Beyond apples and pears: sex-specific genetics of body fat percentage.

Roshandel, Delnaz / Lu, Tianyuan / Paterson, Andrew D / Dash, Satya

Frontiers in endocrinology

2023 Volume 14, Page(s) 1274791

Abstract: Introduction: Biological sex influences both overall adiposity and fat distribution. Further, testosterone and sex hormone binding globulin (SHBG) influence adiposity and metabolic function, with differential effects of testosterone in men and women. ... ...

Abstract	Introduction: Biological sex influences both overall adiposity and fat distribution. Further, testosterone and sex hormone binding globulin (SHBG) influence adiposity and metabolic function, with differential effects of testosterone in men and women. Here, we aimed to perform sex-stratified genome-wide association studies (GWAS) of body fat percentage (BFPAdj) (adjusting for testosterone and sex hormone binding globulin (SHBG)) to increase statistical power. Methods: GWAS were performed in white British individuals from the UK Biobank (157,937 males and 154,337 females). To avoid collider bias, loci associated with SHBG or testosterone were excluded. We investigated association of BFPAdj loci with high density cholesterol (HDL), triglyceride (TG), type 2 diabetes (T2D), coronary artery disease (CAD), and MRI-derived abdominal subcutaneous adipose tissue (ASAT), visceral adipose tissue (VAT) and gluteofemoral adipose tissue (GFAT) using publicly available data from large GWAS. We also performed 2-sample Mendelian Randomization (MR) using identified BFPAdj variants as instruments to investigate causal effect of BFPAdj on HDL, TG, T2D and CAD in males and females separately. Results: We identified 195 and 174 loci explaining 3.35% and 2.60% of the variation in BFPAdj in males and females, respectively at genome-wide significance (GWS, p<5x10 Conclusions: There was limited genetic overlap between BFPAdj in males and females at GWS. BFPAdj loci generally did not have adverse cardiometabolic effects which may reflect the effects of favourable fat distribution and cardiometabolic risk modulation by testosterone and SHBG.
MeSH term(s)	Male ; Humans ; Female ; Sex Hormone-Binding Globulin/genetics ; Sex Hormone-Binding Globulin/metabolism ; Malus/metabolism ; Pyrus/metabolism ; Diabetes Mellitus, Type 2/genetics ; Genome-Wide Association Study ; Obesity ; Testosterone ; Intra-Abdominal Fat/metabolism ; Cardiovascular Diseases
Chemical Substances	Sex Hormone-Binding Globulin ; Testosterone (3XMK78S47O)
Language	English
Publishing date	2023-10-05
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2592084-4
ISSN	1664-2392
ISSN	1664-2392
DOI	10.3389/fendo.2023.1274791
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Article ; Online: HbA1c for type 2 diabetes diagnosis in Africans and African Americans: Personalized medicine NOW!

Paterson, Andrew D

PLoS medicine

2017 Volume 14, Issue 9, Page(s) e1002384

Abstract: Andrew Paterson discusses findings from a new study that shows HbA1c screening for diabetes will leave 2% of African Americans undiagnosed and how personalised medicine is needed. ...

Abstract	Andrew Paterson discusses findings from a new study that shows HbA1c screening for diabetes will leave 2% of African Americans undiagnosed and how personalised medicine is needed.
MeSH term(s)	African Americans ; African Continental Ancestry Group ; Diabetes Mellitus, Type 2/diagnosis ; Diabetes Mellitus, Type 2/ethnology ; Glycated Hemoglobin A/genetics ; Glycated Hemoglobin A/metabolism ; Humans ; Precision Medicine
Chemical Substances	Glycated Hemoglobin A ; hemoglobin A1c protein, human
Language	English
Publishing date	2017-09-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2185925-5
ISSN	1549-1676 ; 1549-1277
ISSN (online)	1549-1676
ISSN	1549-1277
DOI	10.1371/journal.pmed.1002384
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Article: Statistical Learning of Large-Scale Genetic Data: How to Run a Genome-Wide Association Study of Gene-Expression Data Using the 1000 Genomes Project Data.

Sugolov, Anton / Emmenegger, Eric / Paterson, Andrew D / Sun, Lei

Statistics in biosciences

2023 Volume 16, Issue 1, Page(s) 250–264

Abstract: Teaching statistics through engaging applications to contemporary large-scale datasets is essential to attracting students to the field. To this end, we developed a hands-on, week-long workshop for senior high-school or junior undergraduate students, ... ...

Abstract	Teaching statistics through engaging applications to contemporary large-scale datasets is essential to attracting students to the field. To this end, we developed a hands-on, week-long workshop for senior high-school or junior undergraduate students, without prior knowledge in statistical genetics but with some basic knowledge in data science, to conduct their own genome-wide association study (GWAS). The GWAS was performed for open source gene expression data, using publicly available human genetics data. Assisted by a detailed instruction manual, students were able to obtain
Language	English
Publishing date	2023-07-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2497694-5
ISSN	1867-1772 ; 1867-1764
ISSN (online)	1867-1772
ISSN	1867-1764
DOI	10.1007/s12561-023-09375-9
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Article ; Online: Major sex differences in allele frequencies for X chromosomal variants in both the 1000 Genomes Project and gnomAD.

Wang, Zhong / Sun, Lei / Paterson, Andrew D

PLoS genetics

2022 Volume 18, Issue 5, Page(s) e1010231

Abstract: An unexpectedly high proportion of SNPs on the X chromosome in the 1000 Genomes Project phase 3 data were identified with significant sex differences in minor allele frequencies (sdMAF). sdMAF persisted for many of these SNPs in the recently released ... ...

Abstract	An unexpectedly high proportion of SNPs on the X chromosome in the 1000 Genomes Project phase 3 data were identified with significant sex differences in minor allele frequencies (sdMAF). sdMAF persisted for many of these SNPs in the recently released high coverage whole genome sequence of the 1000 Genomes Project that was aligned to GRCh38, and it was consistent between the five super-populations. Among the 245,825 common (MAF>5%) biallelic X-chromosomal SNPs in the phase 3 data presumed to be of high quality, 2,039 have genome-wide significant sdMAF (p-value <5e-8). sdMAF varied by location: non-pseudo-autosomal region (NPR) = 0.83%, pseudo-autosomal regions (PAR1) = 0.29%, PAR2 = 13.1%, and X-transposed region (XTR)/PAR3 = 0.85% of SNPs had sdMAF, and they were clustered at the NPR-PAR boundaries, among others. sdMAF at the NPR-PAR boundaries are biologically expected due to sex-linkage, but have generally been ignored in association studies. For comparison, similar analyses found only 6, 1 and 0 SNPs with significant sdMAF on chromosomes 1, 7 and 22, respectively. Similar sdMAF results for the X chromosome were obtained from the high coverage whole genome sequence data from gnomAD V 3.1.2 for both the non-Finnish European and African/African American samples. Future X chromosome analyses need to take sdMAF into account.
MeSH term(s)	Female ; Gene Frequency ; Genome ; Humans ; Male ; Polymorphism, Single Nucleotide/genetics ; Sex Characteristics ; X Chromosome
Language	English
Publishing date	2022-05-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1010231
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