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1. Genome-wide association study in minority children with asthma implicates DNAH5 in bronchodilator responsiveness

Author

Joo, Jaehyun, Mak, Angel CY, Xiao, Shujie, Sleiman, Patrick M, Hu, Donglei, Huntsman, Scott, Eng, Celeste, Kan, Mengyuan, Diwakar, Avantika R, Lasky-Su, Jessica A, Weiss, Scott T, Sordillo, Joanne E, Wu, Ann C, Cloutier, Michelle, Canino, Glorisa, Forno, Erick, Celedón, Juan C, Seibold, Max A, Hakonarson, Hakon, Williams, L Keoki, Burchard, Esteban G, and Himes, Blanca E

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Epidemiology, Health Sciences, Pharmacology and Pharmaceutical Sciences, Pediatric, Prevention, Clinical Research, Asthma, Health Disparities, Human Genome, Precision Medicine, Biotechnology, Lung, Minority Health, 2.1 Biological and endogenous factors, Respiratory, Good Health and Well Being, Axonemal Dyneins, Bronchodilator Agents, Child, Ethnicity, Genome-Wide Association Study, Hispanic or Latino, Humans, Mexican Americans, Minority Groups, Polymorphism, Single Nucleotide
Abstract

Variability in response to short-acting β2-agonists (e.g., albuterol) among patients with asthma from diverse racial/ethnic groups may contribute to asthma disparities. We sought to identify genetic variants associated with bronchodilator response (BDR) to identify potential mechanisms of drug response and risk factors for worse asthma outcomes. Genome-wide association studies of bronchodilator response (BDR) were performed using TOPMed Whole Genome Sequencing data of the Asthma Translational Genomic Collaboration (ATGC), which corresponded to 1136 Puerto Rican, 656 Mexican and 4337 African American patients with asthma. With the population-specific GWAS results, a trans-ethnic meta-analysis was performed to identify BDR-associated variants shared across the three populations. Replication analysis was carried out in three pediatric asthma cohorts, including CAMP (Childhood Asthma Management Program; n = 560), GACRS (Genetics of Asthma in Costa Rica Study; n = 967) and HPR (Hartford-Puerto Rico; n = 417). A genome-wide significant locus (rs35661809; P = 3.61 × 10-8) in LINC02220, a non-coding RNA gene, was identified in Puerto Ricans. While this region was devoid of protein-coding genes, capture Hi-C data showed a distal interaction with the promoter of the DNAH5 gene in lung tissue. In replication analysis, the GACRS cohort yielded a nominal association (1-tailed P

Published
2022

2. European and multi-ancestry genome-wide association meta-analysis of atopic dermatitis highlights importance of systemic immune regulation

Author

Budu-Aggrey, Ashley, Kilanowski, Anna, Sobczyk, Maria K., Shringarpure, Suyash S., Mitchell, Ruth, Reis, Kadri, Reigo, Anu, Mägi, Reedik, Nelis, Mari, Tanaka, Nao, Brumpton, Ben M., Thomas, Laurent F., Sole-Navais, Pol, Flatley, Christopher, Espuela-Ortiz, Antonio, Herrera-Luis, Esther, Lominchar, Jesus V. T., Bork-Jensen, Jette, Marenholz, Ingo, Arnau-Soler, Aleix, Jeong, Ayoung, Fawcett, Katherine A., Baurecht, Hansjorg, Rodriguez, Elke, Alves, Alexessander Couto, Kumar, Ashish, Sleiman, Patrick M., Chang, Xiao, Medina-Gomez, Carolina, Hu, Chen, Xu, Cheng-jian, Qi, Cancan, El-Heis, Sarah, Titcombe, Philip, Antoun, Elie, Fadista, João, Wang, Carol A., Thiering, Elisabeth, Wu, Baojun, Kress, Sara, Kothalawala, Dilini M., Kadalayil, Latha, Duan, Jiasong, Zhang, Hongmei, Hadebe, Sabelo, Hoffmann, Thomas, Jorgenson, Eric, Choquet, Hélène, Risch, Neil, Njølstad, Pål, Andreassen, Ole A., Johansson, Stefan, Almqvist, Catarina, Gong, Tong, Ullemar, Vilhelmina, Karlsson, Robert, Magnusson, Patrik K. E., Szwajda, Agnieszka, Burchard, Esteban G., Thyssen, Jacob P., Hansen, Torben, Kårhus, Line L., Dantoft, Thomas M., Jeanrenaud, Alexander C.S.N., Ghauri, Ahla, Arnold, Andreas, Homuth, Georg, Lau, Susanne, Nöthen, Markus M., Hübner, Norbert, Imboden, Medea, Visconti, Alessia, Falchi, Mario, Bataille, Veronique, Hysi, Pirro, Ballardini, Natalia, Boomsma, Dorret I., Hottenga, Jouke J., Müller-Nurasyid, Martina, Ahluwalia, Tarunveer S., Stokholm, Jakob, Chawes, Bo, Schoos, Ann-Marie M., Esplugues, Ana, Bustamante, Mariona, Raby, Benjamin, Arshad, Syed, German, Chris, Esko, Tõnu, Milani, Lili A., Metspalu, Andres, Terao, Chikashi, Abuabara, Katrina, Løset, Mari, Hveem, Kristian, Jacobsson, Bo, Pino-Yanes, Maria, Strachan, David P., Grarup, Niels, Linneberg, Allan, Lee, Young-Ae, Probst-Hensch, Nicole, Weidinger, Stephan, Jarvelin, Marjo-Riitta, Melén, Erik, Hakonarson, Hakon, Irvine, Alan D., Jarvis, Deborah, Nijsten, Tamar, Duijts, Liesbeth, Vonk, Judith M., Koppelmann, Gerard H., Godfrey, Keith M., Barton, Sheila J., Feenstra, Bjarke, Pennell, Craig E., Sly, Peter D., Holt, Patrick G., Williams, L. Keoki, Bisgaard, Hans, Bønnelykke, Klaus, Curtin, John, Simpson, Angela, Murray, Clare, Schikowski, Tamara, Bunyavanich, Supinda, Weiss, Scott T., Holloway, John W., Min, Josine L., Brown, Sara J., Standl, Marie, and Paternoster, Lavinia

Published
2023
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4. Lung Function in African American Children with Asthma Is Associated with Novel Regulatory Variants of the KIT Ligand KITLG/SCF and Gene-By-Air-Pollution Interaction

Author

Mak, Angel CY, Sajuthi, Satria, Joo, Jaehyun, Xiao, Shujie, Sleiman, Patrick M, White, Marquitta J, Lee, Eunice Y, Saef, Benjamin, Hu, Donglei, Gui, Hongsheng, Keys, Kevin L, Lurmann, Fred, Jain, Deepti, Abecasis, Gonçalo, Kang, Hyun Min, Nickerson, Deborah A, Germer, Soren, Zody, Michael C, Winterkorn, Lara, Reeves, Catherine, Huntsman, Scott, Eng, Celeste, Salazar, Sandra, Oh, Sam S, Gilliland, Frank D, Chen, Zhanghua, Kumar, Rajesh, Martínez, Fernando D, Wu, Ann Chen, Ziv, Elad, Hakonarson, Hakon, Himes, Blanca E, Williams, L Keoki, Seibold, Max A, and Burchard, Esteban G

Subjects
Biological Sciences, Genetics, Pediatric, Human Genome, Asthma, Precision Medicine, Biotechnology, Lung, 2.1 Biological and endogenous factors, Respiratory, Good Health and Well Being, Adolescent, Black or African American, Air Pollution, Child, Chromosomes, Human, Pair 12, Female, Forced Expiratory Volume, Gene-Environment Interaction, Humans, Linkage Disequilibrium, Male, Nasal Mucosa, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Stem Cell Factor, Young Adult, GWAS, African American, FEV(1)gene-by-environment interaction, GxE, air pollution, KITLG, SCF, FEV1 gene-by-environment interaction, Developmental Biology, Biochemistry and cell biology
Abstract

Baseline lung function, quantified as forced expiratory volume in the first second of exhalation (FEV1), is a standard diagnostic criterion used by clinicians to identify and classify lung diseases. Using whole-genome sequencing data from the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine project, we identified a novel genetic association with FEV1 on chromosome 12 in 867 African American children with asthma (P = 1.26 × 10-8, β = 0.302). Conditional analysis within 1 Mb of the tag signal (rs73429450) yielded one major and two other weaker independent signals within this peak. We explored statistical and functional evidence for all variants in linkage disequilibrium with the three independent signals and yielded nine variants as the most likely candidates responsible for the association with FEV1 Hi-C data and expression QTL analysis demonstrated that these variants physically interacted with KITLG (KIT ligand, also known as SCF), and their minor alleles were associated with increased expression of the KITLG gene in nasal epithelial cells. Gene-by-air-pollution interaction analysis found that the candidate variant rs58475486 interacted with past-year ambient sulfur dioxide exposure (P = 0.003, β = 0.32). This study identified a novel protective genetic association with FEV1, possibly mediated through KITLG, in African American children with asthma. This is the first study that has identified a genetic association between lung function and KITLG, which has established a role in orchestrating allergic inflammation in asthma.

Published
2020

6. Selective Genetic Overlap Between Amyotrophic Lateral Sclerosis and Diseases of the Frontotemporal Dementia Spectrum.

Author

Karch, Celeste M, Wen, Natalie, Fan, Chun C, Yokoyama, Jennifer S, Kouri, Naomi, Ross, Owen A, Höglinger, Gunter, Müller, Ulrich, Ferrari, Raffaele, Hardy, John, Schellenberg, Gerard D, Sleiman, Patrick M, Momeni, Parastoo, Hess, Christopher P, Miller, Bruce L, Sharma, Manu, Van Deerlin, Vivianna, Smeland, Olav B, Andreassen, Ole A, Dale, Anders M, Desikan, Rahul S, and International Frontotemporal Dementia (FTD)–Genomics Consortium, International Collaboration for Frontotemporal Dementia, Progressive Supranuclear Palsy (PSP) Genetics Consortium, and International Parkinson’s Disease Genomics Consortium

Subjects
International Frontotemporal Dementia (FTD)–Genomics Consortium, International Collaboration for Frontotemporal Dementia, Progressive Supranuclear Palsy (PSP) Genetics Consortium, and International Parkinson’s Disease Genomics Consortium, Humans, Basal Ganglia Diseases, Parkinson Disease, Supranuclear Palsy, Progressive, Alzheimer Disease, Amyotrophic Lateral Sclerosis, Genetic Predisposition to Disease, tau Proteins, Vesicular Transport Proteins, Proto-Oncogene Proteins c-bcl-2, Nerve Tissue Proteins, Genome-Wide Association Study, TDP-43 Proteinopathies, Frontotemporal Dementia, Superoxide Dismutase-1, C9orf72 Protein, International Frontotemporal Dementia (FTD)–Genomics Consortium, International Collaboration for Frontotemporal Dementia, Progressive Supranuclear Palsy (PSP) Genetics Consortium, and International Parkinson’s Disease Genomics Consortium, Supranuclear Palsy, Progressive
Abstract

Importance:Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder characterized by loss of upper and lower motor neurons. Although novel ALS genetic variants have been identified, the shared genetic risk between ALS and other neurodegenerative disorders remains poorly understood. Objectives:To examine whether there are common genetic variants that determine the risk for ALS and other neurodegenerative diseases and to identify their functional pathways. Design, Setting, and Participants:In this study conducted from December 1, 2016, to August 1, 2017, the genetic overlap between ALS, sporadic frontotemporal dementia (FTD), FTD with TDP-43 inclusions, Parkinson disease (PD), Alzheimer disease (AD), corticobasal degeneration (CBD), and progressive supranuclear palsy (PSP) were systematically investigated in 124 876 cases and controls. No participants were excluded from this study. Diagnoses were established using consensus criteria. Main Outcomes and Measures:The primary outcomes were a list of novel loci and their functional pathways in ALS, FTD, PSP, and ALS mouse models. Results:Among 124 876 cases and controls, genome-wide conjunction analyses of ALS, FTD, PD, AD, CBD, and PSP revealed significant genetic overlap between ALS and FTD at known ALS loci: rs13302855 and rs3849942 (nearest gene, C9orf72; P = .03 for rs13302855 and P = .005 for rs3849942) and rs4239633 (nearest gene, UNC13A; P = .03). Significant genetic overlap was also found between ALS and PSP at rs7224296, which tags the MAPT H1 haplotype (nearest gene, NSF; P = .045). Shared risk genes were enriched for pathways involving neuronal function and development. At a conditional FDR P

Published
2018

7. Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma

Author

Mak, Angel CY, White, Marquitta J, Eckalbar, Walter L, Szpiech, Zachary A, Oh, Sam S, Pino-Yanes, Maria, Hu, Donglei, Goddard, Pagé, Huntsman, Scott, Galanter, Joshua, Wu, Ann Chen, Himes, Blanca E, Germer, Soren, Vogel, Julia M, Bunting, Karen L, Eng, Celeste, Salazar, Sandra, Keys, Kevin L, Liberto, Jennifer, Nuckton, Thomas J, Nguyen, Thomas A, Torgerson, Dara G, Kwok, Pui-Yan, Levin, Albert M, Celedón, Juan C, Forno, Erick, Hakonarson, Hakon, Sleiman, Patrick M, Dahlin, Amber, Tantisira, Kelan G, Weiss, Scott T, Serebrisky, Denise, Brigino-Buenaventura, Emerita, Farber, Harold J, Meade, Kelley, Lenoir, Michael A, Avila, Pedro C, Sen, Saunak, Thyne, Shannon M, Rodriguez-Cintron, William, Winkler, Cheryl A, Moreno-Estrada, Andrés, Sandoval, Karla, Rodriguez-Santana, Jose R, Kumar, Rajesh, Williams, L Keoki, Ahituv, Nadav, Ziv, Elad, Seibold, Max A, Darnell, Robert B, Zaitlen, Noah, Hernandez, Ryan D, and Burchard, Esteban G

Subjects
Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Health Disparities, Lung, Precision Medicine, Genetics, Biotechnology, Minority Health, Asthma, Human Genome, Pediatric, 2.1 Biological and endogenous factors, Respiratory, Good Health and Well Being, Adolescent, Black or African American, Albuterol, Bronchodilator Agents, Child, Female, Genome-Wide Association Study, Hispanic or Latino, Humans, Male, Mexican Americans, Pharmacogenomic Variants, Polymorphism, Single Nucleotide, Race Factors, United States, albuterol, asthma, minority, NFKB1, Latinos, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Medical and Health Sciences, Respiratory System, Cardiovascular medicine and haematology, Clinical sciences
Abstract

RationaleAlbuterol, a bronchodilator medication, is the first-line therapy for asthma worldwide. There are significant racial/ethnic differences in albuterol drug response.ObjectivesTo identify genetic variants important for bronchodilator drug response (BDR) in racially diverse children.MethodsWe performed the first whole-genome sequencing pharmacogenetics study from 1,441 children with asthma from the tails of the BDR distribution to identify genetic association with BDR.Measurements and main resultsWe identified population-specific and shared genetic variants associated with BDR, including genome-wide significant (P

Published
2018

11. Predictive Utility of Polygenic Risk Scores for Coronary Heart Disease in Three Major Racial and Ethnic Groups

Author

Dikilitas, Ozan, Schaid, Daniel J., Kosel, Matthew L., Carroll, Robert J., Chute, Christopher G., Denny, Joshua C., Fedotov, Alex, Feng, QiPing, Hakonarson, Hakon, Jarvik, Gail P., Lee, Ming Ta Michael, Pacheco, Jennifer A., Rowley, Robb, Sleiman, Patrick M., Stein, C. Michael, Sturm, Amy C., Wei, Wei-Qi, Wiesner, Georgia L., Williams, Marc S., Zhang, Yanfei, Manolio, Teri A., and Kullo, Iftikhar J.

Published
2020
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12. Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4

Author

Grosche, Sarah, Marenholz, Ingo, Esparza-Gordillo, Jorge, Arnau-Soler, Aleix, Pairo-Castineira, Erola, Rüschendorf, Franz, Ahluwalia, Tarunveer S., Almqvist, Catarina, Arnold, Andreas, Baurecht, Hansjörg, Bisgaard, Hans, Bønnelykke, Klaus, Brown, Sara J., Bustamante, Mariona, Curtin, John A., Custovic, Adnan, Dharmage, Shyamali C., Esplugues, Ana, Falchi, Mario, Fernandez-Orth, Dietmar, Ferreira, Manuel A. R., Franke, Andre, Gerdes, Sascha, Gieger, Christian, Hakonarson, Hakon, Holt, Patrick G., Homuth, Georg, Hubner, Norbert, Hysi, Pirro G., Jarvelin, Marjo-Riitta, Karlsson, Robert, Koppelman, Gerard H., Lau, Susanne, Lutz, Manuel, Magnusson, Patrik K. E., Marks, Guy B., Müller-Nurasyid, Martina, Nöthen, Markus M., Paternoster, Lavinia, Pennell, Craig E., Peters, Annette, Rawlik, Konrad, Robertson, Colin F., Rodriguez, Elke, Sebert, Sylvain, Simpson, Angela, Sleiman, Patrick M. A., Standl, Marie, Stölzl, Dora, Strauch, Konstantin, Szwajda, Agnieszka, Tenesa, Albert, Thompson, Philip J., Ullemar, Vilhelmina, Visconti, Alessia, Vonk, Judith M., Wang, Carol A., Weidinger, Stephan, Wielscher, Matthias, Worth, Catherine L., Xu, Chen-Jian, and Lee, Young-Ae

Published
2021
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16. ARAF recurrent mutation causes central conducting lymphatic anomaly treatable with a MEK inhibitor

Author

Li, Dong, March, Michael E., Gutierrez-Uzquiza, Alvaro, Kao, Charlly, Seiler, Christoph, Pinto, Erin, Matsuoka, Leticia S., Battig, Mark R., Bhoj, Elizabeth J., Wenger, Tara L., Tian, Lifeng, Robinson, Nora, Wang, Tiancheng, Liu, Yichuan, Weinstein, Brant M., Swift, Matthew, Jung, Hyun Min, Kaminski, Courtney N., Chiavacci, Rosetta, Perkins, Jonathan A., Levine, Michael A., Sleiman, Patrick M. A., Hicks, Patricia J., Strausbaugh, Janet T., Belasco, Jean B., Dori, Yoav, and Hakonarson, Hakon

Published
2019
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18. Rare copy number variants in over 100,000 European ancestry subjects reveal multiple disease associations

Author

Li, Yun Rose, Glessner, Joseph T., Coe, Bradley P., Li, Jin, Mohebnasab, Maede, Chang, Xiao, Connolly, John, Kao, Charlly, Wei, Zhi, Bradfield, Jonathan, Kim, Cecilia, Hou, Cuiping, Khan, Munir, Mentch, Frank, Qiu, Haijun, Bakay, Marina, Cardinale, Christopher, Lemma, Maria, Abrams, Debra, Bridglall-Jhingoor, Andrew, Behr, Meckenzie, Harrison, Shanell, Otieno, George, Thomas, Alexandria, Wang, Fengxiang, Chiavacci, Rosetta, Wu, Lawrence, Hadley, Dexter, Goldmuntz, Elizabeth, Elia, Josephine, Maris, John, Grundmeier, Robert, Devoto, Marcella, Keating, Brendan, March, Michael, Pellagrino, Renata, Grant, Struan F. A., Sleiman, Patrick M. A., Li, Mingyao, Eichler, Evan E., and Hakonarson, Hakon

Published
2020
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20. The role of TREM2 R47H as a risk factor for Alzheimer's disease, frontotemporal lobar degeneration, amyotrophic lateral sclerosis, and Parkinson's disease

Author

Lill, Christina M., Rengmark, Aina, Pihlstrøm, Lasse, Fogh, Isabella, Shatunov, Aleksey, Sleiman, Patrick M., Wang, Li-San, Liu, Tian, Lassen, Christina F., Meissner, Esther, Alexopoulos, Panos, Calvo, Andrea, Chio, Adriano, Dizdar, Nil, Faltraco, Frank, Forsgren, Lars, Kirchheiner, Julia, Kurz, Alexander, Larsen, Jan P., Liebsch, Maria, Linder, Jan, Morrison, Karen E., Nissbrandt, Hans, Otto, Markus, Pahnke, Jens, Partch, Amanda, Restagno, Gabriella, Rujescu, Dan, Schnack, Cathrin, Shaw, Christopher E., Shaw, Pamela J., Tumani, Hayrettin, Tysnes, Ole-Bjørn, Valladares, Otto, Silani, Vincenzo, van den Berg, Leonard H., van Rheenen, Wouter, Veldink, Jan H., Lindenberger, Ulman, Steinhagen-Thiessen, Elisabeth, Teipel, Stefan, Perneczky, Robert, Hakonarson, Hakon, Hampel, Harald, von Arnim, Christine A.F., Olsen, Jørgen H., Van Deerlin, Vivianna M., Al-Chalabi, Ammar, Toft, Mathias, Ritz, Beate, and Bertram, Lars

Published
2015
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21. Trans-ethnic polygenic risk scores for body mass index: An international hundred K+ cohorts consortium study

Author

Qu, Hui-Qi, Connolly, John J, Kraft, Peter, Long, Jirong, Pereira, Alexandre, Flatley, Christopher, Turman, Constance, Prins, Bram, Mentch, Frank, Lotufo, Paulo A, Magnus, Per, Stampfer, Meir J, Tamimi, Rulla, Eliassen, A Heather, Zheng, Wei, Knudsen, Gun Peggy Stromstad, Helgeland, Oyvind, Butterworth, Adam S, Hakonarson, Hakon, Sleiman, Patrick M, IHCC consortium, Qu, Hui-Qi [0000-0001-9317-4488], Hakonarson, Hakon [0000-0003-2814-7461], and Apollo - University of Cambridge Repository

Subjects
obesity, Multifactorial Inheritance, Risk Factors, polygenic risk score, Humans, body mass index, Bayes Theorem, trans-ethnic, Child, population admixture, Body Mass Index, Genome-Wide Association Study
Abstract

BACKGROUND: While polygenic risk scores hold significant promise in estimating an individual's risk of developing a complex trait such as obesity, their application in the clinic has, to date, been limited by a lack of data from non-European populations. As a collaboration model of the International Hundred K+ Cohorts Consortium (IHCC), we endeavored to develop a globally applicable trans-ethnic PRS for body mass index (BMI) through this relatively new international effort. METHODS: The polygenic risk score (PRS) model was developed, trained and tested at the Center for Applied Genomics (CAG) of The Children's Hospital of Philadelphia (CHOP) based on a BMI meta-analysis from the GIANT consortium. The validated PRS models were subsequently disseminated to the participating sites. Scores were generated by each site locally on their cohorts and summary statistics returned to CAG for final analysis. RESULTS: We show that in the absence of a well powered trans-ethnic GWAS from which to derive marker SNPs and effect estimates for PRS, trans-ethnic scores can be generated from European ancestry GWAS using Bayesian approaches such as LDpred, by adjusting the summary statistics using trans-ethnic linkage disequilibrium reference panels. The ported trans-ethnic scores outperform population specific-PRS across all non-European ancestry populations investigated including East Asians and three-way admixed Brazilian cohort. CONCLUSIONS: Here we show that for a truly polygenic trait such as BMI adjusting the summary statistics of a well powered European ancestry study using trans-ethnic LD reference results in a score that is predictive across a range of ancestries including East Asians and three-way admixed Brazilians.

Published
2023

22. Hereditary Early-Onset Parkinson's Disease Caused by Mutations in PINK1

Author

Valente, Enza Maria, Abou-Sleiman, Patrick M., Caputo, Viviana, Harvey, Kirsten, Gispert, Suzana, Ali, Zeeshan, Del Turco, Domenico, Bentivoglio, Anna Rita, Healy, Daniel G., Albanese, Alberto, Nussbaum, Robert, González-Maldonado, Rafael, Deller, Thomas, Salvi, Sergio, Cortelli, Pietro, Gilks, William P., Latchman, David S., Harvey, Robert J., Dallapiccola, Bruno, Auburger, Georg, and Wood, Nicholas W.

Published
2004

23. Additional file 1 of Rare recurrent copy number variations in metabotropic glutamate receptor interacting genes in children with neurodevelopmental disorders

Author

Glessner, Joseph T., Khan, Munir E., Chang, Xiao, Liu, Yichuan, Otieno, F. George, Lemma, Maria, Slaby, Isabella, Hain, Heather, Mentch, Frank, Li, Jin, Kao, Charlly, Sleiman, Patrick M. A., March, Michael E., Connolly, John, and Hakonarson, Hakon

Abstract

Additional file 1: Supplementary methods. ADHD and Autism Phenotype Query Parameters. Supplementary Table S1. ADHD Inclusion/ Exclusion Table. Supplementary Table S2. Autism Inclusion/ Exclusion Table. Supplementary Table S3. mGluR Interacting Genes (n=273). Supplementary Table S4. CNVs in mGluR interacting gene regions significantly associated in ADHD cases vs. controls. Supplementary Table S5. CNVs in mGluR interacting gene regions significantly associated in ASD cases vs. controls. Supplementary Table S6. CNVs in mGluR interacting gene regions significantly associated in ADHD & ASD cases vs. controls. Supplementary Figure S1. DeepCNV Probability in mGluR CNVs Passing Prior Visual Inspection. Supplementary Figure S2. mGluR CNV Association Study Manhattan Plot.

Published
2023
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26. Trans-ethnic Polygenic Risk Scores for Body Mass Index: An International Hundred K+ Cohorts Consortium Study

Author

Qu, Huiqi, primary, Connolly, John J, additional, Kraft, Peter, additional, Long, Jirong, additional, Pereira, Alexandre, additional, Flatley, Christopher, additional, Turman, Constance, additional, Prins, Bram, additional, Mentch, Frank, additional, Lotufo, Paulo A, additional, Magnus, Per, additional, Stampfer, Meir J, additional, Tamimi, Rulla, additional, Eliassen, A Heather, additional, Zheng, Wei, additional, Knudsen, Gun Peggy Stromstad, additional, Helgeland, Oyvind, additional, Butterworth, Adam S., additional, Hakonarson, Hakon, additional, and Sleiman, Patrick M., additional

Published
2023
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27. Probing the Virtual Proteome to Identify Novel Disease Biomarkers

Author

Mosley, Jonathan D., Benson, Mark D., Smith, J. Gustav, Melander, Olle, Ngo, Debby, Shaffer, Christian M., Ferguson, Jane F., Herzig, Matthew S., McCarty, Catherine A., Chute, Christopher G., Jarvik, Gail P., Gordon, Adam S., Palmer, Melody R., Crosslin, David R., Larson, Eric B., Carrell, David S., Kullo, Iftikhar J., Pacheco, Jennifer A., Peissig, Peggy L., Brilliant, Murray H., Kitchner, Terrie E., Linneman, James G., Namjou, Bahram, Williams, Marc S., Ritchie, Marylyn D., Borthwick, Kenneth M., Kiryluk, Krzysztof, Mentch, Frank D., Sleiman, Patrick M., Karlson, Elizabeth W., Verma, Shefali S., Zhu, Yineng, Vasan, Ramachandran S., Yang, Qiong, Denny, Josh C., Roden, Dan M., Gerszten, Robert E., and Wang, Thomas J.

Published
2018
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28. Trans‐ethnic genomic informed risk assessment for Alzheimer's disease: An International Hundred K+ Cohorts Consortium study.

Author

Sleiman, Patrick M., Qu, Hui‐Qi, Connolly, John J., Mentch, Frank, Pereira, Alexandre, Lotufo, Paulo A., Tollman, Stephen, Choudhury, Ananyo, Ramsay, Michele, Kato, Norihiro, Ozaki, Kouichi, Mitsumori, Risa, Jeon, Jae‐Pil, Hong, Chang Hyung, Son, Sang Joon, Roh, Hyun Woong, Lee, Dong‐gi, Mukadam, Naaheed, Foote, Isabelle F., and Marshall, Charles R.

Abstract

BACKGROUND: As a collaboration model between the International HundredK+ Cohorts Consortium (IHCC) and the Davos Alzheimer's Collaborative (DAC), our aim was to develop a trans‐ethnic genomic informed risk assessment (GIRA) algorithm for Alzheimer's disease (AD). METHODS: The GIRA model was created to include polygenic risk score calculated from the AD genome‐wide association study loci, the apolipoprotein E haplotypes, and non‐genetic covariates including age, sex, and the first three principal components of population substructure. RESULTS: We validated the performance of the GIRA model in different populations. The proteomic study in the participant sites identified proteins related to female infertility and autoimmune thyroiditis and associated with the risk scores of AD. CONCLUSIONS: As the initial effort by the IHCC to leverage existing large‐scale datasets in a collaborative setting with DAC, we developed a trans‐ethnic GIRA for AD with the potential of identifying individuals at high risk of developing AD for future clinical applications. [ABSTRACT FROM AUTHOR]

Published
2023
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29. Phenome-wide association studies across large population cohorts support drug target validation

Author

Diogo, Dorothée, Tian, Chao, Franklin, Christopher S., Alanne-Kinnunen, Mervi, March, Michael, Spencer, Chris C. A., Vangjeli, Ciara, Weale, Michael E., Mattsson, Hannele, Kilpeläinen, Elina, Sleiman, Patrick M. A., Reilly, Dermot F., McElwee, Joshua, Maranville, Joseph C., Chatterjee, Arnaub K., Bhandari, Aman, Nguyen, Khanh-Dung H., Estrada, Karol, Reeve, Mary-Pat, Hutz, Janna, Bing, Nan, John, Sally, MacArthur, Daniel G., Salomaa, Veikko, Ripatti, Samuli, Hakonarson, Hakon, Daly, Mark J., Palotie, Aarno, Hinds, David A., Donnelly, Peter, Fox, Caroline S., Day-Williams, Aaron G., Plenge, Robert M., and Runz, Heiko

Published
2018
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30. Trans-ethnic Genomic Informed Risk Assessment for Alzheimer’s disease: An International Hundred K+ Cohorts Consortium Study

Author

Sleiman, Patrick M., primary, Qu, Hui-Qi, additional, Connolly, John J, additional, Mentch, Frank, additional, Pereira, Alexandre, additional, Lotufo, Paulo A, additional, Tollman, Stephen, additional, Choudhury, Ananyo, additional, Ramsay, Michele, additional, Kato, Norihiro, additional, Ozaki, Kouichi, additional, Mitsumori, Risa, additional, Jeon, Jae-Pil, additional, Hong, Chang Hyung, additional, Son, Sang Joon, additional, Roh, Hyun Woong, additional, Lee, Dong-gi, additional, Mukadam, Naaheed, additional, Foote, Isabelle F, additional, Marshall, Charles R, additional, Butterworth, Adam, additional, Prins, Bram P, additional, Glessner, Joseph T, additional, and Hakonarson, Hakon, additional

Published
2022
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33. COVID-19 in pediatrics: Genetic susceptibility

Author

Glessner, Joseph T., primary, Chang, Xiao, additional, Mentch, Frank, additional, Qu, Huiqi, additional, Abrams, Debra J., additional, Thomas, Alexandria, additional, Sleiman, Patrick M. A., additional, and Hakonarson, Hakon, additional

Published
2022
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35. Identification of Novel Loci Shared by Juvenile Idiopathic Arthritis Subtypes Through Integrative Genetic Analysis

Author

Li, Jin, primary, Li, Yun R., additional, Glessner, Joseph T., additional, Yang, Jie, additional, March, Michael E., additional, Kao, Charlly, additional, Vaccaro, Courtney N., additional, Bradfield, Jonathan P., additional, Li, Junyi, additional, Mentch, Frank D., additional, Qu, Hui‐Qi, additional, Qi, Xiaohui, additional, Chang, Xiao, additional, Hou, Cuiping, additional, Abrams, Debra J., additional, Qiu, Haijun, additional, Wei, Zhi, additional, Connolly, John J., additional, Wang, Fengxiang, additional, Snyder, James, additional, Flatø, Berit, additional, Thompson, Susan D., additional, Langefeld, Carl D., additional, Lie, Benedicte A., additional, Munro, Jane E., additional, Wise, Carol, additional, Sleiman, Patrick M. A., additional, and Hakonarson, Hakon, additional

Published
2022
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36. Strong synaptic transmission impact by copy number variations in schizophrenia

Author

Glessner, Joseph T., Reilly, Muredach P., Kim, Cecilia E., Takahashi, Nagahide, Albano, Anthony, Hou, Cuiping, Bradfield, Jonathan P., Zhang, Haitao, Sleiman, Patrick M. A., Flory, James H., Imielinski, Marcin, Frackelton, Edward C., Chiavacci, Rosetta, Thomas, Kelly A., Garris, Maria, Otieno, Frederick G., Davidson, Michael, Weiser, Mark, Reichenberg, Abraham, Davis, Kenneth L., Friedman, Joseph I., Cappola, Thomas P., Margulies, Kenneth B., Rader, Daniel J., Grant, Struan F. A., Buxbaum, Joseph D., Gur, Raquel E., Hakonarson, Hakon, and Lupski, James R.

Published
2010

37. Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height

Author

Lanktree, Matthew B., Guo, Yiran, Murtaza, Muhammed, Glessner, Joseph T., Bailey, Swneke D., Onland-Moret, N. Charlotte, Lettre, Guillaume, Ongen, Halit, Rajagopalan, Ramakrishnan, Johnson, Toby, Shen, Haiqing, Nelson, Christopher P., Klopp, Norman, Baumert, Jens, Padmanabhan, Sandosh, Pankratz, Nathan, Pankow, James S., Shah, Sonia, Taylor, Kira, Barnard, John, Peters, Bas J., M. Maloney, Cliona, Lobmeyer, Maximilian T., Stanton, Alice, Zafarmand, M. Hadi, Romaine, Simon P.R., Mehta, Amar, van Iperen, Erik P.A., Gong, Yan, Price, Tom S., Smith, Erin N., Kim, Cecilia E., Li, Yun R., Asselbergs, Folkert W., Atwood, Larry D., Bailey, Kristian M., Bhatt, Deepak, Bauer, Florianne, Behr, Elijah R., Bhangale, Tushar, Boer, Jolanda M.A., Boehm, Bernhard O., Bradfield, Jonathan P., Brown, Morris, Braund, Peter S., Burton, Paul R., Carty, Cara, Chandrupatla, Hareesh R., Chen, Wei, Connell, John, Dalgeorgou, Chrysoula, Boer, Anthonius de, Drenos, Fotios, Elbers, Clara C., Fang, James C., Fox, Caroline S., Frackelton, Edward C., Fuchs, Barry, Furlong, Clement E., Gibson, Quince, Gieger, Christian, Goel, Anuj, Grobbee, Diederik E., Hastie, Claire, Howard, Philip J., Huang, Guan-Hua, Johnson, W. Craig, Li, Qing, Kleber, Marcus E., Klein, Barbara E.K., Klein, Ronald, Kooperberg, Charles, Ky, Bonnie, LaCroix, Andrea, Lanken, Paul, Lathrop, Mark, Li, Mingyao, Marshall, Vanessa, Melander, Olle, Mentch, Frank D., J. Meyer, Nuala, Monda, Keri L., Montpetit, Alexandre, Murugesan, Gurunathan, Nakayama, Karen, Nondahl, Dave, Onipinla, Abiodun, Rafelt, Suzanne, Newhouse, Stephen J., Otieno, F. George, Patel, Sanjey R., Putt, Mary E., Rodriguez, Santiago, Safa, Radwan N., Sawyer, Douglas B., Schreiner, Pamela J., Simpson, Claire, Sivapalaratnam, Suthesh, Srinivasan, Sathanur R., Suver, Christine, Swergold, Gary, Sweitzer, Nancy K., Thomas, Kelly A., Thorand, Barbara, Timpson, Nicholas J., Tischfield, Sam, Tobin, Martin, Tomaszweski, Maciej, Verschuren, W.M. Monique, Wallace, Chris, Winkelmann, Bernhard, Zhang, Haitao, Zheng, Dongling, Zhang, Li, Zmuda, Joseph M., Clarke, Robert, Balmforth, Anthony J., Danesh, John, Day, Ian N., Schork, Nicholas J., de Bakker, Paul I.W., Delles, Christian, Duggan, David, Hingorani, Aroon D., Hirschhorn, Joel N., Hofker, Marten H., Humphries, Steve E., Kivimaki, Mika, Lawlor, Debbie A., Kottke-Marchant, Kandice, Mega, Jessica L., Mitchell, Braxton D., Morrow, David A., Palmen, Jutta, Redline, Susan, Shields, Denis C., Shuldiner, Alan R., Sleiman, Patrick M., Smith, George Davey, Farrall, Martin, Jamshidi, Yalda, Christiani, David C., Casas, Juan P., Hall, Alistair S., Doevendans, Pieter A., D. Christie, Jason, Berenson, Gerald S., Murray, Sarah S., Illig, Thomas, Dorn, Gerald W., II, Cappola, Thomas P., Boerwinkle, Eric, Sever, Peter, Rader, Daniel J., Reilly, Muredach P., Caulfield, Mark, Talmud, Philippa J., Topol, Eric, Engert, James C., Wang, Kai, Dominiczak, Anna, Hamsten, Anders, Curtis, Sean P., Silverstein, Roy L., Lange, Leslie A., Sabatine, Marc S., Trip, Mieke, Saleheen, Danish, Peden, John F., Cruickshanks, Karen J., März, Winfried, O'Connell, Jeffrey R., Klungel, Olaf H., Wijmenga, Cisca, Maitland-van der Zee, Anke Hilse, Schadt, Eric E., Johnson, Julie A., Jarvik, Gail P., Papanicolaou, George J., Grant, Struan F.A., Munroe, Patricia B., North, Kari E., Samani, Nilesh J., Koenig, Wolfgang, Gaunt, Tom R., Anand, Sonia S., van der Schouw, Yvonne T., Soranzo, Nicole, FitzGerald, Garret A., Reiner, Alex, Hegele, Robert A., Hakonarson, Hakon, and Keating, Brendan J.

Published
2011
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39. Association of Pathogenic Variants in Hereditary Cancer Genes With Multiple Diseases

Author

Zeng, Chenjie, primary, Bastarache, Lisa A., additional, Tao, Ran, additional, Venner, Eric, additional, Hebbring, Scott, additional, Andujar, Justin D., additional, Bland, Sarah T., additional, Crosslin, David R., additional, Pratap, Siddharth, additional, Cooley, Ayorinde, additional, Pacheco, Jennifer A., additional, Christensen, Kurt D., additional, Perez, Emma, additional, Zawatsky, Carrie L. Blout, additional, Witkowski, Leora, additional, Zouk, Hana, additional, Weng, Chunhua, additional, Leppig, Kathleen A., additional, Sleiman, Patrick M. A., additional, Hakonarson, Hakon, additional, Williams, Marc. S., additional, Luo, Yuan, additional, Jarvik, Gail P., additional, Green, Robert C., additional, Chung, Wendy K., additional, Gharavi, Ali G., additional, Lennon, Niall J., additional, Rehm, Heidi L., additional, Gibbs, Richard A., additional, Peterson, Josh F., additional, Roden, Dan M., additional, Wiesner, Georgia L., additional, and Denny, Joshua C., additional

Published
2022
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41. Additional file 1 of An electronic health record (EHR) phenotype algorithm to identify patients with attention deficit hyperactivity disorders (ADHD) and psychiatric comorbidities

Author

Slaby, Isabella, Hain, Heather S., Abrams, Debra, Mentch, Frank D., Glessner, Joseph T., Sleiman, Patrick M. A., and Hakonarson, Hakon

Subjects
mental disorders
Abstract

Additional file 1: Table S1. ADHD Inclusion/ Exclusion Table. ICD codes and direct terms of ADHD and ADD were used, as well as terms that were specific towards ADHD phenotypes and medications. Table S2. Anxiety Inclusion/ Exclusion Table. ICD codes and terms that were specific towards anxiety phenotypes and medications were used. Table S3. Autism Inclusion/ Exclusion Table. ICD Codes as well as terms that were specific towards autism phenotypes were used. Table S4. Conduct Disorder Inclusion/ Exclusion Table. ICD codes and terms that were specific towards conduct disorder phenotypes were used. Table S5. Oppositional Defiant Disorder Inclusion/ Exclusion Table. ICD codes and terms that were specific towards oppositional defiant disorder phenotypes were used. Table S6. Major Depressive Disorder Inclusion/ Exclusion Table. ICD codes and terms that were specific towards major depression phenotypes and medications were used. Diagnosis of major depressive disorder was present on at least two (2) distinct calendar days that are at least thirty (30) days apart and not more than one hundred and eighty (180) days apart. Table S7. Bipolar Disorder Inclusion/ Exclusion Table. ICD codes and terms that were specific towards bipolar disorder phenotypes and medications were used. Diagnosis of bipolar disorder was present on at least two (2) distinct calendar days that are at least thirty (30) days apart and not more than one hundred and eighty (180) days apart. Table S8. Schizophrenia and Psychoses Inclusion/ Exclusion Table. ICD codes and terms that were specific towards schizophrenia and psychoses phenotypes and medications were used. Table S9. Tic Disorders Inclusion/ Exclusion Table. ICD codes and terms that were specific towards tic disorder phenotypes were used. Table S10. Tourette Syndrome Inclusion/ Exclusion Table. ICD codes and terms that were specific towards Tourette syndrome phenotypes were used. Table S11. Intellectual Disability Inclusion/ Exclusion Table. ICD codes and terms that were specific towards intellectual disability phenotypes were used. Table S12. Learning Disability Inclusion/ Exclusion Table. ICD codes and terms that were specific towards learning disability phenotypes were used. Table S13. Case Exclusion Table. ICD codes and terms used for case exclusions. Table S14. Control Exclusion Table. ICD codes and terms used for control exclusions. Table S15. Control Syndromes Exclusion Table. ICD codes and terms used for control syndrome exclusions. Table S16. Psychiatric Conditions Prevalence in Extracted Subjects. Numbers and percent of psychiatric disorders and comorbidities in all cases and Psych Positive Cases. *has at least of the 10 psychiatric conditions (does not include learning disability or intellectual disability. Table S17. Validation of algorithms. Positive Predictive Values (PPV) of algorithms for each psychiatric disorders and comorbidity of ADHD measured.

Published
2022
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42. Identification of Four Novel Loci in Asthma in European American and African American Populations

Author

Almoguera, Berta, Vazquez, Lyam, Mentch, Frank, Connolly, John, Pacheco, Jennifer A., Sundaresan, Agnes S., Peissig, Peggy L., Linneman, James G., McCarty, Catherine A., Crosslin, David, Carrell, David S., Lingren, Todd, Namjou-Khales, Bahram, Harley, John B., Larson, Eric, Jarvik, Gail P., Brilliant, Murray, Williams, Marc S., Kullo, Iftikhar J., Hysinger, Erik B., Sleiman, Patrick M. A., and Hakonarson, Hakon

Published
2017
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43. Trans‐ethnic polygenic risk scores for body mass index: An international hundred K+ cohorts consortium study.

Author

Qu, Hui‐Qi, Connolly, John J, Kraft, Peter, Long, Jirong, Pereira, Alexandre, Flatley, Christopher, Turman, Constance, Prins, Bram, Mentch, Frank, Lotufo, Paulo A, Magnus, Per, Stampfer, Meir J, Tamimi, Rulla, Eliassen, A Heather, Zheng, Wei, Knudsen, Gun Peggy Stromstad, Helgeland, Oyvind, Butterworth, Adam S., Hakonarson, Hakon, and Sleiman, Patrick M.

Subjects
DISEASE risk factors, MONOGENIC & polygenic inheritance (Genetics), BODY mass index, EAST Asians, CHILDREN'S hospitals
Abstract

Background: While polygenic risk scores hold significant promise in estimating an individual's risk of developing a complex trait such as obesity, their application in the clinic has, to date, been limited by a lack of data from non‐European populations. As a collaboration model of the International Hundred K+ Cohorts Consortium (IHCC), we endeavored to develop a globally applicable trans‐ethnic PRS for body mass index (BMI) through this relatively new international effort. Methods: The polygenic risk score (PRS) model was developed, trained and tested at the Center for Applied Genomics (CAG) of The Children's Hospital of Philadelphia (CHOP) based on a BMI meta‐analysis from the GIANT consortium. The validated PRS models were subsequently disseminated to the participating sites. Scores were generated by each site locally on their cohorts and summary statistics returned to CAG for final analysis. Results: We show that in the absence of a well powered trans‐ethnic GWAS from which to derive marker SNPs and effect estimates for PRS, trans‐ethnic scores can be generated from European ancestry GWAS using Bayesian approaches such as LDpred, by adjusting the summary statistics using trans‐ethnic linkage disequilibrium reference panels. The ported trans‐ethnic scores outperform population specific‐PRS across all non‐European ancestry populations investigated including East Asians and three‐way admixed Brazilian cohort. Conclusions: Here we show that for a truly polygenic trait such as BMI adjusting the summary statistics of a well powered European ancestry study using trans‐ethnic LD reference results in a score that is predictive across a range of ancestries including East Asians and three‐way admixed Brazilians. [ABSTRACT FROM AUTHOR]

Published
2023
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45. Thymic stromal lymphopoietin--elicited basophil responses promote eosinophilic esophagitis

Author

Noti, Mario, Wojno, Elia D. Tait, Kim, Brian S., Siracusa, Mark C., Giacomin, Paul R., Nair, Meera G., Benitez, Alain J., Ruymann, Kathryn R., Muir, Amanda B., Hill, David A., Chikwava, Kudakwashe R., Moghaddam, Amin E., Sattentau, Quentin J., Alex, Aneesh, Zhou, Chao, Yearley, Jennifer H., Menard-Katcher, Paul, Kubo, Masato, Obata-Ninomiya, Kazushige, Karasuyama, Hajime, Comeau, Michael R., Brown-Whitehorn, Terri, de Waal Malefyt, Rene, Sleiman, Patrick M., Hakonarson, Hakon, Cianferoni, Antonella, Falk, Gary W., Wang, Mei-Lun, Spergel, Jonathan M., and Artis, David

Subjects
Care and treatment, Physiological aspects, Development and progression, Genetic aspects, Research, Causes of, Eosinophils -- Physiological aspects -- Genetic aspects -- Research, Basophils -- Physiological aspects -- Genetic aspects -- Research, Esophagitis -- Causes of -- Development and progression -- Genetic aspects -- Care and treatment -- Research
Abstract

Eosinophilic esophagitis (EoE) is a food allergy--associated inflammatory disease characterized by esophageal eosinophilia. Current management strategies for EoE are nonspecific, and thus there is a need to identify specific immunological [...]

Published
2013
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48. A genome-wide study reveals copy number variants exclusive to childhood obesity cases

Author

Glessner, Joseph T., Bradfield, Jonathan P., Kai Wang, Takahashi, Nagahide, Haitao Zhang, Sleiman, Patrick M., Mentch, Frank D., Kim, Cecilia E., Cuiping Hou, Thomas, Kelly A., Garris, Maria L., Deliard, Sandra, Frackelton, Edward C., Otieno, F. George, Jainhua Zhao, Chiavacci, Rosetta M., Mingyao Li, Buxbaum, Joseph D., Berkowitz, Robert I., Hakonarson, Hakon, and Grant, Struan F.A.

Subjects
Obesity in children -- Genetic aspects, Obesity in children -- Demographic aspects, Single nucleotide polymorphisms -- Analysis, Biological sciences
Abstract

A whole-genome copy number variations (CNV) study in a large cohort of child hood-obesity cases and lean controls of European ancestry who were genotyped with the Illumina Infinium II HumanHap550K BeadChip was performed to examine the CNVs in a large pediatric cohort presenting with common obesity that is primarily nonsyndromic. The results indicated that CNVs contributed to the genetic susceptibility of common childhood obesity in subjects of both European and African ancestry.

Published
2010

49. Additional file 1 of MONTAGE: a new tool for high-throughput detection of mosaic copy number variation

Author

Glessner, Joseph T., Chang, Xiao, Yichuan Liu, Li, Jin, Khan, Munir, Wei, Zhi, Sleiman, Patrick M. A., and Hakon Hakonarson

Abstract

Additional file 1: Supplementary Fig. 1. Age Distribution of Studied Cohort. Supplementary Fig. 2. Modeling B-allele Frequency Standard Deviation for Mosaic Copy Number States. Supplementary Table 1. Samples Genotyped on Illumina SNP microarray platforms. Supplementary Table 2. Genotyping Sex. Supplementary Table 3. Genotyping Race.

Published
2021
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