Department of Genetics Publications for June 5th – 18th, 2022

Department of Genetics faculty, postdocs, students and collaborators published 16 papers during June 5^th – 18^th, 2022.

 

SnapHiC2: A computationally efficient loop caller for single cell Hi-C data. 

Li X, Lee L, Abnousi A, Yu M, Liu W, Huang L, Li Y, Hu M.

Comput Struct Biotechnol J. 2022 Jun 1;20:2778-2783. doi: 10.1016/j.csbj.2022.05.046. eCollection 2022.

PMID: 35685374 Free PMC article.

 

Association of protein function-altering variants with cardiometabolic traits: the strong heart study. 

Shan Y, Cole SA, Haack K, Melton PE, Best LG, Bizon C, Kobes S, Köroğlu Ç, Baier LJ, Hanson RL, Sanna S, Li Y, Franceschini N.

Sci Rep. 2022 Jun 4;12(1):9317. doi: 10.1038/s41598-022-12866-2.

PMID: 35665752 Free PMC article.

 

Using liver models generated from human-induced pluripotent stem cells (iPSCs) for evaluating chemical-induced modifications and disease across liver developmental stages. 

Carberry CK, Ferguson SS, Beltran AS, Fry RC, Rager JE.

Toxicol In Vitro. 2022 Jun 7:105412. doi: 10.1016/j.tiv.2022.105412. Online ahead of print.

PMID: 35688329 Review.

 

Clinical Testing for Tumor Cell-Free DNA. 

Devereaux KA, Souers RJ, Merker JD, Lindeman NI, Graham RP, Hameed MR, Vasalos P, Moncur JT, Lockwood CM, Xian RR.

Arch Pathol Lab Med. 2022 Jun 10. doi: 10.5858/arpa.2021-0585-CP. Online ahead of print.

PMID: 35687785

 

Four-Year Laboratory Performance of the First College of American Pathologists In Silico Next-Generation Sequencing Bioinformatics Proficiency Testing Surveys. 

Furtado LV, Souers RJ, Vasalos P, Halley JG, Aisner DL, Nagarajan R, Voelkerding KV, Merker JD, Konnick EQ.

Arch Pathol Lab Med. 2022 Jun 7. doi: 10.5858/arpa.2021-0384-CP. Online ahead of print.

PMID: 35671151

 

A hierarchical spike-and-slab model for pan-cancer survival using pan-omic data. 

Samorodnitsky S, Hoadley KA, Lock EF.

BMC Bioinformatics. 2022 Jun 17;23(1):235. doi: 10.1186/s12859-022-04770-3.

PMID: 35710340

 

Lessons learned and recommendations for data coordination in collaborative research: The CSER consortium experience. 

Muenzen KD, Amendola LM, Kauffman TL, Mittendorf KF, Bensen JT, Chen F, Green R, Powell BC, Kvale M, Angelo F, Farnan L, Fullerton SM, Robinson JO, Li T, Murali P, Lawlor JMJ, Ou J, Hindorff LA, Jarvik GP, Crosslin DR.

HGG Adv. 2022 May 20;3(3):100120. doi: 10.1016/j.xhgg.2022.100120. eCollection 2022 Jul 14.

PMID: 35707062 Free PMC article.

 

Caspase-7 activates ASM to repair gasdermin and perforin pores. 

Nozaki K, Maltez VI, Rayamajhi M, Tubbs AL, Mitchell JE, Lacey CA, Harvest CK, Li L, Nash WT, Larson HN, McGlaughon BD, Moorman NJ, Brown MG, Whitmire JK, Miao EA.

Nature. 2022 Jun 15. doi: 10.1038/s41586-022-04825-8. Online ahead of print.

PMID: 35705808

 

Protective and aggressive bacterial subsets and metabolites modify hepatobiliary inflammation and fibrosis in a murine model of PSC. 

Awoniyi M, Wang J, Ngo B, Meadows V, Tam J, Viswanathan A, Lai Y, Montgomery S, Farmer M, Kummen M, Thingholm L, Schramm C, Bang C, Franke A, Lu K, Zhou H, Bajaj JS, Hylemon PB, Ting J, Popov YV, Hov JR, Francis HL, Sartor RB.

Gut. 2022 Jun 15:gutjnl-2021-326500. doi: 10.1136/gutjnl-2021-326500. Online ahead of print.

PMID: 35705368

 

Impact of schizophrenia GWAS loci converge onto distinct pathways in cortical interneurons vs glutamatergic neurons during development. 

Liu D, Zinski A, Mishra A, Noh H, Park GH, Qin Y, Olorife O, Park JM, Abani CP, Park JS, Fung J, Sawaqed F, Coyle JT, Stahl E, Bendl J, Fullard JF, Roussos P, Zhang X, Stanton PK, Yin C, Huang W, Kim HY, Won H, Cho JH, Chung S.

Mol Psychiatry. 2022 Jun 14. doi: 10.1038/s41380-022-01654-z. Online ahead of print.

PMID: 35701597

 

Prognostic significance of RNA-based TP53 pathway function among estrogen receptor positive and negative breast cancer cases. 

Hurson AN, Abubakar M, Hamilton AM, Conway K, Hoadley KA, Love MI, Olshan AF, Perou CM, Garcia-Closas M, Troester MA.

NPJ Breast Cancer. 2022 Jun 14;8(1):74. doi: 10.1038/s41523-022-00437-7.

PMID: 35701440 Free PMC article.

 

Differential and shared genetic effects on kidney function between diabetic and non-diabetic individuals. 

Winkler TW, Rasheed H, Teumer A, Gorski M, Rowan BX, Stanzick KJ, Thomas LF, Tin A, Hoppmann A, Chu AY, Tayo B, Thio CHL, Cusi D, Chai JF, Sieber KB, Horn K, Li M, Scholz M, Cocca M, Wuttke M, van der Most PJ, Yang Q, Ghasemi S, Nutile T, Li Y, Pontali G, Günther F, Dehghan A, Correa A, Parsa A, Feresin A, de Vries APJ, Zonderman AB, Smith AV, Oldehinkel AJ, De Grandi A, Rosenkranz AR, Franke A, Teren A, Metspalu A, Hicks AA, Morris AP, Tönjes A, Morgan A, Podgornaia AI, Peters A, Körner A, Mahajan A, Campbell A, Freedman BI, Spedicati B, Ponte B, Schöttker B, Brumpton B, Banas B, Krämer BK, Jung B, Åsvold BO, Smith BH, Ning B, Penninx BWJH, Vanderwerff BR, Psaty BM, Kammerer CM, Langefeld CD, Hayward C, Spracklen CN, Robinson-Cohen C, Hartman CA, Lindgren CM, Wang C, Sabanayagam C, Heng CK, Lanzani C, Khor CC, Cheng CY, Fuchsberger C, Gieger C, Shaffer CM, Schulz CA, Willer CJ, Chasman DI, Gudbjartsson DF, Ruggiero D, Toniolo D, Czamara D, Porteous DJ, Waterworth DM, Mascalzoni D, Mook-Kanamori DO, Reilly DF, Daw EW, Hofer E, Boerwinkle E, Salvi E, Bottinger EP, Tai ES, Catamo E, Rizzi F, Guo F, Rivadeneira F, Guilianini F, Sveinbjornsson G, Ehret G, Waeber G, Biino G, Girotto G, Pistis G, Nadkarni GN, Delgado GE, Montgomery GW, Snieder H, Campbell H, White HD, Gao H, Stringham HM, Schmidt H, Li H, Brenner H, Holm H, Kirsten H, Kramer H, Rudan I, Nolte IM, Tzoulaki I, Olafsson I, Martins J, Cook JP, Wilson JF, Halbritter J, Felix JF, Divers J, Kooner JS, Lee JJ, O’Connell J, Rotter JI, Liu J, Xu J, Thiery J, Ärnlöv J, Kuusisto J, Jakobsdottir J, Tremblay J, Chambers JC, Whitfield JB, Gaziano JM, Marten J, Coresh J, Jonas JB, Mychaleckyj JC, Christensen K, Eckardt KU, Mohlke KL, Endlich K, Dittrich K, Ryan KA, Rice KM, Taylor KD, Ho K, Nikus K, Matsuda K, Strauch K, Miliku K, Hveem K, Lind L, Wallentin L, Yerges-Armstrong LM, Raffield LM, Phillips LS, Launer LJ, Lyytikäinen LP, Lange LA, Citterio L, Klaric L, Ikram MA, Ising M, Kleber ME, Francescatto M, Concas MP, Ciullo M, Piratsu M, Orho-Melander M, Laakso M, Loeffler M, Perola M, de Borst MH, Gögele M, Bianca M, Lukas MA, Feitosa MF, Biggs ML, Wojczynski MK, Kavousi M, Kanai M, Akiyama M, Yasuda M, Nauck M, Waldenberger M, Chee ML, Chee ML, Boehnke M, Preuss MH, Stumvoll M, Province MA, Evans MK, O’Donoghue ML, Kubo M, Kähönen M, Kastarinen M, Nalls MA, Kuokkanen M, Ghanbari M, Bochud M, Josyula NS, Martin NG, Tan NYQ, Palmer ND, Pirastu N, Schupf N, Verweij N, Hutri-Kähönen N, Mononen N, Bansal N, Devuyst O, Melander O, Raitakari OT, Polasek O, Manunta P, Gasparini P, Mishra PP, Sulem P, Magnusson PKE, Elliott P, Ridker PM, Hamet P, Svensson PO, Joshi PK, Kovacs P, Pramstaller PP, Rossing P, Vollenweider P, van der Harst P, Dorajoo R, Sim RZH, Burkhardt R, Tao R, Noordam R, Mägi R, Schmidt R, de Mutsert R, Rueedi R, van Dam RM, Carroll RJ, Gansevoort RT, Loos RJF, Felicita SC, Sedaghat S, Padmanabhan S, Freitag-Wolf S, Pendergrass SA, Graham SE, Gordon SD, Hwang SJ, Kerr SM, Vaccargiu S, Patil SB, Hallan S, Bakker SJL, Lim SC, Lucae S, Vogelezang S, Bergmann S, Corre T, Ahluwalia TS, Lehtimäki T, Boutin TS, Meitinger T, Wong TY, Bergler T, Rabelink TJ, Esko T, Haller T, Thorsteinsdottir U, Völker U, Foo VHX, Salomaa V, Vitart V, Giedraitis V, Gudnason V, Jaddoe VWV, Huang W, Zhang W, Wei WB, Kiess W, März W, Koenig W, Lieb W, Gao X, Sim X, Wang YX, Friedlander Y, Tham YC, Kamatani Y, Okada Y, Milaneschi Y, Yu Z; Lifelines cohort study; DiscovEHR/MyCode study; VA Million Veteran Program, Stark KJ, Stefansson K, Böger CA, Hung AM, Kronenberg F, Köttgen A, Pattaro C, Heid IM.

Commun Biol. 2022 Jun 13;5(1):580. doi: 10.1038/s42003-022-03448-z.

PMID: 35697829 Free PMC article.

 

EPIC: Inferring relevant cell types for complex traits by integrating genome-wide association studies and single-cell RNA sequencing. 

Wang R, Lin DY, Jiang Y.

PLoS Genet. 2022 Jun 16;18(6):e1010251. doi: 10.1371/journal.pgen.1010251. Online ahead of print.

PMID: 35709291

 

Race reporting and disparities regarding clinical trials in bladder cancer: a systematic review. 

Freudenburg E, Bagheri I, Srinivas S, Martinez A, Putluri N, Klaassen Z, Kamat AM, Konety BR, Kim WY, Dyrskjøt L, McConkey DJ, Freedland SJ, Black PC, Daneshmand S, Catto JWF, Williams SB.

Cancer Causes Control. 2022 Jun 14. doi: 10.1007/s10552-022-01593-8. Online ahead of print.

PMID: 35699798

 

A mixed-effects two-part model for twin-data and an application on identifying important factors associated with extremely preterm children’s health disorders. 

Zou B, Santos HP, Xenakis JG, O’Shea MM, Fry RC, Zou F.

PLoS One. 2022 Jun 13;17(6):e0269630. doi: 10.1371/journal.pone.0269630. eCollection 2022.

PMID: 35696398 Free PMC article.

 

TwinEQTL: Ultra Fast and Powerful Association Analysis for eQTL and GWAS in Twin Studies. 

Xia K, Shabalin AA, Yin Z, Chung W, Sullivan PF, Wright FA, Styner M, Gilmore JH, Santelli RC, Zou F.

Genetics. 2022 Jun 11:iyac088. doi: 10.1093/genetics/iyac088. Online ahead of print.

PMID: 35689615