faculty
Alice Berger
ahberger@fredhutch.org
Associate Professor
Fred Hutch
,Human Biology
Cancer Biology
Cell Signaling & Cell/Environment Interactions
Computational Biology
Cancer functional genomics
Faculty Contact Information
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.
DEI Statement
My goal for my laboratory is to create a training environment that is diverse and inclusive and enables each trainee to reach their greatest potential. In addition to my own mentorship, I encourage my trainees to build a team of diverse mentors to best support their professional goals. As a mentor, I have been fortunate to train many underrepresented trainees from diverse backgrounds including Black and Latina women, members of the LGBTQ+ community, and those from disadvantaged socioeconomic backgrounds. Of the ten research technicians, graduate students, and postdoctoral fellows that I have trained since starting my independent laboratory, six out of ten trainees identify as members of one or more of these communities. Many of these trainees have received competitive fellowships aimed at increasing diversity in science.
Several ongoing strategies my lab uses to further diversity, equity, and inclusion are:
1. Continuing education and training in diversity, equity, inclusion, and mentorship. I have sought out research training in topics related to diversity, equity, inclusion, or mentoring, and I encourage my trainees to do the same.
2. Implementation of data-driven approaches to mitigate implicit bias in hiring decisions. I have modified my postdoctoral hiring process by implementing a defined scoring rubric that enables me to compare candidates in a quantitative and holistic manner rather than using vague feedback that can allow implicit bias to dominate.
3. Commitment to creating a laboratory environment in which every member feels valued, respected, and able to share their ideas. I actively encourage all lab-members to contribute to scientific discussions, and I solicit feedback from my mentees on lab environment and mentorship using anonymous surveys.
4. Regularly revisiting our lab’s commitment to diversity, equity, and inclusion. I devote special annual lab meetings to discussions of diversity, equity, and inclusion. These meetings inform our stated lab values.
5. Applying principles of diversity equity, and inclusion to selection of research topics. Cancer genomics research has historically been highly biased toward white populations. To help combat this, my lab currently has two ongoing projects in understudied populations: profiling the cancer genome of lung tumors from female lung cancer patients in the U.S. and from lung cancer patients in Uganda.
Training Summary
Bias Mitigation Training (Fred Hutch) – 2021
Race, Bias, and Dissonance Training (UW) – 2021
DEI training for hiring committees (Fred Hutch) – 2020
Cold Spring Harbor Workshop on Leadership in Bioscience (2016)
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Publications
The following publications were retrieved from PubMed:
Author Correction: Massively parallel phenotyping of coding variants in cancer with Perturb-seq.
Ursu O, Neal JT, Shea E, Thakore PI, Jerby-Arnon L, Nguyen L, Dionne D, Diaz C, Bauman J, Mosaad MM, Fagre C, Lo A, McSharry M, Giacomelli AO, Ly SH, Rozenblatt-Rosen O, Hahn WC, Aguirre AJ, Berger AH, Regev A, Boehm JS.
Nat Biotechnol. 2022 Nov; 11(40)1691
All About That Ras: Novel Fusion Drives Ras Pathway Activation in Lung Cancer.
Moorthi S, Berger AH.
Clin Cancer Res. 2022 Jul 15; 14(28)2983-2985
Genome-wide CRISPR screening reveals novel therapeutic targets in RIT1-driven lung cancer.
Riley AK, Berger AH.
Mol Cell Oncol. 2021; 6(8)2000318
Correction to: Oncogenic RIT1 mutations in lung adenocarcinoma.
Berger AH, Imielinski M, Duke F, Wala J, Kaplan N, Shi G-, Andres DA, Meyerson M.
Oncogene. 2022 May; 19(41)2788
Cell Painting predicts impact of lung cancer variants.
Caicedo JC, Arevalo J, Piccioni F, Bray MA, Hartland CL, Wu X, Brooks AN, Berger AH, Boehm JS, Carpenter AE, Singh S.
Mol Biol Cell. 2022 May 15; 6(33)ar49
Massively parallel phenotyping of coding variants in cancer with Perturb-seq.
Ursu O, Neal JT, Shea E, Thakore PI, Jerby-Arnon L, Nguyen L, Dionne D, Diaz C, Bauman J, Mosaad MM, Fagre C, Lo A, McSharry M, Giacomelli AO, Ly SH, Rozenblatt-Rosen O, Hahn WC, Aguirre AJ, Berger AH, Regev A, Boehm JS.
Nat Biotechnol. 2022 Jun; 6(40)896-905
Hovland HN, Al-Adhami R, Ariansen SL, Van Ghelue M, Sjursen W, Lima S, Bolstad M, Berger AH, Høberg-Vetti H, Knappskog P, Haukanes BI, Aukrust I, Ognedal E.
Fam Cancer. 2022 Oct; 4(21)389-398
Multiomic characterization of oncogenic signaling mediated by wild-type and mutant RIT1.
Lo A, Holmes K, Kamlapurkar S, Mundt F, Moorthi S, Fung I, Fereshetian S, Watson J, Carr SA, Mertins P, Berger AH.
Sci Signal. 2021 Nov 30; 711(14)eabc4520
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
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
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
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
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
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
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 CO(2) Adsorption in Diamine-Appended Mg(2)(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.
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. 2016 Aug 8; 2(30)214-228
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
Fox S, Ryan KA, Berger AH, Petro K, Das S, Crowe SE, Ernst PB.
J Inflamm (Lond). 2015; (12)51
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
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
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
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, Spring
Rotation, Winter
Lab Information
Location: Fred Hutchinson Cancer Research Center
Building: Hutchinson building
Room: C2-201
Box: C2-023
https://research.fhcrc.org/berger/en.html
Building: Hutchinson building
Room: C2-201
Box: C2-023
https://research.fhcrc.org/berger/en.html