Rachel Karchin

Assistant Professor, Department of Biomedical Engineering

Address:
3400 N. Charles Street
Computational Science & Engineering Building, Room 217a
Baltimore, MD 21218

Phone: (410) 516-5578
Fax: (410) 516-5294
E-mail: karchin@jhu.edu
Website: http://www.karchinlab.org/

CV

Research Interest Statement

We use computation to study the impact of genetic variation at the molecular level. Genetic variation is critical to human susceptibility to diseases and response to medications. Yet the functional consequences of most genetic variants are unknown. We are working to predict these consequences using computation, by integrating information from molecular modeling and sequence analysis with clinical patient data and in vitro functional studies, through collaborations with physicians, genetic counselors, and experimental biologists. We are particularly interested in inherited cancer susceptibilities and gain of function mutations in tumor genomes.

Current Projects

Computational analysis of protein evolution and structure to aid medical decision making in high-risk breast, ovarian, prostate, and colorectal cancer families

Predicting the impact of somatic variation in cancer genomes with molecular modeling

Large scale annotation of human genetic variation

Molecular modeling of point mutations in proteins

SNPs and X-linked mental retardation

Publications

Karchin R., F. J. Couch, M. Agarwal, A. Sali, M.S. Beattie (2008). "Classification of BRCA2 unclassified variants using protein likelihood ratios." Cancer Informatics, (accepted).

Carvalho M., M.A. Pino, R. Karchin, M. Godinho-Netto, R.D. Mesquita, R.S. Rodarte, D.C. Vaz, V.A. Monteiro, S. Manoukian, M. Colombo, C. Ripamonti, R. Rosenquist-Brandell, G. Suthers, A. Borg, P. Radice, S.A. Grist11, A.N.A. Monteiro, B. Billack (2008). "Analysis of missense, frameshift, and in-frame deletion variants of BRCA1." submitted.

Carvalho M. A., S. M. Marsillac, R. Karchin, S. Manoukian, S. Grist, R. F. Swaby, T. P. Urmenyi, E. Rondinelli, R. Silva, L. Gayol, L. Baumbach, R. Sutphen, J. L. Pickard-Brzosowicz, K. L. Nathanson, A. Sali, D. Goldgar, F. J. Couch, P. Radice, A. N. Monteiro (2007). "Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis." Cancer Research, 67(4): 1494-1501.

Wood L.D., D.W. Parsons, S. Jones, J. Lin, T. Sjoblom, R.J. Leary, D. Shen, S.M. Boca, T. Barber, J. Ptak, N. Silliman, S. Szabo, Z. Dezso, V. Ustyanksky, T. Nikolskaya, Y. Nikolsky, R. Karchin, P.A. Wilson, J.S. Kaminker, Z. Zhang, R. Croshaw, J. Willis, D. Dawson, M. Shipitsin, J.K. Willson, S. Sukumar, K. Polyak, B.H. Park, C.L. Pethiyagoda, P.V. Pant, D.G. Ballinger, A.B. Sparks, J. Hartigan, D.R. Smith, E. Suh, N. Papadopoulos, P. Buckhaults, S.D. Markowitz, G. Parmigiani, K.W. Kinzler, V.E. Velculescu, B. Vogelstein (2007). "The Genomic Landscapes of Human Breast and Colorectal Cancers." Science, 318(5853): 1108-1113.

Karchin R., A. N. Monteiro, M. A. Carvalho, S. V. Tavtigian, A. Sali (2007). "Functional impact of missense mutants in BRCA1 predicted by supervised learning." PLoS Comput Biol., 3(2): e26.

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