Department of Genetics Publications for January 5th – 18th, 2025

Department of Genetics faculty, postdocs, students and collaborators published 18 papers during January 5th – 18th 2025.

 

Response eQTLs, chromatin accessibility, and 3D chromatin structure in chondrocytes provide mechanistic insight into osteoarthritis risk. 

Kramer NE, Byun S, Coryell P, D’Costa S, Thulson E, Kim H, Parkus SM, Bond ML, Klein ER, Shine J, Chubinskaya S, Love MI, Mohlke KL, Diekman BO, Loeser RF, Phanstiel DH.

Cell Genom. 2025 Jan 8;5(1):100738. doi: 10.1016/j.xgen.2024.100738.

PMID: 39788104

 

Gene signatures derived from transcriptomic-causal networks stratify colorectal cancer patients for effective targeted therapy. 

Yazdani A, Lenz HJ, Pillonetto G, Mendez-Giraldez R, Yazdani A, Sanoff H, Hadi R, Samiei E, Venook AP, Ratain MJ, Rashid N, Vincent BG, Qu X, Wen Y, Kosorok M, Symmans WF, Shen JPYC, Lee MS, Kopetz S, Nixon AB, Bertagnolli MM, Perou CM, Innocenti F.

Commun Med (Lond). 2025 Jan 8;5(1):9. doi: 10.1038/s43856-024-00728-z.

PMID: 39779996 Free PMC article.

 

Gaussian processes for time series with lead-lag effects with applications to biology data. 

Mu W, Chen J, Davis ES, Reed K, Phanstiel D, Love MI, Li D.

Biometrics. 2025 Jan 7;81(1):ujae156. doi: 10.1093/biomtc/ujae156.

PMID: 39775854

 

Linking tumor immune infiltration to enhanced longevity in recurrence-free breast cancer. 

Angelats L, Paré L, Rubio-Perez C, Sanfeliu E, González A, Seguí E, Villacampa G, Marín-Aguilera M, Pernas S, Conte B, Albarrán-Fernández V, Martínez-Sáez O, Aguirre Á, Galván P, Fernandez-Martinez A, Cobo S, Rey M, Martínez-Romero A, Walbaum B, Schettini F, Vidal M, Buckingham W, Muñoz M, Adamo B, Agrawal Y, Guedan S, Pascual T, Agudo J, Grzelak M, Borcherding N, Heyn H, Vivancos A, Parker JS, Villagrasa P, Perou CM, Prat A, Brasó-Maristany F.

ESMO Open. 2025 Jan 6;10(1):104109. doi: 10.1016/j.esmoop.2024.104109. Online ahead of print.

PMID: 39765189

 

The expected polygenic risk score (ePRS) framework: an equitable metric for quantifying polygenetic risk via modeling of ancestral makeup. 

Huang YJ, Kurniansyah N, Goodman MO, Spitzer BW, Wang J, Stilp A, Laurie C, de Vries PS, Chen H, Min YI, Sims M, Peloso GM, Guo X, Bis JC, Brody JA, Raffield LM, Smith JA, Zhao W, Rotter JI, Rich SS, Redline S, Fornage M, Kaplan R, Franceschini N, Levy D, Morrison AC, Boerwinkle E, Smith NL, Kooperberg C, Psaty BM, Zöllner S; Trans-Omics in Precision Medicine Consortium; Sofer T.

medRxiv [Preprint]. 2024 Dec 20:2024.03.05.24303738. doi: 10.1101/2024.03.05.24303738.

PMID: 39763564 Free PMC article. Preprint.

 

Functions of the Bloom Syndrome Helicase N-terminal Intrinsically Disordered Region. 

Bereda CC, Dewey EB, Nasr MA, Chirasani VR, Sekelsky J.

Genetics. 2025 Jan 10:iyaf005. doi: 10.1093/genetics/iyaf005. Online ahead of print.

PMID: 39792594

 

Precision Opioid Prescription in ICU Surgery: Insights from an Interpretable Deep Learning Framework. 

Zhu X, Luria I, Tighe P, Zou F, Zou B.

J Surg (Lisle). 2024;9(15):11189. doi: 10.29011/2575-9760.11189. Epub 2024 Nov 27.

PMID: 39781484 Free PMC article.

 

Rho(D) immune globulin shortage and fetal Rh(D) screening with cell-free DNA. 

Grace MR, Goodhue B, Vora NL.

Curr Opin Obstet Gynecol. 2024 Dec 30. doi: 10.1097/GCO.0000000000001011. Online ahead of print.

PMID: 39774459

 

Cell-free DNA Screening and Maternal Cancer. 

Vora NL.

N Engl J Med. 2024 Dec 5;391(22):2168-2169. doi: 10.1056/NEJMe2412259.

PMID: 39774319 No abstract available.

 

X-Chromosome-Linked miRNAs Regulate Sex Differences in Cardiac Physiology. 

Emerson JI, Shi W, Paredes-Larios J, Walker WG, Hutton JE, Cristea IM, Marzluff WF, Conlon FL.

Circ Res. 2024 Dec 30. doi: 10.1161/CIRCRESAHA.124.325447. Online ahead of print.

PMID: 39772608

 

SLC35A2 loss of function variants affect glycomic signatures, neuronal fate, and network dynamics. 

Lai D, Sosicka P, Williams DJ, Bowyer ME, Ressler AK, Kohrt SE, Muron SJ, Crino PB, Freeze HH, Boland MJ, Heinzen EL.

bioRxiv [Preprint]. 2024 Dec 27:2024.12.27.630524. doi: 10.1101/2024.12.27.630524.

PMID: 39763953 Free PMC article. Preprint.

 

Cranial, Renal, and Skeletal Anomalies in a Fetus With a Pathogenic Variant in the TAFAZZIN Gene. 

Muir CR, Gilmore KL, Singh S, Vora NL.

Prenat Diagn. 2025 Jan 5. doi: 10.1002/pd.6736. Online ahead of print.

PMID: 39757347

 

Mitochondria and NLRP3: To die or inflame. 

Yang S, Huang G, Ting JP.

Immunity. 2025 Jan 14;58(1):5-7. doi: 10.1016/j.immuni.2024.12.007.

PMID: 39813994

 

General Kernel Machine Methods for Multi-Omics Integration and Genome-Wide Association Testing With Related Individuals. 

Little A, Zhao N, Mikhaylova A, Zhang A, Ling W, Thibord F, Johnson AD, Raffield LM, Curran JE, Blangero J, O’Connell JR, Xu H, Rotter JI, Rich SS, Rice KM, Chen MH, Reiner A, Kooperberg C, Vu T, Hou L, Fornage M, Loos RJF, Kenny E, Mathias R, Becker L, Smith AV, Boerwinkle E, Yu B, Thornton T, Wu MC.

Genet Epidemiol. 2025 Jan;49(1):e22610. doi: 10.1002/gepi.22610.

PMID: 39812506

 

Genomic and phenotypic correlates of mosaic loss of chromosome Y in blood. 

Jakubek YA, Ma X, Stilp AM, Yu F, Bacon J, Wong JW, Aguet F, Ardlie K, Arnett DK, Barnes K, Bis JC, Blackwell T, Becker LC, Boerwinkle E, Bowler RP, Budoff MJ, Carson AP, Chen J, Cho MH, Coresh J, Cox NJ, de Vries PS, DeMeo DL, Fardo DW, Fornage M, Guo X, Hall ME, Heard-Costa N, Hidalgo B, Irvin MR, Johnson AD, Jorgenson E, Kenny EE, Kessler MD, Levy D, Li Y, Lima JAC, Liu Y, Locke AE, Loos RJF, Machiela MJ, Mathias RA, Mitchell BD, Murabito JM, Mychaleckyj JC, North KE, Orchard P, Parker SCJ, Pershad Y, Peyser PA, Pratte KA, Psaty BM, Raffield LM, Redline S; Regeneron Genetics Center; Rich SS, Rotter JI, Shah SJ, Smith JA, Smith AP, Smith A, Taub MA, Tiwari HK, Tracy R, Tuftin B; NHLBI Trans-Omics for Precision Medicine Consortium; Bick AG, Sankaran VG, Reiner AP, Scheet P, Auer PL.

Am J Hum Genet. 2025 Jan 6:S0002-9297(24)00456-7. doi: 10.1016/j.ajhg.2024.12.014. Online ahead of print.

PMID: 39809269

 

Design and implementation of an action plan for justice, equity, diversity, and inclusion within the Clinical Genome Resource. 

Popejoy AB, Ritter DI, Azzariti D, Berg JS, Bulkley JE, Cho M, Gonzaga-Jauregui C, Klein TE, Martschenko DO, Oni-Orisan A, Ramos EM, Rehm HL, Riggs ER, Wright MW, Yudell M, Plon SE, Morales J.

Am J Hum Genet. 2025 Jan 7:S0002-9297(24)00451-8. doi: 10.1016/j.ajhg.2024.12.009. Online ahead of print.

PMID: 39793579 Review.

 

Atp1a2 and Kcnj9 Are Candidate Genes Underlying Sensitivity to Oxycodone-Induced Locomotor Activation and Withdrawal-Induced Anxiety-Like Behaviors in C57BL/6 Substrains. 

Goldberg LR, Baskin BM, Beierle JA, Adla Y, Kelliher JC, Yao EJ, Kirkpatrick SL, Reed ER, Jenkins DF, Cox J, Luong AM, Luttik KP, Scotellaro JA, Drescher TA, Crotts SB, Yazdani N, Ferris MT, Johnson WE, Mulligan MK, Bryant CD.

Genes Brain Behav. 2025 Feb;24(1):e70009. doi: 10.1111/gbb.70009.

PMID: 39801366 Free PMC article.

 

A deep learning feature importance test framework for integrating informative high-dimensional biomarkers to improve disease outcome prediction. 

Zou B, Xenakis JG, Xiao M, Ribeiro A, Divaris K, Wu D, Zou F.

Brief Bioinform. 2024 Nov 22;26(1):bbae709. doi: 10.1093/bib/bbae709.

PMID: 39815828 Free PMC article.