Department of Genetics Publications for Oct. 7-20, 2018

Department of Genetics faculty, postdocs, students and collaborators published ten papers during Oct. 7-20, 2018.

ClinGen Variant Curation Expert Panel experiences and standardized processes for disease and gene-level specification of the ACMG/AMP guidelines for sequence variant interpretation.

Rivera-Muñoz EA, Milko LV, Harrison SM, Azzariti DR, Kurtz CL, Lee K, Mester JL, Weaver MA, Currey E, Craigen W, Eng C, Funke B, Hegde M, Hershberger RE, Mao R, Steiner RD, Vincent LM, Martin CL, Plon SE, Ramos E, Rehm HL, Watson M, Berg JS.

Hum Mutat. 2018 Nov;39(11):1614-1622. doi: 10.1002/humu.23645.

PMID: 30311389

Evidence-based assessments of clinical actionability in the context of secondary findings: Updates from ClinGen’s Actionability Working Group.

Webber EM, Hunter JE, Biesecker LG, Buchanan AH, Clarke EV, Currey E, Dagan-Rosenfeld O, Lee K, Lindor NM, Martin CL, Milosavljevic A, Mittendorf KF, Muessig KR, O’Daniel JM, Patel RY, Ramos EM, Rego S, Slavotinek AM, Sobriera NLM, Weaver MA, Williams MS, Evans JP, Goddard KAB; ClinGen Resource.

Hum Mutat. 2018 Nov;39(11):1677-1685. doi: 10.1002/humu.23631.

PMID: 30311382

The progression of the ClinGen gene clinical validity classification over time.

McGlaughon JL, Goldstein JL, Thaxton C, Hemphill SE, Berg JS.

Hum Mutat. 2018 Nov;39(11):1494-1504. doi: 10.1002/humu.23604.

PMID: 30311372

Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis.

Gralinski LE, Sheahan TP, Morrison TE, Menachery VD, Jensen K, Leist SR, Whitmore A, Heise MT, Baric RS.

MBio. 2018 Oct 9;9(5). pii: e01753-18. doi: 10.1128/mBio.01753-18.

PMID: 30301856

Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps.

Mahajan A, Taliun D, Thurner M, Robertson NR, Torres JM, Rayner NW, Payne AJ, Steinthorsdottir V, Scott RA, Grarup N, Cook JP, Schmidt EM, Wuttke M, Sarnowski C, Mägi R, Nano J, Gieger C, Trompet S, Lecoeur C, Preuss MH, Prins BP, Guo X, Bielak LF, Below JE, Bowden DW, Chambers JC, Kim YJ, Ng MCY, Petty LE, Sim X, Zhang W, Bennett AJ, Bork-Jensen J, Brummett CM, Canouil M, Ec Kardt KU, Fischer K, Kardia SLR, Kronenberg F, Läll K, Liu CT, Locke AE, Luan J, Ntalla I, Nylander V, Schönherr S, Schurmann C, Yengo L, Bottinger EP, Brandslund I, Christensen C, Dedoussis G, Florez JC, Ford I, Franco OH, Frayling TM, Giedraitis V, Hackinger S, Hattersley AT, Herder C, Ikram MA, Ingelsson M, Jørgensen ME, Jørgensen T, Kriebel J, Kuusisto J, Ligthart S, Lindgren CM, Linneberg A, Lyssenko V, Mamakou V, Meitinger T,Mohlke KL, Morris AD, Nadkarni G, Pankow JS, Peters A, Sattar N, Stančáková A, Strauch K, Taylor KD, Thorand B, Thorleifsson G, Thorsteinsdottir U, Tuomilehto J, Witte DR, Dupuis J, Peyser PA, Zeggini E, Loos RJF, Froguel P, Ingelsson E, Lind L, Groop L, Laakso M, Collins FS, Jukema JW, Palmer CNA, Grallert H, Metspalu A, Dehghan A, Köttgen A, Abecasis GR, Meigs JB, Rotter JI, Marchini J, Pedersen O, Hansen T, Langenberg C, Wareham NJ, Stefansson K, Gloyn AL, Morris AP, Boehnke M, McCarthy MI.

Nat Genet. 2018 Oct 8. doi: 10.1038/s41588-018-0241-6. [Epub ahead of print]

PMID: 30297969

Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline CDH1 sequence variants.

Lee K, Krempely K, Roberts ME, Anderson MJ, Carneiro F, Chao E, Dixon K, Figueiredo J, Ghosh R, Huntsman D, Kaurah P, Kesserwan C, Landrith T, Li S, Mensenkamp AR, Oliveira C, Pardo C, Pesaran T, Richardson M, Slavin TP, Spurdle AB, Trapp M, Witkowski L, Yi CS, Zhang L, Plon SE, Schrader KA, Karam R.

Hum Mutat. 2018 Nov;39(11):1553-1568. doi: 10.1002/humu.23650.

PMID: 30311375

ClinGen Allele Registry links information about genetic variants.

Pawliczek P, Patel RY, Ashmore LR, Jackson AR, Bizon C, Nelson T, Powell B, Freimuth RR, Strande N, Shah N, Paithankar S, Wright MW, Dwight S, Zhen J, Landrum M, McGarvey P, Babb L, Plon SE, Milosavljevic A; Clinical Genome (ClinGen) Resource.

Hum Mutat. 2018 Nov;39(11):1690-1701. doi: 10.1002/humu.23637.

PMID: 30311374

Integrative Molecular Characterization of Malignant Pleural Mesothelioma.

Hmeljak J, Sanchez-Vega F, Hoadley KA, Shih J, Stewart C, Heiman DI, Tarpey P, Danilova L, Drill E, Gibb EA, Bowlby R, Kanchi R, Osmanbeyoglu HU, Sekido Y, Takeshita J, Newton Y, Graim K, Gupta M, Gay CM, Diao L, Gibbs DL, Thorsson V, Iype L, Kantheti HS, Severson DT, Ravegnini G, Desmeules P, Jungbluth AA, Travis WD, Dacic S, Chirieac LR, Galateau-Salle F, Fujimoto J, Husain AN, Silveira HC, Rusch VW, Rintoul RC, Pass H, Kindler H, Zauderer MG, Kwiatkowski DJ, Bueno R, Tsao AS, Creaney J, Lichtenberg T, Leraas K, Bowen J, Research Network T, Felau I, Zenklusen JC, Akbani R, Cherniack AD, Byers LA, Noble MS, Fletcher JA, Robertson G, Shen R, Aburatani H, Robinson BW, Campbell P, Ladanyi M.

Cancer Discov. 2018 Oct 15. pii: CD-18-0804. doi: 10.1158/2159-8290.CD-18-0804. [Epub ahead of print]

PMID: 30322867

Phase II trial of palbociclib in patients with metastatic urothelial cancer after failure of first-line chemotherapy.

Rose TL, Chism DD, Alva AS, Deal AM, Maygarden SJ, Whang YE, Kardos J, Drier A, Basch E, Godley PA, Dunn MW, Kim WY, Milowsky MI.

Br J Cancer. 2018 Oct 8. doi: 10.1038/s41416-018-0229-0. [Epub ahead of print]

PMID: 30293995

The Cancer/Testes (CT) Antigen HORMAD1 promotes Homologous Recombinational DNA Repair and Radioresistance in Lung adenocarcinoma cells.

Gao Y, Kardos J, Yang Y, Tamir TY, Mutter-Rottmayer E, Weissman B, Major MB, Kim WY, Vaziri C.

Sci Rep. 2018 Oct 17;8(1):15304. doi: 10.1038/s41598-018-33601-w.

PMID: 30333500