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Posts Tagged ‘10X genomics’

Real Time Conferecence Coverage: Advancing Precision Medicine Conference Philadelphia PA November 1,2 2024  Deliverables

Curator: Stephen J. Williams, Ph.D.

Below are deliverables in form of real Time conference coverage from the Advancing Precision Medicine Confererence held this year in Philadelphia, PA.  The meeting brought together scientists and clinicians to discuss the challenges faced in implementing genomics and proteomics into precision medicine decision making workflow.  As summarized by a future release at the 2025 ASCO, there are many issues and hindrances to incorporating data obtained from sequencing to make a personalized medicine strategy.  The meeting focused on two main disease states: oncology and cardiovascular however most of  the live meeting notes are from the oncology tract.  In general it was discussed there are three areas which need to be addressed to correctly and more frequently incorporate precision medicine and genomic panel testing into clinical decision making workflow:

  1.  access to testing panels and testing methodology for both doctors and patients
  2. expert interpretation of results including algorithms needed to analyze the data
  3. more education of molecular biology and omics data and methodology in medical school to address knowledge gaps between clinicians and scientists

The issues can be summarized by a JCO report to ASCO in 2022:

 Helen Sadik, PhDDaryl Pritchard, PhD https://orcid.org/0000-0003-2675-0371 dpritchard@personalizedmedicinecoalition.orgDerry-Mae Keeling, BScFrank Policht, PhDPeter Riccelli, PhDGretta Stone, BSKira Finkel, MSPHJeff Schreier, MBA, and Susanne Munksted, MS.  Impact of Clinical Practice Gaps on the Implementation of Personalized Medicine in Advanced Non–Small-Cell Lung Cancer. 2022: JCO Precision Oncology; Volume 6. https://doi.org/10.1200/PO.22.00246

Personalized medicine presents new opportunities for patients with cancer. However, many patients do not receive the most effective personalized treatments because of challenges associated with integrating predictive biomarker testing into clinical care. Patients are lost at various steps along the precision oncology pathway because of operational inefficiencies, limited understanding of biomarker strategies, inappropriate testing result usage, and access barriers. We examine the impact of various clinical practice gaps associated with diagnostic testing-informed personalized medicine strategies on the treatment of advanced non–small-cell lung cancer (aNSCLC).

The authors used a  Diaceutics’ Data Repository, a multisource database including commercial and Medicare claims and laboratory data from over 500,000 patients with non–small-cell lung cancer in the United States. They  analyzed the number of patients with newly diagnosed aNSCLC who could have, but did not, benefit from a personalized treatment. The analysis was focused on identifying the gaps and at which steps during care did gaps existed which precipitated either lack of use of precision medicine testing or incorrect interpretation of results.

Their conclusions were alarming:

Most patients with aNSCLC eligible for precision oncology treatments do not benefit from them because of clinical practice gaps. This finding is likely reflective of similar gaps in other cancer types. An increased understanding of the impact of each practice gap can inform strategies to improve the delivery of precision oncology, helping to fully realize the promise of personalized medicine.

The links to the live meeting notes are given below and collection of tweets follow (please note this meeting did not have a Twitter hashtag)

Real Time Coverage Advancing Precision Medicine Annual Conference, Philadelphia PA November 1,2 2024

https://pharmaceuticalintelligence.com/2024/11/01/real-time-coverage-advancing-precision-medicine-annual-conference-philadelphia-pa-november-12-2024/

Real Time Coverage Morning Session on Precision Oncology: Advancing Precision Medicine Annual Conference, Philadelphia PA November 1 2024

https://pharmaceuticalintelligence.com/2024/11/01/real-time-coverage-morning-session-on-precision-oncology-advancing-precision-medicine-annual-conference-philadelphia-pa-november-1-2024/

Real Time Coverage Afternoon Session on Precision Oncology: Advancing Precision Medicine Annual Conference, Philadelphia PA November 1 2024

https://pharmaceuticalintelligence.com/2024/11/01/real-time-coverage-afternoon-session-on-precision-oncology-advancing-precision-medicine-annual-conference-philadelphia-pa-november-1-2024/ 

Real Time Coverage Morning Session on Precision Oncology: Advancing Precision Medicine Annual Conference, Philadelphia PA November 2 2024

https://pharmaceuticalintelligence.com/2024/11/04/real-time-coverage-morning-session-on-precision-oncology-advancing-precision-medicine-annual-conference-philadelphia-pa-november-2-2024/ 

Tweet Collection

Tweet Collection Advancing Precision Medicine Conference November 1,2 2024 Philadelphia PA

 

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Real Time Coverage Morning Session on Precision Oncology: Advancing Precision Medicine Annual Conference, Philadelphia PA November 2 2024

Reporter: Stephen J. Williams, Ph.D.

9:20-9:50

How Can We Close the Clinical Practice Gaps in Precision Medicine?

Susanne Munksted, Diaceutics

Studies are showing that genetic tests are being ordered at a sufficient rate however it appears there are problems in interpretation and developing treatment plans based on omics testing results

 

  • 30 % of patients in past and now currently half of all patients are not being given the proper treatment based on genomic testing results (ASCO)
  • E.g. only 1.5% with NTRK fusions received a NTRK based therapy (this was > 4000 patients receiving wrong therapy)
  • A lung oncologist may only see one patient with NTRK fusion in three years

 

Precision Medicine Practice Gaps

48% of oncologist surveyed  agreed pathologist needs to be more informed and relevant in the decision making process with regard to tests needing to be ordered

95% said need to flip cost issues ; what does it cost not to get a test … i.e. what is the cost of the wrong therapy

We need a new commercialization model for therapeutic development for this new era of “n of one” patient

9:50-10:15

Implementation of a CLIA-based Reverse Phase Protein Array Assay for Precision Oncology Applications: Proteomics and Phosphoproteomics at the Bedside (CME Eligible)

Emanuel Petricoin, George Mason University

There are some tumor markers approved by FDA that cant just be measured by NGS and are correlated with a pathologic complete response

 

  • Many point mutations will have no actionable drug
  • Many alterations are post-genomic meaning there is a post translational component to many prognostic biomarkers
  • Prevalence of point mutation with no actionable mutation is a limit of NGS
  • It is important to look at phospho protein spectrum as a potential biomarker

 

Reverse phase protein proteomic analysis

  • Made into CLIA based array
  • They trained centers around the US on the technology and analysis
  • Basing proteomics or protein markers by traditional IHC requires much antibody validation so if the mass spectrometry field can catch up it would be very powerful
  • With multiple MRM.MS there is too low abundance of phosphoproteins to allow for good detection

 

They  conducted the I-SPY2 trial for breast cancer and determining if phosphoproteins could be a good biomarker panel

  • They found they could predict a HER2 response better than NGS
  • There were patients who were predicted HER2 negative that actually had an activated HER2 signaling pathway by proteomics so NGS must have had a series of false negatives
  • HER2 co phosphorylation predicts pathologic complete response and predicts therapy by herceptin
  • They found patients classified as HER2 negative by FISH were HER2 positive by proteomics and had HER2 activation

10:15-11:10

Liquid Biopsy MRD to Escalate or De-escalate Therapy (CME Eligible)

Adrian Lee

Adrian Lee, UPMC

Marija Balic, UPMC

Howard McLeod

Howard McLeod, Utah Tech University

Muhammed, Murtaza, University of Wisconsin-Madison

 

11:15-11:25  PRODUCT PRESENTATION  204A

SpaceIQ™ – Powering Next Generation Precision Therapeutics with AI-Driven Spatial Biomarkers

Dusty Majumdar, PredxBio 

Single Cell and Spatial Omics

 

  • Single cell transcriptomics technology have been scaled up very nicely over the past ten years
  • Spatial informatics field is lacking in innovations
  • Can get a terabyte worth of data from analysis of one slide

11:25-11:35  PRODUCT PRESENTATION  204C

10x Genomics

11:40-12:35

Transcriptomics and AI in Transforming Precision Diagnosis

Maher Albitar, Genomic Testing Cooperative

Transciptomica and AI:Transforming Precision diagnosis

-The Genomics Testing Coopererative at www.genomictestingcooperative.com

 

Advantages of transcriptomics

– mutation frequency and allele variant detection now at 80% (higher sensitivity in mutation detection)

 

– transcriptomics has good detection of chromosomal translocations

– great surrogate for IHC and detect splicing alterations

– can use AI to predict % of PDL1 in tumor cells versus immune cells

– they have developed a software UMAP (uniform manifold approximation and projection) to supervise cluster analysis

– the group has used AI to predict prognosis and survival using transcriptomics data

Marija Balic, UPMC

Andrew Pecora, Hackensack University Medical Center 

12:35-1:00

The Impact of Multi-Omics in the Context of the APOLLO-2 Moonshot Program (CME Eligible)

 

 

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