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Publications

Indel variant analysis of short-read sequencing data with Scalpel

As the second most common type of variation in the human genome, insertions and deletions (indels) have been linked to many diseases, but the discovery of indels of more than a few bases in size from short-read sequencing data remains...

Authors:  Michael Zody   Giuseppe Narzisi   Kanika Arora  

PGBD5 promotes site-specific oncogenic mutations in human tumors.

Nat Genet. 2017 May 15. doi: 10.1038/ng.3866. Genomic rearrangements are a hallmark of human cancers. Here, we identify the piggyBac transposable element derived 5 (PGBD5) gene as encoding an active DNA transposase expressed in the majority of childhood...

Authors:  Kanika Arora   Minita Shah  

Next-Generation Rapid Autopsies Enable Tumor Evolution Tracking and Generation of Preclinical Models

Purpose:

Patients with cancer who graciously consent for autopsy represent an invaluable resource for the study of cancer biology. To advance the study of tumor evolution, metastases, and resistance to treatment, we developed a next-generation rapid autopsy program integrated within a...

Authors:  Nicolas Robine  

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid...

Authors:  Andre Corvelo  

Immunohistochemical analysis of T-type calcium channels in acquired melanocytic nevi and melanoma.

BACKGROUND AND OBJECTIVES: Cutaneous malignant melanoma arises from transformed melanocytes de novo or from congenital or acquired melanocytic nevi. We have recently reported that T-type Ca2+ channels (TTCs) are upregulated in human melanoma and play an important role on cell proliferation....

Authors: 

Genetic Determinants of Cisplatin Resistance in Patients With Advanced Germ Cell Tumors

Owing to its exquisite chemotherapy sensitivity, most patients with metastatic germ cell tumors (GCTs) are cured with cisplatin-based chemotherapy. However, up to 30% of patients with advanced GCT exhibit cisplatin resistance,...

Authors:  Dayna Oschwald   Kanika Arora  

Targeting renal cell carcinoma with a HIF-2 antagonist

Clear cell renal cell carcinoma (ccRCC) is characterized by inactivation of the von Hippel-Lindau tumour suppressor gene (VHL). Because no other gene is mutated as frequently in ccRCC and VHL mutations are truncal, VHL inactivation is regarded as the governing...

Authors:  Heather Geiger  

Structural insights into mis-regulation of protein kinase A in human tumors

The extensively studied cAMP-dependent protein kinase A (PKA) is involved in the regulation of critical cell processes, including metabolism, gene expression, and cell proliferation; consequentially, mis-regulation of PKA signaling is implicated in tumorigenesis. Recent genomic studies have identified recurrent mutations...

Authors:  Nicolas Robine  

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