Department of Genetics Publications for March 2nd – 29th, 2025

Department of Genetics faculty, postdocs, students and collaborators published 30 papers during March 2nd – 29th 2025.

 

Opportunities and Challenges in Using Electronic Health Record Systems to Study Postacute Sequelae of SARS-CoV-2 Infection: Insights From the NIH RECOVER Initiative. 

Mandel HL, Shah SN, Bailey LC, Carton T, Chen Y, Esquenazi-Karonika S, Haendel M, Hornig M, Kaushal R, Oliveira CR, Perlowski AA, Pfaff E, Rao S, Razzaghi H, Seibert E, Thomas GL, Weiner MG, Thorpe LE, Divers J; RECOVER EHR Cohort.

J Med Internet Res. 2025 Mar 5;27:e59217. doi: 10.2196/59217.

PMID: 40053748

 

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

Choi SH, Jurgens SJ, Xiao L, Hill MC, Haggerty CM, Sveinbjörnsson G, Morrill VN, Marston NA, Weng LC, Pirruccello JP, Arnar DO, Gudbjartsson DF, Mantineo H, von Falkenhausen AS, Natale A, Tveit A, Geelhoed B, Roselli C, Van Wagoner DR, Darbar D, Haase D, Soliman EZ, Davogustto GE, Jun G, Calkins H, Anderson JL, Brody JA, Halford JL, Barnard J, Hokanson JE, Smith JD, Bis JC, Young K, Johnson LSB, Risch L, Gula LJ, Kwee LC, Chaffin MD, Kühne M, Preuss M, Gupta N, Nafissi NA, Smith NL, Nilsson PM, van der Harst P, Wells QS, Judy RL, Schnabel RB, Johnson R, Smit RAJ, Gabriel S, Knight S, Furukawa T, Blackwell TW, Nauffal V, Wang X, Min YI, Yoneda ZT, Laksman ZWM, Bezzina CR, Alonso A, Psaty BM, Albert CM, Arking DE, Roden DM, Chasman DI, Rader DJ, Conen D, McManus DD, Fatkin D, Benjamin EJ, Boerwinkle E, Marcus GM, Christophersen IE, Smith JG, Roberts JD, Raffield LM, Shoemaker MB, Cho MH, Cutler MJ, Rienstra M, Chung MK, S Olesen M, Sinner MF, Sotoodehnia N, Kirchhof P, Loos RJF, Nazarian S, Mohanty S, Damrauer SM, Kaab S, Heckbert SR, Redline S, Shah SH, Tanaka T, Ebana Y; Regeneron Genetics Center; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Holm H, Stefansson K, Ruff CT, Sabatine MS, Lunetta KL, Lubitz SA, Ellinor PT.

Nat Genet. 2025 Mar 6. doi: 10.1038/s41588-025-02074-9. Online ahead of print.

PMID: 40050430

 

A covalent chemical probe for Chikungunya nsP2 cysteine protease with antialphaviral activity and proteome-wide selectivity. 

Ghoshal A, Tse EG, Hossain MA, Asressu KH, Merten EM, Sears JD, Howell S, Perveen S, Burdick J, Morales NL, Martinez SA, Law I, Davenport BJ, Morrison TE, Streblow ZJ, Streblow DN, Mordant AL, Webb TS, Cabrera A, Herring LE, Arrowsmith CH, Pearce KH, Moorman NJ, Heise MT, Couñago RM, Brown PJ, Willson TM.

Sci Rep. 2025 Mar 1;15(1):7264. doi: 10.1038/s41598-025-91673-x.

PMID: 40025188 Free PMC article.

 

Association Between Polygenic Risk and Symptom Severity Change After Cognitive Behavioral Therapy for Obsessive-Compulsive Disorder. 

Bäckman J, Wallert J, Halvorsen M, Roelstraete B, de Schipper E, Strom NI, Eide TO, Höffler KD, Mattheisen M, Hansen B, Kvale G, Hagen K, Haavik J; Nordic OCD and Related Disorders Consortium (NORDiC); Mataix-Cols D, Rück C, Crowley JJ.

Am J Med Genet B Neuropsychiatr Genet. 2025 Mar 7:e33026. doi: 10.1002/ajmg.b.33026. Online ahead of print.

PMID: 40052195

 

Predictors of new persistent opioid use after surgery in adults. 

Gessner KH, Preisser JS, Pfaff E, Wang R, Walters K, Bradford R, Clark M, Ehlers M, Nielsen M.

Anesthesiol Perioper Sci. 2025;3(1):2. doi: 10.1007/s44254-024-00083-1. Epub 2025 Jan 17.

PMID: 40051586 Free PMC article.

 

Epigenetics as a link between environmental factors and dementia risk. 

Koulouri A, Zannas AS.

J Alzheimers Dis Rep. 2024 Oct 18;8(1):1372-1380. doi: 10.1177/25424823241284227. eCollection 2024.

PMID: 40034348 Free PMC article. Review.

 

A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines. 

Chen Y, Davidson NM, Wan YK, Yao F, Su Y, Gamaarachchi H, Sim A, Patel H, Low HM, Hendra C, Wratten L, Hakkaart C, Sawyer C, Iakovleva V, Lee PL, Xin L, Ng HEV, Loo JM, Ong X, Ng HQA, Wang J, Koh WQC, Poon SYP, Stanojevic D, Tran HD, Lim KHE, Toh SY, Ewels PA, Ng HH, Iyer NG, Thiery A, Chng WJ, Chen L, DasGupta R, Sikic M, Chan YS, Tan BOP, Wan Y, Tam WL, Yu Q, Khor CC, Wüstefeld T, Lezhava A, Pratanwanich PN, Love MI, Goh WSS, Ng SB, Oshlack A; SG-NEx consortium; Göke J.

Nat Methods. 2025 Mar 13. doi: 10.1038/s41592-025-02623-4. Online ahead of print.

PMID: 40082608

 

LILRB3 genetic variation is associated with kidney transplant failure in African American recipients. 

Sun Z, Yi Z, Wei C, Wang W, Ren T, Cravedi P, Tedla F, Ward SC, Azeloglu E, Schrider DR, Li Y, Khan A, Zanoni F, Fu J, Ali S, Liu S, Liang D, Liu T, Li H, Xi C, Vy TH, Mosoyan G, Sun Q, Kumar A, Zhang Z, Farouk S, Campell K, Ochando J, Lee K, Coca S, Xiang J, Connolly P, Gallon L, O’Connell PJ, Colvin R, Menon MC, Nadkarni G, He JC, Kraft M, Jiang X, Zhang X, Kiryluk K, Cherukuri A, Lakkis FG, Zhang W, Chen SH, Heeger PS, Zhang W.

Nat Med. 2025 Mar 10. doi: 10.1038/s41591-025-03568-z. Online ahead of print.

PMID: 40065170

 

TBC1D30 regulates proinsulin and insulin secretion and is the target of a genomic association signal for proinsulin. 

Parsons VA, Vadlamudi S, Voos KM, Rohy AE, Moxley AH, Cannon ME, Rosen JD, Mills CA, Herring LE, Broadaway KA, Lorenzo DN, Mohlke KL.

Diabetologia. 2025 Mar 10. doi: 10.1007/s00125-025-06391-w. Online ahead of print.

PMID: 40064677

 

Prognostic and molecular multi-platform analysis of CALGB 40603 (Alliance) and public triple-negative breast cancer datasets. 

Felsheim BM, Fernandez-Martinez A, Fan C, Pfefferle AD, Hayward MC, Hoadley KA, Rashid NU, Tolaney SM, Somlo G, Carey LA, Sikov WM, Perou CM.

NPJ Breast Cancer. 2025 Mar 8;11(1):24. doi: 10.1038/s41523-025-00740-z.

PMID: 40057511 Free PMC article.

 

Significance in scale space for Hi-C data. 

Liu R, Zhang Z, Won H, Marron JS.

Bioinformatics. 2025 Mar 4;41(3):btaf026. doi: 10.1093/bioinformatics/btaf026.

PMID: 40036585 Free PMC article.

 

Highlights from the breakout session: transcriptomic approaches to the study of systemic vasculitis. 

Ciavatta DJ, Kain R, Inrueangsri N, Croci S, Karabayas M, Zulcinski M, Morgan AW.

Rheumatology (Oxford). 2025 Mar 1;64(Supplement_1):i109-i111. doi: 10.1093/rheumatology/keae387.

PMID: 40071404 Review.

 

A randomized phase II/III study of paclitaxel/carboplatin/metformin versus paclitaxel/carboplatin/placebo as initial therapy for measurable stage III or IVA, stage IVB, or recurrent endometrial cancer: An NRG oncology/GOG study. 

Bae-Jump VL, Sill MW, Gehrig PA, Merker JD, Corcoran DL, Pfefferle AD, Hayward MC, Walker JL, Hagemann AR, Waggoner SE, O’Cearbhaill RE, McDonald ME, Edelson MI, DiSilvestro PA, McNally AL, Fleury A, Littell RD, Ueland FR, Lankes HA, Aghajanian C.

Gynecol Oncol. 2025 Mar 7;195:66-74. doi: 10.1016/j.ygyno.2025.03.003. Online ahead of print.

PMID: 40056832

 

Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A. 

Jain S, Trinidad M, Nguyen TB, Jones K, Neto SD, Ge F, Glagovsky A, Jones C, Moran G, Wang B, Rahimi K, Çalıcı SZ, Cedillo LR, Berardelli S, Özden B, Chen K, Katsonis P, Williams A, Lichtarge O, Rana S, Pradhan S, Srinivasan R, Sajeed R, Joshi D, Faraggi E, Jernigan R, Kloczkowski A, Xu J, Song Z, Özkan S, Padilla N, de la Cruz X, Acuna-Hidalgo R, Grafmüller A, Barrón LTJ, Manfredi M, Savojardo C, Babbi G, Martelli PL, Casadio R, Sun Y, Zhu S, Shen Y, Pucci F, Rooman M, Cia G, Raimondi D, Hermans P, Kwee S, Chen E, Astore C, Kamandula A, Pejaver V, Ramola R, Velyunskiy M, Zeiberg D, Mishra R, Sterling T, Goldstein JL, Lugo-Martinez J, Kazi S, Li S, Long K, Brenner SE, Bakolitsa C, Radivojac P, Suhr D, Suhr T, Clark WT.

Hum Genet. 2025 Mar 8. doi: 10.1007/s00439-025-02731-3. Online ahead of print.

PMID: 40055237

 

Meningeal Lymphatic and Glymphatic Structures in a Pelagic Delphinid (Delphinus delphis). 

Jackson ON, Keenan TF, Nelson-Maney NP, Rommel SA, McLellan WA, Pabst DA, Costidis AM, Caron KM, Kernagis DN, Rotstein DS, Thayer VG, Harms CA, Piscitelli-Doshkov MA, Doshkov P, Schweikert LE, Yopak KE, Braun M, Tift MS.

Animals (Basel). 2025 Mar 4;15(5):729. doi: 10.3390/ani15050729.

PMID: 40076012 Free PMC article.

 

Hepato-selective dihydroquinolizinones active against hepatitis A virus in vitro and in vivo. 

Misumi I, Yue Z, Jiang Z, Karampoori A, Whitmire JK, Cullen JM, Block T, Lemon SM, Du Y, Li Y.

Antiviral Res. 2025 Mar 19:106145. doi: 10.1016/j.antiviral.2025.106145. Online ahead of print.

PMID: 40118118

 

TRIP13 protects pancreatic cancer cells against intrinsic and therapy-induced DNA replication stress. 

Anand JR, Droby GN, Joseph S, Patel U, Zhang X, Klomp JA, Der CJ, Purvis JE, Wolff SC, Bowser JL, Vaziri C.

NAR Cancer. 2025 Mar 20;7(1):zcaf009. doi: 10.1093/narcan/zcaf009. eCollection 2025 Mar.

PMID: 40115747 Free PMC article.

 

Crafted experiments to evaluate feature selection methods for single-cell RNA-seq data. 

Liu S, Corcoran DL, Garcia-Recio S, Marron JS, Perou CM.

NAR Genom Bioinform. 2025 Mar 19;7(1):lqaf023. doi: 10.1093/nargab/lqaf023. eCollection 2025 Mar.

PMID: 40109353 Free PMC article.

 

The Unified Phenotype Ontology : a framework for cross-species integrative phenomics. 

Matentzoglu N, Bello SM, Stefancsik R, Alghamdi SM, Anagnostopoulos AV, Balhoff JP, Balk MA, Bradford YM, Bridges Y, Callahan TJ, Caufield H, Cuzick A, Carmody LC, Caron AR, de Souza V, Engel SR, Fey P, Fisher M, Gehrke S, Grove C, Hansen P, Harris NL, Harris MA, Harris L, Ibrahim A, Jacobsen JOB, Köhler S, McMurry JA, Munoz-Fuentes V, Munoz-Torres MC, Parkinson H, Pendlington ZM, Pilgrim C, Robb SMC, Robinson PN, Seager J, Segerdell E, Smedley D, Sollis E, Toro S, Vasilevsky N, Wood V, Haendel MA, Mungall CJ, McLaughlin JA, Osumi-Sutherland D.

Genetics. 2025 Mar 17;229(3):iyaf027. doi: 10.1093/genetics/iyaf027.

PMID: 40048704 Free PMC article.

 

Characterization of the phenotypic consequences of the Duffy-null genotype. 

Hysong MR, Shuey MM, Huffman JE, Auer P, Reiner A, Raffield LM.

Blood Adv. 2025 Mar 25;9(6):1452-1462. doi: 10.1182/bloodadvances.2024014399.

PMID: 39825822

 

Isogenic comparison of Airn and Xist reveals core principles of Polycomb recruitment by lncRNAs. 

Trotman JB, Abrash EW, Murvin MM, Braceros AK, Li S, Boyson SP, Salcido RT, Cherney RE, Bischoff SR, Kaufmann K, Eberhard QE, Zhang Z, Cowley DO, Calabrese JM.

Mol Cell. 2025 Mar 20;85(6):1117-1133.e14. doi: 10.1016/j.molcel.2025.02.014.

PMID: 40118040

 

Editorial: Global approaches to molecular diagnostics for pediatric cancer. 

Wang JR, Alexander TB.

Front Oncol. 2025 Mar 6;15:1578509. doi: 10.3389/fonc.2025.1578509. eCollection 2025.

PMID: 40115010 Free PMC article. No abstract available.

 

Can Pharmacogenetics Be Used to Predict the Response to Fesoterodine Fumarate? 

Wu JM, Siddiqui NY, Wiltshire T, Voora D, Schmader K.

Urogynecology (Phila). 2025 Feb 14. doi: 10.1097/SPV.0000000000001668. Online ahead of print.

PMID: 40105750

 

Community Collaboration in Public Health Genetic Literacy: Methods for Co-Designing Educational Resources for Equitable Genomics Research and Practice. 

Salunke J, Byfield G, Powell SN, Torres DF, Leon-Lozano G, Jackson J, Orphanides AK, Shaw J, Owens T, Berg JS, Branch E, Caro L, Giric S, O’Daniel JM, Powell BC, Ray K, Robinson C, Schilling S, Shaw N, Song E, Waltz M, Roberts MC, Foreman AKM, Foss K, Milko LV.

Public Health Genomics. 2025;28(1):66-84. doi: 10.1159/000543227. Epub 2024 Dec 19.

PMID: 40144343

 

Demographic and Clinical Factors Associated With SARS-CoV-2 Anti-Nucleocapsid Antibody Response Among Previously Infected US Adults: The C4R Study. 

Demmer RT, Wu C, Kim JS, Sun Y, Balte P, Cushman M, Boyle R, Tracy RP, Styer LM, Bell TD, Anderson MR, Allen NB, Schreiner PJ, Bowler R, Schwartz DA, Lee JS, Xanthakis V, Rock JM, Bievenue R, Pirzada A, Doyle M, Regan EA, Make BJ, Kanaya AM, Kandula NR, Wenzel SE, Coresh J, Isasi CR, Raffield LM, Elkind MSV, Howard VJ, Ortega VE, Woodruff P, Cole SA, Henderson JM, Mantis NJ, Oelsner EC.

Open Forum Infect Dis. 2025 Mar 20;12(3):ofaf123. doi: 10.1093/ofid/ofaf123. eCollection 2025 Mar.

PMID: 40124199 Free PMC article.

 

Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval – Phenotypic inference Evaluation framework. 

Bridges Y, Souza V, Cortes KG, Haendel M, Harris NL, Korn DR, Marinakis NM, Matentzoglu N, McLaughlin JA, Mungall CJ, Odell A, Osumi-Sutherland D, Robinson PN, Smedley D, Jacobsen JOB.

BMC Bioinformatics. 2025 Mar 22;26(1):87. doi: 10.1186/s12859-025-06105-4.

PMID: 40121479 Free PMC article.

 

Rare damaging CCR2 variants are associated with lower lifetime cardiovascular risk. 

Georgakis MK, Malik R, Bounkari OE, Hasbani NR, Li J, Huffman JE, Shakt G, Tack RWP, Kimball TN, Asare Y, Morrison AC, Tsao NL, Judy R, Mitchell BD, Xu H, Montasser ME, Do R, Kenny EE, Loos RJF, Terry JG, Carr JJ, Bis JC, Psaty BM, Longstreth WT, Young KA, Lutz SM, Cho MH, Broome J, Khan AT, Wang FF, Heard-Costa N, Seshadri S, Vasan RS, Palmer ND, Freedman BI, Bowden DW, Yanek LR, Kral BG, Becker LC, Peyser PA, Bielak LF, Ammous F, Carson AP, Hall ME, Raffield LM, Rich SS, Post WS, Tracy RP, Taylor KD, Guo X, Mahaney MC, Curran JE, Blangero J, Clarke SL, Haessler JW, Hu Y, Assimes TL, Kooperberg C, Bernhagen J, Anderson CD, Damrauer SM, Zand R, Rotter JI, de Vries PS, Dichgans M.

Genome Med. 2025 Mar 21;17(1):27. doi: 10.1186/s13073-025-01456-2.

PMID: 40119478 Free PMC article.

 

How people undergoing genomic sequencing interpret and react to varied secondary findings with limited actionability. 

Yan H, Rini CM, Foreman AKM, Berg JS, Henderson GE, Lee K, O’Daniel JM, Roche M, Waltz M.

Per Med. 2025 Apr;22(2):93-101. doi: 10.1080/17410541.2025.2476392. Epub 2025 Mar 18.

PMID: 40100039

 

Lymphatic Activation of ACKR3 Signaling Regulates Lymphatic Response After Ischemic Heart Injury. 

Balint L, Patel S, Serafin DS, Zhang H, Quinn KE, Aghajanian A, Kistner BM, Caron KM.

Arterioscler Thromb Vasc Biol. 2025 Mar 27. doi: 10.1161/ATVBAHA.124.322288. Online ahead of print.

PMID: 40143814

 

Real-time genomic characterization of pediatric acute leukemia using adaptive sampling. 

Geyer J, Opoku KB, Lin J, Ramkissoon L, Mullighan C, Bhakta N, Alexander TB, Wang JR.

Leukemia. 2025 Mar 24. doi: 10.1038/s41375-025-02565-y. Online ahead of print.

PMID: 40128561