faculty

Alice Berger

ahberger@fredhutch.org

Assistant Professor

Fred Hutch

Human Biology

Cancer Biology

Cell Signaling & Cell/Environment Interactions

Computational Biology

Cancer functional genomics

Faculty Contact Information

Box: C2-023 https://www.fredhutch.org/en/labs/profiles/berger-alice.html

Research Summary

The goal of the Berger laboratory is to enable precision medicine by systematically uncovering the molecular alterations in cancer, determining the function of these variant alleles, and understanding how these alleles modulate response to targeted or immune-based therapies. We combine functional genomics, computational biology, biochemistry, and genetics to understand the mechanism of somatic cancer variants. Our goal is to identify drug targets and biomarkers and to translate this knowledge into clinical benefit for patients.

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Publications

The following publications were retrieved from PubMed:

Transcriptional Changes in Regulatory T Cells From Patients With Autoimmune Polyendocrine Syndrome Type 1 Suggest Functional Impairment of Lipid Metabolism and Gut Homing.

Berger AH, Bratland E, Sjøgren T, Heimli M, Tyssedal T, Bruserud Ø, Johansson S, Husebye ES, Oftedal BE, Wolff ASB.

Front Immunol. 2021; (12)722860

Discovery of synthetic lethal and tumor suppressor paralog pairs in the human genome.

Parrish PCR, Thomas JD, Gabel AM, Kamlapurkar S, Bradley RK, Berger AH.

Cell Rep. 2021 Aug 31; 9(36)109597

Integrative oncogene-dependency mapping identifies RIT1 vulnerabilities and synergies in lung cancer.

Vichas A, Riley AK, Nkinsi NT, Kamlapurkar S, Parrish PCR, Lo A, Duke F, Chen J, Fung I, Watson J, Rees M, Gabel AM, Thomas JD, Bradley RK, Lee JK, Hatch EM, Baine MK, Rekhtman N, Ladanyi M, Piccioni F, Berger AH.

Nat Commun. 2021 Aug 9; 1(12)4789

Loss of MGA repression mediated by an atypical polycomb complex promotes tumor progression and invasiveness.

Mathsyaraja H, Catchpole J, Freie B, Eastwood E, Babaeva E, Geuenich M, Cheng PF, Ayers J, Yu M, Wu N, Moorthi S, Poudel KR, Koehne A, Grady W, Houghton AM, Berger AH, Shiio Y, MacPherson D, Eisenman RN.

Elife. 2021 Jul 8; (10)

eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants.

Thornton AM, Fang L, Lo A, McSharry M, Haan D, O'Brien C, Berger AH, Giannakis M, Brooks AN.

PLoS Comput Biol. 2021 Jul; 7(17)e1009132

Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway.

Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, Wong CK, Choi HY, Felau I, Robertson AG, Castro MAA, Bao L, Rheinbay E, Liu EM, Trieu T, Haan D, Yau C, Hinoue T, Liu Y, Shapira O, Kumar K, Mungall KL, Zhang H, June-Koo Lee J, Berger A, Gao GF, Zhitomirsky B, Liang WW, Zhou M, Moorthi S, Berger AH, Collisson EA, Zody MC, Ding L, Cherniack AD, Getz G, Elemento O, Benz CC, Stuart J, Zenklusen JC, Beroukhim R, Chang JC, Campbell JD, Hayes DN, Yang L, Laird PW, Weinstein JN, Kwiatkowski DJ, Tsao MS, Travis WD, Khurana E, Berman BP, Hoadley KA, Robine N, TCGA Research Network., Meyerson M, Govindan R, Imielinski M.

Cell Rep. 2021 Feb 23; 8(34)108784

CRISPR base editor screens identify variant function at scale.

Parrish PCR, Berger AH.

Mol Cell. 2021 Feb 18; 4(81)647-648

GWAS for autoimmune Addison's disease identifies multiple risk loci and highlights AIRE in disease susceptibility.

Eriksson D, Røyrvik EC, Aranda-Guillén M, Berger AH, Landegren N, Artaza H, Hallgren Å, Grytaas MA, Ström S, Bratland E, Botusan IR, Oftedal BE, Breivik L, Vaudel M, Helgeland Ø, Falorni A, Jørgensen AP, Hulting AL, Svartberg J, Ekwall O, Fougner KJ, Wahlberg J, Nedrebø BG, Dahlqvist P, Norwegian Addison Registry Study Group., Swedish Addison Registry Study Group., Knappskog PM, Wolff ASB, Bensing S, Johansson S, Kämpe O, Husebye ES.

Nat Commun. 2021 Feb 11; 1(12)959

Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway.

Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, Wong CK, Choi HY, Felau I, Robertson AG, Castro MAA, Bao L, Rheinbay E, Liu EM, Trieu T, Haan D, Yau C, Hinoue T, Liu Y, Shapira O, Kumar K, Mungall KL, Zhang H, Lee JJ, Berger A, Gao GF, Zhitomirsky B, Liang WW, Zhou M, Moorthi S, Berger AH, Collisson EA, Zody MC, Ding L, Cherniack AD, Getz G, Elemento O, Benz CC, Stuart J, Zenklusen JC, Beroukhim R, Chang JC, Campbell JD, Hayes DN, Yang L, Laird PW, Weinstein JN, Kwiatkowski DJ, Tsao MS, Travis WD, Khurana E, Berman BP, Hoadley KA, Robine N, TCGA Research Network., Meyerson M, Govindan R, Imielinski M.

Cell Rep. 2021 Feb 2; 5(34)108707

RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons.

Thomas JD, Polaski JT, Feng Q, De Neef EJ, Hoppe ER, McSharry MV, Pangallo J, Gabel AM, Belleville AE, Watson J, Nkinsi NT, Berger AH, Bradley RK.

Nat Genet. 2020 Jan; 1(52)84-94

Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation.

Gelman H, Dines JN, Berg J, Berger AH, Brnich S, Hisama FM, James RG, Rubin AF, Shendure J, Shirts B, Fowler DM, Starita LM, Brotman Baty Institute Mutational Scanning Working Group..

Genome Med. 2019 Dec 20; 1(11)85

Compound haploinsufficiency of Dok2 and Dusp4 promotes lung tumorigenesis.

Chen M, Zhang J, Berger AH, Diolombi MS, Ng C, Fung J, Bronson RT, Castillo-Martin M, Thin TH, Cordon-Cardo C, Plevin R, Pandolfi PP.

J Clin Invest. 2019 Jan 2; 1(129)215-222

Oncogenic Signaling Pathways in The Cancer Genome Atlas.

Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M, Cancer Genome Atlas Research Network., Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N.

Cell. 2018 Apr 5; 2(173)321-337.e10

High-throughput Phenotyping of Lung Cancer Somatic Mutations.

Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Watson J, Kaplan N, Campbell JD, Singh S, Root DE, Narayan R, Natoli T, Lahr DL, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub TR, Meyerson M, Boehm JS.

Cancer Cell. 2017 Dec 11; 6(32)884

A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.

Subramanian A, Narayan R, Corsello SM, Peck DD, Natoli TE, Lu X, Gould J, Davis JF, Tubelli AA, Asiedu JK, Lahr DL, Hirschman JE, Liu Z, Donahue M, Julian B, Khan M, Wadden D, Smith IC, Lam D, Liberzon A, Toder C, Bagul M, Orzechowski M, Enache OM, Piccioni F, Johnson SA, Lyons NJ, Berger AH, Shamji AF, Brooks AN, Vrcic A, Flynn C, Rosains J, Takeda DY, Hu R, Davison D, Lamb J, Ardlie K, Hogstrom L, Greenside P, Gray NS, Clemons PA, Silver S, Wu X, Zhao WN, Read-Button W, Wu X, Haggarty SJ, Ronco LV, Boehm JS, Schreiber SL, Doench JG, Bittker JA, Root DE, Wong B, Golub TR.

Cell. 2017 Nov 30; 6(171)1437-1452.e17

Controlling Cooperative CO₂ Adsorption in Diamine-Appended Mg₂(dobpdc) Metal-Organic Frameworks.

Siegelman RL, McDonald TM, Gonzalez MI, Martell JD, Milner PJ, Mason JA, Berger AH, Bhown AS, Long JR.

J Am Chem Soc. 2017 Aug 2; 30(139)10526-10538

MET Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma.

Lu X, Peled N, Greer J, Wu W, Choi P, Berger AH, Wong S, Jen KY, Seo Y, Hann B, Brooks A, Meyerson M, Collisson EA.

Cancer Res. 2017 Aug 15; 16(77)4498-4505

Institutional implementation of clinical tumor profiling on an unselected cancer population.

Sholl LM, Do K, Shivdasani P, Cerami E, Dubuc AM, Kuo FC, Garcia EP, Jia Y, Davineni P, Abo RP, Pugh TJ, van Hummelen P, Thorner AR, Ducar M, Berger AH, Nishino M, Janeway KA, Church A, Harris M, Ritterhouse LL, Campbell JD, Rojas-Rudilla V, Ligon AH, Ramkissoon S, Cleary JM, Matulonis U, Oxnard GR, Chao R, Tassell V, Christensen J, Hahn WC, Kantoff PW, Kwiatkowski DJ, Johnson BE, Meyerson M, Garraway LA, Shapiro GI, Rollins BJ, Lindeman NI, MacConaill LE.

JCI Insight. 2016 Nov 17; 19(1)e87062

High-throughput Phenotyping of Lung Cancer Somatic Mutations.

Cancer Cell. 2016 Aug 8; 2(30)214-228

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas.

Campbell JD, Alexandrov A, Kim J, Wala J, Berger AH, Pedamallu CS, Shukla SA, Guo G, Brooks AN, Murray BA, Imielinski M, Hu X, Ling S, Akbani R, Rosenberg M, Cibulskis C, Ramachandran A, Collisson EA, Kwiatkowski DJ, Lawrence MS, Weinstein JN, Verhaak RG, Wu CJ, Hammerman PS, Cherniack AD, Getz G, Cancer Genome Atlas Research Network., Artyomov MN, Schreiber R, Govindan R, Meyerson M.

Nat Genet. 2016 Jun; 6(48)607-16

The role of C1q in recognition of apoptotic epithelial cells and inflammatory cytokine production by phagocytes during Helicobacter pylori infection.

Fox S, Ryan KA, Berger AH, Petro K, Das S, Crowe SE, Ernst PB.

J Inflamm (Lond). 2015; (12)51

Inpatient versus outpatient vincristine, dactinomycin, and cyclophosphamide for pediatric cancers: Quality and cost implications.

Beaty RS, Bernhardt MB, Berger AH, Hesselgrave JE, Russell HV, Okcu MF.

Pediatr Blood Cancer. 2015 Nov; 11(62)1925-8

Suppression of CHK1 by ETS Family Members Promotes DNA Damage Response Bypass and Tumorigenesis.

Lunardi A, Varmeh S, Chen M, Taulli R, Guarnerio J, Ala U, Seitzer N, Ishikawa T, Carver BS, Hobbs RM, Quarantotti V, Ng C, Berger AH, Nardella C, Poliseno L, Montironi R, Castillo-Martin M, Cordon-Cardo C, Signoretti S, Pandolfi PP.

Cancer Discov. 2015 May; 5(5)550-63

Comprehensive molecular profiling of lung adenocarcinoma.

Cancer Genome Atlas Research Network.

Nature. 2014 Jul 31; 7511(511)543-50

Brain angiogenesis inhibitor 1 is expressed by gastric phagocytes during infection with Helicobacter pylori and mediates the recognition and engulfment of human apoptotic gastric epithelial cells.

Das S, Sarkar A, Ryan KA, Fox S, Berger AH, Juncadella IJ, Bimczok D, Smythies LE, Harris PR, Ravichandran KS, Crowe SE, Smith PD, Ernst PB.

FASEB J. 2014 May; 5(28)2214-24

Oncogenic RIT1 mutations in lung adenocarcinoma.

Berger AH, Imielinski M, Duke F, Wala J, Kaplan N, Shi GX, Andres DA, Meyerson M.

Oncogene. 2014 Aug 28; 35(33)4418-23

BCR-ABL disrupts PTEN nuclear-cytoplasmic shuttling through phosphorylation-dependent activation of HAUSP.

Morotti A, Panuzzo C, Crivellaro S, Pergolizzi B, Familiari U, Berger AH, Saglio G, Pandolfi PP.

Leukemia. 2014 Jun; 6(28)1326-33

DOK2 inhibits EGFR-mutated lung adenocarcinoma.

Berger AH, Chen M, Morotti A, Janas JA, Niki M, Bronson RT, Taylor BS, Ladanyi M, Van Aelst L, Politi K, Varmus HE, Pandolfi PP.

PLoS One. 2013; 11(8)e79526

Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing.

Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, Cho J, Suh J, Capelletti M, Sivachenko A, Sougnez C, Auclair D, Lawrence MS, Stojanov P, Cibulskis K, Choi K, de Waal L, Sharifnia T, Brooks A, Greulich H, Banerji S, Zander T, Seidel D, Leenders F, Ansén S, Ludwig C, Engel-Riedel W, Stoelben E, Wolf J, Goparju C, Thompson K, Winckler W, Kwiatkowski D, Johnson BE, Jänne PA, Miller VA, Pao W, Travis WD, Pass HI, Gabriel SB, Lander ES, Thomas RK, Garraway LA, Getz G, Meyerson M.

Cell. 2012 Sep 14; 6(150)1107-20

Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2.

Greulich H, Kaplan B, Mertins P, Chen TH, Tanaka KE, Yun CH, Zhang X, Lee SH, Cho J, Ambrogio L, Liao R, Imielinski M, Banerji S, Berger AH, Lawrence MS, Zhang J, Pho NH, Walker SR, Winckler W, Getz G, Frank D, Hahn WC, Eck MJ, Mani DR, Jaffe JD, Carr SA, Wong KK, Meyerson M.

Proc Natl Acad Sci U S A. 2012 Sep 4; 36(109)14476-81

In silico screening of carbon-capture materials.

Lin LC, Berger AH, Martin RL, Kim J, Swisher JA, Jariwala K, Rycroft CH, Bhown AS, Deem MW, Haranczyk M, Smit B.

Nat Mater. 2012 May 27; 7(11)633-41

Dosage and tumour suppression.

Berger AH, Knudson AG, Pandolfi PP.

J Pathol. 2012 Jun; 2(227)e1; author reply e2

A continuum model for tumour suppression.

Berger AH, Knudson AG, Pandolfi PP.

Nature. 2011 Aug 10; 7359(476)163-9

Haplo-insufficiency: a driving force in cancer.

Berger AH, Pandolfi PP.

J Pathol. 2011 Jan; 2(223)137-46

Identification of DOK genes as lung tumor suppressors.

Berger AH, Niki M, Morotti A, Taylor BS, Socci ND, Viale A, Brennan C, Szoke J, Motoi N, Rothman PB, Teruya-Feldstein J, Gerald WL, Ladanyi M, Pandolfi PP.

Nat Genet. 2010 Mar; 3(42)216-23

Animal-to-Human Transplants: The Ethics of Xenotransplantation: a review.

Berger AH

Sci Eng Ethics. 1996 Oct; 4(2)481-2

Accepting Students For:

Rotation, Autumn

Rotation, Spring

Rotation, Summer

Rotation, Winter

Permanent

Lab Information

Location: Fred Hutchinson Cancer Research Center
Building: Hutchinson building
Room: C2-201
Box: C2-023
https://research.fhcrc.org/berger/en.html