Next generation plasma proteome profiling to monitor health and disease

AbstractThe need for precision medicine approaches to monitor health and disease makes it important to develop sensitive and accurate assays for proteome profiles in blood. Here, we describe an approach for plasma profiling based on proximity extension assay combined with next generation sequencing. First, we analyze the variability of plasma profiles between and within healthy individuals in a longitudinal wellness study, including the influence of genetic variations on plasma levels. Second, we follow patients newly diagnosed with type 2 diabetes before and during therapeutic intervention using plasma proteome profiling. The studies show that healthy individuals have a unique and stable proteome profile and indicate that a panel of proteins could potentially be used for early diagnosis of diabetes, including stratification of patients with regards to response to metformin treatment. Although validation in larger cohorts is needed, the analysis demonstrates the usefulness of comprehensive plasma profiling for precision medicine efforts.

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Faculty Opinions recommendation of Bioinformatory-assisted analysis of next-generation sequencing data for precision medicine in pancreatic cancer.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.727775566.793536095 ◽

2017 ◽

Author(s):

Steve Pereira

Keyword(s):

Pancreatic Cancer ◽

Next Generation Sequencing ◽

Precision Medicine ◽

Next Generation Sequencing Data ◽

Next Generation ◽

Sequencing Data ◽

Assisted Analysis ◽

Generation Sequencing

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The integration of emerging omics approaches to advance precision medicine: How can regulatory science help?

Journal of Clinical and Translational Science ◽

10.1017/cts.2018.330 ◽

2018 ◽

Vol 2 (5) ◽

pp. 295-300

Author(s):

Joan E. Adamo ◽

Robert V. Bienvenu ◽

F. Owen Fields ◽

Soma Ghosh ◽

Christina M. Jones ◽

...

Keyword(s):

Next Generation Sequencing ◽

Precision Medicine ◽

Working Group ◽

Regulatory Science ◽

Translational Science ◽

Next Generation ◽

Clinical Validity ◽

Knowledge Gaps ◽

Recent Advances ◽

Generation Sequencing

Building on the recent advances in next-generation sequencing, the integration of genomics, proteomics, metabolomics, and other approaches hold tremendous promise for precision medicine. The approval and adoption of these rapidly advancing technologies and methods presents several regulatory science considerations that need to be addressed. To better understand and address these regulatory science issues, a Clinical and Translational Science Award Working Group convened the Regulatory Science to Advance Precision Medicine Forum. The Forum identified an initial set of regulatory science gaps. The final set of key findings and recommendations provided here address issues related to the lack of standardization of complex tests, preclinical issues, establishing clinical validity and utility, pharmacogenomics considerations, and knowledge gaps.

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The Important Role of Breast Microbiota in Breast Cancer

10.20944/preprints202010.0437.v1 ◽

2020 ◽

Author(s):

Kar-Yan Su ◽

Wai-Leng Lee ◽

Vinod Balasubramaniam

Keyword(s):

Breast Cancer ◽

Next Generation Sequencing ◽

Racial Differences ◽

Breast Tissue ◽

Bacterial Species ◽

Cancer Therapies ◽

Next Generation ◽

Sequencing Technologies ◽

Health And Disease ◽

Generation Sequencing

One in eight women will be diagnosed with breast cancer (BC) in their lifetime, resulting in over 2 million cases annually. BC is the most common cancer among women. Unfortunately, the etiology of majority of cases remains unknown. Recently, evidence has shown that the human microbiota plays an important role in health and disease. Intriguingly, studies have revealed the presence of microorganisms in human breast tissue, which was previously presumed to be sterile. Next-generation sequencing technologies have paved way for the investigation of breast microbiota, uncovering bacterial signatures that are associated with BC. Some of the bacterial species were found to possess pro-carcinogenic and/or anti-carcinogenic properties, suggesting that the breast microbiota has potentially crucial roles in maintenance of breast health. In this review, we summarize the recent findings on breast tissue microbiota and its interplay with BC. Bacterial signatures identified via next-generation sequencing as well as their impact on breast carcinogenesis and cancer therapies are reviewed. Correlation of breast tissue microbiota and other factors, such as geographical and racial differences, in BC is discussed. Additionally, we discuss the future directions of research on breast microbiota as well as its potential role in prevention, diagnosis and treatment of BC.

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Brain Tumor Biobank Development for Precision Medicine: Role of the Neurosurgeon

Frontiers in Oncology ◽

10.3389/fonc.2021.662260 ◽

2021 ◽

Vol 11 ◽

Author(s):

Emilie Darrigues ◽

Benjamin W. Elberson ◽

Annick De Loose ◽

Madison P. Lee ◽

Ebonye Green ◽

...

Keyword(s):

Brain Tumor ◽

Next Generation Sequencing ◽

Precision Medicine ◽

Critical Role ◽

First Year ◽

Histopathological Diagnosis ◽

Next Generation ◽

Cancer Predisposition Syndrome ◽

Generation Sequencing

Neuro-oncology biobanks are critical for the implementation of a precision medicine program. In this perspective, we review our first year experience of a brain tumor biobank with integrated next generation sequencing. From our experience, we describe the critical role of the neurosurgeon in diagnosis, research, and precision medicine efforts. In the first year of implementation of the biobank, 117 patients (Female: 62; Male: 55) had 125 brain tumor surgeries. 75% of patients had tumors biobanked, and 16% were of minority race/ethnicity. Tumors biobanked were as follows: diffuse gliomas (45%), brain metastases (29%), meningioma (21%), and other (5%). Among biobanked patients, 100% also had next generation sequencing. Eleven patients qualified for targeted therapy based on identification of actionable gene mutations. One patient with a hereditary cancer predisposition syndrome was also identified. An iterative quality improvement process was implemented to streamline the workflow between the operating room, pathology, and the research laboratory. Dedicated tumor bank personnel in the department of neurosurgery greatly improved standard operating procedure. Intraoperative selection and processing of tumor tissue by the neurosurgeon was integral to increasing success with cell culture assays. Currently, our institutional protocol integrates standard histopathological diagnosis, next generation sequencing, and functional assays on surgical specimens to develop precision medicine protocols for our patients. This perspective reviews the critical role of neurosurgeons in brain tumor biobank implementation and success as well as future directions for enhancing precision medicine efforts.

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