Is insourcing NGS testing worth it?
Dartmouth-Hitchcock has experienced nearly 40% savings by bringing NGS testing in-house. A recent AMP study using non-small cell lung cancer as an example cites $2.7 million in anticipated savings.
In-house NGS testing is the foundation of any modern precision medicine program. It can have a profound effect on patient care. And, as these examples show, a strong business case can be made.
How have Dartmouth-Hitchcock and other progressive institutions been so successful despite myriad challenges?
Join us for a webinar on May 31st at 12pm ET as Eric Loo, MD (Dartmouth-Hitchcock) and Rakesh Nagarajan, MD, PhD (PierianDx) explore answers to this question and more.
In this webinar you will learn:
How recent precision medicine trends are driving strong market growth for clinical NGS and other complex molecular testing.
How to make a strong business case for in-house NGS testing.
Challenges your institution is likely to face by insourcing.
Blueprints for overcoming these challenges, including reimbursement.
Cancer is a leading cause of death in developed countries. In this webcast Dr. Andreas Scherer will explain how personalized medicine can transform our approach to fighting this disease. He will also discuss current roadblocks and diagnostic challenges, and the pivotal role of Next Gen Sequencing to overcome these challenges.
The webcast will inform about best practices to design and implement a cancer testing pipeline: from sample preparation, to sequencing, to secondary and tertiary analysis of sequencing data. The goal is to rapidly identify clinically actionable data that allows an oncologist to quickly determine the best available treatment options.
The webcast will include demonstrations of the Golden Helix VarSeq software in the context of analyzing cancer gene panels and somatic mutations.
Forensic Sciences (DNA Fingerprinting) STR Typing - Case Reportnarmeenarshad
Identification of Human Remains by DNA Analysis of the gastrointestinal contents of Fly Larvae
A case Report that has been explained in form of presentation.
Talk from the SciLifeLab NGI NovaSeq seminar in September 2018. I describe how differences in illumina sequencing on the new NovaSeq 6000 can affect your sequencing, with illustrated examples from qcfail.com
Explain the basic mechanisms involved in DNA extraction.
Describe the steps involved in gDNA extraction from blood.
Explain the processes involved in quality and quantity check of extracted DNA using nanodrop technique.
Decribe the steps of quantity check of amplicon using flurometer.
Decribe the principle of dilution of amplicon.
Presented by,
Dr. Md. Mohiuddin Masum
Guided by,
Prof. Laila Anjuman Banu
State v. Mott: A Case Study in Forensic Sciencegcpolando
Presentation to Manchester College\'s Science Department; describes the legal aspects of forensic science in a trial presented by my elected prosecutor, Curtis Hill, and chief deputy, Vicki Becker.
Cancer is a leading cause of death in developed countries. In this webcast Dr. Andreas Scherer will explain how personalized medicine can transform our approach to fighting this disease. He will also discuss current roadblocks and diagnostic challenges, and the pivotal role of Next Gen Sequencing to overcome these challenges.
The webcast will inform about best practices to design and implement a cancer testing pipeline: from sample preparation, to sequencing, to secondary and tertiary analysis of sequencing data. The goal is to rapidly identify clinically actionable data that allows an oncologist to quickly determine the best available treatment options.
The webcast will include demonstrations of the Golden Helix VarSeq software in the context of analyzing cancer gene panels and somatic mutations.
Forensic Sciences (DNA Fingerprinting) STR Typing - Case Reportnarmeenarshad
Identification of Human Remains by DNA Analysis of the gastrointestinal contents of Fly Larvae
A case Report that has been explained in form of presentation.
Talk from the SciLifeLab NGI NovaSeq seminar in September 2018. I describe how differences in illumina sequencing on the new NovaSeq 6000 can affect your sequencing, with illustrated examples from qcfail.com
Explain the basic mechanisms involved in DNA extraction.
Describe the steps involved in gDNA extraction from blood.
Explain the processes involved in quality and quantity check of extracted DNA using nanodrop technique.
Decribe the steps of quantity check of amplicon using flurometer.
Decribe the principle of dilution of amplicon.
Presented by,
Dr. Md. Mohiuddin Masum
Guided by,
Prof. Laila Anjuman Banu
State v. Mott: A Case Study in Forensic Sciencegcpolando
Presentation to Manchester College\'s Science Department; describes the legal aspects of forensic science in a trial presented by my elected prosecutor, Curtis Hill, and chief deputy, Vicki Becker.
Fundamentals of Fluorescence in situ Hybridization Amartya Pradhan
This presentation provides an insight into the fundamentals of in situ hybridization (ISH), especially fluorescence in situ hybridization. It is ideal for classroom lecture.
Explore the Illumina workflow, including sequencing by synthesis (SBS) technology, in 3-dimensional detail. Go from sample preparation, to cluster generation, to sequencing on a system flow cell with the proprietary SBS process.
"SNP and STR analysis using NGS
Niels Morling, MD DMSc
Professor of Forensic Genetics
Chairman & Director
Department of Forensic Medicine
Faculty of Health and Medical Sciences
University of Copenhagen
Denmark"
Fluorescent in situ hybridization (FISH) is a molecular cytogenetic technique that uses fluorescent probes that bind to only those parts of the chromosome with a high degree of sequence complementarity. Creative Bioarray provides comprehensive FISH services and products to our clients.
Optimizing the Output of Your Molecular Pathology LaboratoryJosh Forsythe
If you are a clinical lab looking to build or accelerate your NGS testing capability where do you start? The components of success can be overwhelming - planning, assay design, validation, clinical lab workflow, informatics, and interpretation.
During this one-hour webinar, BG Jones, SVP of Business Development for PierianDx, who has 23 years of experience in healthcare IT and genomics technology, will demonstrate how to pull it all together using "Actionable Intelligence" - a combination of machine learning and human expertise to achieve clinically actionable insights.
Rakesh Nagarajan, MD, PhD and founder of PierianDx, discusses the rise of precision medicine programs and makes the business case for healthcare institutions to build their own clinical NGS testing programs.
Fundamentals of Fluorescence in situ Hybridization Amartya Pradhan
This presentation provides an insight into the fundamentals of in situ hybridization (ISH), especially fluorescence in situ hybridization. It is ideal for classroom lecture.
Explore the Illumina workflow, including sequencing by synthesis (SBS) technology, in 3-dimensional detail. Go from sample preparation, to cluster generation, to sequencing on a system flow cell with the proprietary SBS process.
"SNP and STR analysis using NGS
Niels Morling, MD DMSc
Professor of Forensic Genetics
Chairman & Director
Department of Forensic Medicine
Faculty of Health and Medical Sciences
University of Copenhagen
Denmark"
Fluorescent in situ hybridization (FISH) is a molecular cytogenetic technique that uses fluorescent probes that bind to only those parts of the chromosome with a high degree of sequence complementarity. Creative Bioarray provides comprehensive FISH services and products to our clients.
Optimizing the Output of Your Molecular Pathology LaboratoryJosh Forsythe
If you are a clinical lab looking to build or accelerate your NGS testing capability where do you start? The components of success can be overwhelming - planning, assay design, validation, clinical lab workflow, informatics, and interpretation.
During this one-hour webinar, BG Jones, SVP of Business Development for PierianDx, who has 23 years of experience in healthcare IT and genomics technology, will demonstrate how to pull it all together using "Actionable Intelligence" - a combination of machine learning and human expertise to achieve clinically actionable insights.
Rakesh Nagarajan, MD, PhD and founder of PierianDx, discusses the rise of precision medicine programs and makes the business case for healthcare institutions to build their own clinical NGS testing programs.
Challenges and Opportunities for Digital PCR in the CLIA Laboratory of the Mo...Kate Barlow
Anthony Magliocco, Chair of Anatomical Pathology, Moffitt Cancer Center, USA
The Moffit Cancer Center is one of the largest NCI designated comprehensive free-standing cancer centers in the USA. The center has developed one of the most advanced personalized cancer medicine treatment programs in the world. This program is supported by a comprehensive and advanced CLIA molecular diagnostics. Digital PCR assays are currently being developed for several clinical applications including TKI resistance monitoring in patients with advanced lung cancer. The challenges and opportunities in deploying digital PCR into clinical practice will be discussed.
Peter Hamilton on Next generation Imaging and Computer Vision in Pathology: p...Cirdan
Automated image analysis has had a long history but continues to grow with massive improvements in algorithms, speed, performance, and with emerging opportunities for high throughput tissue biomarker analysis and automated decision support for primary diagnostics. Of particular importance is the development of computer vision and image analysis for H&E stained samples. This talk will outline recent advances in automated tissue analysis for biomarker discovery and diagnostics and how adoption of digital pathology will drive the demand for quantitative imaging and decision support.
As an example, PathXL have developed TissueMark for the automated identification and analysis of tumour in lung, colon, breast and prostate cancer digital H&E slides. The conventional pathological estimation of % tumour nuclei in H&E samples shows gross variation between pathologists, undermining the quality of next generation sequencing, molecular testing and patient therapy and potential of false negative diagnoses. TissueMark uses a combination of pattern recognition, glandular analysis and nuclear segmentation to identify premaligant and invasive cancer patterns in H&E stained tissues and use this to assess tumour cell numbers and annotate samples for nucleic acid extraction and molecular profiling. Benchmark data was generated to validate TissueMark technology and showed concordance of automated data with manual counts, accelerating tumour markup and improving sample quality assessment. This represents an example of how automated imaging of tissue samples can be of immense value in quantitative tumour analysis for molecular diagnostics, thereby improving reliability in discovery and diagnostics.
This together with other examples in pathology research and practice will demonstrate that next generation tissue imaging technology in digital pathology could radically change how pathology is practiced.
Development of a new venture pioneering medical screening tests for a number of diseases simply though breath samples. This technology is changing the way people check on their health and will save millions of lives through the early detection of Lung cancer alone.
Next Generation Companion Diagnostics; Adoption, Drivers, and Moderators of N...Andrew Aijian
Analysis and synthesis of a pulse survey conducted across >140 oncologists, pathologists, and lab directors regarding current adoption and trends associated with emerging oncology biomarkers and companion diagnostics (CDx), with an emphasis on next-generation sequencing (NGS)-based CDx.
Personalized Medicine Through Tumor SequencingGolden Helix
One of the main recent advances in cancer therapy is the identification of medications that target specific gene mutations. In 2001 Gleevec was approved to treat patients with the BCR-ABL fusion in chronic myelogenous leukemia (CML), but since then many more drugs have been developed. Currently, there are numerous ongoing trials to identify tumor drivers that can be attacked by a drug. In order to identify the mutations driving a tumor, the tumor needs to be sequenced. There are a range of different approaches for sequencing tumors ranging from the sequencing of a few genes in the tumor up to paired whole-exome sequencing in both the tumor and adjacent normal tissue. Each type of sequencing has benefits and drawbacks and a balance needs to be made between cost and usability of the results. We have developed a clinical workflow for a 50 gene panel that identifies mutations in hotspots in known cancer genes. This workflow uses BaseSpace, VarSeq and N-Of-One to provide insight for our physicians and patients.
New & Improved COSMIC Database for NGS Cancer AnalysesGolden Helix
With Next-Gen Sequencing becoming a routine method of rapidly investigating cancer mutations, having access to accurate and large somatic variant catalogs is paramount. We at Golden Helix are excited to announce our newly released COSMIC 87 track. This updated version of the world's largest and most comprehensive somatic track provides a number of significant improvements. This includes not only an increase of ~1.1 million variants but also improvements on evidence accessibility and as always maintaining data quality. As a result of our 20+ years of bioinformatics experience, users have come to trust and rely on our data curation since our goal is to ensure highly efficient and accurate variant analysis. With this webcast, we are going to focus on the new capabilities users have when integrating COSMIC into their cancer workflow. We will also discuss the implications and value of relying on top data quality data curation maintained here at Golden Helix. Please join us as we seek to inform you on methods to optimize your cancer variant analysis!
Medical Deep Learning: Clinical, Technical, & Regulatory Challenges and How t...Devon Bernard
Deep Learning is proving to be a powerful tool that can improve healthcare for both patients and care-providers. In this talk I’ll cover an intro to some of the medical problems currently being solved by deep learning, market adoption, healthcare challenges (e.g regulation, data quality, data acquisition), deep learning challenges (e.g. model stability, training/convergence time, scalable training environment), and tips learned by tackling these problems head-on.
This talk was presented Oct 15, 2017 at http://ai.withthebest.com/.
Title: Sense of Taste
Presenter: Dr. Faiza, Assistant Professor of Physiology
Qualifications:
MBBS (Best Graduate, AIMC Lahore)
FCPS Physiology
ICMT, CHPE, DHPE (STMU)
MPH (GC University, Faisalabad)
MBA (Virtual University of Pakistan)
Learning Objectives:
Describe the structure and function of taste buds.
Describe the relationship between the taste threshold and taste index of common substances.
Explain the chemical basis and signal transduction of taste perception for each type of primary taste sensation.
Recognize different abnormalities of taste perception and their causes.
Key Topics:
Significance of Taste Sensation:
Differentiation between pleasant and harmful food
Influence on behavior
Selection of food based on metabolic needs
Receptors of Taste:
Taste buds on the tongue
Influence of sense of smell, texture of food, and pain stimulation (e.g., by pepper)
Primary and Secondary Taste Sensations:
Primary taste sensations: Sweet, Sour, Salty, Bitter, Umami
Chemical basis and signal transduction mechanisms for each taste
Taste Threshold and Index:
Taste threshold values for Sweet (sucrose), Salty (NaCl), Sour (HCl), and Bitter (Quinine)
Taste index relationship: Inversely proportional to taste threshold
Taste Blindness:
Inability to taste certain substances, particularly thiourea compounds
Example: Phenylthiocarbamide
Structure and Function of Taste Buds:
Composition: Epithelial cells, Sustentacular/Supporting cells, Taste cells, Basal cells
Features: Taste pores, Taste hairs/microvilli, and Taste nerve fibers
Location of Taste Buds:
Found in papillae of the tongue (Fungiform, Circumvallate, Foliate)
Also present on the palate, tonsillar pillars, epiglottis, and proximal esophagus
Mechanism of Taste Stimulation:
Interaction of taste substances with receptors on microvilli
Signal transduction pathways for Umami, Sweet, Bitter, Sour, and Salty tastes
Taste Sensitivity and Adaptation:
Decrease in sensitivity with age
Rapid adaptation of taste sensation
Role of Saliva in Taste:
Dissolution of tastants to reach receptors
Washing away the stimulus
Taste Preferences and Aversions:
Mechanisms behind taste preference and aversion
Influence of receptors and neural pathways
Impact of Sensory Nerve Damage:
Degeneration of taste buds if the sensory nerve fiber is cut
Abnormalities of Taste Detection:
Conditions: Ageusia, Hypogeusia, Dysgeusia (parageusia)
Causes: Nerve damage, neurological disorders, infections, poor oral hygiene, adverse drug effects, deficiencies, aging, tobacco use, altered neurotransmitter levels
Neurotransmitters and Taste Threshold:
Effects of serotonin (5-HT) and norepinephrine (NE) on taste sensitivity
Supertasters:
25% of the population with heightened sensitivity to taste, especially bitterness
Increased number of fungiform papillae
micro teaching on communication m.sc nursing.pdfAnurag Sharma
Microteaching is a unique model of practice teaching. It is a viable instrument for the. desired change in the teaching behavior or the behavior potential which, in specified types of real. classroom situations, tends to facilitate the achievement of specified types of objectives.
These simplified slides by Dr. Sidra Arshad present an overview of the non-respiratory functions of the respiratory tract.
Learning objectives:
1. Enlist the non-respiratory functions of the respiratory tract
2. Briefly explain how these functions are carried out
3. Discuss the significance of dead space
4. Differentiate between minute ventilation and alveolar ventilation
5. Describe the cough and sneeze reflexes
Study Resources:
1. Chapter 39, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 34, Ganong’s Review of Medical Physiology, 26th edition
3. Chapter 17, Human Physiology by Lauralee Sherwood, 9th edition
4. Non-respiratory functions of the lungs https://academic.oup.com/bjaed/article/13/3/98/278874
The prostate is an exocrine gland of the male mammalian reproductive system
It is a walnut-sized gland that forms part of the male reproductive system and is located in front of the rectum and just below the urinary bladder
Function is to store and secrete a clear, slightly alkaline fluid that constitutes 10-30% of the volume of the seminal fluid that along with the spermatozoa, constitutes semen
A healthy human prostate measures (4cm-vertical, by 3cm-horizontal, 2cm ant-post ).
It surrounds the urethra just below the urinary bladder. It has anterior, median, posterior and two lateral lobes
It’s work is regulated by androgens which are responsible for male sex characteristics
Generalised disease of the prostate due to hormonal derangement which leads to non malignant enlargement of the gland (increase in the number of epithelial cells and stromal tissue)to cause compression of the urethra leading to symptoms (LUTS
Couples presenting to the infertility clinic- Do they really have infertility...Sujoy Dasgupta
Dr Sujoy Dasgupta presented the study on "Couples presenting to the infertility clinic- Do they really have infertility? – The unexplored stories of non-consummation" in the 13th Congress of the Asia Pacific Initiative on Reproduction (ASPIRE 2024) at Manila on 24 May, 2024.
Flu Vaccine Alert in Bangalore Karnatakaaddon Scans
As flu season approaches, health officials in Bangalore, Karnataka, are urging residents to get their flu vaccinations. The seasonal flu, while common, can lead to severe health complications, particularly for vulnerable populations such as young children, the elderly, and those with underlying health conditions.
Dr. Vidisha Kumari, a leading epidemiologist in Bangalore, emphasizes the importance of getting vaccinated. "The flu vaccine is our best defense against the influenza virus. It not only protects individuals but also helps prevent the spread of the virus in our communities," he says.
This year, the flu season is expected to coincide with a potential increase in other respiratory illnesses. The Karnataka Health Department has launched an awareness campaign highlighting the significance of flu vaccinations. They have set up multiple vaccination centers across Bangalore, making it convenient for residents to receive their shots.
To encourage widespread vaccination, the government is also collaborating with local schools, workplaces, and community centers to facilitate vaccination drives. Special attention is being given to ensuring that the vaccine is accessible to all, including marginalized communities who may have limited access to healthcare.
Residents are reminded that the flu vaccine is safe and effective. Common side effects are mild and may include soreness at the injection site, mild fever, or muscle aches. These side effects are generally short-lived and far less severe than the flu itself.
Healthcare providers are also stressing the importance of continuing COVID-19 precautions. Wearing masks, practicing good hand hygiene, and maintaining social distancing are still crucial, especially in crowded places.
Protect yourself and your loved ones by getting vaccinated. Together, we can help keep Bangalore healthy and safe this flu season. For more information on vaccination centers and schedules, residents can visit the Karnataka Health Department’s official website or follow their social media pages.
Stay informed, stay safe, and get your flu shot today!
These lecture slides, by Dr Sidra Arshad, offer a quick overview of physiological basis of a normal electrocardiogram.
Learning objectives:
1. Define an electrocardiogram (ECG) and electrocardiography
2. Describe how dipoles generated by the heart produce the waveforms of the ECG
3. Describe the components of a normal electrocardiogram of a typical bipolar leads (limb II)
4. Differentiate between intervals and segments
5. Enlist some common indications for obtaining an ECG
Study Resources:
1. Chapter 11, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 9, Human Physiology - From Cells to Systems, Lauralee Sherwood, 9th edition
3. Chapter 29, Ganong’s Review of Medical Physiology, 26th edition
4. Electrocardiogram, StatPearls - https://www.ncbi.nlm.nih.gov/books/NBK549803/
5. ECG in Medical Practice by ABM Abdullah, 4th edition
6. ECG Basics, http://www.nataliescasebook.com/tag/e-c-g-basics
New Directions in Targeted Therapeutic Approaches for Older Adults With Mantl...i3 Health
i3 Health is pleased to make the speaker slides from this activity available for use as a non-accredited self-study or teaching resource.
This slide deck presented by Dr. Kami Maddocks, Professor-Clinical in the Division of Hematology and
Associate Division Director for Ambulatory Operations
The Ohio State University Comprehensive Cancer Center, will provide insight into new directions in targeted therapeutic approaches for older adults with mantle cell lymphoma.
STATEMENT OF NEED
Mantle cell lymphoma (MCL) is a rare, aggressive B-cell non-Hodgkin lymphoma (NHL) accounting for 5% to 7% of all lymphomas. Its prognosis ranges from indolent disease that does not require treatment for years to very aggressive disease, which is associated with poor survival (Silkenstedt et al, 2021). Typically, MCL is diagnosed at advanced stage and in older patients who cannot tolerate intensive therapy (NCCN, 2022). Although recent advances have slightly increased remission rates, recurrence and relapse remain very common, leading to a median overall survival between 3 and 6 years (LLS, 2021). Though there are several effective options, progress is still needed towards establishing an accepted frontline approach for MCL (Castellino et al, 2022). Treatment selection and management of MCL are complicated by the heterogeneity of prognosis, advanced age and comorbidities of patients, and lack of an established standard approach for treatment, making it vital that clinicians be familiar with the latest research and advances in this area. In this activity chaired by Michael Wang, MD, Professor in the Department of Lymphoma & Myeloma at MD Anderson Cancer Center, expert faculty will discuss prognostic factors informing treatment, the promising results of recent trials in new therapeutic approaches, and the implications of treatment resistance in therapeutic selection for MCL.
Target Audience
Hematology/oncology fellows, attending faculty, and other health care professionals involved in the treatment of patients with mantle cell lymphoma (MCL).
Learning Objectives
1.) Identify clinical and biological prognostic factors that can guide treatment decision making for older adults with MCL
2.) Evaluate emerging data on targeted therapeutic approaches for treatment-naive and relapsed/refractory MCL and their applicability to older adults
3.) Assess mechanisms of resistance to targeted therapies for MCL and their implications for treatment selection
- Video recording of this lecture in English language: https://youtu.be/lK81BzxMqdo
- Video recording of this lecture in Arabic language: https://youtu.be/Ve4P0COk9OI
- Link to download the book free: https://nephrotube.blogspot.com/p/nephrotube-nephrology-books.html
- Link to NephroTube website: www.NephroTube.com
- Link to NephroTube social media accounts: https://nephrotube.blogspot.com/p/join-nephrotube-on-social-media.html
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Explore natural remedies for syphilis treatment in Singapore. Discover alternative therapies, herbal remedies, and lifestyle changes that may complement conventional treatments. Learn about holistic approaches to managing syphilis symptoms and supporting overall health.
5. The Inflection Point
CMS finalized a National
Coverage Determination that
covers diagnostic laboratory
tests using Next Generation
Sequencing (NGS) for patients
with advanced cancer.
CMS.gov
Kymriah is the first gene therapy
approved in the US, to treat
children with advanced leukemia.
Merck’s Keytruda is the first
immunotherapy treatment
approved for all solid tumors
based on a genomic biomarker.
Sep’17
Aug’17
Nov’17
Nov’17
Oncomine Dx, MSK-IMPACT, and
FoundationOne CDx are the
first NGS tumor profiling assays
to gain FDA approval.
Mar’18
Jun’17
6. Strong Growth Underway
Clinical genetic testing labs
% of total commercial vs. hospital
Source: Epstein Health
% of somatic testing among 4 labs vs all other labs
$8.0B
5.5 MM
Tests
2017
1.1MM
NGS
2020
3.2MM
NGS
$11B
8.0 MM
Tests
Quest, LabCorp, Genomic Health, Foundation Medicine
12-15% per annum
revenue growth
20% NGS in 2017
40% NGS in 2020
8. Precision Medicine & The Learning Health System
Insourcing has allowed Intermountain to
“control all genomic and associated
clinical data and has reduced turnaround
time and lowered costs.”
“Clinical and molecular information from
patients who undergo NGS testing is
included in a centralized, longitudinal
data registry used for clinical treatment
decision support and research.”
Stanford program not only improves
patient outcomes but also support its
efforts to “improve its position in the
clinical marketplace.”
Control
Institutional
Learning
Competitive
Advantage
12. Ex. Non-Small Cell Lung Cancer (NSCLC) 6% 13%
83% 20%
207 138
4% 54%
7% 13%
$8.4MM $2.2MM
$1.1MM $2.3MM
$ N/A $N/A
$? $2.7MM
$? $.06MM
EGFR and ALK
Mutational Analysis
GSP (81445)
5-50 Gene Tumor
Panel
Targeted
Clinical Trial
(Targeted)
Non Targeted
Hospice
Targeted
Therapy
Clinical Trial
Selection
Non Targeted
Selection
Hospice Care $10.2MM $7.5MM
$2.7 Million
anticipated
savings for a
health plan
covering
1 million lives
13. Growing Body of Evidence
8900 Patients diagnosed with
melanoma per year in US
$79.5 million annuals savings
155 quality-adjusted life years
Overall Survival:
25.8 weeks vs. 51.7 weeks
Cost Savings:
$733 per week of survival
Sequential Exclusionary Panel NGS
Total Cost $3,721,368 $3,584,177 $4,331,295 $2,190,499
Savings $1,530,869 $1,393,678 $2,140,795
Total Costs $747,771 $624,178 $871,211 $620,369
Savings $127, 402 $3,809 $250,842
CMS
Private
Pay
15. Build Strategic Capabilities
Amount of data to curate
Validation of
clinical testing protocols
Scarcity of informatics expertise
Expense of implementation
Rapidly changing
nature of technologies
In the “new molecular biology”
excellence in analytics and data will be
the source of long-term clinical value.
‟
Difficulty of getting first
“application” deployed
20. Library
Extraction,
Sample Prep
Sequencing
Variant Calling
(Bioinformatic
Pipelines)
Variant
Annotation &
Classification
Data
Visualization,
QC Analysis
Final Report &
Medical
Director
Sign-out
Data
Integration
EMR, 3rd
Party
Clinical
Interpretation
& Reporting
Take an Economical, Modular Approach
A CLIA/CAP certified lab is allowed to
outsource any of the three components
to another CLIA/CAP certified lab.
ProfessionalDry LabWet Lab
22. PierianDx Gateway Lab Services
Indication # of Genes
Solid Tumors 122
Heme Disorders 54
Breast Tumors 42
CNS Tumors 48
Genitourinary Tumors 50
Head and Neck Tumors 41
Melanoma 38
Thoracic Tumors 36
Indication # of Genes
Myeloid 65
Lymphoid 61
Indication # of Genes
Inherited Cancer 94
Indication # of Genes
Cardiomyopathy 91
3rd Party Bill Available
23. Assay Validation
Minimum # of variants assessed per type to
achieve certain confidence level ✓
Assess limitations by variant type (e.g. max
length of indels detected by the assay) ✓
Determine acceptance and rejection criteria
based on analytical validation ✓
Determine lower limit of detection as a function
of coverage and variant allele fraction ✓
New in 2017
24. Final
Report
REF Call
Filtering
Splice Variant
Filter
Re-
Classification
Sequence
Alignment
Variant
Identification
CNV
Conversion
Fusion
Identification
VCF Tag
Display
Primary
Variant Filter
Panel Filters
Medical
Interpretation
Therapies
Clinical Trials
Auto
Classification
Review
Patient Data
Run QC
DNA Only RNA Only DNA/RNA
Lung
Subpanel
GIST
Subpanel
CNS
Subpanel
Colorectal
Subpanel
Melanoma
Subpanel
All Genes
Review Case
Data
DNA QC
Report
Fastq
DNA
BAM
RNA
BAM
DNA/RNA
BAM
Raw
Variant
Calls
Final
VCF
RNA QC
Report
Draft
Report
Auto
Interpretation
Variant QC
HGVS
Annotation
Robust Informatics Solutions
Illumina TST170 Example
25. Putting it All Together
Insourcing Success “Working with PierianDx has been an ideal partnership.
They have been with us since the early onset of our
program, providing both the technology and services that
allowed us to ramp our program much faster.”
— Dr. Anthony Magliocco
Exec. Director, Esoteric Laboratory Services
#18
Solid tumor & heme
NGS tests go live
1st patient cases run
Moffitt partners with
PierianDx
PierianDx Lab Services
added, increases
Moffitt’s capacity
Interpretation Services
added
NGS informatics
upgraded
>120,000 enrolled in Total
Cancer Care Study
First TST 170 assay
validated for clinical use
#9
May 2014 Oct 2014 Nov 2015 Jan 2016 Jan 2017 Today
27. 417 bed acute/3° care hospital
19,479 admissions last year
8,376 input + 10,961 outpt surgeries
NCI CCC: Norris Cancer Center
Children’s Hospital at Dartmouth (CHaD)
28. Dartmouth-Hitchcock
Dartmouth-Hitchcock
Androscoggin Valley Hospital
Weeks Medical Center
Upper Connecticut Valley Hospital
Speare Memorial Hospital
Valley Regional Hospital
Alice Peck Day Hospital
Colebrook
BerlinLancaster
New London
Claremont
Concord
Manchester
Keene
Cheshire Medical Center
PlymouthNew London Hospital
Lebanon
Nashua
Mt. Ascutney Hospital
Windsor, VT
Woodsville
Cottage Hospital
29. Why Invest in NGS?
Clinical Mission
Oncologists are going to order and
use testing results
Would have to provide access
internally or externally
Question: Can we make it for less
than what we “buy” it for?
Academic Mission
Advance health through research
and education
30. Clinical Genomics & Advanced Technology (CGAT) Disciplines
CMS
Reportable
CMS
Non-Reportable
Chemistry 4,300,000 0
Hematology 418,544 30,627
Microbiology 240,000 2,711
Anatomic Pathology 229,247 1,110
Transfusion Medicine 31,492 0
Point of Care 25,000 390,000
CGAT 23,636 0
Chemistry - Special 7,506 24,407
Flow-Cytometry 3,375 17,210
Cytogenomics 2,301 0
‘16 Total DHMC Vol. 43,981,101 466,065
Goals
Keep send-out volume <5% of total
Keep send-out expense <7-8% of
total lab expenses
Plan
Make vs. Buy
Test utilization
Aggressive contracting with
reference labs
31. CGAT Testing
Breast CA
Panel
“Cancer” Panel
Colorectal
Panel
Glioma
Panel
Lung CA
Panel
Myeloid
Neoplasm
Panel
23%33% 23% 21%
Solid Tumor “Genetic” Infectious D. Heme
9%81%
6
%
4
%
Solid Tumor
“Genetic”
Infectious Disease
Heme
32. Make vs. Buy
81445 vs 81450 Myeloid ~$600 ~$2,000 ~$2,700 122
81445 vs 81445 Lung CA ~$300 ~$800 ~$1,400 219
81445 vs 81445 Melanoma ~$300 ~$800 ~$1,500 60
81445 vs 81450 Myeloid ~$75,000 ~$215,000 ~$325,000
81445 vs 81445 Lung CA ~$70,000 ~$175,000 ~$300,000
81445 vs 81445 Melanoma ~$20,000 ~$50,000 ~$90,000
~$165,000 ~$440,000 ~$715,000
Savings 76.79% 38.57%*
To Lab To Institution *Dollar figures were altered for
confidentiality. Savings are accurate.
33. CGAT Clinical Workflow
Clinical
Interpretation
Send Report to
Interp Serv
Re-
classification
Run QC
Accession
Case Data
Hybridization
of Oligo Pool
DNA QC
Report
Fastq
File
BAM
File
Final
VCF
Remove Un-
bound Oligos
Final
Report
Extend Ligate
Bound Oligos
PCR
Amplification
Library
Normalization
PCR Cleanup
Library
Quantification
LIbrary Pooling
Sequencing
Prepare,
Upload Files
Upload Run
Details
Queue Run
Analysis
Variant QC
Return
Report
Review,
Analyze Report
Sign Out
Report
Draft
Report 2
ProfessionalDry BenchWet Bench
Technician Technician Bioinformatician Genomic Analyst
CGAT Faculty
PierianDx
Interp. Services
CGAT Faculty
Draft
Report 1
34. CGAT Dry Lab Workflow
Re-
Classification
Sequence
Alignment
Variant
Identification
Filter
Medical
Interpretation
Therapies
Clinical Trials
Auto
Classification
Run QC
DNA QC
Report
Fastq
File
BAM
File
Raw
Variant
Calls
Draft
Report 1
Auto
Interpretation
Variant QC
HGVS
Annotation
Final
VCF
Review
Patient Data
Cancer
Subpanels
All Genes
Review Case
Data
Draft
Report2
ServicesSoftware Reports Data
Final
Report
35. Uniform Structure of Interpretation
Note: The case disease is provided as 'Myeloproliferative
neoplasmv(MPN)'. The WHO classification of MPN includes following
sub-categories: Chronic myeloid leukemia, BCR-ABL1 positive; Chronic
neutrophilic leukemia (CNL); Polycythemia vera (PV); Primary
myelofibrosis (PMF); Essential Thrombocythemia (ET); Chronic
eosinophilic leukemia, not otherwise specified (NOS); Myeloproliferative
neoplasm, unclassifiable (PMID: 27069254). Myelofibrosis (MF),
polycythemia vera (PV) and Essential Thrombocythemia (ET) are a group
of heterogeneous disorders of the hematopoietic system collectively
known as Philadelphia chromosome-negative myeloproliferative
neoplasms (MPN) (NCCN, MPN v2.2017).
Interpretation: ASXL1 is a member of the polycomb group of proteins,
which are necessary for the maintenance of stable repression of homeotic
and other loci. The protein is thought to disrupt chromatin in localized
areas, enhancing transcription of certain genes while repressing the
transcription of other genes(RefSeq, Sep 2009). Somatic ASXL1
mutations are found in primary myelofibrosis (PMF), chronic
myelomonocytic leukemia (CMML), myelodysplastic syndromes (MDS),
and acute myeloid leukemia (AML) (PMID: 22436456).
An insertion in ASXL1 leading to a frameshift truncation (G646Wfs*12) is
identified in this patient with a VAF 38.54%. Codon 646 lies in exon 12 of
ASXL1 and G646Wfs*12 is expected to result in loss of the
C-terminalhistone/DNA-binding plant homeodomain (PHD) (PMID:
19609284). Mutations resulting in the deletion of the PHD domain of SXL1
are known to result in the loss-of-function
(Ref:http://www.bloodjournal.org/content/120/21/2393?sso-checked=true).
ASXL1 G646Wfs*12 is one of the frequently reported ASXL1 mutation in
hematopoietic neoplasms (COSMIC, accessed June 2017). A recent
study reported that ASXL1 mutations are more frequently identified in
PMF and PV as compared to ET (PMID: 28419183).
ASXL1 mutations are independently associated with inferior overall
survival and leukemia-free survival in PMF (NCCN, MPN v2.2017). Per
NCCN, in PMF, survival is shortest in CALR(-)ASXL1(+) patients (median
2.3 years) (NCCN, MPN v2.2017). ASXL1 mutations are also associated
with inferior overall survival, leukemia-free survival or fibrosis-free survival
in PV (PMID:27991718).
We try to maintain a uniform structure to
the interpretation to keep uniformity in
reports across signout pathologists.
We are in the process of creating
“canned” comments for recurring
scenarios.
Not shown are sections 5: Approved/Emerging Therapies) and
6: Concluding Remarks or Other Comments).
36. Biobanking and Big Data
DHMC Biobank
Managed by Pathology Dept
Pair genomic data to all banked specimens
for research and collaboration
BC Platforms
Research / Industry collaboration
Sample & clinical data management
Genotype knowledge base for pharma
37. Technical staff
Administration
Management
NGS Takes a Team Effort
Ideally: 3 clinical lab
scientists
Ideally: At least 2
bioinformaticians
IT support staff
Molecular genetics
boarded physicians
and scientists
38. Advanced Technologies
CGAT is using reagent rental
E.g. machines for extraction, RT-PCR,
robots to automate portions such as
library prep, etc
39. IT and Informatics
Lab IT
Integration
Cloud must be
HIPAA
Compliant
Data warehousing,
storage and
redundancy
EMR
Integration
Informatics and
Reporting
Hospital Lab
40. In-house testing met educational
mission and made financial sense
Could be feasible if specimen
volumes are high enough
It IS an investment (money, time,
personnel, IT resources, etc)
Not everything in the pipeline needs
to be done in-house
Can keep pace with ‘wet-lab’
work, but explosion of data is
difficult to manage
Need more staff positions, but
not granted due to institutional
budgetary constraints
And...
In Summary
42. MolDX Program*
Other Regional MAC LCDs
CMS National Coverage Decision
Reimbursement
Major health plans utilize laboratory
benefits management (LBM) programs
Insurers realizing they lack the expertise in
this field to rein in fraud & abuse
Potential cost-savings in driving business
to preferred in-network labs
43. MolDX and MACs
JF
Noridian
JE
Noridian
J5 WPS
JH
Novitas
J6 NGS
J8 WPS
JK NGS
JL
NovitasJ15
CGS
JM
Palmetto
JJ
Palmetto
JN
FSCO
All labs performing
MolDX testing and
submitting claims to
Medicare are
affected
Palmetto GBA
maintains “Master
Edit File” that’s
updated weekly
and distributed to
participating MACs.
Participating
Palmetto MACs
44. AMA Codes Code Category/Description ‘18 MolDX CPT Code Range
Tier 1 81105-81112, 81120-81121,
81161-81383
Tier 2 81400-81408
Genomic Sequencing Procedures 81410-81471
Molecular Multianalyte Assays 81490-81595
MAAA Admin. Codes All Codes
Immunology 86152-86153
PLA All Codes
Cytology 88120-88121
Not otherwise classified (NOC) 81479, 81599, 84999, 85999,
86849, 87999, 88199, 88299,
88399, and 89398
If in a jurisdiction with MolDX and
want to submit a MDT claim, you’re
going to need a “Z-code”
Z-code = unique identifier for your
lab’s assay
If assay is a LDT, getting registered
can be rather onerous
45. Dealing with Prior Auth
Revenue cycle management services
Generate list of denials → ID insurance groups
to target
Work with payers to determine the patient
subset where auth is needed
Team for submitting prior-auth requests for
lab-generated testing
Run test cases to ID the true turnaround time
for authorization
46. CGAT
CGAT- Admin
Heather Steinmetz
Amber Erskine
Samantha Allen
Mohammad Azim
Greg Tsongalis
Wendy Wells
CGAT- Fellows
Aaron Atkinson
M. Rabie Al-Turkmani
Precision Summer Interns
Rachel Barney – UVM
Sarah Benware – UNH
Jamie Dinulos – Dartmouth
Mackenzie Keegan – Northeastern
CGAT-Core
Natasha Aekus
Jing Bao
Leanne Cook
Sophie Deharvengt
Betty Dokus
Torrey Gallagher
Justin Giffin
Kelley Godwin
Donald Green
Cameron Griffin
Arnold Hawk
Brianna Houde
Guohong Huang
Edward Hughes
Michael Johnston
Kathryn Kearns
Collin Keegan
Jennifer Kilburn
Elizabeth Melchiona
Jason Peterson
Jenna Schofield
James Stevens
Stephanie Vallee
Terri Wilson
CGAT- Histology
David Beck
Rebecca O’Meara
Scott Palisoul
CGAT- Clinical
Mark Cervinski
Francine de Abreu
Deana Denault
Mary Beth Dinulos
Joel Lefferts
Carol Liu
Eric Loo
Robert Nerenz
Bing Ren
Laura Tafe
47. Ready to Get Started?
1
3
4
Now is the time.
Invest intelligently.
Build critical competencies.
2 Establish a leadership strategy.
5 Practice better medicine.
Dedicated curation and
interpretation team
Expert validation services
World-class PhDs and MDs
Robust informatics and reporting
Partner with leading assay vendors
Proven, successful deployments
48. We Learn from the Best
We leverage the expertise of the
most advanced labs and
productize for every hospital.
49. PierianDx
Neha Agarwal
Sachin Agre
Shubham Aher
Madiha Ahmed
Sonalee Athavankar
Shabbir Bata
Matts Bell
Andy Bredemeyer
Erin Buck
Chris Callahan
Bryce Daines
Indraneel Damle
Vishal Dawange
Sumit Deshmukh Bela
Dhamangaonkar
Dnyaneshwar Ekande
Josh Forsythe
Swapnil Gaikwad
Amruta Gandhe
Suprita Ghode
Sayali Gokhale
Brad Herrick
Harshal Inamdar
Shweta Jangam
Anuja Jedhe
BJ Jones
Aditya Joshi
Prachi A. Joshi
Prachi P. Joshi
Sneha Joshi
Pavan Kalantri
Ankita Kathal
Mamata Khirade
Ram Kotta
Rujuta Kshirsagar
Vinay Kusuma
Sufiya Lathiwale
Bhakti Limaye
Kedar Limbkar
Michelle Marcial
Tyler Marquart
Shweta Mohite
Will Moller
Andy Olson
Susan Pais
Bhushan Patil
Suarabh Patil
Pramila Phadtare
Aditi Phatak
Aditya Phatak
Samuel Pillay
Neha Purandare
Deepthi Rajagopalan
Nandini Sahasrabuddhe
Prachi Salgude
Niharika Sane
Rishikesh Sarode
Nilam Satpute
Sukanya Sengupta
Mukesh Sharma
Kalyanee Shirlekar
Savita Shrivistava
Gaurav Singh
Neeraj Singh
Vivek Suradkar
Jack VanDover
Rhucha Vatturkar
Shalini Verma
Gautam Wad
Lisa Weingartner
Abby Whitson
Jia Zhou
Junfei Zhu
50. Eric Loo, MD
Assistant Professor, Pathology &
Lab Medicine, Dartmouth-Hitchcock
eric.y.loo@hitchcock.org
Rakesh Nagarajan, MD, PhD
Chief Executive Officer and Founder
PierianDx
rakesh@pieriandx.com
Thank You
Type questions here
51. Offer for Webinar Attendees
To Qualify*
1. Attend this webinar (great job!)
2. Must be from a health institution
or laboratory (i.e. no vendors)
3. Participate in an introductory
consult (via phone)
To Apply
1. Email forsythe@pieriandx.com
2. Provide a brief description of your
program and interest in NGS
*Limit to the first 10 who qualify