616.234.5000

Publications

Laird Laboratory

Selected Publications

For a full list of Dr. Laird’s publications, please visit PubMed.

Hoadley KA, Yau C, Hinoue T…Laird PW. 2018. Cell-of-origin patterns molecular classification of 10,000 tumors from 33 types of cancer. Cell 173(2):291–304.
*One of three theme papers for the
PanCancer Atlas

Sanchez-Vega F, Mina M, Armenia J…Zhou W, Shen H, Laird PW…Schultz N. 2018. Oncogenic signaling pathways in The Cancer Genome Atlas. Cell 173(2):321–337.
*One of three theme papers for the PanCancer Atlas

Malta TM, Sokolov A…Laird PW, Noushmehr H, Wizernowicz M. 2018. Machine learning identifies stemness features associated with oncogenic dedifferentiation. Cell 173(2):338–354.

Liu Y, Sethi NS, Hinoue T, Schneider BG…Thorsson V, Bass AJ, Laird PW. 2018. Comparative molecular analysis of gastrointestinal adenocarcinomas. Can Cell 33(4):721–735.

Berger AC, Korkut A, Kanchi RS…Fan H, Shen H…Akbani R. 2018. A comprehensive pan-cancer molecular study of gynecological and breast cancers. Can Cell 33(4):690–705.

Knijnenburg T, Wang L, Zimmerman MT, Chambwe N…Fan H, Shen H…Laird PW…Wang C. 2018. Genomic and molecular landscape of DNA damage repair deficiency across The Cancer Genome Atlas. Cell Rep 23(1):239–254.

Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C…Shen H…Laird PW…Waes CV. 2018. Genomic, pathway network, and immunologic features distinguishing squamous carcinomas. Cell Rep 23(1):194–212.

Ricketts CJ…Fan H…Shen H…Laird PW…Spellman P, Rathmell K, Linehan WM. 2018. Comprehensive molecular characterization of renal cell carcinoma. Cell Rep 23(1):313–326.

Zhou W, Dinh HQ, Ramjan Z, Weisenberger DJ, Nicolet CM, Shen H, Laird PW, Berman BP. 2018. DNA methylation loss in late-replicating domains is linked to mitotic cell division. Nat Gen 50:591–602.

The Cancer Genome Atlas Research Network. 2017. Comprehensive and integrative genomic characterization of hepatocellular carcinomaCell 169(7):1327–1341.

Farshidfar F…The Cancer Genome Atlas Research Network…Laird PW…Andersen JB, Bardeesy N, Roberts LR, Kwong LN. 2017. Integrative genomic analysis of cholangiocarcinoma identifies distinct IDH-mutant molecular profilesCell Rep 18(11):2780–2794.

Cherniack AD, Shen H…Laird PW…The Cancer Genome Atlas Research Network..Akbani R, Levine DA. 2017. Integrated molecular characterization of uterine carcinomaCan Cell 31(3):411–423.

The Cancer Genome Atlas Research Network. 2017. Integrated genomic characterization of oesophageal carcinomaNature 541:169–175.

Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA; TCGA Research Network, Perou CM. 2015. Comprehensive molecular portraits of invasive lobular breast cancerCell 163(2):506–519.
*Laird PW is one of 126 collaborators.

Cancer Genome Atlas Network. 2015. Genomic classification of cutaneous melanomaCell 161(7):1681–1696

Kim H, Zheng S, Amini SA, Virk SM, Mikkelsen T, Brat DJ, Grimsby J, Sougnez C, Muller F, Hu J, Sloan AE, Cohen ML, Van Meir EG, Scarpace L, Laird PW, Weinstein JN, Lander ES, Gabriel S, Getz G, Meyerson M, Chin L, Barnholtz-Sloan JS, Verhaak RGW. 2015. Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolutionGenome Res 25(3): 316–327.

Yao L, Shen H, Laird PW, Farnham PJ, Berman BP. 2015. Inferring regulatory element landscapes and transcription factor networks from cancer methylomesGenome Biol 16:105.

Kim SE, Hinoue T, Kim MS, Sohn KJ, Cho RC, Cole PD, Weisenberger DJ, Laird PW, Kim YI. 2015. γ-Glutamyl hydrolase modulation significantly influences global and gene-specific DNA methylation and gene expression in human colon and breast cancer cellsGenes Nutr 10(1):444.

Weisenberger DJ, Levine AJ, Long TI, Buchanan DD, Walters R, Clendenning M, Rosty C, Joshi AD, Stern MC, Le Marchand L, Lindor NM, Daftary D, Gallinger S, Selander T, Bapat B, Newcomb PA, Campbell PT, Casey G, Ahnen DJ, Baron JA, Haile RW, Hopper JL, Young JP, Laird PW, Siegmund KD; for the Colon Cancer Family Registry. 2015. Association of the colorectal CpG island methylator phenotype with molecular features, risk factors, and family historyCancer Epidemiol Biomarkers Prev 24(3):512–519.

Cancer Genome Atlas Network. 2015. Comprehensive genomic characterization of head and neck squamous cell carcinomasNature 517(7536):576–582.
*Laird PW is one of 348 co-authors

Kim H, Zheng S, Amini SS, Virk SM, Mikkelsen T, Brat DJ, Grimsby J, Sougnez C, Muller F, Hu J, Sloan AE, Cohen ML, Van Meir EG, Scarpace L, Laird PW, Weinstein JN, Lander ES, Gabriel S, Getz G, Meyerson M, Chin L, Barnholtz-Sloan JS, Verhaak RG. 2015. Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolutionGenome Res 25(3):316–327.

Phipps AI, Limburg PJ, Baron JA, Burnett-Hartman AN, Weisenberger DJ, Laird PW, Sinicrope FA, Rosty C, Buchanan DD, Potter JD, Newcomb PA. 2014. Association between molecular subtypes of colorectal cancer and patient survivalGastroenterology 148(1):77–87.

Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R; Cancer Genome Atlas Network*. 2014. Characterization of HPV and host genome interactions in primary head and neck cancersProc Natl Acad Sci USA 111(43):15544–15549.       
*Laird PW is included among 340 collaborators

Cancer Genome Atlas Network*. 2014. Integrated genomic characterization of papillary thyroid carcinomaCell 159(3):676–690.      
*Laird PW is one of 243 co-authors

Cancer Genome Atlas Network*. 2014. Comprehensive molecular characterization of gastric adenocarcinomaNature 513(7517):202–209.
*Laird PW was one of three co-chairs for this project and was one of 315 co-authors as well as a member of the writing team and analysis working group.

Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC,  Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA; The Cancer Genome Atlas Research Network, Chin L, Meyerson M, Kucherlapati R, Park WY, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ; Cancer Genome Atlas Research Network. 2014. The somatic genomic landscape of chromophobe renal cell carcinomaCancer Cell 26(3):319–330.

Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MD, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, Van’t Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA, Cancer Genome Atlas Research Network, Benz CC, Perou CM, Stuart JM. 2014. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of originCell 158(4):929–944.

Cancer Genome Atlas Network. 2014. Comprehensive molecular profiling of lung adenocarcinomaNature 511(7511):543–550.
*Laird PW is one of 383 co-authors and member of the writing team and analysis working group

Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AF, Wessels LF, Laird PW, Aderem A, Shmulevich I. 2014. Multiscale representation of genomic signals.  Nat Methods 11:689–694.

Wang X, Laird PW, Hinoue T, Groshen S, Siegmund KD. 2014. Non-specific filtering of beta-distributed dataBMC Bioinformatics 15:199.

Cancer Genome Atlas Network*. 2014. Comprehensive molecular characterization of urothelial bladder carcinomaNature 507: 315-322.
*Laird PW is one of 366 co-authors and member of the writing team and analysis working group

Kim TM, Laird PW, Park PJ. 2013. The landscape of microsatellite instability in colorectal and endometrial cancer genomesCell 155(4):858–868.

Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O’Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L; TCGA Research Network. 2013. The somatic genomic landscape of glioblastomaCell 155(2):462–477.

Yoshihara K, Shahmoradgoli M, Martínez E, Vegesna R, Kim H, Torres-Garcia W, Treviño V, Shen H, Laird PW, Levine DA, Carter SL, Getz G, Stemke-Hale K, Mills GB, Verhaak RG. 2013. Inferring tumour purity and stromal and immune cell admixture from expression dataNat Commun 4:2612.

Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhang CZ, Wala J, Mermel CH, Sougnez C, Gabriel SB, Hernandez B, Shen H, Laird PW, Getz G, Meyerson M, Beroukhim R. 2013. Pan-cancer patterns of somatic copy number alteration. Nat Genet 45(10):1134–1140.    PubMed

Cancer Genome Atlas Research Network; Genome Characterization Center, Chang K, Creighton CJ,…, Hinoue T, Laird PW, Rhie SK, Shen H,…, Sander C, Stuart JM. 2013. The Cancer Genome Atlas pan-cancer analysis projectNat Genet 45(10):1113–1120.

Cancer Genome Atlas Network*. 2013. Comprehensive molecular characterization of clear cell renal cell carcinomaNature 499(7456):43–49.
*Laird PW is one of 346 co-authors and member of the writing team and analysis working group

Cancer Genome Atlas Research Network*. 2013. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemiaN Engl J Med 368(22):2059–2074.    PubMed
*Laird PW is one of 139 co-authors

Shen H, Laird PW. 2013. Interplay between the cancer genome and epigenomeCell 153(1):38-55.

Shen H, Fridley BL, Song H,…, Australian Ovarian Cancer Study Group; Australian Cancer Study,…, Laird PW, Goode EL, Leigh Pearce C. 2013. Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancerNat Commun 4:1628.

Triche TJ Jr, Weisenberger DJ, Van Den Berg D, Laird PW, Siegmund KD. 2013. Low-level processing of Illumina Infinium DNA Methylation BeadArraysNucleic Acids Res 41(7):e90.

Lange CP, Campan M, Hinoue T, Schmitz RF, van der Meulen-de Jong AE, Slingerland H, Kok PJ, van Dijk CM, Weisenberger DJ, Shen H, Tollenaar RA, Laird PW. 2012. Genome-scale discovery of DNA-methylation biomarkers for blood-based detection of colorectal cancerPLoS One 7(11):e50266.

Cancer Genome Atlas Network*. 2012. Comprehensive molecular portraits of human breast tumoursNature 490(7418):61–70.
*Laird PW is one of 357 co-authors

Cancer Genome Atlas Network. 2012. Comprehensive genomic characterization of squamous cell lung cancersNature 489(7417):519–525.
*Laird PW is one of 412 co-authors

Cancer Genome Atlas Network. 2012. Comprehensive molecular characterization of human colon and rectal cancerNature 487(7407):330–337.
*Laird PW is one of 326 co-authors

Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, Laird PW, Onofrio RC, Winckler W, Weir BA, Beroukhim R, Pellman D, Levine DA, Lander ES, Meyerson M, Getz G. 2012. Absolute quantification of somatic DNA alterations in human cancerNat Biotechnol 30(5):413–421.

Shen H, Laird PW. 2012. In epigenetic therapy, less is moreCell Stem Cell 10(4):353–354.

Hinoue T, Weisenberger DJ, Lange CPE, Shen H, Byun HM, Van Den Berg D, Malik S, Pan F, Noushmehr H, van Dijk CM, Tollenaar RAEM, and Laird PW. 2012. Genome-scale analysis of aberrant DNA methylation in colorectal cancerGenome Res 22(2):271–282.

Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, Noushmehr H, Lange CP, van Dijk CM, Tollenaar RA, Van Den Berg D, Laird PW. 2011. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domainsNat Genet 44(1):40-46.
*Cited in Genome Biology (Vol 12, 137) as one of the most important papers published in 2011

Cancer Genome Atlas Research Network*. 2011. Integrated genomic analyses of ovarian carcinoma. Nature 474(7353):609–615.
*Laird PW is one of 297 co-authors; also listed among co-authors who contributed substantively to the writing of the manuscript
**Cited more than 700 times (ISI)

Noushmehr H, Weisenberger DJ, Diefes K, Phillips HS, Pujara K, Berman BP, Pan F, Pelloski CE, Sulman EP, Bhat KP, Verhaak RG, Hoadley KA, Hayes DN, Perou CM, Schmidt HK, Ding L, Wilson RK, Van Den Berg D, Shen H, Bengtsson H, Neuvial P, Cope LM, Buckley J, Herman JG, Baylin SB, Laird PW*, Aldape K*, The Cancer Genome Atlas Research Network. 2010. Identification of a CpG island methylator phenotype that defines a distinct subgroup of gliomaCancer Cell 17(5):510–522.
*Corresponding author, equal contribution
**Cancer Cell Preview: Wright KD, Gilbertson JD. 2010. To infinium, and beyond! Cancer Cell 17(5):419–420.
**Faculty of 1000 Citation “Must Read”
**Listed as “Hot Paper” by ISI**Listed as “Highly Cited Paper in the Past Decade” by ISI
**Listed among Top Five Papers for Cancer Cell 10th Anniversary

Laird PW. 2010. Principles and challenges of genomewide DNA methylation analysisNat Rev Genet 11(3):191–203.
*Listed as “Highly Cited Paper in the Past Decade” by ISI

Cancer Genome Atlas Research Network*. 2008. Comprehensive genomic characterization defines human glioblastoma genes and core pathwaysNature 455(7216):1061–1068.
Laird PW is one of 231 co-authors
**Listed as “Highly Cited Paper in the Past Decade” by ISI
**Cited more than 1,600 times (ISI)

Weisenberger DJ, Trinh BN, Campan M, Sharma S, Long TI, Ananthnarayan S, Liang G, Esteva FJ, Hortobagyi GN, McCormick F, Jones PA, Laird PW. 2008. DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLightNucleic Acids Res 36(14):4689–4698.

Widschwendter M, Fiegl H, Egle D, Mueller-Holzner E, Spizzo G, Marth C, Weisenberger DJ, Campan M, Young J, Jacobs I, Laird PW. 2007. Epigenetic stem cell signature in cancerNat Genet 39(2):157–158.
*Highlighted in Research Highlights: Nature Reviews Genetics 8, 90-91, 2007
*Faculty of 1000 Citation
*Listed as “Highly Cited Paper in the Past Decade” by ISI
*Cited more than 500 times (ISI)

Sodir NM, Chen X, Park R, Nickel AE, Conti PS, Moats R, Bading JR, Shibata D, Laird PW. 2006. Smad3 deficiency promotes tumorigenesis in the distal colon of ApcMin/+ miceCancer Res 66(1):8430–8438.

Weisenberger DJ, Siegmund KD, Campan M, Young J, Long TI, Faasse MA, Kang GH, Widschwendter M, Weener D, Buchanan D, Koh H, Simms L, Barker M, Leggett B, Levine J, Kim M, French AJ, Thibodeau SN, Jass J, Haile R, Laird PW. 2006. CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancerNat Genet 38(7):787–793.
*Highlighted in News and Views: Schuebel et al. Nature Genetics 38,706-708, 2006
*Selected Summary in Gastroenterology 132, 1184-1195, 2007
*Listed as “Highly Cited Paper in the Past Decade” by ISI

Weisenberger DJ, Campan M, Long TI, Kim M, Woods C, Fiala E, Ehrlich M, Laird PW. 2005. Analysis of repetitive element DNA methylation by MethyLightNucleic Acids Res 33(21):6823–6836.
*Selected as “Recent Hot Paper” by Nucleic Acids Research*Listed as “Highly Cited Paper in the Past Decade” by ISI
*Cited More Than 700 Times (ISI)

Laird PW. 2003. The power and the promise of DNA methylation markersNat Rev Cancer 3(4):253–266.
*Highlighted in “Nature Reviews Focus on DNA methylation”
*Listed as “Highly Cited Paper in the Past Decade” by ISI
*Cited More Than 700 Times (ISI)

Eads CA, Nickel AE, Laird PW. 2002. Complete genetic suppression of polyp formation and reduction in CpG-island hypermethylation in Apc (Min/+) Dnmt1-hypomorphic miceCancer Res 62(5):1296–1299.

Eads CA, Danenberg KD, Kawakami K, Saltz LB, Blake C, Shibata D, Danenberg PV, Laird PW. 2000. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res 28(8):E32.
*Cited more than 500 times (ISI)

Jones PA, Laird PW. 1999. Cancer epigenetics comes of ageNat Genet 21(2):163–167.
*Listed until 2010 as the highest cited paper of all Nature Genetics papers in the past decade among ISI “Highly Cited Papers”
*Cited more than 1,600 times (ISI)

Xiong Z, Laird PW. 1997. COBRA – A sensitive and quantitative DNA methylation assayNucleic Acids Res 25(12):2532–2534.
*Cited more than 700 times (ISI)

Laird PW*, Jackson-Grusby L*, Fazeli A*, Dickinson SL, Jung WE, Li E, Weinberg RA, Jaenisch R. 1995. Suppression of intestinal neoplasia by DNA hypomethylationCell 81(2):197–205.    PubMed
*Equal contribution
**Cited in “Milestones in Cancer” in Nature, April 2006 (Milestone 19)**Cited more than 500 times (ISI)

Laird PW, Zijderveld A, Linders K, Rudnicki MA, Jaenisch R, Berns A. 1991. Simplified mammalian DNA isolation procedureNucleic Acids Res 19(15):4293.
*Cited more than 1,100 times (ISI)