Department of Genetics Publications for August 18th – 31st, 2024

Department of Genetics faculty, postdocs, students and collaborators published 18 papers during August 18th – 31st, 2024.

 

Liver eQTL meta-analysis illuminates potential molecular mechanisms of cardiometabolic traits. 

Broadaway KA, Brotman SM, Rosen JD, Currin KW, Alkhawaja AA, Etheridge AS, Wright F, Gallins P, Jima D, Zhou YH, Love MI, Innocenti F, Mohlke KL.

Am J Hum Genet. 2024 Aug 18:S0002-9297(24)00261-1. doi: 10.1016/j.ajhg.2024.07.017. Online ahead of print.

PMID: 39173627

 

Measure of Strength of Evidence for Visually Observed Differences between Subpopulations. 

Yang X, Hannig J, Hoadley KA, Carmichael I, Marron JS.

J Comput Graph Stat. 2024;33(2):736-748. doi: 10.1080/10618600.2023.2276113. Epub 2023 Dec 26.

PMID: 39170642

 

Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis. 

Aygün N, Vuong C, Krupa O, Mory J, Le BD, Valone JM, Liang D, Shafie B, Zhang P, Salinda A, Wen C, Gandal MJ, Love MI, Torre-Ubieta L, Stein JL.

Am J Hum Genet. 2024 Aug 10:S0002-9297(24)00259-3. doi: 10.1016/j.ajhg.2024.07.015. Online ahead of print.

PMID: 39168119

 

Generating Clinical-Grade Gene-Disease Validity Classifications Through the ClinGen Data Platforms. 

Wright MW, Thaxton CL, Nelson T, DiStefano MT, Savatt JM, Brush MH, Cheung G, Mandell ME, Wulf B, Ward TJ, Goehringer S, O’Neill T, Weller P, Preston CG, Keseler IM, Goldstein JL, Strande NT, McGlaughon J, Azzariti DR, Cordova I, Dziadzio H, Babb L, Riehle K, Milosavljevic A, Martin CL, Rehm HL, Plon SE, Berg JS, Riggs ER, Klein TE.

Annu Rev Biomed Data Sci. 2024 Aug;7(1):31-50. doi: 10.1146/annurev-biodatasci-102423-112456. Epub 2024 Jul 24.

PMID: 38663031 Review.

 

Transcriptome profiling of pediatric extracranial solid tumors and lymphomas enables rapid low-cost diagnostic classification. 

Opoku KB, Santiago T, Kumar P, Roush SM, Fedoriw Y, Tomoka T, Leventaki V, Furtado LV, Bhakta N, Alexander TB, Wang JR.

Sci Rep. 2024 Aug 21;14(1):19456. doi: 10.1038/s41598-024-70541-0.

PMID: 39169157 Free PMC article.

 

The challenges and opportunities of offering and integrating training in clinical molecular genetics and clinical cytogenetics: A survey of LGG Fellowship Program Directors. 

Deignan JL, Aggarwal V, Bale AE, Bellissimo DB, Booker JK, Cao Y, Crooks KR, Deak KL, Del Gaudio D, Funke B, Hoppman NL, Horner V, Hufnagel RB, Jackson-Cook C, Koduru P, Leung ML, Li S, Liu P, Luo M, Mao R, Mason-Suares H, Mikhail FM, Moore SR, Naeem RC, Pollard LM, Repnikova EA, Shao L, Shaw BM, Shetty S, Smolarek TA, Spiteri E, Van Ziffle J, Vance GH, Vnencak-Jones CL, Williams ES.

Genet Med Open. 2024;2:101820. doi: 10.1016/j.gimo.2024.101820. Epub 2024 Feb 1.

PMID: 39175871 Free PMC article.

 

Towards Preanalytical Best Practices for Liquid Biopsy Studies: A BLOODPAC Landscape Analysis. 

Lockwood CM, Merker JD, Bain E, Compton C, Grossman RL, Johann D, Jones F, Jones G, Kreifels M, LeBlang S, Lee JSH, Lyle J, Martini JF, Saunders L, Scher H, Somiari S, Stewart M, Vinson J, Leiman LC.

Clin Pharmacol Ther. 2024 Aug 20. doi: 10.1002/cpt.3416. Online ahead of print.

PMID: 39164947 Review.

 

Design of the SPIROMICS Study of Early COPD Progression: SOURCE Study. 

Curtis JL, Bateman LA, Murray S, Couper DJ, Labaki WW, Freeman CM, Arnold KB, Christenson SA, Alexis NE, Kesimer M, Boucher RC, Kaner RJ, Barjaktarevic I, Cooper CB, Hoffman EA, Barr RG, Bleecker ER, Bowler RP, Comellas A, Dransfield MT, Freedman MB, Hansel NN, Krishnan JA, Marchetti N, Meyers DA, Ohar J, O’Neal WK, Ortega VE, Paine Iii R, Peters SP, Smith BM, Wedzicha JA, Wells JM, Woodruff PG, Han MK, Martinez FJ.

Chronic Obstr Pulm Dis. 2024 Aug 16. doi: 10.15326/jcopdf.2023.0490. Online ahead of print.

PMID: 39159077

 

Nodal Response and Survival After Neoadjuvant Endocrine Therapy in Hormone Receptor-Positive Breast Cancer: 20-Year Experience from a Single Institution. 

An SJ, Thai CHNC, Ismail S, Agala CB, Hoang V, Feeney T, Lillie M, Wheless A, Selfridge JM, Ollila DW, Gallagher KK, Carey LA, Spanheimer PM.

Ann Surg Oncol. 2024 Aug 17. doi: 10.1245/s10434-024-16059-1. Online ahead of print.

PMID: 39154153

 

Adjuvants restore colistin sensitivity in mouse models of highly colistin-resistant isolates, limiting bacterial proliferation and dissemination. 

Koller BH, Jania LA, Li H, Barker WT, Melander RJ, Melander C.

Antimicrob Agents Chemother. 2024 Aug 28:e0067124. doi: 10.1128/aac.00671-24. Online ahead of print.

PMID: 39194205

 

Host response to influenza infections in human blood: association of influenza severity with host genetics and transcriptomic response. 

Schughart K, Smith AM, Tsalik EL, Threlkeld SC, Sellers S, Fischer WA 2nd, Schreiber J, Lücke E, Cornberg M, Debarry J, Woods CW, McClain MT, Heise M.

Front Immunol. 2024 Aug 13;15:1385362. doi: 10.3389/fimmu.2024.1385362. eCollection 2024.

PMID: 39192977 Free PMC article.

 

A single-dose intranasal live-attenuated codon deoptimized vaccine provides broad protection against SARS-CoV-2 and its variants. 

Liu X, Ng WH, Zusinaite E, Freitas J, Taylor A, Yerragunta V, Aavula SM, Gorriparthi S, Ponsekaran S, Bonda RL, Mani P, Nimmagadda SV, Wang S, Lello LS, Zaid A, Dua U, Taft-Benz SA, Anderson E, Baxter VK, Sarkar S, Ling ZL, Ashhurst TM, Cheng SMS, Pattnaik P, Kanakasapapathy AK, Baric RS, Burt FJ, Peiris M, Heise MT, King NJC, Merits A, Lingala R, Mahalingam S.

Nat Commun. 2024 Aug 26;15(1):7225. doi: 10.1038/s41467-024-51535-y.

PMID: 39187479 Free PMC article.

 

Stain SAN: simultaneous augmentation and normalization for histopathology images. 

Kim T, Li Y, Calhoun BC, Thennavan A, Carey LA, Symmans WF, Troester MA, Perou CM, Marron JS.

J Med Imaging (Bellingham). 2024 Jul;11(4):044006. doi: 10.1117/1.JMI.11.4.044006. Epub 2024 Aug 23.

PMID: 39185474

 

Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture. 

Glass MR, Waxman EA, Yamashita S, Lafferty M, Beltran AA, Farah T, Patel NK, Singla R, Matoba N, Ahmed S, Srivastava M, Drake E, Davis LT, Yeturi M, Sun K, Love MI, Hashimoto-Torii K, French DL, Stein JL.

Stem Cell Reports. 2024 Aug 6:S2213-6711(24)00217-0. doi: 10.1016/j.stemcr.2024.07.008. Online ahead of print.

PMID: 39178845

 

Renal Cell Carcinoma: A Review. 

Rose TL, Kim WY.

JAMA. 2024 Aug 28. doi: 10.1001/jama.2024.12848. Online ahead of print.

PMID: 39196544

 

CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression. 

Lewis MW, King CM, Wisniewska K, Regner MJ, Coffey A, Kelly MR, Mendez-Giraldez R, Davis ES, Phanstiel DH, Franco HL.

Cancer Res. 2024 Aug 26. doi: 10.1158/0008-5472.CAN-23-3995. Online ahead of print.

PMID: 39186674

 

Age-associated contraction of tumor-specific T cells impairs antitumor immunity. 

Georgiev P, Han S, Huang AY, Nguyen TH, Drijvers JM, Creasey H, Pereira JA, Yao CH, Park JS, Conway TS, Fung ME, Liang D, Peluso M, Joshi S, Rowe JH, Miller BC, Freeman GJ, Sharpe AH, Haigis MC, Ringel AE.

Cancer Immunol Res. 2024 Aug 24. doi: 10.1158/2326-6066.CIR-24-0463. Online ahead of print.

PMID: 39186561

 

PurIST Pancreatic Cancer Classifier: Analytic Validation of a 16-RNA Expression Signature Distinguishing Basal and Classical Subtypes. 

Li Y, Merker JD, Kshatriya R, Trembath DG, Morrison AB, Kuhlers PC, Rashid NU, Yeh JJ, Gulley ML.

J Mol Diagn. 2024 Aug 22:S1525-1578(24)00180-6. doi: 10.1016/j.jmoldx.2024.07.002. Online ahead of print.

PMID: 39181325