Full Text Journal Articles by
Author Rebecca F Halperin

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Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas.

Michael E Berens, Anup Sood, Jill S Barnholtz-Sloan, John F Graf, Sanghee Cho, Seungchan Kim, Jeffrey Kiefer, Sara A Byron, Rebecca F Halperin, Sara Nasser, Jonathan Adkins, Lori Cuyugan, Karen Devine, Quinn Ostrom, Marta Couce, Leo Wolansky, Elizabeth McDonough, Shannon Schyberg, Sean Dinn, Andrew E Sloan, Michael Prados, Joanna J Phillips, Sarah J Nelson, Winnie S Liang, Yousef Al-Kofahi, Mirabela Rusu, Maria I Zavodszky, Fiona Ginty,

Glioma is recognized to be a highly heterogeneous CNS malignancy, whose diverse cellular composition and cellular interactions have not been well characterized. To gain new clinical- and biological-insights into the genetically-bifurcated IDH1 mutant (mt) vs wildtype (wt) forms of glioma, we integrated data from protein, genomic and MR imaging from ... Read more >>

PLoS ONE (PloS one)
[2019, 14(12):e0219724]

Cited: 0 times

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PD-1-Associated Gene Expression Signature of Neoadjuvant Trastuzumab-Treated Tumors Correlates with Patient Survival in HER2-Positive Breast Cancer.

William P D Hendricks, Natalia Briones, Rebecca F Halperin, Salvatore Facista, Paul R Heaton, Daruka Mahadevan, Suwon Kim,

The therapeutic HER2-targeting antibody trastuzumab has been shown to elicit tumor immune response in a subset of HER2-positive (HER2+) breast cancer. We performed genomic and immunohistochemical profiling of tumors from eight patients who have completed multiple rounds of neoadjuvant trastuzumabb to identify predictive biomarkers for trastuzumab-elicited tumor immune responses. Immunohistochemistry ... Read more >>

Cancers (Basel) (Cancers)
[2019, 11(10):]

Cited: 0 times

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Leveraging Spatial Variation in Tumor Purity for Improved Somatic Variant Calling of Archival Tumor Only Samples.

Rebecca F Halperin, Winnie S Liang, Sidharth Kulkarni, Erica E Tassone, Jonathan Adkins, Daniel Enriquez, Nhan L Tran, Nicole C Hank, James Newell, Chinnappa Kodira, Ronald Korn, Michael E Berens, Seungchan Kim, Sara A Byron,

Archival tumor samples represent a rich resource of annotated specimens for translational genomics research. However, standard variant calling approaches require a matched normal sample from the same individual, which is often not available in the retrospective setting, making it difficult to distinguish between true somatic variants and individual-specific germline variants. ... Read more >>

Front Oncol (Frontiers in oncology)
[2019, 9:119]

Cited: 2 times

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Prospective Feasibility Trial for Genomics-Informed Treatment in Recurrent and Progressive Glioblastoma.

Sara A Byron, Nhan L Tran, Rebecca F Halperin, Joanna J Phillips, John G Kuhn, John F de Groot, Howard Colman, Keith L Ligon, Patrick Y Wen, Timothy F Cloughesy, Ingo K Mellinghoff, Nicholas A Butowski, Jennie W Taylor, Jennifer L Clarke, Susan M Chang, Mitchel S Berger, Annette M Molinaro, Gerald M Maggiora, Sen Peng, Sara Nasser, Winnie S Liang, Jeffrey M Trent, Michael E Berens, John D Carpten, David W Craig, Michael D Prados,

Purpose: Glioblastoma is an aggressive and molecularly heterogeneous cancer with few effective treatment options. We hypothesized that next-generation sequencing can be used to guide treatment recommendations within a clinically acceptable time frame following surgery for patients with recurrent glioblastoma.Experimental Design: We conducted a prospective genomics-informed feasibility trial in adults with ... Read more >>

Clin. Cancer Res. (Clinical cancer research : an official journal of the American Association for Cancer Research)
[2018, 24(2):295-305]

Cited: 8 times

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A method to reduce ancestry related germline false positives in tumor only somatic variant calling.

Rebecca F Halperin, John D Carpten, Zarko Manojlovic, Jessica Aldrich, Jonathan Keats, Sara Byron, Winnie S Liang, Megan Russell, Daniel Enriquez, Ana Claasen, Irene Cherni, Baffour Awuah, Joseph Oppong, Max S Wicha, Lisa A Newman, Evelyn Jaigge, Seungchan Kim, David W Craig,

BACKGROUND:Significant clinical and research applications are driving large scale adoption of individualized tumor sequencing in cancer in order to identify tumors-specific mutations. When a matched germline sample is available, somatic mutations may be identified using comparative callers. However, matched germline samples are frequently not available such as with archival tissues, ... Read more >>

BMC Med Genomics (BMC medical genomics)
[2017, 10(1):61]

Cited: 7 times

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Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma.

Winnie S Liang, William Hendricks, Jeffrey Kiefer, Jessica Schmidt, Shobana Sekar, John Carpten, David W Craig, Jonathan Adkins, Lori Cuyugan, Zarko Manojlovic, Rebecca F Halperin, Adrienne Helland, Sara Nasser, Christophe Legendre, Laurence H Hurley, Karthigayini Sivaprakasam, Douglas B Johnson, Holly Crandall, Klaus J Busam, Victoria Zismann, Valerie Deluca, Jeeyun Lee, Aleksandar Sekulic, Charlotte E Ariyan, Jeffrey Sosman, Jeffrey Trent,

Genomic analyses of cutaneous melanoma (CM) have yielded biological and therapeutic insights, but understanding of non-ultraviolet (UV)-derived CMs remains limited. Deeper analysis of acral lentiginous melanoma (ALM), a rare sun-shielded melanoma subtype associated with worse survival than CM, is needed to delineate non-UV oncogenic mechanisms. We thus performed comprehensive genomic ... Read more >>

Genome Res. (Genome research)
[2017, 27(4):524-532]

Cited: 12 times

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GuiTope: an application for mapping random-sequence peptides to protein sequences.

Rebecca F Halperin, Phillip Stafford, Jack S Emery, Krupa Arun Navalkar, Stephen Albert Johnston,

BACKGROUND: Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. ... Read more >>

BMC Bioinformatics (BMC bioinformatics)
[2012, 13:1]

Cited: 143 times

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Exploring antibody recognition of sequence space through random-sequence peptide microarrays.

Rebecca F Halperin, Phillip Stafford, Stephen Albert Johnston,

A universal platform for efficiently mapping antibody epitopes would be of great use for many applications, ranging from antibody therapeutic development to vaccine design. Here we tested the feasibility of using a random peptide microarray to map antibody epitopes. Although peptide microarrays are physically constrained to ∼10(4) peptides per array, ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2011, 10(3):M110.000786]

Cited: 18 times

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GRM7 variants confer susceptibility to age-related hearing impairment.

Rick A Friedman, Lut Van Laer, Matthew J Huentelman, Sonal S Sheth, Els Van Eyken, Jason J Corneveaux, Waibhav D Tembe, Rebecca F Halperin, Ashley Q Thorburn, Sofie Thys, Sarah Bonneux, Erik Fransen, Jeroen Huyghe, Ilmari Pyykkö, Cor W R J Cremers, Hannie Kremer, Ingeborg Dhooge, Dafydd Stephens, Eva Orzan, Markus Pfister, Michael Bille, Agnete Parving, Martti Sorri, Paul H Van de Heyning, Linna Makmura, Jeffrey D Ohmen, Frederick H Linthicum, Jose N Fayad, John V Pearson, David W Craig, Dietrich A Stephan, Guy Van Camp,

Age-related hearing impairment (ARHI), or presbycusis, is the most prevalent sensory impairment in the elderly. ARHI is a complex disease caused by an interaction between environmental and genetic factors. Here we describe the results of the first whole genome association study for ARHI. The study was performed using 846 cases ... Read more >>

Hum. Mol. Genet. (Human molecular genetics)
[2009, 18(4):785-796]

Cited: 79 times

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Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studies.

John V Pearson, Matthew J Huentelman, Rebecca F Halperin, Waibhav D Tembe, Stacey Melquist, Nils Homer, Marcel Brun, Szabolcs Szelinger, Keith D Coon, Victoria L Zismann, Jennifer A Webster, Thomas Beach, Sigrid B Sando, Jan O Aasly, Reinhard Heun, Frank Jessen, Heike Kolsch, Magdalini Tsolaki, Makrina Daniilidou, Eric M Reiman, Andreas Papassotiropoulos, Michael L Hutton, Dietrich A Stephan, David W Craig,

We report the development and validation of experimental methods, study designs, and analysis software for pooling-based genomewide association (GWA) studies that use high-throughput single-nucleotide-polymorphism (SNP) genotyping microarrays. We first describe a theoretical framework for establishing the effectiveness of pooling genomic DNA as a low-cost alternative to individually genotyping thousands of ... Read more >>

Am. J. Hum. Genet. (American journal of human genetics)
[2007, 80(1):126-139]

Cited: 110 times

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Whole-genome analysis of sporadic amyotrophic lateral sclerosis.

Travis Dunckley, Matthew J Huentelman, David W Craig, John V Pearson, Szabolcs Szelinger, Keta Joshipura, Rebecca F Halperin, Chelsea Stamper, Kendall R Jensen, David Letizia, Sharon E Hesterlee, Alan Pestronk, Todd Levine, Tulio Bertorini, Michael C Graves, Tahseen Mozaffar, Carlayne E Jackson, Peter Bosch, April McVey, Arthur Dick, Richard Barohn, Catherine Lomen-Hoerth, Jeffrey Rosenfeld, Daniel T O'connor, Kuixing Zhang, Richard Crook, Henrik Ryberg, Michael Hutton, Jonathan Katz, Ericka P Simpson, Hiroshi Mitsumoto, Robert Bowser, Robert G Miller, Stanley H Appel, Dietrich A Stephan,

BACKGROUND: Approximately 90% of persons with amyotrophic lateral sclerosis (ALS) have the sporadic form, which may be caused by the interaction of multiple environmental factors and previously unknown genes. METHODS: We performed a genomewide association analysis using 766,955 single-nucleotide polymorphisms (SNPs) found in 386 white patients with sporadic ALS and ... Read more >>

N. Engl. J. Med. (The New England journal of medicine)
[2007, 357(8):775-788]

Cited: 144 times

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Sorl1 as an Alzheimer's disease predisposition gene?

Jennifer A Webster, Amanda J Myers, John V Pearson, David W Craig, Diane Hu-Lince, Keith D Coon, Victoria L Zismann, Thomas Beach, Doris Leung, Leslie Bryden, Rebecca F Halperin, Lauren Marlowe, Mona Kaleem, Matthew J Huentelman, Keta Joshipura, Douglas Walker, Christopher B Heward, Rivka Ravid, Joseph Rogers, Andreas Papassotiropoulos, John Hardy, Eric M Reiman, Dietrich A Stephan,

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressively disabling impairments in memory, cognition, and non-cognitive behavioural symptoms. Sporadic AD is multifactorial and genetically complex. While several monogenic mutations cause early-onset AD and gene alleles have been suggested as AD susceptibility factors, the only extensively validated susceptibility gene for ... Read more >>

Neurodegener Dis (Neuro-degenerative diseases)
[2008, 5(2):60-64]

Cited: 43 times

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Cognitive dysfunction in NF1 knock-out mice may result from altered vesicular trafficking of APP/DRD3 complex.

Elizabeth A Donarum, Rebecca F Halperin, Dietrich A Stephan, Vinodh Narayanan,

It has been estimated that more than 50% of patients with Neurofibromatosis type 1 (NF1) have neurobehavioral impairments which include attention deficit/hyperactivity disorder, visual/spatial learning disabilities, and a myriad of other cognitive developmental problems. The biological mechanisms by which NF1 gene mutations lead to such cognitive deficits are not well ... Read more >>

BMC Neurosci (BMC neuroscience)
[2006, 7:22]

Cited: 10 times

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A high-density whole-genome association study reveals that APOE is the major susceptibility gene for sporadic late-onset Alzheimer's disease.

Keith D Coon, Amanda J Myers, David W Craig, Jennifer A Webster, John V Pearson, Diane Hu Lince, Victoria L Zismann, Thomas G Beach, Doris Leung, Leslie Bryden, Rebecca F Halperin, Lauren Marlowe, Mona Kaleem, Douglas G Walker, Rivka Ravid, Christopher B Heward, Joseph Rogers, Andreas Papassotiropoulos, Eric M Reiman, John Hardy, Dietrich A Stephan,

OBJECTIVE:While the apolipoprotein E (APOE) epsilon allele is a well-established risk factor for late-onset Alzheimer's disease (AD), initial genome scans using microsatellite markers in late-onset AD failed to identify this locus on chromosome 19. Recently developed methods for the simultaneous assessment of hundreds of thousands of single nucleotide polymorphisms (SNPs) ... Read more >>

J Clin Psychiatry (The Journal of clinical psychiatry)
[2007, 68(4):613-618]

Cited: 231 times

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