Friday, May 17, 2024

AI Corner: Can AI Fix Bad Molecular Pathology Writing so CMS Can Read It?


Many labs are preparing their "crosswalk presentations" for CMS pricing meetings.  The decks are due May 30 and will presented on June 25.

Labs face the challenge of crafting applications that resonate with diverse audiences. These audiences include (1) CMS physicians, (2) CMS staff without clinical backgrounds, and (3) the CMS lab expert panel, which is composed of expert industry professionals.

Writing a presentation that satisfies all these groups can be daunting, plus, your presentation has to "register" amidst 100 other presentations.  It's like speed dating.  

The CMS PowerPoint template covers several sections, but for this post, I'll focus on "Background,"  "Purpose and Method," and"Resources." To illustrate how AI can assist with this task, I've asked Chat GPT to create a fictional test case, written in the three sections.  

  • First, AI generates a hypothetical molecular test, and writes a verbose version with overly long sentences and digressions.   
    • (Believe me, this is AI first draft is scary close to human first drafts I've seen.)
  • Then, AI rewrites the text at "college freshman" and "college junior" levels, demonstrating how AI can enhance clarity, brevity, and focus in scientific writing.




The evolution of cancer diagnostics has witnessed a significant breakthrough with the introduction of the OncoGen 5000, a state-of-the-art molecular diagnostic test meticulously crafted by Precision Genomics Inc. This innovative test employs a highly advanced technique known as next-generation sequencing (NGS), which is capable of sequencing DNA at an unprecedented scale and speed. The OncoGen 5000 meticulously analyzes over 800 genes that are known to be associated with various types of cancers, identifying mutations, copy number variations, and gene fusions that are pivotal for accurate cancer diagnosis, prognosis, and therapeutic decision-making. By generating an extensive genomic profile of the tumor, this test provides unparalleled insights into the genetic underpinnings of cancer. The results are compared against a vast and meticulously curated reference database, encompassing genetic data from a diverse cohort of cancer patients worldwide. This comparison not only enhances the accuracy of the diagnosis but also facilitates the development of personalized treatment regimens tailored to the unique genetic makeup of each patient's tumor. The significance of comprehensive genomic profiling in modern oncology is underscored by endorsements from leading medical organizations such as the American Society of Clinical Oncology (ASCO) and the National Comprehensive Cancer Network (NCCN), which advocate for the integration of such advanced diagnostic tools into clinical practice to optimize patient outcomes and advance the field of personalized medicine.


Background of the Test: The OncoGen 5000 test helps doctors understand the genetic changes in cancer cells. It looks at over 800 genes related to cancer to find important mutations and changes. This test uses next-generation sequencing (NGS) to compare a patient's tumor DNA with a database of genetic information from other cancer patients. The clinician can diagnose the cancer better and decide on the best treatment plan.


Background of the Test: The OncoGen 5000 is an advanced molecular diagnostic test designed to analyze genetic mutations in cancer cells using next-generation sequencing (NGS). It examines over 800 genes related to cancer, identifying mutations, copy number variations, and gene fusions. The test compares the tumor's genetic profile with a reference database containing genetic data from a diverse group of cancer patients. This approach, recommended in 2024 guidelines from ASCO and NCCN, aids in precise cancer diagnosis and personalized treatment planning, enhancing therapeutic outcomes.



Precision Genomics Inc. has developed the OncoGen 5000 with the primary objective of revolutionizing the precision of cancer diagnosis and the personalization of treatment strategies. This test leverages the capabilities of next-generation sequencing (NGS) to conduct a comprehensive analysis of genetic alterations present in tumor DNA. The workflow begins with the extraction of DNA from a tumor biopsy, followed by NGS, which sequences the DNA to identify genetic mutations, copy number variations, and gene fusions that are critical for understanding the molecular characteristics of the cancer. The extensive data generated from sequencing is processed through a sophisticated bioinformatics pipeline, which includes steps such as data alignment, variant calling, and annotation of genetic alterations. The test's advanced machine learning algorithms then compare the patient's genomic profile to an extensive and meticulously curated reference database. This comparison yields a detailed report that provides insights into the molecular underpinnings of the tumor, highlighting actionable mutations that can inform targeted therapy decisions. The precise genomic profiling enabled by the OncoGen 5000 is essential for tailoring treatment strategies to the individual patient, thereby optimizing therapeutic efficacy and minimizing adverse effects. This approach is in line with the principles of personalized medicine, which aims to provide tailored healthcare solutions based on the unique genetic makeup of each patient.


Purpose and Methodology of the Test: The OncoGen 5000 test helps doctors diagnose and treat cancer more accurately.  The method analyzes genetic changes in tumor DNA using next-generation sequencing (NGS). DNA is extracted from the tumor and sequenced to find mutations.  Results are compared to a large database. This helps doctors understand specific characteristics of the cancer and choose the best treatment.


Purpose and Methodology of the Test: The OncoGen 5000 is designed to improve cancer diagnosis and treatment by providing a detailed analysis of genetic mutations in tumors using next-generation sequencing (NGS). The process involves extracting DNA from a tumor sample, running quality controls, sequencing the DNA to identify mutations, and comparing the results to a validated reference database. Advanced algorithms then interpret the data, offering insights into the tumor's molecular profile and guiding personalized treatment strategies.  The process is both CAP- and New York State-validated.  This precise genomic profiling helps doctors make informed decisions about the best treatment options for each patient.



The successful implementation of the OncoGen 5000 test necessitates the availability of several critical resources, which are essential for conducting a comprehensive genomic analysis. Initially, a tumor tissue sample must be obtained through a biopsy, and high-quality DNA must be extracted from this sample. The extracted DNA undergoes next-generation sequencing (NGS) using highly specialized sequencing platforms, which are capable of generating vast amounts of genetic data in a relatively short time frame. The sequencing data is then processed through a series of bioinformatics pipelines that include crucial steps such as data alignment, variant calling, and the annotation of genetic mutations. The bioinformatics analysis is further supported by a proprietary reference database that contains genomic information from thousands of cancer patients, ensuring that the comparison is robust and clinically relevant. Additionally, the test requires advanced computational infrastructure to handle the large-scale data processing and the application of machine learning algorithms, which are vital for interpreting the genomic data. The entire workflow is conducted in a certified laboratory equipped with state-of-the-art technology and staffed by personnel with expertise in molecular biology, genetics, and bioinformatics. This combination of resources and expertise is paramount to ensuring the accuracy, reliability, and clinical utility of the OncoGen 5000 test results.


Resources Required to Run the Test: To conduct the OncoGen 5000 test, a sample of the tumor tissue is needed. The DNA is extracted from this tissue and analyzed using next-generation sequencing (NGS) technology. The test requires specialized sequencing machines, a large database for comparison, and advanced software to interpret the results. This process is done in a lab with skilled scientists.


Resources Required to Run the Test: The OncoGen 5000 test requires specific laboratory capabilities, including the extraction of high-quality DNA from tumor samples, next-generation sequencing (NGS) technology for analyzing the DNA, comprising a 500 MB data output, and advanced bioinformatics tools for data interpretation. The test also relies on a comprehensive reference database and sophisticated computational infrastructure. This analysis is conducted in certified laboratories staffed with experts in molecular biology, genetics, and bioinformatics. The combination of these extensive and regularly updated resources ensures the test's accuracy and reliability in providing clinically useful results.


Results were perhaps more impressive starting with "real" client text, which I couldn't share.  Similar approaches to re-writing might be used for tech assessment dossiers.   Also, when you've seen AI do these re-writes, authors might learn to write better first drafts the next time.