Publications by authors named "S M Foltz"
Somatic mutation phasing informs our understanding of cancer-related events, like driver mutations. We generated linked-read whole genome sequencing data for 23 samples across disease stages from 14 multiple myeloma (MM) patients and systematically assigned somatic mutations to haplotypes using linked-reads. Here, we report the reconstructed cancer haplotypes and phase blocks from several MM samples and show how phase block length can be extended by integrating samples from the same individual.
View Article and Find Full Text PDFThe use of adeno-associated viruses (AAVs) as gene delivery vectors has vast potential for the treatment of many severe human diseases. Over one hundred naturally existing AAV capsid variants have been described and classified into phylogenetic clades based on their sequences. AAV8, AAV9, AAVrh.
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- DNA methylation is crucial for maintaining cellular identity, but it's often disrupted in tumors and linked with other genetic changes.
- Researchers analyzed 687 tumors and adjacent normal tissues across various organs to create a Pan-Cancer catalog, highlighting specific methylation patterns.
- They discovered that certain methylation changes are associated with cancer characteristics, such as hypomethylated FGFR2 in endometrial cancer and hypermethylated STAT5A leading to immune suppression in squamous tumors, revealing the importance of methylation in tumor behavior.
Article Synopsis
- - The National Cancer Institute's CPTAC focuses on analyzing tumors using a proteogenomic approach, which combines genomic data with proteomic information to better understand cancer.
- - The consortium has developed a comprehensive dataset that includes genomic, transcriptomic, proteomic, and clinical data from over 1000 tumors across 10 different groups, aimed at enhancing cancer research.
- - The CPTAC team addresses challenges in integrating and analyzing multi-omics data, especially the complexities arising from combining nucleotide sequencing with mass spectrometry proteomics information.
Pediatric brain and spinal cancers are collectively the leading disease-related cause of death in children; thus, we urgently need curative therapeutic strategies for these tumors. To accelerate such discoveries, the Children's Brain Tumor Network (CBTN) and Pacific Pediatric Neuro-Oncology Consortium (PNOC) created a systematic process for tumor biobanking, model generation, and sequencing with immediate access to harmonized data. We leverage these data to establish OpenPBTA, an open collaborative project with over 40 scalable analysis modules that genomically characterize 1,074 pediatric brain tumors.
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