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To date, a significant amount of work has been performed on the human microbiome to evaluate its composition and influence on physiology; this research has led to additional studies on microbiomes localized at specific sites of the human body (e.g., skin, oral, vaginal). Given that fungi are ubiquitous and live in symbiosis with the human body, researchers are now actively looking into the role of the mycobiome in human health and disease. Recent advancements in sequencing technologies have enabled the community profiling of fungi; however, the complexities associated with metagenomics sequencing analyses have posed significant challenges toward standardization. To address this need, ATCC has developed genomic DNA and whole cell mock microbial communities comprising ten medically relevant fungal species mixed in even proportions. In this proof-of-concept study, we demonstrate the use these standards in evaluating DNA extraction and sequencing methods for mycobiome analysis.

Scientific progress depends on a strong foundation of data credibility. Yet, research is frequently limited by the lack of reliable reference materials. With microbiological research entering the ‘omics era, scientists are now equipped with tools such as whole-genome sequencing (WGS), which has diverse applications in the areas of microbiome research, clinical diagnostics, public health, and therapeutics development. Translational studies in these areas necessitate the need for authenticated standards along with high-quality reference genomes. Despite the availability of publicly available genomic data, the quality, authenticity, and accuracy of the data are inadequate and the lack of official standards for determining genome quality exacerbates these underlying issues. In this workshop, we discuss the importance of credible reference materials in microbial genomics with a particular focus on microbiome and phylogenetic studies. We also preview ATCC’s genome portal of high-quality assembled genomes for advancing the authentication of ATCC strains.

Making Sense Out of Microbiome Data

The Importance of Standardized Reference Materials

11/1/2018 — 11/3/2018

Next-generation sequencing technologies have influenced microbiome analyses in tremendous ways, opening up applications in the areas of clinical, diagnostic, therapeutic, and environmental research. However, the complexities involved in 16S rRNA community profiling and shotgun metagenomics methods often result in the introduction of biases throughout the workflow, ultimately impacting data interpretation and reproducibility. To address this, ATCC has developed fully sequenced, authenticated microbiome standards that can be used in assay standardization or as daily run controls. This workshop will highlight the utility of these standards and will focus on the assays and sequencing tools from Illumina that facilitate microbiome research.

ATCC Corporate Workshop

Association of Molecular Pathology (AMP) Annual Meeting

11/16/2017 — 11/18/2017

The complexities involved in 16S rRNA and shotgun metagenomic analysis methods pose significant challenges for microbiome research and frequently result in the introduction of biases. One of the primary obstacles in assay standardization is the limited availability of reference materials and robust analytical tools. To support this need, ATCC has developed mock microbial communities from fully sequenced and characterized ATCC strains, selected based on their phenotypic and genotypic attributes or relevance in disease-specific research. These mock communities mimic mixed metagenomics samples and offer a universal control for microbiome analyses and assay development.

ATCC is among the world’s leading biological resource centers, supporting both the academic and commercial research and development communities. The organization houses and supplies a wide range of biological materials and research tools, including continuous cell lines, primary cells, and hTERT-immortalized cell lines, as well as bacteria, viruses, fungi, and protists. In addition, ATCC develops and supplies microbial and tumor cell panels, certified reference materials, culture media and sera, and other research materials. This module examines the use of ATCC materials in two areas: molecular-based assays for cancer detection and analysis; and assay development for infectious diseases.

Genetic sequencing advances and molecular diagnostics are fostering the development of personalized medicine research and care. This has amplified the need for reliable biological certified reference materials for use as controls in cancer research and elsewhere. ATCC has developed a host of research materials, including authenticated cell lines and cell derivatives to support molecular-based assay development. Examples include cell lines with well-characterized mutations relevant to cancer study and purified genomic DNA preparations with key oncological biomarkers.

Several key aspects of infectious disease assay development are aided by well-characterized and authenticated biological materials. These assay-development activities include sourcing organisms with known traits and relevant genes, establishing inclusivity/exclusivity parameters, and determining sensitivity and limits of detection. The ATCC portfolio contains an extensive collection of microbial cultures and genetic material designed to support assay development in infectious disease and public health research. Among the tools are microbial cultures of known source of isolation, fully sequenced strains, cultures with clinically relevant phenotypic characteristics, and synthetic nucleic acids with clinically relevant gene sequences. ATCC also holds cultures grouped by toxin production, serotype, and drug-resistance. All of these materials and tools are developed and handled in conditions that have been certified and accredited to four relevant ISO standards.

ATCC Molecular Signature Panels

Powerful tools for the genomics age

12/14/2013 — 12/18/2013

ATCC molecular signature panels focus on key components of cell signaling pathways such as EGFR, AKT, PI3K, PTEN, or p53. This section will describe how we generated these panels using authenticated cell lines containing critical gene copy number changes and site mutations, as well as how each panel was experimentally validated for genetic alterations, protein expression, and cell functionality.

Transfex

for hard to transfect cells

12/14/2013 — 12/18/2013

ATCC offers a superior lipid-based transfection reagent (TransfeX) that can be used to transfect difficult cell types, like primary and stem cells, and uncomplicated continuous cell lines. In this section, we will show how TransfeX provides higher transfection efficiency and lower cytotoxicity than other commercially available transfection reagents. We will also describe the HEKPlus Expression System for protein expression.

Induced Pluripotent and Mesenchymal Stem Cells

Cells with a lot of potential

12/14/2013 — 12/18/2013

ATCC has a wide selection of induced pluripotent and mesenchymal stem cells along with an array of associated culture media and reagents. This section will provide an overview of the ATCC stem cell collection and describe how these resources can be used in cell biology studies.

hTERT Immortalized Cells

Unique tools for tissue-relevant research

12/14/2013 — 12/18/2013

ATCC Human telomerase (hTERT) immortalized cell lines combine the in vivo nature of primary cells and the long culture life of continuous cell lines. This section will provide an overview of the hTERT-immortalized cell line collection, and will examine the use of RPTEC/TERT1 (ATCC® No. CRL-4031™) and TIME (ATCC® No. CRL-4025™) cell lines to demonstrate how hTERT-immortalized cell lines can help you reach your research goals.

Development of the PI3K Pathway Inhibitors

How to choose the right cell line

10/1/2012 — 10/3/2012

The phosphatidylinositol 3-kinase (PI3K) cell signal transduction pathway plays a central role in critical cell processes, such as proliferation, apoptosis, metabolism, and angiogenesis. But mutations in several of the enzymes in the PI3K pathway have been implicated in the pathogenesis of several types of cancer. As such, the family of enzymes comprising the PI3K pathway presents an opportunity for potential cancer therapies. Targeted development of PI3K pathway inhibitors is a complicated endeavor, but recent cancer genome research has opened new treatment targets and drug-development paradigms with relevance to PI3K. Tumor cell panels offer a platform for evaluating anticancer agents. ATCC has developed several cell panels with tumor cell lines that feature mutations along the PI3K pathway. Also, ATCC has created gene mutation lists that contain annotations of its tumor cell line collection with data from the Sanger Institute COSMIC database. These research tools inform the use of the cell lines as model systems and for drug development. This module discusses the PI3K pathway mutation cell lines and gene mutations lists.