A5051491336- Cancer Genomics and Diagnostics
- Prostate Cancer Treatment and Research
- Genomic variations and chromosomal abnormalities
- Pancreatic and Hepatic Oncology Research
- Acute Myeloid Leukemia Research
- Lung Cancer Treatments and Mutations
- Genetic factors in colorectal cancer
- Lymphoma Diagnosis and Treatment
- Chronic Myeloid Leukemia Treatments
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Acute Lymphoblastic Leukemia research
- Genomics and Rare Diseases
- Occupational and environmental lung diseases
- Chronic Lymphocytic Leukemia Research
- Medical Imaging and Pathology Studies
- Molecular Biology Techniques and Applications
- Glioma Diagnosis and Treatment
- Cancer Immunotherapy and Biomarkers
- Renal cell carcinoma treatment
- Antimicrobial Resistance in Staphylococcus
- Microbial infections and disease research
- Cancer Cells and Metastasis
- bioluminescence and chemiluminescence research
- T-cell and Retrovirus Studies
- Myeloproliferative Neoplasms: Diagnosis and Treatment
Mayo Clinic
2016-2025
Mayo Clinic in Arizona
2013-2025
WinnMed
2014-2024
Manipal Hospital
2024
Kasturba Medical College, Manipal
2024
University of Auckland
2013-2023
Qiagen (United Kingdom)
2023
Auburn University
2020
Center for Discovery
2018
Mayo Clinic in Florida
2014-2018
The Alaskan Layered Pollution And Chemical Analysis (ALPACA) field experiment was a collaborative study designed to improve understanding of pollution sources and chemical processes during winter (cold climate low-photochemical activity), investigate indoor pollution, dispersion as affected by frequent temperature inversions. A number the research goals were motivated questions raised residents Fairbanks, Alaska, where held. This paper describes measurement strategies conditions encountered...
Distinguishing independent primary tumors from intrapulmonary metastases in non-small-cell carcinoma remains a clinical dilemma with significant implications. Using next-generation DNA sequencing, we developed chromosomal rearrangement-based approach to differentiate multiple metastasis.Tumor specimens patients known and metastatic lesions were used for lineage test development, which was then applied multifocal tumors. Laser capture microdissection performed separately each tumor. Genomic...
IntroductionMalignant pleural mesothelioma is a disease primarily associated with exposure to the carcinogen asbestos. Whereas other carcinogen-related tumors are high tumor mutation burden, not. We sought resolve this discrepancy.MethodsWe used mate-pair (n = 22), RNA 28), and T cell receptor sequencing along in silico predictions immunologic assays understand how structural variants of chromosomes affect transcriptome.ResultsWe observed that inter- or intrachromosomal rearrangements were...
Abstract Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants chromosomal abnormalities. Unfortunately, the mapping alignment of mate-pair read pairs to a reference genome challenging time-consuming process most next-generation programs. Large insert sizes, introduction preparation protocol artifacts (biotin junction reads, paired-end contamination, chimeras, etc.) presence variant breakpoints within reads increase complexity....
Massively parallel sequencing analyses have revealed a common mutation within the MYD88 gene (MYD88L265P) occurring at high frequencies in many non-Hodgkin lymphomas (NHLs) including rare lymphoplasmacytic lymphoma, Waldenström's macroglobulinemia (WM). Using whole-exome sequencing, Sanger and allele-specific PCR, we validate initial studies detect MYD88L265P tumor genome of 97% WM patients analyzed (n=39). Due to frequency other NHL, its known effects on malignant B-cell survival,...
IntroductionGenomic technologies present a promising mechanism of resolving the clinical dilemma distinguishing independent primary tumors from intrapulmonary metastases in NSCLC. We evaluated utility discordant mapping somatic junctions chromosomal rearrangements diagnosing metastatic disease compared to current standard histologic review.Material and MethodsMate-pair sequencing was performed on DNA extracted 76 distinct 37 cases multiple lung cancers. Discordant copy levels were assessed...
BackgroundInflammatory myofibroblastic tumors (IMTs) are rare sarcomas that can occur at any age. Surgical resection is the primary treatment for patients with localized disease; however, these frequently recur. Less commonly, IMTs develop or present metastatic disease. There no standard of care and traditional cytotoxic therapy largely ineffective. Most associated oncogenic ALK, ROS1 PDGFRβ fusions may benefit from targeted therapy.Patient methodsWe sought to understand genomic...
Abstract Recently, the use of a liquid biopsy has shown promise in monitoring tumor burden. While point mutations have been extensively studied, chromosomal rearrangements demonstrated greater specificity. Such can be identified and subsequently detected plasma patients using quantitative PCR (qPCR). In this study we used whole-genome mate-pair protocol to characterize landscape genomic primary tumors ten ovarian cancer patients. Individualized tumor-specific primer panels aberrant junctions...
More effective antibiotics and a protective vaccine are desperately needed to combat the 'superbug' Staphylococcus aureus. While in vivo pathogenicity studies routinely involve infection of mice with human S. aureus isolates, recent genetic have demonstrated that lineages largely host-specific. The use such animal-adapted strains may therefore be promising approach for developing more clinically relevant animal models. We isolated mouse-adapted strain (JSNZ) which caused severe outbreak...
Chromosomal translocations leading to expression of abnormal fusion proteins play a major role in the pathogenesis various hematologic malignancies. The recent development high‐throughput, “deep” sequencing has allowed discovery novel rapid increase understanding these diseases. Translocations involving anaplastic lymphoma kinase ( ALK ) gene originally were discovered large cell lymphomas (ALCLs). Among ALCLs, NPM1‐ALK fusions are most common and lead nuclear localization protein. Here, we...
Common fragile sites (CFS) are chromosome regions that prone to form gaps or breaks in response DNA replication stress. They often found as hotspots for sister chromatid exchanges, deletions, and amplifications different cancers. Many of the CFS span genes whose genomic sequence is greater than 1 Mb, some which have been demonstrated function important tumor suppressors. also human papillomavirus (HPV) integrations cervical cancer. We used mate-pair sequencing examine HPV integration events...
ABSTRACT Rapid identification of the causative pathogens central nervous system infections is essential for providing appropriate management and improving patient outcomes. The performance QIAstat-Dx Meningitis/Encephalitis (ME) Panel—a multiplex PCR testing platform—in detecting implicated in meningitis and/or encephalitis was evaluated using BioFire FilmArray ME Panel as a comparator method. This multicenter study analyzed 585 retrospective residual cerebrospinal fluid specimens 367...
Gleason score 7 (GS7) prostate cancer [tumors with both patterns 3 (GP3) and 4 (GP4)] portends a significantly more aggressive tumor than 6 (GS6). It is, therefore, critical to understand the molecular relationship of adjacent GP3 GP4 cell populations relate abnormalities disease progression. To decipher relatedness, we used laser capture microdissection (LCM) whole-genome amplification (WGA) separately collect amplify DNA from 14 cases GS7 cancer. We then carried out massively parallel...
Overexpression of TOP2A is associated with risk systemic progression in prostate cancer patients, and higher levels were found hormone-resistant cases. To elucidate the mechanism by which high contribute to tumor we generated overexpressing cell lines. We show that promotes aggressiveness inducing chromosomal rearrangements genes a more invasive phenotype. Anti-androgen treatment alone was ineffective killing cells due activation an androgen receptor network. poisons killed efficiently early...
Copy number variation (CNV) is a common form of structural detected in human genomes, occurring as both constitutional and somatic events. Cytogenetic techniques like chromosomal microarray (CMA) are widely used analyzing CNVs. However, CMA cannot resolve the full nature these variations (i.e. orientation location associated breakpoint junctions) must be combined with other cytogenetic techniques, such karyotyping or FISH, to do so. This makes development next-generation sequencing (NGS)...
Abstract PURPOSE: Monitoring disease progression in patients with high-grade gliomas (HGGs) is challenging due to treatment-related changes on imaging and the requirement for neurosurgical intervention obtain diagnostic tissue. DNA junctions HGGs often amplify oncogenes, making these fragments potentially more abundant blood than monoallelic mutations. Herein, we piloted a cell-free approach detection plasma of by leveraging patient-specific associated oncogene amplifications. EXPERIMENTAL...