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GenomeWebinars

Senior Research Associate,
Lawrence Berkeley National Laboratory

This webinar will discuss a streamlined library preparation method for next-generation sequencing (NGS) that improves quality control testing capability while reducing the total number of steps compared to conventional multiplexed library workflows.

NGS library preparation methods typically entail quality control testing at the end of the workflow, which can be laborious, particularly for high-throughput applications. The streamlined modification discussed in this webinar, Fluorescent Amplification for Next Generation Sequencing (FA-NGS), replaces PCR with real-time qPCR and SYBR Green to save time and implement single tube and single reagent QC.

FA-NGS enables in situ monitoring of library amplification and replaces the need for a separate quantification step of individual libraries. Additionally, FA-NGS allows for melting curve analysis as an intermediate library quality control step to aid in troubleshooting library failures prior to sequencing.

Attendees of this webinar will learn:

  • How to integrate qPCR and melting curve analysis into high-throughput NGS library preparation
  • Potential applications to various library workflows
Sponsored by
Thu
Sep
24
11:00 am2020
Sponsored by
ArcherDX

New Insights Underscore the Need to Identify NTRK Fusions in Childhood Tumors

GenomeWebinar

Professor of Pediatrics and Professor of Clinical Pathology and Laboratory Medicine,
University of Pennsylvania Perelman School of Medicine

NTRK fusions are oncogenic drivers in a variety of tumors. The Food and Drug Administration has recently approved the NTRK inhibitors larotrectinib and entrectinib for the treatment of pediatric and adult patients with NTRK fusion positive advanced solid tumors regardless of tumor histology.

In children, the incidence of NTRK fusions is high (more than 90 percent) in certain tumors, such as infantile fibrosarcoma, congenital mesoblastic nephroma, and secretory carcinoma; lower (between 5 percent and 26 percent) in other tumors such as pediatric papillary thyroid carcinomas and a subset of pediatric gliomas; and rarely seen in different acute leukemia.

In this webinar, Marilyn M. Li of the Children’s Hospital of Philadelphia will discuss a study of a large cohort of pediatric tumors using custom-designed DNA- and RNA-based next-generation sequencing panels. The team found that NTRK fusions are more common in pediatric tumors compared to adult tumors and involve a broader panel of fusion partners and a wider range of tumors than previously recognized.

The identification of these NTRK fusions is essential for precise tumor diagnosis and accurate tumor treatment. Therefore, it is crucial to include NTRK fusions as part of tumor genomic profiling for pediatric cancer patients to facilitate pediatric precision cancer care.

For Research Only. Not for use in diagnostics procedures.

Sponsored by

Computational Biologist and Senior Director of the Data Sciences Platform, Institute Scientist, Broad Institute

The Broad Institute and Illumina have partnered to co-develop and improve upon genomic analysis pipelines, starting with integrating methods from Illumina’s DRAGEN (Dynamic Read Analysis for GENomics) hardware-accelerated informatics platform into the Broad Institute’s GATK (Genomic Analysis ToolKit) Best Practices small variant pipeline, resulting in DRAGEN-GATK Best Practices.

In this webinar, Eric Banks of the Broad Institute will describe some of the issues the development team encountered as it investigated the differences between DRAGEN and GATK tools, highlighting the improvements to methods implemented in the new Best Practices pipeline.

He will also explain how the team assessed functional equivalency between the open source and licensed (hardware-accelerated) version of the pipeline, showing results between the two methods on the same source input.

Sponsored by
Wed
Sep
30
12:00 pm2020
Sponsored by
LGC SeraCare Life Sciences

Moving from Non-Invasive Prenatal Screening to Prenatal Diagnostics: An Expert Panel Discussion

GenomeWebinar

Chief Medical Officer, Bionano Genomics

Clinical Associate Professor, Obstetrics & Gynecology, Maternal Fetal Medicine


Consultant Clinical Scientist
Director of GenQA

Non-invasive prenatal testing (NIPT) continues to expand globally to support maternal-fetal patient care. With a growing number of available assays and more labs offering testing, it is essential to have consistency in reporting and the ability to compare results and validate current or new methods.

This webinar will feature a panel of experts in the field who will provide key insights into the current needs in prenatal testing, the complexities of selecting an assay format and performing quality control, as well as other challenges that labs face when setting up and validating an NIPT assay.

The panelists bring a wealth of expertise and differing viewpoints in clinical laboratory practice, diagnosis of pregnancy complications, and new molecular methods for diagnosis and treatment of pregnancy anomalies and complications. Each speaker will have an opportunity to share their perspectives on this topic, which will be moderated by Dr. Russell Garlick, Chief Scientific Officer at LGC SeraCare. The presentation will be followed by a live Q&A to allow attendees to address the experts directly.

Sponsored by
Thu
Oct
1
1:00 pm2020
Sponsored by
Adaptive Biotechnologies

Immune Repertoire Sequencing to Uncover SARS-CoV-2-Specific T Cell Responses and Dynamics

GenomeWebinar

Chief of the Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases at the National Institutes of Health

Bioinformatician, NIAID Collaborative Bioinformatics Resource (NCBR)/Leidos

VP Research for immunoSEQ Dx, Adaptive Biotechnologies

T cells are the adaptive immune system’s first responders to any virus, circulating in the blood to detect and quickly multiply to attack the virus, and also support the development of antibodies by B cells. This central role for T cells makes them a desirable target for assessing the immune response to SARS-CoV-2 infection. 

In this webinar we’ll discuss:

  • Information and early insights from Adaptive Biotechnologies’ open-access ImmuneCODE COVID-19 database
  • Demonstrate how high-throughput sequencing of the T-cell receptor beta repertoire may reveal SARS-CoV-2-specific clonotypes
  • Describe the epidemiology of COVID-19 in a cohort of patient samples from Northern Italy
  • Discuss the presence of public SARS-CoV-2-specific clonotypes in COVID-19 patient samples and controls
  • Analyze differences in the clonal distribution of SARS-CoV-2-specific T cell clonotypes according to different degrees of disease severity
  • Reveal changes in frequency (expansions vs. contractions) of SARS-CoV-2 clonotypes during evolution of the disease

For Research Use Only. Not for use in Diagnostic Procedures.

Sponsored by
Tue
Oct
6
11:00 am2020
Sponsored by
10x Genomics

Understanding Human Pulmonary Fibrosis using Single-Cell Technologies

GenomeWebinar

Boehringer-Ingelheim Endowed Professor of Internal Medicine,
Chief of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Yale School of Medicine

Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease characterized by irreversible scarring of the distal lung, leading to respiratory failure. Currently, there is no cure for the disease and while studies have pointed to possible distinguishing molecular features, high-resolution cellular insights are still needed.

Harnessing technologies such as single-cell RNA-sequencing (scRNA-seq) may enable a better understanding of the cellular and molecular processes that determine the IPF lung phenotype, and lead to the identification of novel, cell type-specific therapies and biomarkers. 

In this webinar, Dr. Naftali Kaminski of Yale University will describe research that leveraged scRNA-seq to uncover the diversity and complexity of aberrant cellular populations in the IPF lung.

Dr. Naftali Kaminski will discuss details of the study and its findings, including:

  • Steps to generate a comprehensive IPF lung cell atlas from 312,928 cells collected from human IPF lungs, chronic obstructive pulmonary disease lungs, and control donor lungs
  • Identification of a previously undescribed aberrant basaloid cell type highly expressing genes implicated in the pathogenesis of IPF and marked by features characteristic of cells involved in distal airway development and repair
  • Resulting hypotheses on the relationships between the transcriptional profiles of cells identified in IPF lung tissues, function, localization in tissue, and disease pathophysiology
 
Sponsored by

Chief Medical Officer, Basilea Pharmaceutica International

President and CEO, GeneCentric Therapeutics

This webinar, Part 3 of the “Advances in RNA-based Biomarker Development for Precision Oncology” webinar series sponsored by GeneCentric Therapeutics, will discuss novel and emerging applications of RNA-based genomic analysis in precision oncology, form characterizing the tumor microenvironment to informing the development of immuno-oncology treatments.

Marc Engelhardt of Basilea Pharmaceutica International will discuss work showing that differential induction of gene expression may explain differences in reported adverse event profiles of targeted anticancer agents. His talk will detail the analysis of gene expression induction in safety relevant normal tissues from patient-derived xenograft models as an approach to rationalize and identify the molecular basis of adverse event profiles of targeted anticancer agents.

Michael Milburn, President and CEO of GeneCentric, will follow with a discussion of the utility of bulk tumor RNA-seq analysis in drug development. In particular, he will cover aspects of specimen and study design for bulk tumor genomics, as well as advantages and challenges of RNA-based diagnostics over DNA variations.  Development of immunogenomic analyses and GeneCentric’s overall technology approach will be highlighted.  This includes looking beyond RNA transcriptomics and utilizing RNA sequence data in drug development.

Sponsored by

As cases of COVID-19 continued to grow this spring and summer in the US, so too did the number of Emergency Use Authorizations from the FDA for clinical diagnostic tests aimed at detecting current and past infections. The agency's policies for granting EUAs for both molecular and antibody tests evolved over time as more was learned about SARS-CoV-2 and its spread, and diagnostics firms and labs needed to adapt to these changes.

Dr. Elizabeth Hillebrenner, associate director for scientific and regulatory programs at the FDA's Center for Devices and Radiological Health, will kick off this virtual roundtable with an overview of the EUA program, how it evolved, and how lessons learned during the current pandemic may shape future policies and actions by the FDA. She will then take part in a panel discussion that will include a variety of stakeholders from the diagnostics and clinical lab industries. Panelists will include Dr. Robert Boorstein, Medical Director of Lenco Diagnostic Laboratories; Danelle Miller, VP, Global Regulatory Policy and Intelligence for Roche Diagnostics; Dr. Jeffrey Klausner, Professor of Medicine and Public Health at UCLA David Geffen School of Medicine and Fielding School of Public Health; and Gail Javitt, Director at Hyman, Phelps & McNamara.

Sponsored by

Principal Investigator, CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences

This webinar will outline the use of targeted protein degradation (TPD) to understand transcriptional processes at a high kinetic resolution.

TPD is a new therapeutic modality based on small molecules, called degraders, that destabilize proteins by inducing their proximity to E3 ubiquitin ligases. The ubiquinated proteins are then degraded by the proteasome. 

In this webinar, Georg Winter of CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences, will discuss his team’s efforts to chart the function of the human Mediator complex by combining acute protein ablation with nascent RNA sequencing approaches. 

Dr. Winter will discuss how his team develops phenotypic drug screens to find novel small-molecule degraders that function as “molecular glues,” which can degrade otherwise unligandable proteins by orchestrating direct interactions between target and ligase. 

He will also describe a scalable strategy toward glue degrader discovery that is based on chemical screening in hyponeddylated cells coupled to a multi-omics target deconvolution campaign. This approach led the CeMM team to identify compounds that induce ubiquitination and degradation of cyclin K by prompting an interaction of CDK12–cyclin K with a CRL4B ligase complex. Notably, this interaction is independent of a dedicated substrate receptor, thus functionally segregating this mechanism from all described degraders. 

The presentation will outline a versatile and broadly applicable strategy to identify degraders with nonobvious mechanisms and thus empower future drug discovery efforts.

Sponsored by

Lower Gastrointestinal Medical Oncology and Trials Lead,
Peter MacCallum Cancer Centre

Circulating tumor DNA (ctDNA) can allow clinicians and researchers to better understand which patients are at high risk of recurrence and should be offered intensified chemotherapy or selected for clinical trials. Those with low-risk disease may be able to avoid chemotherapy and its associated side effects.

Methods for ctDNA detection require very high-sensitivity approaches in order to detect microscopic disease after surgery or treatment. Methods have been developed that utilize genomic profiling of tumor tissue based on patient-specific next-generation sequencing (NGS) panels. High-sensitivity personalized panels allow detection of residual disease and serial monitoring for detection of recurrence.

This webinar will discuss the use of such panels to test for residual disease and recurrence in the treatment of colorectal cancer.

Sponsored by
Thu
Oct
15
11:00 am2020
Sponsored by
Agena Bioscience

A Comparison of cfDNA Approaches to Guide Targeted Therapy in NSCLC

GenomeWebinar

Professor of Molecular Oncological Pathology
University Medical Center Groningen

Staff Scientist, Scientific Affairs
Agena Bioscience

In non-small cell lung cancer (NSCLC), early detection of emerging resistance mutations such as EGFR T790M is important in order to determine the appropriate targeted therapeutic strategy.

In this webinar, Prof. Ed Schuuring of University Medical Center Groningen will report on a comparison study for the detection of mutations in plasma DNA of NSCLC patients using the Roche Cobas EGFR v2.0 Mutation Test, BioRad droplet digital PCR, and the Agena Bioscience UltraSEEK Lung Panel. Prof. Schuuring will discuss the detection sensitivity of clinically relevant markers across the platforms and will also highlight the relevance of pre-analytical quality and quantity assessment of cfDNA.

Dr. Alexander Sartori from Agena Bioscience will follow with an overview of the MALDI-TOF based MassARRAY System and available mutation panels for both tissue and plasma DNA in various cancers.

Sponsored by

Scientist – Platform responsible dPCR,
Department of Molecular Diagnostics and Flow Cytometry (MOC), Blood Transfusion Service Zurich, Swiss Red Cross

Field Application Scientist,
Stilla Technologies Europe

This webinar will discuss a new method that relies on Crystal digital PCR from Stilla Technologies to monitor chimerism in patients after stem cell transplantation, which is a key part of surveillance for impending clinical relapse.

The new method relies on target detection by Stilla’s Crystal dPCR with the Naica system. The process allows for single nucleotide variant detection in up to 20,000 partitions per reaction, with up to 48 reactions per run.

Elise Gourri of the Blood Transfusion Service Zurich will discuss the validation and implementation of the Naica system for routine chimerism monitoring.

Her presentation will discuss how the Department of Molecular Diagnostics and Flow Cytometry confirmed the reliability of the dPCR platform on samples from previously monitored patients as well as external quality assessment samples. They could provide reproducible quantification of the minor allele, even below 0.25 percent, and, notably, the clinically required 0.5 percent minor allele sensitivity was achieved with only 5 ng of input DNA.

The webinar will detail the department’s conclusion that the Naica system is fast, convenient, and highly accurate.

Sponsored by

Assistant Professor, University of Lorraine,
Tumor Molecular Biology Unit, Institut de Cancérologie de Lorraine

This webinar will share the Lorraine Cancer Institute's experience in implementing a novel targeted solution to accurately assess homologous recombination repair (HRR) deficiency by analyzing a series of genes, beyond BRCA, and calling multiple types of variants, including copy number variants (CNVs). In the past, HRR deficiency has been commonly associated with BRCA mutations, but recent evidence shows that HRR deficiency detection should not exclusively focus on BRCA, single nucleotide variants (SNPs), and insertions/deletions (indels).

The Lorraine Cancer Center is currently participating in a guideline-defining multicenter study on ovarian cancer, investigating the correlations between a larger range of genomic alterations linked to HRR, clinical evolution, and therapeutic impact.

Dr. Alexandre Harlé, from the institute's Tumor Biology Unit, will describe the adoption of a next-generation sequencing (NGS) solution for broad HRR-deficiency-analysis, additionally enabling CNV detection. He will discuss:

• Why the institute chose a broad and future-proof HRR-deficiency-analysis approach

• How a single NGS workflow can assess a large range of HRR-related variants

• The methods used to confirm the analytical performance of the solution

• The challenges lying ahead and how can they be solved

Sponsored by
Mon
Oct
26
11:00 am2020
Sponsored by
Sophia Genetics

Robust CNV Detection Using Whole-Exome Sequencing for Complex Cases

GenomeWebinar

Scientific Director, Chief Genetic Officer, Co-founder
Genotypos Science Labs

This webinar will discuss Genotypos Science Labs’ experience with a whole-exome sequencing solution supporting the detection of copy number variants (CNVs) for the management of complex cases.

CNVs are a well-established cause of human genetic disease. Karyotype and microarray analyses have served as gold standards in molecular diagnostics for CNVs, but the increasing number and complexity of possible genomic changes require more sensitive testing.

Whole-exome analysis is emerging as a reliable tool in the study of genetic disorders and has proven to be particularly effective in identifying disease-associated genes that are refractory to linkage analysis. However, the detection of CNVs in whole-exome analyses presents unique challenges due to the large number of genomic changes present, resulting in noise and biases. Hence there is a need for a tailored and robust analytical solution for the detection and exome-wide analysis of CNVs.

In this webinar, Dr. Pantelis Constantoulakis, Director and Chief Genetic Officer of Genotypos Science Labs, will present his experience with whole-exome sequencing (WES). In particular, he will describe:

  • How WES leads to improved results
  • A streamlined workflow enabling the sensitive detection of CNVs
  • A concrete case of a de novo CNV detection linked to growth retardation and hearing loss
Sponsored by
Tue
Oct
27
11:00 am2020
Sponsored by
LGC SeraCare Life Sciences

The Promise of Liquid Biopsy for Cancer Diagnostics and Therapeutic Monitoring: Are We There Yet?

GenomeWebinar

Professor of Molecular Oncological Pathology,
University of Groningen

Consultant Clinical Scientist and Director,
Genomics Quality Assessment

Scientific Associate
Institute of Pathology, Charité – Universitätsmedizin Berlin

This webinar brings together an expert panel of stakeholders in cancer diagnostics and clinical care who will discuss the promise and challenges of liquid biopsy technologies in cancer diagnosis, monitoring, and patient care management.

The use of circulating tumor DNA (ctDNA) as a surrogate sample type for tumor tissue is an area of significant clinical interest. ctDNA has been demonstrated to mirror the solid tumor mutational landscape and has the potential for early diagnosis of cancer as well as monitoring and tracking biomarkers associated with residual disease over time.

Despite this promise, there are still open questions regarding the best way to implement liquid biopsy approaches in the clinical setting. Our panel brings together academic, clinical, and industry experts in liquid biopsy technologies who will describe the applications of this technique and discuss its benefits and shortcomings in the context of cancer care.

Sponsored by

Associate Professor and Associate Department Head
Department of Agronomy and Horticulture, University of Nebraska-Lincoln

Director of Operations,
Agriplex Genomics

Director of Genomics Solutions,
NRGene

Molecular breeding methods such as genomic selection and genome-wide association studies often require high-density genotypic data from many samples, but the cost and complexity of genotyping at this scale may be prohibitive.

This presentation will outline three areas for improvement that can be combined for greatest impact: marker optimization, efficient genotyping, and data imputation. 

The challenge with marker optimization is to control cost by minimizing the number of SNPs genotyped yet obtaining an accurate description of each individual genome analyzed and capture the diversity within the breeding germplasm. We will offer methods for minimizing genotyping, allowing the analysis of more individuals, and data imputation generating high density data from sparse genotyping.

The development of a 1K SNP set for genomic selection in soy is presented as an example. The 1,000 soy SNPs were selected to provide maximum informativeness in US North Central Soy public breeding programs. The SNPs were developed into molecular inversion probes, a low-cost genotyping-by-sequencing method. This approach is cost-effective and provides high-quality genotypic data.

This presentation will next discuss PlexSeq, a novel approach for efficient mid-density SNP genotyping. PlexSeq uses artificial intelligence algorithms to create highly multiplexed genotyping assays followed by a unique and effective workflow. This technology has advantages in terms of efficiency and cost.

Next, the webinar will address SNPer, a method of SNP optimization and data imputation in three steps: 1) analysis of the breeding germplasm sequence and haplotype diversity; 2) optimization of SNP targets for genotyping by minimizing the number of targets and maximizing the information gained from each;  and 3) imputation of data at ungenotyped SNP loci. The result is a complete and accurate description of each sample genome.

Sponsored by
Thu
Oct
29
10:00 am2020
Sponsored by
Illumina

How to Train Your DRAGEN for Pathology Informatics

GenomeWebinar

Laboratory Director,
Xing Cancer Care

Illumina’s BaseSpace Sequence Hub (BSSH) supports primary and secondary analysis of massively parallel sequencing data and can be applied to gene panel data that is generated as part of a clinical cancer assay performed in a pathology lab.

In this webinar, Lynn Fink of Xing Cancer Care will discuss how her ISO15189-accredited lab has used BSSH to support informatics data analysis as part its routine testing and will share details of why the lab chose this platform over other options.

In particular, Lynn will share how the lab uses the BSSH-hosted DRAGEN (Dynamic Read Analysis for Genomics) apps — Enrichment, Germline, and Somatic — to perform in-depth coverage analyses of a 1,000 cancer gene panel, germline alteration calling, and tumor-normal paired somatic alteration calling, respectively. These apps support about 95 percent of the lab’s analytical needs.

Sponsored by

Lead Scientist, Molecular Profiling, NEO New Oncology

Molecular tumor profiling has provided extensive value, both in tumor biology and oncology, with the development of new technologies to identify biomarkers. While conventional technologies, such as FISH and PCR, allow accurate low-throughput detection (e.g., EML4-ALK fusion), next-generation sequencing-based approaches enable comprehensive and simultaneous identification of various alterations (single nucleotide variants, insertions/deletions, fusions, copy number alterations) and genomic signatures (microsatellite instability, tumor mutational burden).

Compared to conventional technologies, NGS-based approaches overcome the challenge of limited materials and reduce the turnaround time. However, further improvements are still needed due to the complex structure of the genome, including repetitive regions and high GC/AT content.

In this webinar, Dr. Judith Müller-Eisert of NEO New Oncology will discuss a collaboration with Agilent Technologies to develop several hybrid capture-based assays for various tumor entities using the SureSelect XT HS2 chemistry. She will share details of the kit’s performance and discuss its use as a powerful tool for cancer profiling.

For Research Use Only. Not for use in diagnostic procedures.

Sponsored by

Professor of Cancer Prevention,
Hutchison-MRC Research Centre, University of Cambridge

This webinar will provide an overview of novel proximal and distal sampling methods that have promise to improve patient outcomes from esophageal cancer.

Esophageal cancer is a global public health concern due to late presentation and poor patient outcomes. Esophageal adenocarcinoma has increased six-fold over the past 30 years in the UK, northwest Europe, Australia, and North America and it is generally preceded by a premalignant condition called Barrett’s esophagus.

In this webinar, Rebecca Fitzgerald of the Hutchison-MRC Research Center at the University of Cambridge, will discuss two non-endoscopic methods that show promise for improving patient care.

The first method relates to earlier diagnosis. Traditional diagnosis relies on endoscopy for those patients presenting with persistent heartburn unresponsive to medication, or alarm symptoms such as weight loss and dysphagia. Non-endoscopic methods that are affordable, acceptable, and easy to provide in the primary care setting could improve early detection. The Cytosponge-TFF3 test, combines a minimally invasive cell sampling device with immunohistochemical staining for the biomarker trefoil factor 3. The approach is a promising non-endoscopic method with substantial evidence to underpin its use, and Dr. Fitzgerald will present data from the recent randomized controlled trial BEST3.

For those patients diagnosed with invasive adenocarcinoma, earlier detection of relapse and indicators of response to therapy would help to tailor treatment. Blood biopsy to detect circulating tumor DNA is one such approach and Dr. Fitzgerald will present data to show the potential of a ctDNA mutation panel to detect relapse post-surgery in patients with esophageal adenocarcinoma in a retrospective study.

Sponsored by

Rachford and Carlota A. Harris Professor,
Department of Pathology, Stanford University

Most recent single-cell and spatial biology studies have focused on the network of interactions between different cell types and their spatial context. However, studying tumor biology at two different levels — the interacting cell types as well as the tissue regions within which they are organized — can give further insight into tumor progression and immunotherapy response.

Dr. Garry Nolan and his team at Stanford University collaborated with the University of Bern to conduct deep single-cell phenotyping and spatial analysis on a cohort of colorectal cancer formalin-fixed, paraffin-embedded samples using the CODEX (CO-Detection by indEXing) platform from Akoya Biosciences. As a result, the authors discovered nine distinct cellular neighborhoods, each uniquely composed of certain immune and cancer cell types. These cellular neighborhoods were found to interact with one another in a manner that correlated with disease progression and prognosis.

In this webinar, Dr. Nolan will discuss the findings from the study and present an analytical framework to analyze high-dimensional imaging data that can reveal new insights into how the tumor microenvironment is organized.

Learning objectives:

  • How to use high-dimensional imaging to study tumor biology at the single-cell and tissue architecture levels
  • How spatial interactions between cellular aggregates in the tumor microenvironment contribute to disease progression and prognosis in colorectal cancer
Sponsored by