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de Vries PS, Conomos MP, Singh K, Nicholson CJ, Jain D, Hasbani NR, Jiang W, Lee S, Cardenas CLL, Lutz SM, Wong D, Guo X, Yao J, Young EP, Tcheandjieu C, Hilliard AT, Bis JC, Bielak LF, Brown MR, Musharoff S, Clarke SL, Terry JG, Palmer ND, Yanek LR, Xu H, Heard-Costa N, Wessel J, Selvaraj MS, Li RH, Sun X, Turner AW, Stilp AM, Khan A, Newman AB, Rasheed A, Freedman BI, Kral BG, McHugh CP, Hodonsky C, Saleheen D, Herrington DM, Jacobs DR, Nickerson DA, Boerwinkle E, Wang FF, Heiss G, Jun G, Kinney GL, Sigurslid HH, Doddapaneni H, Hall IM, Bensenor IM, Broome J, Crapo JD, Wilson JG, Smith JA, Blangero J, Vargas JD, Mosquera JV, Smith JD, Viaud-Martinez KA, Ryan KA, Young KA, Taylor KD, Lange LA, Emery LS, Bittencourt MS, Budoff MJ, Montasser ME, Yu M, Mahaney MC, Mahamdeh MS, Fornage M, Franceschini N, Lotufo PA, Natarajan P, Wong Q, Mathias RA, Gibbs RA, Do R, Mehran R, Tracy RP, Kim RW, Nelson SC, Damrauer SM, Kardia SL, Rich SS, Fuster V, Napolioni V, Zhao W, Tian W, Yin X, Min YI, Manning AK, Peloso G, Kelly TN, O’Donnell CJ, Morrison AC, Curran JE, Zapol WM, Bowden DW, Becker LC, Correa A, Mitchell BD, Psaty BM, Carr JJ, Pereira AC, Assimes TL, Stitziel NO, Hokanson JE, Laurie CA, Rotter JI, Vasan RS, Post WS, Peyser PA, Miller CL, Malhotra R. Whole-genome sequencing uncovers two loci for coronary artery calcification and identifies ARSE as a regulator of vascular calcification. NATURE CARDIOVASCULAR RESEARCH 2023; 2:1159-1172. [PMID: 38817323 PMCID: PMC11138106 DOI: 10.1038/s44161-023-00375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/25/2023] [Indexed: 06/01/2024]
Abstract
Coronary artery calcification (CAC) is a measure of atherosclerosis and a well-established predictor of coronary artery disease (CAD) events. Here we describe a genome-wide association study (GWAS) of CAC in 22,400 participants from multiple ancestral groups. We confirmed associations with four known loci and identified two additional loci associated with CAC (ARSE and MMP16), with evidence of significant associations in replication analyses for both novel loci. Functional assays of ARSE and MMP16 in human vascular smooth muscle cells (VSMCs) demonstrate that ARSE is a promoter of VSMC calcification and VSMC phenotype switching from a contractile to a calcifying or osteogenic phenotype. Furthermore, we show that the association of variants near ARSE with reduced CAC is likely explained by reduced ARSE expression with the G allele of enhancer variant rs5982944. Our study highlights ARSE as an important contributor to atherosclerotic vascular calcification, and a potential drug target for vascular calcific disease.
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Li T, Ferraro N, Strober BJ, Aguet F, Kasela S, Arvanitis M, Ni B, Wiel L, Hershberg E, Ardlie K, Arking DE, Beer RL, Brody J, Blackwell TW, Clish C, Gabriel S, Gerszten R, Guo X, Gupta N, Johnson WC, Lappalainen T, Lin HJ, Liu Y, Nickerson DA, Papanicolaou G, Pritchard JK, Qasba P, Shojaie A, Smith J, Sotoodehnia N, Taylor KD, Tracy RP, Van Den Berg D, Wheeler MT, Rich SS, Rotter JI, Battle A, Montgomery SB. The functional impact of rare variation across the regulatory cascade. CELL GENOMICS 2023; 3:100401. [PMID: 37868038 PMCID: PMC10589633 DOI: 10.1016/j.xgen.2023.100401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/08/2023] [Accepted: 08/10/2023] [Indexed: 10/24/2023]
Abstract
Each human genome has tens of thousands of rare genetic variants; however, identifying impactful rare variants remains a major challenge. We demonstrate how use of personal multi-omics can enable identification of impactful rare variants by using the Multi-Ethnic Study of Atherosclerosis, which included several hundred individuals, with whole-genome sequencing, transcriptomes, methylomes, and proteomes collected across two time points, 10 years apart. We evaluated each multi-omics phenotype's ability to separately and jointly inform functional rare variation. By combining expression and protein data, we observed rare stop variants 62 times and rare frameshift variants 216 times as frequently as controls, compared to 13-27 times as frequently for expression or protein effects alone. We extended a Bayesian hierarchical model, "Watershed," to prioritize specific rare variants underlying multi-omics signals across the regulatory cascade. With this approach, we identified rare variants that exhibited large effect sizes on multiple complex traits including height, schizophrenia, and Alzheimer's disease.
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Pinard A, Ye W, Fraser SM, Rosenfeld JA, Pichurin P, Hickey SE, Guo D, Cecchi AC, Boerio ML, Guey S, Aloui C, Lee K, Kraemer M, Alyemni SO, Bamshad MJ, Nickerson DA, Tournier-Lasserve E, Haider S, Jin SC, Smith ER, Kahle KT, Jan LY, He M, Milewicz DM. Rare variants in ANO1, encoding a calcium-activated chloride channel, predispose to moyamoya disease. Brain 2023; 146:3616-3623. [PMID: 37253099 PMCID: PMC10473557 DOI: 10.1093/brain/awad172] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/24/2023] [Accepted: 04/16/2023] [Indexed: 06/01/2023] Open
Abstract
Moyamoya disease, a cerebrovascular disease leading to strokes in children and young adults, is characterized by progressive occlusion of the distal internal carotid arteries and the formation of collateral vessels. Altered genes play a prominent role in the aetiology of moyamoya disease, but a causative gene is not identified in the majority of cases. Exome sequencing data from 151 individuals from 84 unsolved families were analysed to identify further genes for moyamoya disease, then candidate genes assessed in additional cases (150 probands). Two families had the same rare variant in ANO1, which encodes a calcium-activated chloride channel, anoctamin-1. Haplotype analyses found the families were related, and ANO1 p.Met658Val segregated with moyamoya disease in the family with an LOD score of 3.3. Six additional ANO1 rare variants were identified in moyamoya disease families. The ANO1 rare variants were assessed using patch-clamp recordings, and the majority of variants, including ANO1 p.Met658Val, displayed increased sensitivity to intracellular Ca2+. Patients harbouring these gain-of-function ANO1 variants had classic features of moyamoya disease, but also had aneurysm, stenosis and/or occlusion in the posterior circulation. Our studies support that ANO1 gain-of-function pathogenic variants predispose to moyamoya disease and are associated with unique involvement of the posterior circulation.
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Liu Q, Zhou Y, Cogan JD, Mitchell DB, Sheng Q, Zhao S, Bai Y, Ciombor KK, Sabusap CM, Malabanan MM, Markin CR, Douglas K, Ding G, Banovich NE, Nickerson DA, Blue EE, Bamshad MJ, Brown KK, Schwartz DA, Phillips JA, Martinez-Barricarte R, Salisbury ML, Shyr Y, Loyd JE, Kropski JA, Blackwell TS. The Genetic Landscape of Familial Pulmonary Fibrosis. Am J Respir Crit Care Med 2023; 207:1345-1357. [PMID: 36622818 PMCID: PMC10595451 DOI: 10.1164/rccm.202204-0781oc] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 01/09/2023] [Indexed: 01/10/2023] Open
Abstract
Rationale and Objectives: Up to 20% of idiopathic interstitial lung disease is familial, referred to as familial pulmonary fibrosis (FPF). An integrated analysis of FPF genetic risk was performed by comprehensively evaluating for genetic rare variants (RVs) in a large cohort of FPF kindreds. Methods: Whole-exome sequencing and/or candidate gene sequencing from affected individuals in 569 FPF kindreds was performed, followed by cosegregation analysis in large kindreds, gene burden analysis, gene-based risk scoring, cell-type enrichment analysis, and coexpression network construction. Measurements and Main Results: It was found that 14.9-23.4% of genetic risk in kindreds could be explained by RVs in genes previously linked to FPF, predominantly telomere-related genes. New candidate genes were identified in a small number of families-including SYDE1, SERPINB8, GPR87, and NETO1-and tools were developed for evaluation and prioritization of RV-containing genes across kindreds. Several pathways were enriched for RV-containing genes in FPF, including focal adhesion and mitochondrial complex I assembly. By combining single-cell transcriptomics with prioritized candidate genes, expression of RV-containing genes was discovered to be enriched in smooth muscle cells, type II alveolar epithelial cells, and endothelial cells. Conclusions: In the most comprehensive FPF genetic study to date, the prevalence of RVs in known FPF-related genes was defined, and new candidate genes and pathways relevant to FPF were identified. However, new RV-containing genes shared across multiple kindreds were not identified, thereby suggesting that heterogeneous genetic variants involving a variety of genes and pathways mediate genetic risk in most FPF kindreds.
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Jun G, English AC, Metcalf GA, Yang J, Chaisson MJP, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YDI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJ, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. RESEARCH SQUARE 2023:rs.3.rs-2515453. [PMID: 36778386 PMCID: PMC9915771 DOI: 10.21203/rs.3.rs-2515453/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hematologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.
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Esterhuizen AI, Tiffin N, Riordan G, Wessels M, Burman RJ, Aziz MC, Calhoun JD, Gunti J, Amiri EE, Ramamurthy A, Bamshad MJ, Mefford HC, Ramesar R, Wilmshurst JM, Carvill GL, Leal SM, Nickerson DA, Anderson P, Bacus TJ, Blue EE, Brower K, Buckingham KJ, Chong JX, Cornejo Sánchez D, Davis CP, Davis CJ, Frazar CD, Gomeztagle-Burgess K, Gordon WW, Horike-Pyne M, Hurless JR, Jarvik GP, Johanson E, Thomas Kolar J, Marvin CT, McGee S, McGoldrick DJ, Mekonnen B, Nielsen PM, Patterson K, Radhakrishnan A, Richardson MA, Roote GT, Ryke EL, Schrauwen I, Shively KM, Smith JD, Tackett M, Wang G, Weiss JM, Wheeler MM, Yi Q, Zhang X. Precision medicine for developmental and epileptic encephalopathies in Africa-strategies for a resource-limited setting. Genet Med 2023; 25:100333. [PMID: 36480001 DOI: 10.1016/j.gim.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Sub-Saharan Africa bears the highest burden of epilepsy worldwide. A presumed proportion is genetic, but this etiology is buried under the burden of infections and perinatal insults in a setting of limited awareness and few options for testing. Children with developmental and epileptic encephalopathies (DEEs) are most severely affected by this diagnostic gap in Africa, because the rate of actionable findings is highest in DEE-associated genes. METHODS We tested 234 genetically naive South African children diagnosed with/possible DEE using gene panels, exome sequencing, and chromosomal microarray. Statistical comparison of electroclinical features in children with and children without candidate variants was performed to identify characteristics most likely predictive of a positive genetic finding. RESULTS Of the 41 (of 234) children with likely/pathogenic variants, 26 had variants supporting precision therapy. Multivariate regression modeling highlighted neonatal or infantile-onset seizures and movement abnormalities as predictive of a positive genetic finding. We used this, coupled with an emphasis on precision medicine outcomes, to propose the pragmatic "Think-Genetics" strategy for early recognition of a possible genetic etiology. CONCLUSION Our findings emphasize the importance of an early genetic diagnosis in DEE. We designed the Think-Genetics strategy for early recognition, appropriate interim management, and genetic testing for DEE in resource-constrained settings.
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Jun G, English AC, Metcalf GA, Yang J, Chaisson MJP, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen YDI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung YJ, Kane JP, Kaplan R, Kim W, Loos RJ, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525428. [PMID: 36747810 PMCID: PMC9900832 DOI: 10.1101/2023.01.25.525428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hemotologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.
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Wheeler MM, Stilp AM, Rao S, Halldórsson BV, Beyter D, Wen J, Mihkaylova AV, McHugh CP, Lane J, Jiang MZ, Raffield LM, Jun G, Sedlazeck FJ, Metcalf G, Yao Y, Bis JB, Chami N, de Vries PS, Desai P, Floyd JS, Gao Y, Kammers K, Kim W, Moon JY, Ratan A, Yanek LR, Almasy L, Becker LC, Blangero J, Cho MH, Curran JE, Fornage M, Kaplan RC, Lewis JP, Loos RJF, Mitchell BD, Morrison AC, Preuss M, Psaty BM, Rich SS, Rotter JI, Tang H, Tracy RP, Boerwinkle E, Abecasis GR, Blackwell TW, Smith AV, Johnson AD, Mathias RA, Nickerson DA, Conomos MP, Li Y, Þorsteinsdóttir U, Magnússon MK, Stefansson K, Pankratz ND, Bauer DE, Auer PL, Reiner AP. Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program. Nat Commun 2022; 13:7592. [PMID: 36481753 PMCID: PMC9732337 DOI: 10.1038/s41467-022-35354-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies have identified thousands of single nucleotide variants and small indels that contribute to variation in hematologic traits. While structural variants are known to cause rare blood or hematopoietic disorders, the genome-wide contribution of structural variants to quantitative blood cell trait variation is unknown. Here we utilized whole genome sequencing data in ancestrally diverse participants of the NHLBI Trans Omics for Precision Medicine program (N = 50,675) to detect structural variants associated with hematologic traits. Using single variant tests, we assessed the association of common and rare structural variants with red cell-, white cell-, and platelet-related quantitative traits and observed 21 independent signals (12 common and 9 rare) reaching genome-wide significance. The majority of these associations (N = 18) replicated in independent datasets. In genome-editing experiments, we provide evidence that a deletion associated with lower monocyte counts leads to disruption of an S1PR3 monocyte enhancer and decreased S1PR3 expression.
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Chung E, Magedson A, Emanuels A, Luiten K, Pfau B, Truong M, Chow EJ, Hughes JP, Uyeki TM, Englund JA, Nickerson DA, Lockwood CM, Shendure J, Starita LM, Chu HY. SARS-CoV-2 Screening Testing in Schools: A Comparison of School- Vs. Home-Based Collection Methods. J Pediatric Infect Dis Soc 2022; 11:522-524. [PMID: 36082698 PMCID: PMC9494399 DOI: 10.1093/jpids/piac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We implemented a voluntary SARS-CoV-2 screening testing study for kindergarten-2nd grade students in a Washington School district. Weekly SARS-CoV-2 testing participation was higher for students with staff-collected nasal swabs at school than for students with parent-collected swabs at home.
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Patel RA, Musharoff SA, Spence JP, Pimentel H, Tcheandjieu C, Mostafavi H, Sinnott-Armstrong N, Clarke SL, Smith CJ, Durda PP, Taylor KD, Tracy R, Liu Y, Johnson WC, Aguet F, Ardlie KG, Gabriel S, Smith J, Nickerson DA, Rich SS, Rotter JI, Tsao PS, Assimes TL, Pritchard JK. Genetic interactions drive heterogeneity in causal variant effect sizes for gene expression and complex traits. Am J Hum Genet 2022; 109:1286-1297. [PMID: 35716666 PMCID: PMC9300878 DOI: 10.1016/j.ajhg.2022.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/26/2022] [Indexed: 01/09/2023] Open
Abstract
Despite the growing number of genome-wide association studies (GWASs), it remains unclear to what extent gene-by-gene and gene-by-environment interactions influence complex traits in humans. The magnitude of genetic interactions in complex traits has been difficult to quantify because GWASs are generally underpowered to detect individual interactions of small effect. Here, we develop a method to test for genetic interactions that aggregates information across all trait-associated loci. Specifically, we test whether SNPs in regions of European ancestry shared between European American and admixed African American individuals have the same causal effect sizes. We hypothesize that in African Americans, the presence of genetic interactions will drive the causal effect sizes of SNPs in regions of European ancestry to be more similar to those of SNPs in regions of African ancestry. We apply our method to two traits: gene expression in 296 African Americans and 482 European Americans in the Multi-Ethnic Study of Atherosclerosis (MESA) and low-density lipoprotein cholesterol (LDL-C) in 74K African Americans and 296K European Americans in the Million Veteran Program (MVP). We find significant evidence for genetic interactions in our analysis of gene expression; for LDL-C, we observe a similar point estimate, although this is not significant, most likely due to lower statistical power. These results suggest that gene-by-gene or gene-by-environment interactions modify the effect sizes of causal variants in human complex traits.
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Gaik M, Kojic M, Stegeman MR, Öncü‐Öner T, Kościelniak A, Jones A, Mohamed A, Chau PYS, Sharmin S, Chramiec‐Głąbik A, Indyka P, Rawski M, Biela A, Dobosz D, Millar A, Chau V, Ünalp A, Piper M, Bellingham MC, Eichler EE, Nickerson DA, Güleryüz H, Abbassi NEH, Jazgar K, Davis MJ, Mercimek‐Andrews S, Cingöz S, Wainwright BJ, Glatt S. Functional divergence of the two Elongator subcomplexes during neurodevelopment. EMBO Mol Med 2022; 14:e15608. [PMID: 35698786 PMCID: PMC9260213 DOI: 10.15252/emmm.202115608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 12/11/2022] Open
Abstract
The highly conserved Elongator complex is a translational regulator that plays a critical role in neurodevelopment, neurological diseases, and brain tumors. Numerous clinically relevant variants have been reported in the catalytic Elp123 subcomplex, while no missense mutations in the accessory subcomplex Elp456 have been described. Here, we identify ELP4 and ELP6 variants in patients with developmental delay, epilepsy, intellectual disability, and motor dysfunction. We determine the structures of human and murine Elp456 subcomplexes and locate the mutated residues. We show that patient-derived mutations in Elp456 affect the tRNA modification activity of Elongator in vitro as well as in human and murine cells. Modeling the pathogenic variants in mice recapitulates the clinical features of the patients and reveals neuropathology that differs from the one caused by previously characterized Elp123 mutations. Our study demonstrates a direct correlation between Elp4 and Elp6 mutations, reduced Elongator activity, and neurological defects. Foremost, our data indicate previously unrecognized differences of the Elp123 and Elp456 subcomplexes for individual tRNA species, in different cell types and in different key steps during the neurodevelopment of higher organisms.
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Shimada S, Ng BG, White AL, Nickander KK, Turgeon C, Liedtke KL, Lam CT, Font-Montgomery E, Lourenço CM, He M, Peck DS, Umaña LA, Uhles CL, Haynes D, Wheeler PG, Bamshad MJ, Nickerson DA, Cushing T, Gates R, Gomez-Ospina N, Byers HM, Scalco FB, Martinez NN, Sachdev R, Smith L, Poduri A, Malone S, Harris R, Scheffer IE, Rosenzweig SD, Adams DR, Gahl WA, Malicdan MCV, Raymond KM, Freeze HH, Wolfe LA. Clinical, biochemical and genetic characteristics of MOGS-CDG: a rare congenital disorder of glycosylation. J Med Genet 2022; 59:jmedgenet-2021-108177. [PMID: 35790351 PMCID: PMC9813274 DOI: 10.1136/jmedgenet-2021-108177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/18/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE To summarise the clinical, molecular and biochemical phenotype of mannosyl-oligosaccharide glucosidase-related congenital disorders of glycosylation (MOGS-CDG), which presents with variable clinical manifestations, and to analyse which clinical biochemical assay consistently supports diagnosis in individuals with bi-allelic variants in MOGS. METHODS Phenotypic characterisation was performed through an international and multicentre collaboration. Genetic testing was done by exome sequencing and targeted arrays. Biochemical assays on serum and urine were performed to delineate the biochemical signature of MOGS-CDG. RESULTS Clinical phenotyping revealed heterogeneity in MOGS-CDG, including neurological, immunological and skeletal phenotypes. Bi-allelic variants in MOGS were identified in 12 individuals from 11 families. The severity in each organ system was variable, without definite genotype correlation. Urine oligosaccharide analysis was consistently abnormal for all affected probands, whereas other biochemical analyses such as serum transferrin analysis was not consistently abnormal. CONCLUSION The clinical phenotype of MOGS-CDG includes multisystemic involvement with variable severity. Molecular analysis, combined with biochemical testing, is important for diagnosis. In MOGS-CDG, urine oligosaccharide analysis via matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry can be used as a reliable biochemical test for screening and confirmation of disease.
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Li J, Yang W, Wang YJ, Ma C, Curry CJ, McGoldrick D, Nickerson DA, Chong JX, Blue EE, Mullikin JC, Reefhuis J, Nembhard WN, Romitti PA, Werler MM, Browne ML, Olshan AF, Finnell RH, Feldkamp ML, Pangilinan F, Almli LM, Bamshad MJ, Brody LC, Jenkins MM, Shaw GM. Exome sequencing identifies genetic variants in anophthalmia and microphthalmia. Am J Med Genet A 2022; 188:2376-2388. [PMID: 35716026 PMCID: PMC9283271 DOI: 10.1002/ajmg.a.62874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 11/10/2022]
Abstract
Anophthalmia and microphthalmia (A/M) are rare birth defects affecting up to 2 per 10,000 live births. These conditions are manifested by the absence of an eye or reduced eye volumes within the orbit leading to vision loss. Although clinical case series suggest a strong genetic component in A/M, few systematic investigations have been conducted on potential genetic contributions owing to low population prevalence. To overcome this challenge, we utilized DNA samples and data collected as part of the National Birth Defects Prevention Study (NBDPS). The NBDPS employed multi-center ascertainment of infants affected by A/M. We performed exome sequencing on 67 family trios and identified numerous genes affected by rare deleterious nonsense and missense variants in this cohort, including de novo variants. We identified 9 nonsense changes and 86 missense variants that are absent from the reference human population (Genome Aggregation Database), and we suggest that these are high priority candidate genes for A/M. We also performed literature curation, single cell transcriptome comparisons, and molecular pathway analysis on the candidate genes and performed protein structure modeling to determine the potential pathogenic variant consequences on PAX6 in this disease.
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Cingöz S, Soydemir D, Öner TÖ, Karaca E, Özden B, Kurul SH, Bayram E, Coe BP, Nickerson DA, Eichler EE. Novel biallelic variants affecting the OTU domain of the gene OTUD6B associate with severe intellectual disability syndrome and molecular dynamics simulations. Eur J Med Genet 2022; 65:104497. [PMID: 35430327 PMCID: PMC9448893 DOI: 10.1016/j.ejmg.2022.104497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 02/13/2022] [Accepted: 03/29/2022] [Indexed: 01/25/2023]
Abstract
Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies (IDDFSDA) is an autosomal recessive multisystem disorder caused by compound heterozygous or homozygous variants in the gene OTUD6B. Herein, we describe novel pathogenic compound heterozygous variants in OTUD6B identified via whole-exome sequencing in an index case exhibited the severe IDDFSDA phenotype. The potential pathogenicity of the novel frameshift and missense variants in the index case was investigated using in silico tools. The truncating frameshift variant in one allele was predicted to undergo degradation via nonsense-mediated decay of the mRNA molecule. To predict the severity of the damage to the protein caused by the missense variant in the other allele and its effects on phenotypic severity was further investigated together with a previously reported first homozygous missense variant in the same domain in another patient with a less severe IDDFSDA phenotype using structural modeling and molecular dynamics (MD) simulations for the first time. Based on these analyzes, it is anticipated that Tyr216Cys in the earlier reported case with less severe IDDFSDA will lead to localized destabilization, whereas Ile274Arg in the presented index case with the severe IDDFSDA phenotype will lead to significant distortion in the overall fold of OTUD6B. Our findings suggest that compound LOF and ultrarare missense variants may be contribute to the underlying variability expressivity associated with this disorder. In conclusion, our findings support that the clinical severity could be related with the predicted functional severity of the variations in OTUD6B. However, additional functional studies are required.
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Hu X, Qiao D, Kim W, Moll M, Balte PP, Lange LA, Bartz TM, Kumar R, Li X, Yu B, Cade BE, Laurie CA, Sofer T, Ruczinski I, Nickerson DA, Muzny DM, Metcalf GA, Doddapaneni H, Gabriel S, Gupta N, Dugan-Perez S, Cupples LA, Loehr LR, Jain D, Rotter JI, Wilson JG, Psaty BM, Fornage M, Morrison AC, Vasan RS, Washko G, Rich SS, O'Connor GT, Bleecker E, Kaplan RC, Kalhan R, Redline S, Gharib SA, Meyers D, Ortega V, Dupuis J, London SJ, Lappalainen T, Oelsner EC, Silverman EK, Barr RG, Thornton TA, Wheeler HE, Cho MH, Im HK, Manichaikul A. Polygenic transcriptome risk scores for COPD and lung function improve cross-ethnic portability of prediction in the NHLBI TOPMed program. Am J Hum Genet 2022; 109:857-870. [PMID: 35385699 PMCID: PMC9118106 DOI: 10.1016/j.ajhg.2022.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/04/2022] [Indexed: 12/17/2022] Open
Abstract
While polygenic risk scores (PRSs) enable early identification of genetic risk for chronic obstructive pulmonary disease (COPD), predictive performance is limited when the discovery and target populations are not well matched. Hypothesizing that the biological mechanisms of disease are shared across ancestry groups, we introduce a PrediXcan-derived polygenic transcriptome risk score (PTRS) to improve cross-ethnic portability of risk prediction. We constructed the PTRS using summary statistics from application of PrediXcan on large-scale GWASs of lung function (forced expiratory volume in 1 s [FEV1] and its ratio to forced vital capacity [FEV1/FVC]) in the UK Biobank. We examined prediction performance and cross-ethnic portability of PTRS through smoking-stratified analyses both on 29,381 multi-ethnic participants from TOPMed population/family-based cohorts and on 11,771 multi-ethnic participants from TOPMed COPD-enriched studies. Analyses were carried out for two dichotomous COPD traits (moderate-to-severe and severe COPD) and two quantitative lung function traits (FEV1 and FEV1/FVC). While the proposed PTRS showed weaker associations with disease than PRS for European ancestry, the PTRS showed stronger association with COPD than PRS for African Americans (e.g., odds ratio [OR] = 1.24 [95% confidence interval [CI]: 1.08-1.43] for PTRS versus 1.10 [0.96-1.26] for PRS among heavy smokers with ≥ 40 pack-years of smoking) for moderate-to-severe COPD. Cross-ethnic portability of the PTRS was significantly higher than the PRS (paired t test p < 2.2 × 10-16 with portability gains ranging from 5% to 28%) for both dichotomous COPD traits and across all smoking strata. Our study demonstrates the value of PTRS for improved cross-ethnic portability compared to PRS in predicting COPD risk.
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Cornejo-Sanchez DM, Acharya A, Bharadwaj T, Marin-Gomez L, Pereira-Gomez P, Nouel-Saied LM, Nickerson DA, Bamshad MJ, Mefford HC, Schrauwen I, Carrizosa-Moog J, Cornejo-Ochoa W, Pineda-Trujillo N, Leal SM. SCN1A Variants as the Underlying Cause of Genetic Epilepsy with Febrile Seizures Plus in Two Multi-Generational Colombian Families. Genes (Basel) 2022; 13:754. [PMID: 35627139 PMCID: PMC9140479 DOI: 10.3390/genes13050754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022] Open
Abstract
Genetic epilepsy with febrile seizures plus (GEFS+) is an autosomal dominant disorder with febrile or afebrile seizures that exhibits phenotypic variability. Only a few variants in SCN1A have been previously characterized for GEFS+, in Latin American populations where studies on the genetic and phenotypic spectrum of GEFS+ are scarce. We evaluated members in two multi-generational Colombian Paisa families whose affected members present with classic GEFS+. Exome and Sanger sequencing were used to detect the causal variants in these families. In each of these families, we identified variants in SCN1A causing GEFS+ with incomplete penetrance. In Family 047, we identified a heterozygous variant (c.3530C > G; p.(Pro1177Arg)) that segregates with GEFS+ in 15 affected individuals. In Family 167, we identified a previously unreported variant (c.725A > G; p.(Gln242Arg)) that segregates with the disease in a family with four affected members. Both variants are located in a cytoplasmic loop region in SCN1A and based on our findings the variants are classified as pathogenic and likely pathogenic, respectively. Our results expand the genotypic and phenotypic spectrum associated with SCN1A variants and will aid in improving molecular diagnostics and counseling in Latin American and other populations.
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Paredes MI, Lunn SM, Famulare M, Frisbie LA, Painter I, Burstein R, Roychoudhury P, Xie H, Mohamed Bakhash SA, Perez R, Lukes M, Ellis S, Sathees S, Mathias PC, Greninger A, Starita LM, Frazar CD, Ryke E, Zhong W, Gamboa L, Threlkeld M, Lee J, McDermot E, Truong M, Nickerson DA, Bates DL, Hartman ME, Haugen E, Nguyen TN, Richards JD, Rodriguez JL, Stamatoyannopoulos JA, Thorland E, Melly G, Dykema PE, MacKellar DC, Gray HK, Singh A, Peterson JM, Russell D, Marcela Torres L, Lindquist S, Bedford T, Allen KJ, Oltean HN. Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study. Clin Infect Dis 2022; 75:e536-e544. [PMID: 35412591 PMCID: PMC9047245 DOI: 10.1093/cid/ciac279] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Indexed: 12/22/2022] Open
Abstract
Background The coronavirus disease 2019 (COVID-19) pandemic is dominated by variant viruses; the resulting impact on disease severity remains unclear. Using a retrospective cohort study, we assessed the hospitalization risk following infection with 7 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Methods Our study includes individuals with positive SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) in the Washington Disease Reporting System with available viral genome data, from 1 December 2020 to 14 January 2022. The analysis was restricted to cases with specimens collected through sentinel surveillance. Using a Cox proportional hazards model with mixed effects, we estimated hazard ratios (HR) for hospitalization risk following infection with a variant, adjusting for age, sex, calendar week, and vaccination. Results In total, 58 848 cases were sequenced through sentinel surveillance, of which 1705 (2.9%) were hospitalized due to COVID-19. Higher hospitalization risk was found for infections with Gamma (HR 3.20, 95% confidence interval [CI] 2.40–4.26), Beta (HR 2.85, 95% CI 1.56–5.23), Delta (HR 2.28 95% CI 1.56–3.34), or Alpha (HR 1.64, 95% CI 1.29–2.07) compared to infections with ancestral lineages; Omicron (HR 0.92, 95% CI .56–1.52) showed no significant difference in risk. Following Alpha, Gamma, or Delta infection, unvaccinated patients show higher hospitalization risk, while vaccinated patients show no significant difference in risk, both compared to unvaccinated, ancestral lineage cases. Hospitalization risk following Omicron infection is lower with vaccination. Conclusions Infection with Alpha, Gamma, or Delta results in a higher hospitalization risk, with vaccination attenuating that risk. Our findings support hospital preparedness, vaccination, and genomic surveillance.
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Baxter SM, Posey JE, Lake NJ, Sobreira N, Chong JX, Buyske S, Blue EE, Chadwick LH, Coban-Akdemir ZH, Doheny KF, Davis CP, Lek M, Wellington C, Jhangiani SN, Gerstein M, Gibbs RA, Lifton RP, MacArthur DG, Matise TC, Lupski JR, Valle D, Bamshad MJ, Hamosh A, Mane S, Nickerson DA, Rehm HL, O'Donnell-Luria A. Centers for Mendelian Genomics: A decade of facilitating gene discovery. Genet Med 2022; 24:784-797. [PMID: 35148959 PMCID: PMC9119004 DOI: 10.1016/j.gim.2021.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/08/2021] [Accepted: 12/12/2021] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Mendelian disease genomic research has undergone a massive transformation over the past decade. With increasing availability of exome and genome sequencing, the role of Mendelian research has expanded beyond data collection, sequencing, and analysis to worldwide data sharing and collaboration. METHODS Over the past 10 years, the National Institutes of Health-supported Centers for Mendelian Genomics (CMGs) have played a major role in this research and clinical evolution. RESULTS We highlight the cumulative gene discoveries facilitated by the program, biomedical research leveraged by the approach, and the larger impact on the research community. Beyond generating a list of gene-phenotype relationships and participating in widespread data sharing, the CMGs have created resources, tools, and training for the larger community to foster understanding of genes and genome variation. The CMGs have participated in a wide range of data sharing activities, including deposition of all eligible CMG data into the Analysis, Visualization, and Informatics Lab-space (AnVIL), sharing candidate genes through the Matchmaker Exchange and the CMG website, and sharing variants in Genotypes to Mendelian Phenotypes (Geno2MP) and VariantMatcher. CONCLUSION The work is far from complete; strengthening communication between research and clinical realms, continued development and sharing of knowledge and tools, and improving access to richly characterized data sets are all required to diagnose the remaining molecularly undiagnosed patients.
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Pitsava G, Feldkamp ML, Pankratz N, Lane J, Kay DM, Conway KM, Hobbs C, Shaw GM, Reefhuis J, Jenkins MM, Almli LM, Moore C, Werler M, Browne ML, Cunniff C, Olshan AF, Pangilinan F, Brody LC, Sicko RJ, Finnell RH, Bamshad MJ, McGoldrick D, Nickerson DA, Mullikin JC, Romitti PA, Mills JL. Exome sequencing identifies variants in infants with sacral agenesis. Birth Defects Res 2022; 114:215-227. [PMID: 35274497 PMCID: PMC9338687 DOI: 10.1002/bdr2.1987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 01/22/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND Sacral agenesis (SA) consists of partial or complete absence of the caudal end of the spine and often presents with additional birth defects. Several studies have examined gene variants for syndromic forms of SA, but only one has examined exomes of children with non-syndromic SA. METHODS Using buccal cell specimens from families of children with non-syndromic SA, exomes of 28 child-parent trios (eight with and 20 without a maternal diagnosis of pregestational diabetes) and two child-father duos (neither with diagnosis of maternal pregestational diabetes) were exome sequenced. RESULTS Three children had heterozygous missense variants in ID1 (Inhibitor of DNA Binding 1), with CADD scores >20 (top 1% of deleterious variants in the genome); two children inherited the variant from their fathers and one from the child's mother. Rare missense variants were also detected in PDZD2 (PDZ Domain Containing 2; N = 1) and SPTBN5 (Spectrin Beta, Non-erythrocytic 5; N = 2), two genes previously suggested to be associated with SA etiology. Examination of variants with autosomal recessive and X-linked recessive inheritance identified five and two missense variants, respectively. Compound heterozygous variants were identified in several genes. In addition, 12 de novo variants were identified, all in different genes in different children. CONCLUSIONS To our knowledge, this is the first study reporting a possible association between ID1 and non-syndromic SA. Although maternal pregestational diabetes has been strongly associated with SA, the missense variants in ID1 identified in two of three children were paternally inherited. These findings add to the knowledge of gene variants associated with non-syndromic SA and provide data for future studies.
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Gaedigk A, Boone EC, Scherer SE, Lee SB, Numanagić I, Sahinalp C, Smith JD, McGee S, Radhakrishnan A, Qin X, Wang WY, Farrow EG, Gonzaludo N, Halpern AL, Nickerson DA, Miller NA, Pratt VM, Kalman LV. CYP2C8, CYP2C9, and CYP2C19 Characterization Using Next-Generation Sequencing and Haplotype Analysis: A GeT-RM Collaborative Project. J Mol Diagn 2022; 24:337-350. [PMID: 35134542 PMCID: PMC9069873 DOI: 10.1016/j.jmoldx.2021.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/09/2021] [Accepted: 12/28/2021] [Indexed: 01/13/2023] Open
Abstract
Pharmacogenetic tests typically target selected sequence variants to identify haplotypes that are often defined by star (∗) allele nomenclature. Due to their design, these targeted genotyping assays are unable to detect novel variants that may change the function of the gene product and thereby affect phenotype prediction and patient care. In the current study, 137 DNA samples that were previously characterized by the Genetic Testing Reference Material (GeT-RM) program using a variety of targeted genotyping methods were recharacterized using targeted and whole genome sequencing analysis. Sequence data were analyzed using three genotype calling tools to identify star allele diplotypes for CYP2C8, CYP2C9, and CYP2C19. The genotype calls from next-generation sequencing (NGS) correlated well to those previously reported, except when novel alleles were present in a sample. Six novel alleles and 38 novel suballeles were identified in the three genes due to identification of variants not covered by targeted genotyping assays. In addition, several ambiguous genotype calls from a previous study were resolved using the NGS and/or long-read NGS data. Diplotype calls were mostly consistent between the calling algorithms, although several discrepancies were noted. This study highlights the utility of NGS for pharmacogenetic testing and demonstrates that there are many novel alleles that are yet to be discovered, even in highly characterized genes such as CYP2C9 and CYP2C19.
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Sajuthi SP, Everman JL, Jackson ND, Saef B, Rios CL, Moore CM, Mak ACY, Eng C, Fairbanks-Mahnke A, Salazar S, Elhawary J, Huntsman S, Medina V, Nickerson DA, Germer S, Zody MC, Abecasis G, Kang HM, Rice KM, Kumar R, Zaitlen NA, Oh S, Rodríguez-Santana J, Burchard EG, Seibold MA. Nasal airway transcriptome-wide association study of asthma reveals genetically driven mucus pathobiology. Nat Commun 2022; 13:1632. [PMID: 35347136 PMCID: PMC8960819 DOI: 10.1038/s41467-022-28973-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/10/2022] [Indexed: 12/13/2022] Open
Abstract
To identify genetic determinants of airway dysfunction, we performed a transcriptome-wide association study for asthma by combining RNA-seq data from the nasal airway epithelium of 681 children, with UK Biobank genetic association data. Our airway analysis identified 95 asthma genes, 58 of which were not identified by transcriptome-wide association analyses using other asthma-relevant tissues. Among these genes were MUC5AC, an airway mucin, and FOXA3, a transcriptional driver of mucus metaplasia. Muco-ciliary epithelial cultures from genotyped donors revealed that the MUC5AC risk variant increases MUC5AC protein secretion and mucus secretory cell frequency. Airway transcriptome-wide association analyses for mucus production and chronic cough also identified MUC5AC. These cis-expression variants were associated with trans effects on expression; the MUC5AC variant was associated with upregulation of non-inflammatory mucus secretory network genes, while the FOXA3 variant was associated with upregulation of type-2 inflammation-induced mucus-metaplasia pathway genes. Our results reveal genetic mechanisms of airway mucus pathobiology.
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22
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Chau AS, Cole BL, Debley JS, Nanda K, Rosen ABI, Bamshad MJ, Nickerson DA, Torgerson TR, Allenspach EJ. Correction to: Heme oxygenase-1 deficiency presenting with interstitial lung disease and hemophagocytic flares. Pediatr Rheumatol Online J 2022; 20:19. [PMID: 35287710 PMCID: PMC8922765 DOI: 10.1186/s12969-021-00661-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
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Geyer RE, Kotnik JH, Lyon V, Brandstetter E, Zigman Suchsland M, Han PD, Graham C, Ilcisin M, Kim AE, Chu HY, Nickerson DA, Starita LM, Bedford T, Lutz B, Thompson MJ. Diagnostic Accuracy of an At-Home, Rapid Self-test for Influenza: Prospective Comparative Accuracy Study. JMIR Public Health Surveill 2022; 8:e28268. [PMID: 35191852 PMCID: PMC8905479 DOI: 10.2196/28268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 11/02/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Background Rapid diagnostic tests (RDTs) for influenza used by individuals at home could potentially expand access to testing and reduce the impact of influenza on health systems. Improving access to testing could lead to earlier diagnosis following symptom onset, allowing more rapid interventions for those who test positive, including behavioral changes to minimize spread. However, the accuracy of RDTs for influenza has not been determined in self-testing populations. Objective This study aims to assess the accuracy of an influenza RDT conducted at home by lay users with acute respiratory illness compared with that of a self-collected sample by the same individual mailed to a laboratory for reference testing. Methods We conducted a comparative accuracy study of an at-home influenza RDT (Ellume) in a convenience sample of individuals experiencing acute respiratory illness symptoms. Participants were enrolled in February and March 2020 from the Greater Seattle region in Washington, United States. Participants were mailed the influenza RDT and reference sample collection materials, which they completed and returned for quantitative reverse-transcription polymerase chain reaction influenza testing in a central laboratory. We explored the impact of age, influenza type, duration, and severity of symptoms on RDT accuracy and on cycle threshold for influenza virus and ribonuclease P, a marker of human DNA. Results A total of 605 participants completed all study steps and were included in our analysis, of whom 87 (14.4%) tested positive for influenza by quantitative reverse-transcription polymerase chain reaction (70/87, 80% for influenza A and 17/87, 20% for influenza B). The overall sensitivity and specificity of the RDT compared with the reference test were 61% (95% CI 50%-71%) and 95% (95% CI 93%-97%), respectively. Among individuals with symptom onset ≤72 hours, sensitivity was 63% (95% CI 48%-76%) and specificity was 94% (95% CI 91%-97%), whereas, for those with duration >72 hours, sensitivity and specificity were 58% (95% CI 41%-74%) and 96% (95% CI 93%-98%), respectively. Viral load on reference swabs was negatively correlated with symptom onset, and quantities of the endogenous marker gene ribonuclease P did not differ among reference standard positive and negative groups, age groups, or influenza subtypes. The RDT did not have higher sensitivity or specificity among those who reported more severe illnesses. Conclusions The sensitivity and specificity of the self-test were comparable with those of influenza RDTs used in clinical settings. False-negative self-test results were more common when the test was used after 72 hours of symptom onset but were not related to inadequate swab collection or severity of illness. Therefore, the deployment of home tests may provide a valuable tool to support the management of influenza and other respiratory infections.
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Little A, Hu Y, Sun Q, Jain D, Broome J, Chen MH, Thibord F, McHugh C, Surendran P, Blackwell TW, Brody JA, Bhan A, Chami N, de Vries PS, Ekunwe L, Heard-Costa N, Hobbs BD, Manichaikul A, Moon JY, Preuss MH, Ryan K, Wang Z, Wheeler M, Yanek LR, Abecasis GR, Almasy L, Beaty TH, Becker LC, Blangero J, Boerwinkle E, Butterworth AS, Choquet H, Correa A, Curran JE, Faraday N, Fornage M, Glahn DC, Hou L, Jorgenson E, Kooperberg C, Lewis JP, Lloyd-Jones DM, Loos RJF, Min YI, Mitchell BD, Morrison AC, Nickerson DA, North KE, O'Connell JR, Pankratz N, Psaty BM, Vasan RS, Rich SS, Rotter JI, Smith AV, Smith NL, Tang H, Tracy RP, Conomos MP, Laurie CA, Mathias RA, Li Y, Auer PL, Thornton T, Reiner AP, Johnson AD, Raffield LM. Whole genome sequence analysis of platelet traits in the NHLBI Trans-Omics for Precision Medicine (TOPMed) initiative. Hum Mol Genet 2022; 31:347-361. [PMID: 34553764 PMCID: PMC8825339 DOI: 10.1093/hmg/ddab252] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 12/15/2022] Open
Abstract
Platelets play a key role in thrombosis and hemostasis. Platelet count (PLT) and mean platelet volume (MPV) are highly heritable quantitative traits, with hundreds of genetic signals previously identified, mostly in European ancestry populations. We here utilize whole genome sequencing (WGS) from NHLBI's Trans-Omics for Precision Medicine initiative (TOPMed) in a large multi-ethnic sample to further explore common and rare variation contributing to PLT (n = 61 200) and MPV (n = 23 485). We identified and replicated secondary signals at MPL (rs532784633) and PECAM1 (rs73345162), both more common in African ancestry populations. We also observed rare variation in Mendelian platelet-related disorder genes influencing variation in platelet traits in TOPMed cohorts (not enriched for blood disorders). For example, association of GP9 with lower PLT and higher MPV was partly driven by a pathogenic Bernard-Soulier syndrome variant (rs5030764, p.Asn61Ser), and the signals at TUBB1 and CD36 were partly driven by loss of function variants not annotated as pathogenic in ClinVar (rs199948010 and rs571975065). However, residual signal remained for these gene-based signals after adjusting for lead variants, suggesting that additional variants in Mendelian genes with impacts in general population cohorts remain to be identified. Gene-based signals were also identified at several genome-wide association study identified loci for genes not annotated for Mendelian platelet disorders (PTPRH, TET2, CHEK2), with somatic variation driving the result at TET2. These results highlight the value of WGS in populations of diverse genetic ancestry to identify novel regulatory and coding signals, even for well-studied traits like platelet traits.
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Taub MA, Conomos MP, Keener R, Iyer KR, Weinstock JS, Yanek LR, Lane J, Miller-Fleming TW, Brody JA, Raffield LM, McHugh CP, Jain D, Gogarten SM, Laurie CA, Keramati A, Arvanitis M, Smith AV, Heavner B, Barwick L, Becker LC, Bis JC, Blangero J, Bleecker ER, Burchard EG, Celedón JC, Chang YPC, Custer B, Darbar D, de las Fuentes L, DeMeo DL, Freedman BI, Garrett ME, Gladwin MT, Heckbert SR, Hidalgo BA, Irvin MR, Islam T, Johnson WC, Kaab S, Launer L, Lee J, Liu S, Moscati A, North KE, Peyser PA, Rafaels N, Seidman C, Weeks DE, Wen F, Wheeler MM, Williams LK, Yang IV, Zhao W, Aslibekyan S, Auer PL, Bowden DW, Cade BE, Chen Z, Cho MH, Cupples LA, Curran JE, Daya M, Deka R, Eng C, Fingerlin TE, Guo X, Hou L, Hwang SJ, Johnsen JM, Kenny EE, Levin AM, Liu C, Minster RL, Naseri T, Nouraie M, Reupena MS, Sabino EC, Smith JA, Smith NL, Lasky-Su J, Taylor JG, Telen MJ, Tiwari HK, Tracy RP, White MJ, Zhang Y, Wiggins KL, Weiss ST, Vasan RS, Taylor KD, Sinner MF, Silverman EK, Shoemaker MB, Sheu WHH, Sciurba F, Schwartz DA, Rotter JI, Roden D, Redline S, Raby BA, Psaty BM, Peralta JM, Palmer ND, Nekhai S, Montgomery CG, Mitchell BD, Meyers DA, McGarvey ST, Mak AC, Loos RJ, Kumar R, Kooperberg C, Konkle BA, Kelly S, Kardia SL, Kaplan R, He J, Gui H, Gilliland FD, Gelb BD, Fornage M, Ellinor PT, de Andrade M, Correa A, Chen YDI, Boerwinkle E, Barnes KC, Ashley-Koch AE, Arnett DK, Albert C, Laurie CC, Abecasis G, Nickerson DA, Wilson JG, Rich SS, Levy D, Ruczinski I, Aviv A, Blackwell TW, Thornton T, O’Connell J, Cox NJ, Perry JA, Armanios M, Battle A, Pankratz N, Reiner AP, Mathias RA. Genetic determinants of telomere length from 109,122 ancestrally diverse whole-genome sequences in TOPMed. CELL GENOMICS 2022; 2:S2666-979X(21)00105-1. [PMID: 35530816 PMCID: PMC9075703 DOI: 10.1016/j.xgen.2021.100084] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 09/03/2021] [Accepted: 12/10/2021] [Indexed: 01/16/2023]
Abstract
Genetic studies on telomere length are important for understanding age-related diseases. Prior GWAS for leukocyte TL have been limited to European and Asian populations. Here, we report the first sequencing-based association study for TL across ancestrally-diverse individuals (European, African, Asian and Hispanic/Latino) from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program. We used whole genome sequencing (WGS) of whole blood for variant genotype calling and the bioinformatic estimation of telomere length in n=109,122 individuals. We identified 59 sentinel variants (p-value <5×10-9) in 36 loci associated with telomere length, including 20 newly associated loci (13 were replicated in external datasets). There was little evidence of effect size heterogeneity across populations. Fine-mapping at OBFC1 indicated the independent signals colocalized with cell-type specific eQTLs for OBFC1 (STN1). Using a multi-variant gene-based approach, we identified two genes newly implicated in telomere length, DCLRE1B (SNM1B) and PARN. In PheWAS, we demonstrated our TL polygenic trait scores (PTS) were associated with increased risk of cancer-related phenotypes.
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