During the last three weeks, Department of Genetics faculty members, along with their colleagues, have published 21 manuscripts on a wide variety of topics.

A survey of current practices for genomic sequencing test interpretation and reporting processes in US laboratories.

O’Daniel JM, McLaughlin HM, Amendola LM, Bale SJ, Berg JS, Bick D, Bowling KM, Chao EC, Chung WK, Conlin LK, Cooper GM, Das S, Deignan JL, Dorschner MO, Evans JP, Ghazani AA, Goddard KA, Gornick M, Farwell Hagman KD, Hambuch T, Hegde M, Hindorff LA, Holm IA, Jarvik GP, Knight Johnson A, Mighion L, Morra M, Plon SE, Punj S, Richards CS, Santani A, Shirts BH, Spinner NB, Tang S, Weck KE, Wolf SM, Yang Y, Rehm HL.
Genet Med. 2016 Nov 3. doi: 10.1038/gim.2016.152. [Epub ahead of print] MID: 27811861

A Mouse Model of Chronic West Nile Virus Disease.

Graham JB, Swarts JL, Wilkins C, Thomas S, Green R, Sekine A, Voss KM, Ireton RC, Mooney M, Choonoo G, Miller DR, Treuting PM, Pardo Manuel de Villena F, Ferris MT, McWeeney S, Gale M Jr, Lund JM.
PLoS Pathog. 2016 Nov 2;12(11):e1005996. doi: 10.1371/journal.ppat.1005996.
PMID: 27806117

Molecular classification of Crohn’s disease reveals two clinically relevant subtypes.

Weiser M, Simon JM, Kochar B, Tovar A, Israel JW, Robinson A, Gipson GR, Schaner MS, Herfarth HH, Sartor RB, McGovern DP, Rahbar R, Sadiq TS, Koruda MJ, Furey TS, Sheikh SZ.
Gut. 2016 Oct 14. pii: gutjnl-2016-312518. doi: 10.1136/gutjnl-2016-312518. [Epub ahead of print] PMID: 27742763

Ultra-rare disruptive and damaging mutations influence educational attainment in the general population.

Ganna A, Genovese G, Howrigan DP, Byrnes A, Kurki MI, Zekavat SM, Whelan CW, Kals M, Nivard MG, Bloemendal A, Bloom JM, Goldstein JI, Poterba T, Seed C, Handsaker RE, Natarajan P, Mägi R, Gage D, Robinson EB, Metspalu A, Salomaa V, Suvisaari J, Purcell SM, Sklar P, Kathiresan S, Daly MJ, McCarroll SA, Sullivan PF, Palotie A, Esko T, Hultman CM, Neale BM.
Nat Neurosci. 2016 Oct 3. doi: 10.1038/nn.4404. [Epub ahead of print] PMID: 27694993

A Novel Tobacco Use Phenotype Suggests the 15q25 and 19q13 Loci May be Differentially Associated With Cigarettes per Day and Tobacco-Related Problems.

Richmond-Rakerd LS, Otto JM, Slutske WS, Ehlers CL, Wilhelmsen KC, Gizer IR.
Nicotine Tob Res. 2016 Sep 23. pii: ntw260. [Epub ahead of print] PMID: 27663783

No Reliable Association between Runs of Homozygosity and Schizophrenia in a Well-Powered Replication Study.

Johnson EC, Bjelland DW, Howrigan DP, Abdellaoui A, Breen G, Borglum A, Cichon S, Degenhardt F, Forstner AJ, Frank J, Genovese G, Heilmann-Heimbach S, Herms S, Hoffman P, Maier W, Mattheisen M, Morris D, Mowry B, Müller-Mhysok B, Neale B, Nenadic I, Nöthen MM, O’Dushlaine C, Rietschel M, Ruderfer DM, Rujescu D, Schulze TG, Simonson MA, Stahl E, Strohmaier J, Witt SH; Schizophrenia Working Group of the Psychiatric Genomics Consortium., Sullivan PF, Keller MC.
PLoS Genet. 2016 Oct 28;12(10):e1006343. doi: 10.1371/journal.pgen.1006343.
PMID: 27792727

Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains.

Starmer J, Magnuson T.
BMC Bioinformatics. 2016 Mar 24;17:144. doi: 10.1186/s12859-016-0991-z.
PMID: 27009150

Identification of mRNA isoform switching in breast cancer.

Zhao W, Hoadley KA, Parker JS, Perou CM.
BMC Genomics. 2016 Mar 3;17:181. doi: 10.1186/s12864-016-2521-9.
PMID: 26939613

Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses.

Clark SL, McClay JL, Adkins DE, Aberg KA, Kumar G, Nerella S, Xie L, Collins AL, Crowley JJ, Quakenbush CR, Hillard CE, Gao G, Shabalin AA, Peterson RE, Copeland WE, Silberg JL, Maes H,Sullivan PF, Costello EJ, van den Oord EJ.
Nicotine Tob Res. 2016 May;18(5):626-31. doi: 10.1093/ntr/ntv166.
PMID: 26283763

Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer.

Gomez NC, Hepperla AJ, Dumitru R, Simon JM, Fang F, Davis IJ.
Cell Rep. 2016 Nov 1;17(6):1607-1620. doi: 10.1016/j.celrep.2016.10.011.
PMID: 27806299

ATR maintains chromosomal integrity during postnatal cerebellar neurogenesis and is required for medulloblastoma formation.

Lang PY, Nanjangud GJ, Sokolsky-Papkov M, Shaw C, Hwang D, Parker JS, Kabanov AV, Gershon TR.
Development. 2016 Nov 1;143(21):4038-4052.
PMID: 27803059

Draft Genome Sequence of Bacillus luciferensis Isolated from Soil.

Townsley L, Caro L, Kelkar H, Shank EA.
Genome Announc. 2016 Oct 20;4(5). pii: e01140-16. doi: 10.1128/genomeA.01140-16.
PMID: 27795273

The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts.

Saini N, Roberts SA, Klimczak LJ, Chan K, Grimm SA, Dai S, Fargo DC, Boyer JC, Kaufmann WK, Taylor JA, Lee E, Cortes-Ciriano I, Park PJ, Schurman SH, Malc EP, Mieczkowski PA, Gordenin DA.
PLoS Genet. 2016 Oct 27;12(10):e1006385. doi: 10.1371/journal.pgen.1006385.
PMID: 27788131

Implication of LRRC4C and DPP6 in neurodevelopmental disorders.

Maussion G, Cruceanu C, Rosenfeld JA, Bell SC, Jollant F, Szatkiewicz J, Collins RL, Hanscom C, Kolobova I, de Champfleur NM, Blumenthal I, Chiang C, Ota V, Hultman C, O’Dushlaine C, McCarroll S, Alda M, Jacquemont S, Ordulu Z, Marshall CR, Carter MT, Shaffer LG, Sklar P, Girirajan S, Morton CC, Gusella JF, Turecki G, Stavropoulos DJ, Sullivan PF, Scherer SW, Talkowski ME, Ernst C.
Am J Med Genet A. 2016 Oct 19. doi: 10.1002/ajmg.a.38021. [Epub ahead of print] PMID: 27759917

Subtyping sub-Saharan esophageal squamous cell carcinoma by comprehensive molecular analysis.

Liu W, Snell JM, Jeck WR, Hoadley KA, Wilkerson MD, Parker JS, Patel N, Mlombe YB, Mulima G, Liomba NG, Wolf LL, Shores CG, Gopal S, Sharpless NE.
JCI Insight. 2016 Oct 6;1(16):e88755.
PMID: 27734031

The Mouse Universal Genotyping Array: From Substrains to Subspecies.

Morgan AP, Fu CP, Kao CY, Welsh CE, Didion JP, Yadgary L, Hyacinth L, Ferris MT, Bell TA, Miller DR,Giusti-Rodriguez P, Nonneman RJ, Cook KD, Whitmire JK, Gralinski LE, Keller M, Attie AD, Churchill GA, Petkov P, Sullivan PF, Brennan JR, McMillan L, Pardo-Manuel de Villena F.
G3 (Bethesda). 2015 Dec 18;6(2):263-79. doi: 10.1534/g3.115.022087.
PMID: 26684931

The ‘Omics’ of Voluntary Exercise: Systems Approaches to a Complex Phenotype.

Kelly SA, Villena FP, Pomp D.
Trends Endocrinol Metab. 2015 Dec;26(12):673-5. doi: 10.1016/j.tem.2015.10.002.
PMID: 26555601

Genome- and exome-wide association study of serum lipoprotein (a) in the Jackson Heart Study.

Li J, Lange LA, Sabourin J, Duan Q, Valdar W, Willis MS, Li Y, Wilson JG, Lange EM.
J Hum Genet. 2015 Dec;60(12):755-61. doi: 10.1038/jhg.2015.107.
PMID: 26377243

Chromatin profiling of Drosophila CNS subpopulations identifies active transcriptional enhancers.

Pearson JC, McKay DJ, Lieb JD, Crews ST.
Development. 2016 Oct 15;143(20):3723-3732.
PMID: 27802137

Ecdysone signaling induces two phases of cell cycle exit in Drosophila cells.

Guo Y, Flegel K, Kumar J, McKay DJ, Buttitta LA.
Biol Open. 2016 Oct 13. pii: bio.017525. doi: 10.1242/bio.017525. [Epub ahead of print] PMID: 27737823

A phase I/II study of intrathecal idursulfase-IT in children with severe mucopolysaccharidosis II.

Muenzer J, Hendriksz CJ, Fan Z, Vijayaraghavan S, Perry V, Santra S, Solanki GA, Mascelli MA, Pan L, Wang N, Sciarappa K, Barbier AJ.
Genet Med. 2016 Jan;18(1):73-81. doi: 10.1038/gim.2015.36.
PMID: 25834948