Fallacies and Pitfalls in Genome-Wide Association Studies*

Authors: Hecker, Julian, Craig, Adam, Hughes, Andrew, Neidich, Julie, Taswell, Carl, Laird, Nan

Source: 2023 Guardians Workshop (Guardians) Guardians Workshop (Guardians), 2023. :1-7 Oct, 2023

Relation: 2023 Guardians Workshop (Guardians)

miRNAome-metabolome wide association study reveals effects of miRNA regulation in eosinophilia and airflow obstruction in childhood asthma

Authors: Sharma, Rinku ^a, Mendez, Kevin ^{a, b}, Begum, Sofina ^a, Chu, Su ^a, Prince, Nicole ^a, Hecker, Julian ^a, Kelly, Rachel S. ^a, Chen, Qingwen ^a, Wheelock, Craig E. ^{c, d}, Celedón, Juan C. ^e, Clish, Clary ^f, Gertszen, Robert ^g, Tantisira, Kelan G. ^h, Weiss, Scott T. ^a, Lasky-Su, Jessica ^{a, i}, McGeachie, Michael ^{a, i, ∗}

Source: In eBioMedicine February 2025 112

Polygenic and transcriptional risk scores identify chronic obstructive pulmonary disease subtypes in the COPDGene and ECLIPSE cohort studies

Authors: Moll, Matthew, Hecker, Julian, Platig, John, Zhang, Jingzhou, Ghosh, Auyon J., Pratte, Katherine A., Wang, Rui-Sheng, Hill, Davin, Konigsberg, Iain R., Chiles, Joe W., III, Hersh, Craig P., Castaldi, Peter J., Glass, Kimberly, Dy, Jennifer G., Sin, Don D., Tal-Singer, Ruth, Mouded, Majd, Rennard, Stephen I., Anderson, Gary P., Kinney, Gregory L., Bowler, Russell P., Curtis, Jeffrey L., McDonald, Merry-Lynn, Silverman, Edwin K., Hobbs, Brian D., Cho, Michael H.

Source: In eBioMedicine December 2024 110

Assessing the contribution of rare genetic variants to phenotypes of chronic obstructive pulmonary disease using whole-genome sequence data

Authors: Kim, Wonji, Hecker, Julian, Barr, R Graham, Boerwinkle, Eric, Cade, Brian, Correa, Adolfo, Dupuis, Josée, Gharib, Sina A, Lange, Leslie, London, Stephanie J, Morrison, Alanna C, O'Connor, George T, Oelsner, Elizabeth C, Psaty, Bruce M, Vasan, Ramachandran S, Redline, Susan, Rich, Stephen S, Rotter, Jerome I, Yu, Bing, Lange, Christoph, Manichaikul, Ani, Zhou, Jin J, Sofer, Tamar, Silverman, Edwin K, Qiao, Dandi, Cho, Michael H

Source: Human molecular genetics. 31(22):3873-3885

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100164793700.0x000001&indx=1&recIds=ETOCvdc_100164793700.0x000001

Local and Global Stratification Analysis in Whole Genome Sequencing (WGS) Studies Using LocStra
9th International conference on Computational advances in bio and medical sciences, ICCABS

Authors: Hahn, Georg, Lutz, Sharon Marie, Hecker, Julian, Prokopenko, Dmitry, Lange, Christoph

Source: Lecture notes in computer science. 12029:159-170

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCCN606158917&indx=1&recIds=ETOCCN606158917

Genome‐wide association analysis of COVID‐19 mortality risk in SARS‐CoV‐2 genomes identifies mutation in the SARS‐CoV‐2 spike protein that colocalizes with P.1 of the Brazilian strain

Authors: Hahn, Georg, Wu, Chloe M., Lee, Sanghun, Lutz, Sharon M., Khurana, Surender, Baden, Lindsey R., Haneuse, Sebastien, Qiao, Dandi, Hecker, Julian, DeMeo, Dawn L., Tanzi, Rudolph E., Choudhary, Manish C., Etemad, Behzad, Mohammadi, Abbas, Esmaeilzadeh, Elmira, Cho, Michael H., Li, Jonathan Z., Randolph, Adrienne G., Laird, Nan M., Weiss, Scott T., Silverman, Edwin K., Ribbeck, Katharina, Lange, Christoph

Source: Genetic epidemiology. 45(7):685-693

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100132987757.0x000001&indx=1&recIds=ETOCvdc_100132987757.0x000001

An interaction of the 17q12‐21 locus with mold exposure in childhood asthma

Authors: Lee, Sanghun, Lasky‐Su, Jessica, Kim, Wonji, Won, Sungho, Laurie, Cecelia, Celedón, Juan C., Lange, Christoph, Weiss, Scott T., Hecker, Julian

Source: Pediatric allergy and immunology. 32(2):373-376

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100122963904.0x000001&indx=1&recIds=ETOCvdc_100122963904.0x000001

LocStra: Fast analysis of regional/global stratification in whole‐genome sequencing studies

Authors: Hahn, Georg, Lutz, Sharon M., Hecker, Julian, Prokopenko, Dmitry, Cho, Michael H., Silverman, Edwin K., Weiss, Scott T., Lange, Christoph

Source: Genetic epidemiology. 45(1):82-98

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100114738197.0x000001&indx=1&recIds=ETOCvdc_100114738197.0x000001

Assessing polyomic risk to predict Alzheimer's disease using a machine learning model.

Authors: Ngai, Tiffany, Willett, Julian, Waqas, Mohammad, Fishbein, Lucas H., Choi, Younjung, Hahn, Georg, Mullin, Kristina, Lange, Christoph, Hecker, Julian, Tanzi, Rudolph E., Prokopenko, Dmitry

Source: Alzheimer's & Dementia: The Journal of the Alzheimer's Association; Dec2024, Vol. 20 Issue 12, p8700-8714, 15p

Whole Genome Sequencing Identifies CRISPLD2 as a Lung Function Gene in Children With Asthma

Authors: Abe, Namiko, Abecasis, Goncalo, Albert, Christine, Palmer Allred, Nicholette (Nichole), Almasy, Laura, Alonso, Alvaro, Ament, Seth, Anderson, Peter, Anugu, Pramod, Applebaum-Bowden, Deborah, Arking, Dan, Arnett, Donna K., Ashley-Koch, Allison, Aslibekyan, Stella, Assimes, Tim, Auer, Paul, Avramopoulos, Dimitrios, Barnard, John, Barnes, Kathleen, Barr, R. Graham, Barron-Casella, Emily, Beaty, Terri, Becker, Diane, Becker, Lewis, Beer, Rebecca, Begum, Ferdouse, Beitelshees, Amber, Benjamin, Emelia, Bezerra, Marcos, Bielak, Larry, Bis, Joshua, Blackwell, Thomas, Blangero, John, Boerwinkle, Eric, Borecki, Ingrid, Bowler, Russell, Brody, Jennifer, Broeckel, Ulrich, Broome, Jai, Bunting, Karen, Burchard, Esteban, Cardwell, Jonathan, Carty, Cara, Casaburi, Richard, Casella, James, Chaffin, Mark, Chang, Christy, Chasman, Daniel, Chavan, Sameer, Chen, Bo-Juen, Chen, Wei-Min, Chen, Yii-Der Ida, Cho, Michael H., Choi, Seung Hoan, Chuang, Lee-Ming, Chung, Mina, Cornell, Elaine, Correa, Adolfo, Crandall, Carolyn, Crapo, James, Cupples, L. Adrienne, Curran, Joanne, Curtis, Jeffrey, Custer, Brian, Damcott, Coleen, Darbar, Dawood, Das, Sayantan, David, Sean, Davis, Colleen, Daya, Michelle, de Andrade, Mariza, DeBaun, Michael, Deka, Ranjan, DeMeo, Dawn, Devine, Scott, Do, Ron, Duan, Qing, Duggirala, Ravi, Durda, Peter, Dutcher, Susan, Eaton, Charles, Ekunwe, Lynette, Ellinor, Patrick, Emery, Leslie, Farber, Charles, Farnam, Leanna, Fingerlin, Tasha, Flickinger, Matthew, Fornage, Myriam, Franceschini, Nora, Fu, Mao, Fullerton, Stephanie M., Fulton, Lucinda, Gabriel, Stacey, Gan, Weiniu, Gao, Yan, Gass, Margery, Gelb, Bruce, Geng, Xiaoqi (Priscilla), Germer, Soren, Gignoux, Chris, Gladwin, Mark, Glahn, David, Gogarten, Stephanie, Gong, Da-Wei, Goring, Harald, Gu, C. Charles, Guan, Yue, Guo, Xiuqing, Haessler, Jeff, Hall, Michael, Harris, Daniel, Hawley, Nicola, He, Jiang, Heavner, Ben, Heckbert, Susan, Hernandez, Ryan, Herrington, David, Hersh, Craig, Hidalgo, Bertha, Hixson, James, Hokanson, John, Holly, Kramer, Hong, Elliott, Hoth, Karin, (Agnes) Hsiung, Chao, Huston, Haley, Hwu, Chii Min, Irvin, Marguerite Ryan, Jackson, Rebecca, Jain, Deepti, Jaquish, Cashell, Jhun, Min A., Johnsen, Jill, Johnson, Andrew, Johnson, Craig, Johnston, Rich, Jones, Kimberly, Kachroo, Priyadarshini, Kang, Hyun Min, Kaplan, Robert, Kardia, Sharon, Kathiresan, Sekar, Kaufman, Laura, Kelly, Shannon, Kenny, Eimear, Kessler, Michael, Khan, Alyna, Kinney, Greg, Konkle, Barbara, Kooperberg, Charles, Krauter, Stephanie, Lange, Christoph, Lange, Ethan, Lange, Leslie, Laurie, Cathy, Laurie, Cecelia, LeBoff, Meryl, Lee, Seunggeun Shawn, Lee, Wen-Jane, LeFaive, Jonathon, Levine, David, Levy, Dan, Lewis, Joshua, Li, Yun, Lin, Honghuang, Lin, Keng Han, Liu, Simin, Liu, Yongmei, Loos, Ruth, Lubitz, Steven, Lunetta, Kathryn, Luo, James, Mahaney, Michael, Make, Barry, Manichaikul, Ani, Manson, JoAnn, Margolin, Lauren, Martin, Lisa, Mathai, Susan, Mathias, Rasika, McArdle, Patrick, McDonald, Merry-Lynn, McFarland, Sean, McGarvey, Stephen, Mei, Hao, Meyers, Deborah A., Mikulla, Julie, Min, Nancy, Minear, Mollie, Minster, Ryan L., Mitchell, Braxton, Montasser, May E., Musani, Solomon, Mwasongwe, Stanford, Mychaleckyj, Josyf C., Nadkarni, Girish, Naik, Rakhi, Natarajan, Pradeep, Nekhai, Sergei, Nickerson, Deborah, North, Kari, O'Connell, Jeff, O'Connor, Tim, Ochs-Balcom, Heather, Pankow, James, Papanicolaou, George, Parker, Margaret, Parsa, Afshin, Penchev, Sara, Peralta, Juan Manuel, Perez, Marco, Perry, James, Peters, Ulrike, Peyser, Patricia, Phillips, Lawrence S., Phillips, Sam, Pollin, Toni, Post, Wendy, Becker, Julia Powers, Boorgula, Meher Preethi, Preuss, Michael, Prokopenko, Dmitry, Psaty, Bruce, Qasba, Pankaj, Qiao, Dandi, Qin, Zhaohui, Rafaels, Nicholas, Raffield, Laura, Ramachandran, Vasan, Rao, D.C., Rasmussen-Torvik, Laura, Ratan, Aakrosh, Redline, Susan, Reed, Robert, Regan, Elizabeth, Reiner, Alex, Rice, Ken, Rich, Stephen, Roden, Dan, Roselli, Carolina, Rotter, Jerome, Ruczinski, Ingo, Russell, Pamela, Ruuska, Sarah, Ryan, Kathleen, Sakornsakolpat, Phuwanat, Salimi, Shabnam, Salzberg, Steven, Sandow, Kevin, Sankaran, Vijay, Scheller, Christopher, Schmidt, Ellen, Schwander, Karen, Schwartz, David, Sciurba, Frank, Seidman, Christine, Seidman, Jonathan, Sheehan, Vivien, Shetty, Amol, Shetty, Aniket, Sheu, Wayne Hui-Heng, Shoemaker, M. Benjamin, Silver, Brian, Silverman, Edwin, Smith, Jennifer, Smith, Josh, Smith, Nicholas, Smith, Tanja, Smoller, Sylvia, Snively, Beverly, Sofer, Tamar, Sotoodehnia, Nona, Stilp, Adrienne, Streeten, Elizabeth, Sung, Yun Ju, Su-Lasky, Jessica, Sylvia, Jody, Szpiro, Adam, Sztalryd, Carole, Taliun, Daniel, Tang, Hua, Taub, Margaret, Taylor, Kent, Taylor, Simeon, Telen, Marilyn, Thornton, Timothy A., Tinker, Lesley, Tirschwell, David, Tiwari, Hemant, Tracy, Russell, Tsai, Michael, Vaidya, Dhananjay, VandeHaar, Peter, Vrieze, Scott, Walker, Tarik, Wallace, Robert, Walts, Avram, Wan, Emily, Wang, Fei Fei, Watson, Karol, Weeks, Daniel E., Weir, Bruce, Weiss, Scott, Weng, Lu-Chen, Willer, Cristen, Williams, Kayleen, Williams, L. Keoki, Wilson, Carla, Wilson, James, Wong, Quenna, Xu, Huichun, Yanek, Lisa, Yang, Ivana, Yang, Rongze, Zaghloul, Norann, Zekavat, Maryam, Zhang, Yingze, Zhao, Snow Xueyan, Zhao, Wei, Zheng, Xiuwen, Zhi, Degui, Zhou, Xiang, Zody, Michael, Zoellner, Sebastian, Hecker, Julian, Chawes, Bo L., Ahluwalia, Tarunveer S., Kelly, Rachel S., Chu, Su H., Virkud, Yamini V., Huang, Mengna, Barnes, Kathleen C., Burchard, Esteban G., Eng, Celeste, Hu, Donglei, Celedón, Juan C., Levin, Albert M., Gui, Hongsheng, Forno, Erick, Mak, Angel C.Y., Avila, Lydiana, Soto-Quiros, Manuel E., Cloutier, Michelle M., Acosta-Pérez, Edna, Canino, Glorisa, Bønnelykke, Klaus, Bisgaard, Hans, Raby, Benjamin A., Weiss, Scott T., Lasky-Su, Jessica A.

Source: In Chest December 2019 156(6):1068-1079

A flexible and nearly optimal sequential testing approach to randomized testing: QUICK‐STOP

Authors: Hecker, Julian, Ruczinski, Ingo, Cho, Michael H., Silverman, Edwin K., Coull, Brent, Lange, Christoph

Source: Genetic epidemiology. 44(2):139-147

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100102917455.0x000001&indx=1&recIds=ETOCvdc_100102917455.0x000001

Prediction of disease-free survival for precision medicine using cooperative learning on multi-omic data.

Authors: Hahn, Georg¹, ghahn@hsph.harvard.edu, Prokopenko, Dmitry², Hecker, Julian³, Lutz, Sharon M¹, Mullin, Kristina², Sejour, Leinal⁴, Hide, Winston⁴, Vlachos, Ioannis⁴, DeSantis, Stacia⁵, Tanzi, Rudolph E², Lange, Christoph¹

Source: Briefings in Bioinformatics; Jul2024, Vol. 25 Issue 4, p1-15, 15p

Association of PHACTR1 with Coronary Artery Calcium Differs by Sex and Cigarette Smoking.

Authors: Voorhies, Kirsten, Young, Kendra, Hsu, Fang-Chi, Palmer, Nicholette D., McDonald, Merry-Lynn N., Lee, Sanghun, Hahn, Georg, Hecker, Julian, Prokopenko, Dmitry, Wu, Ann Chen, Regan, Elizabeth A., DeMeo, Dawn, Kinney, Greg L., Crapo, James D., Cho, Michael H., Silverman, Edwin K., Lange, Christoph, Budoff, Matthew J., Hokanson, John E., Lutz, Sharon M.

Source: Journal of Cardiovascular Development & Disease (JCDD); Jul2024, Vol. 11 Issue 7, p194, 11p

Urine metabolomics signature reveals novel determinants of adrenal suppression in children taking inhaled corticosteroids to control asthma symptoms.

Authors: Tran, Dung T., Chen, Yulu, Zheng, Yi, Hecker, Julian, Hawcutt, Daniel B., Pirmohamed, Munir, Lasky‐Su, Jessica, Wu, Ann C., Tantisira, Kelan G., McGeachie, Michael J., Weiss, Scott T., Dahlin, Amber

Source: Immunity, Inflammation & Disease; Jul2024, Vol. 12 Issue 7, p1-16, 16p

Subject Terms: ASTHMATICS, FATTY acid oxidation, ASTHMA in children, METABOLOMICS, METABOLITES

A robust and adaptive framework for interaction testing in quantitative traits between multiple genetic loci and exposure variables.

Authors: Hecker, Julian^1,2 (AUTHOR) rejhe@channing.harvard.edu, Prokopenko, Dmitry^2,3 (AUTHOR), Moll, Matthew^1,2,4 (AUTHOR), Lee, Sanghun^5,6 (AUTHOR), Kim, Wonji^1,2 (AUTHOR), Qiao, Dandi^1,2 (AUTHOR), Voorhies, Kirsten^2,7 (AUTHOR), Kim, Woori^2,8,9 (AUTHOR), Vansteelandt, Stijn^10,11 (AUTHOR), Hobbs, Brian D.^1,2,4 (AUTHOR), Cho, Michael H.^1,2,4 (AUTHOR), Silverman, Edwin K.^1,2,4 (AUTHOR), Lutz, Sharon M.^2,6,7 (AUTHOR), DeMeo, Dawn L.^1,2 (AUTHOR), Weiss, Scott T.^1,2 (AUTHOR), Lange, Christoph^1,2,6 (AUTHOR)

Source: PLoS Genetics. 11/16/2022, Vol. 18 Issue 11, p1-19. 19p.

Subject Terms: *GENOTYPE-environment interaction, *DISEASE risk factors, *ROBUST statistics, *FALSE positive error, *GENETIC variation, *STATISTICAL learning

Geographic Terms: UNITED Kingdom

Letter to the editor: critical evaluation of the reliability of DNA methylation probes on the illumina MethylationEPIC v1.0 BeadChip microarrays.

Authors: Hecker, Julian¹ (AUTHOR) rejhe@channing.harvard.edu, Weiss, Scott T.¹ (AUTHOR), Lasky-Su, Jessica A.¹ (AUTHOR), DeMeo, Dawn L.¹ (AUTHOR), Lange, Christoph^1,2 (AUTHOR)

Source: Epigenetics. Dec2024, Vol. 19 Issue 1, p1-3. 3p.

Enhancing Asthma Pharmacogenetics Through Subtype‐Specific Associations.

Authors: Piparia, Shraddha¹ (AUTHOR), Hecker, Julian² (AUTHOR), Srivastava, Upasna³ (AUTHOR), Sharma, Rinku² (AUTHOR), Khare, Manaswitha⁴ (AUTHOR), Kho, Alvin⁵ (AUTHOR), Weiss, Scott T.² (AUTHOR), McGeachie, Michael² (AUTHOR), Tantisira, Kelan^1,6 (AUTHOR) ktantisira@health.ucsd.edu

Source: Clinical & Experimental Allergy. Oct2024, p1. 3p. 1 Illustration.

Subject Terms: *GENOME-wide association studies, *RECEIVER operating characteristic curves, *HUMAN genetics, *ASTHMA in children, *MOLECULAR genetics

Whole Genome Sequencing Identifies CRISPLD2 as a Lung Function Gene in Children With Asthma

Authors: Kachroo, Priyadarshini, Hecker, Julian, Chawes, Bo L., Ahluwalia, Tarunveer S., Cho, Michael H., Qiao, Dandi, Kelly, Rachel S., Chu, Su H., Virkud, Yamini V., Huang, Mengna, Barnes, Kathleen C., Burchard, Esteban G., Eng, Celeste, Hu, Donglei, Celedón, Juan C., Daya, Michelle, Levin, Albert M., Gui, Hongsheng, Williams, L. Keoki, Forno, Erick, Mak, Angel C.Y., Avila, Lydiana, Soto-Quiros, Manuel E., Cloutier, Michelle M., Acosta-Pérez, Edna, Canino, Glorisa, Bønnelykke, Klaus, Bisgaard, Hans, Raby, Benjamin A., Lange, Christoph, Weiss, Scott T., Lasky-Su, Jessica A.

Source: Chest. 156(6):1068-1079

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100094779581.0x000001&indx=1&recIds=ETOCvdc_100094779581.0x000001

Effect of population stratification on SNP‐by‐environment interaction

Authors: An, Jaehoon, Won, Sungho, Lutz, Sharon M., Hecker, Julian, Lange, Christoph

Source: Genetic epidemiology. 43(8):1046-1055

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100092765953.0x000001&indx=1&recIds=ETOCvdc_100092765953.0x000001

Genetic Advances in Chronic Obstructive Pulmonary Disease: Insights from COPDGene

Authors: Ragland, Margaret F., Benway, Christopher J., Lutz, Sharon M., Bowler, Russell P., Hecker, Julian, Hokanson, John E., Crapo, James D., Castaldi, Peter J., DeMeo, Dawn L., Hersh, Craig P.

Source: American journal of respiratory and critical care medicine. 200(6):677-690

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN621484355&indx=1&recIds=ETOCRN621484355