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Genetics Faculty

Thomas LaFramboise
Associate Professor
Ph.D. Training Faculty
Department of Genetics
School of Medicine
Case Western Reserve University
Biomedical Research Building 625
2109 Adelbert Road
Cleveland, Ohio 44106-4955
Tel: (216) 368-0150
Fax: (216) 368-3432

About Thomas LaFramboise

Tom LaFramboise earned his B.S. from the University of Michigan at Ann Arbor and his Ph.D. from the University of Illinois at Urbana-Champaign, both degrees being in theoretical mathematics. Subsequently, he spent several years as Assistant and Associate Professor in the mathematics department at Marietta College in Marietta, OH. In 2002, Tom decided to retrain in biostatistics, earning a Master's degree at the Harvard School of Public Health, which led to a postdoctoral position in cancer genomics in the laboratory of Matthew Meyerson at the Dana-Farber Cancer Institute and the Broad Institute of Harvard/MIT. He joined the department in August 2006.


Broadly, Dr. LaFramboise is interested in developing and applying computational tools to identify molecular variants - both inherited and somatic - that contribute to cancer and related diseases in humans. His postdoctoral work centered on the statistical modeling of data from SNP microarrays to detect DNA copy number changes in tumors, and he has written a number of R software packages designed to draw biological inferences from genomic data. His group is currently developing and applying methods to mine high-dimensional data sets, with the goal of generating hypotheses regarding gene function in tumor initiation, progression, and metastasis. We then test these hypotheses in the laboratory using human cancer cells.

Selected Publications

Yavas G, Koyuturk M, Gould MP, McMahon S, Laframboise T (2014)
DB2: a probabilistic approach for accurate detection of tandem duplication breakpoints using paired-end reads.
BMC Genomics;15(1):175
See PubMed abstract

McMahon S, Laframboise T (2014)
Mutational patterns in the breast cancer mitochondrial genome, with clinical correlates.
See PubMed abstract

Dewal N, Hu Y, Freedman ML, Laframboise T, Pe'er I (2011)
Calling amplified haplotypes in next generation tumor sequence data.
Genome Res;:
See PubMed abstract

Wilkins K, Laframboise T (2011)
Losing Balance: Hardy-Weinberg Disequilibrium as a Marker for Recurrent Loss-of-Heterozygosity in Cancer.
Hum Mol Genet;:
See PubMed abstract

Ruffalo M, LaFramboise T, Koyuturk M (2011)
Comparative analysis of algorithms for next-generation sequencing read alignment.
See PubMed abstract

Sivakumaran TA, Igo RP, Kidd JM, Itsara A, Kopplin LJ, Chen W, Hagstrom SA, Peachey NS, Francis PJ, Klein ML, Chew EY, Ramprasad VL, Tay WT, Mitchell P, Seielstad M, Stambolian DE, Edwards AO, Lee KE, Leontiev DV, Jun G, Wang Y, Tian L, Qiu F, Henning AK, Laframboise T, Sen P, Aarthi M, George R, Raman R, Das MK, Vijaya L, Kumaramanickavel G, Wong TY, Swaroop A, Abecasis GR, Klein R, Klein BE, Nickerson DA, Eichler EE, Iyengar SK (2011)
A 32 kb Critical Region Excluding Y402H in CFH Mediates Risk for Age-Related Macular Degeneration.
PLoS One;6(10):e25598
See PubMed abstract

Laframboise T, Dewal N, Wilkins K, Pe'er I, Freedman ML (2010)
Allelic selection of amplicons in glioblastoma revealed by combining somatic and germline analysis.
PLoS Genet;6(9):
See PubMed abstract

Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG, Adams DJ, Flicek P, Crawford GE, Laframboise T, Tesar P, Wei CL, Scacheri PC (2010)
CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.
PLoS Genet;6(7):e1001023
See PubMed abstract

Yavaş G, Koyutürk M, Ozsoyoğlu M, Gould MP, Laframboise T (2010)
Cokgen: a software for the identification of rare copy number variation from SNP microarrays.
Pac Symp Biocomput;:371-82
See PubMed abstract

Zhang Z, Kobayashi S, Borczuk AC, Leidner RS, Laframboise T, Levine AD, Halmos B (2010)
Dual specificity phosphatase 6 (DUSP6) is an ETS-regulated negative feedback mediator of oncogenic ERK-signaling in lung cancer cells.
See PubMed abstract

Dewal N, Freedman ML, Laframboise T, Pe'er I (2009)
Power to Detect Selective Allelic Amplification in Genome-wide Scans of Tumor Data.
See PubMed abstract

Yavas G, Koyuturk M, Ozsoyoglu M, Gould M, Laframboise T (2009)
An Optimization Framework for Unsupervised Identification of Rare Copy Number Variation from SNP Array Data.
Genome Biol;10(10):R119
See PubMed abstract

LaFramboise T (2009)
Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances.
Nucleic Acids Res;37(13):4181-93
See PubMed abstract

Sos ML, Michel K, Zander T, Weiss J, Frommolt P, Peifer M, Li D, Ullrich R, Koker M, Fischer F, Shimamura T, Rauh D, Mermel C, Fischer S, Stückrath I, Heynck S, Beroukhim R, Lin W, Winckler W, Shah K, Laframboise T, Moriarty WF, Hanna M, Tolosi L, Rahnenführer J, Verhaak R, Chiang D, Getz G, Hellmich M, Wolf J, Girard L, Peyton M, Weir BA, Chen TH, Greulich H, Barretina J, Shapiro GI, Garraway LA, Gazdar AF, Minna JD, Meyerson M, Wong KK, Thomas RK (2009)
Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions.
J Clin Invest;:
See PubMed abstract

LaFramboise T, Winckler W, Thomas RK (2009)
A flexible rank-based framework for detecting copy number aberrations from array data.
See PubMed abstract

Schnetz MP, Bartels CF, Shastri K, Balasubramanian D, Zentner GE, Balaji R, Zhang X, Song L, Wang Z, Laframboise T, Crawford GE, Scacheri PC (2009)
Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns.
Genome Res;19(4):590-601
See PubMed abstract

Rozenblatt-Rosen O, Nagaike T, Francis JM, Kaneko S, Glatt KA, Hughes CM, Laframboise T, Manley JL, Meyerson M (2009)
The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3' mRNA processing factors.
Proc Natl Acad Sci U S A;:
See PubMed abstract

Assié G, LaFramboise T, Platzer P, Bertherat J, Stratakis CA, Eng C (2008)
SNP arrays in heterogeneous tissue: highly accurate collection of both germline and somatic genetic information from unpaired single tumor samples.
Am J Hum Genet;82(4):903-15
See PubMed abstract

Assié G, LaFramboise T, Platzer P, Eng C (2008)
Frequency of germline genomic homozygosity associated with cancer cases.
See PubMed abstract

Zhang X, Guo C, Chen Y, Shulha HP, Schnetz MP, LaFramboise T, Bartels CF, Markowitz S, Weng Z, Scacheri PC, Wang Z (2008)
Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies.
Nat Methods;5(2):163-5
See PubMed abstract

Macconaill LE, Aldred MA, Lu X, Laframboise T (2007)
Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation.
BMC Genomics;8(1):211
See PubMed abstract

Thomas RK, Baker AC, DeBiasi RM, Winckler W, LaFramboise T, Lin WM, Feng W, Wang M, MacConnaill LE, Lee JC, Nicoletti R, Hatton C, Goyette M, Girard L, Majmudar K, Ziaugra L, Wong KK, Gabriel S, Beroukhim R, Peyton M, Barretina J, Dutt A, Emery C, Greulich H, Shah K, Sasaki H, Gazdar AF, Minna J, Armstrong SA, Mellinghoff IK, Hodi FS, Dranoff G, Mischel PS, Cloughesy TF, Nelson SF, Liau LM, Mertz K, Rubin MA, Moch H, Loda M, Catalona W, Fletcher J, Signoretti S, Kaye F, Anderson KC, Demetri GD, Dummer R, Wagner S, Herlyn M, Sellers WR, Meyerson M, Garraway LA (2007)
High-throughput oncogene mutation profiling in human cancer
Nature Genetics;(In Press)

Minami Y, Shimamura T, Shah K, LaFramboise T, Glatt KA, Liniker E, Borgman CL, Haringsma HJ, Feng W, Weir BA, Lowell AM, Lee JC, Wolf J, Shapiro GI, Wong KK, Meyerson M, Thomas RK (2007)
The major lung cancer-derived mutants of ERBB2 are oncogenic and are associated with sensitivity to the irreversible EGFR/ ERBB2 inhibitor HKI-272
Oncogene;(In Press)

Tengs T, Lee JC, Guillermo Paez J, Zhao X, LaFramboise T, Giannoukos G, Thomas RK (2006)
A transforming MET mutation discovered in non-small cell lung cancer using microarray-based resequencing
Cancer Lett;239(2):227-33
See PubMed abstract

Thomas RK, Nickerson E, Simons JF, Janne PA, Tengs T, Yuza Y, Garraway LA, LaFramboise T, Lee JC, Shah K, O'neill K, Sasaki H, Lindeman N, Wong KK, Borras AM, Gutmann EJ, Dragnev KH, Debiasi R, Chen TH, Glatt KA, Greulich H, Desany B, Lubeski CK, Brockman W, Alvarez P, Hutchison SK, Leamon JH, Ronan MT, Turenchalk GS, Egholm M, Sellers WR, Rothberg JM, Meyerson M (2006)
Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing
Nat Med;12(7):852-855
See PubMed abstract

LaFramboise T, Harrington D, Weir BA (2006)
PLASQ: A Generalized Linear Model-Based Procedure to Determine Allelic Dosage in Cancer Cells from SNP Array Data
See PubMed abstract

LaFramboise T, Weir BA, Zhao X, Beroukhim R, Li C, Harrington D, Sellers WR, Meyerson M. (2005)
Allele-specific amplification in cancer revealed by SNP array analysis
PLoS Comput Biol;1(6):e65
See PubMed abstract

Zhao, X., Weir, B., LaFramboise, T., Lin, M., Beroukhim, R., Garraway, L., Beheshti, J., Lee, J., Naoki, K., Chen, F., et al. (2005)
Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis
Cancer Research;65: 5561 - 5570
See PubMed abstract

Balasubramanian R, LaFramboise T, Scholtens D, Gentleman R. (2004)
A graph-theoretic approach to testing associations between disparate sources of functional genomics data
See PubMed abstract

Tengs T, LaFramboise T, Den RB, Hayes DN, Zhang J, DebRoy S, Gentleman RC, O'Neill K, Birren B, Meyerson M. (2004)
Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments
Nucleic Acids Res;32(15):e121
See PubMed abstract

LaFramboise TL, Hayes DN, Tengs T. (2004)
Statistical analysis of genomic tag data
Stat Appl Genet Mol Biol;3(1):Article34
See PubMed abstract

Contributing author to Comprehensive Dictionary of Mathematics (2001)
CRC Press.;