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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 E-mail: thomas.laframboise@case.edu |
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.
Research
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
| 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. |
| Bioinformatics;: |
| 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. |
| Carcinogenesis;: |
| 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. |
| Bioinformatics;: |
| 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. |
| Bioinformatics;25(6):722-8 |
| 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. |
| JAMA;299(12):1437-45 |
| 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 |
| Biostatistics; |
| 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 |
| Bioinformatics;20:3353-62 |
| 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.; |