L

Leslie Cope

Johns Hopkins University

ORCID: 0000-0002-4098-3289

Publishes on Epigenetics and DNA Methylation, Cancer Genomics and Diagnostics, Pancreatic and Hepatic Oncology Research. 685 papers and 99.4k citations.

685Publications
99.4kTotal Citations

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Top publicationsby citations

Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade
Cited by 6.6k

The genomes of cancers deficient in mismatch repair contain exceptionally high numbers of somatic mutations. In a proof-of-concept study, we previously showed that colorectal cancers with mismatch repair deficiency were sensitive to immune checkpoint blockade with antibodies to programmed death receptor-1 (PD-1). We have now expanded this study to evaluate the efficacy of PD-1 blockade in patients with advanced mismatch repair-deficient cancers across 12 different tumor types. Objective radiographic responses were observed in 53% of patients, and complete responses were achieved in 21% of patients. Responses were durable, with median progression-free survival and overall survival still not reached. Functional analysis in a responding patient demonstrated rapid in vivo expansion of neoantigen-specific T cell clones that were reactive to mutant neopeptides found in the tumor. These data support the hypothesis that the large proportion of mutant neoantigens in mismatch repair-deficient cancers make them sensitive to immune checkpoint blockade, regardless of the cancers' tissue of origin.

affy—analysis of <i>Affymetrix GeneChip</i> data at the probe level
Laurent Gautier, Leslie Cope, Benjamin M. Bolstad et al.|Bioinformatics|2004
Cited by 5.4kOpen Access

MOTIVATION: The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used. RESULTS: The affy package is an R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. The package is currently in its second release, affy provides the user with extreme flexibility when carrying out an analysis and make it possible to access and manipulate probe intensity data. In this paper, we present the main classes and functions in the package and demonstrate how they can be used to process probe-level data. We also demonstrate the importance of probe-level analysis when using the Affymetrix GeneChip platform.