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Precision Diagnostics in Oncology

Pioneering Early Cancer Detection with Liquid Biopsy in Egypt - An ASRT Initiative in Association with Oncophenomics, USA

Executive Summary

We are proposing to upgrade any existing routine biochemistry/pathology / molecular biology lab into a full-fledged Next Generation Sequencing lab at the partner location. We will supply all the instruments, kits, reagents, and consumables as a one-stop source for the complete lab setup. The primary focus will be on advanced cancer diagnostics tests and medical genetics using the latest in NGS technology - Nanopore Sequencing. We will install a GridION + P2 Solo setup so that we will have the flexibility to run 5 MinION flowcells at the same time, plus two bigger capacity PromethION flowcells when needed, thereby increasing our operational capacity from 30GB to 300GB TMO. With this setup, we can provide various NGS services to the entire hospital and diagnostics lab network in Egypt. As the sample volumes grow, we can upgrade to a PromethION 24 or 48 model in the future.
GridION plus P2 Solo gives the advantage of mix and match small, medium, and high volume samples ~48 samples simultaneously per batch run for 72 hours.
PromethION 24 model, we can go up to 1440 samples in one batch of 72 hours - $250,000 upgrade cost, not included in the current budget.
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Directory of Services

1. Medical Genetics - Pediatrics

Rare Diseases
De Novo Sequencing
Trios Analysis - Mother, Father, Child
Pathogenic Variant Detection according to ACMG, AMP, CAP, and CLIA Guidelines

2. Reproductive Medicine - Carrier Screening

Preimplantation Genetics - PGD, PGS, Carrier Screening, known history of genetic illness
IVF Clinics - Embryo Screening and selection of healthy embryos for implantation (need PCPNDT license and neonatalogist approval)
NIPT - Comprehensive Non-Invasive Prenatal Diagnostic testing - not just aneuploidies but a complete list of known pediatric diseases
Newborn Screening - as per ACMG guidelines
3. MCED - Multi Cancer Early Detection - Self Ordered, No need for doctor's prescription
An innovative Liquid Biopsy cancer screening test (7.5 ml Whole EDTA Blood sample) for >50 cancers in men and women aged 45 and above. Similar to the Galleri test offered by Grail Inc. (Illumina)

4. Clinical Cancer Diagnostics - Physician-Ordered Tests

Both Tissue and Liquid Biopsy sample types
Clinical Whole Exome Sequencing
Clinical Metagenomics
Pan-Cancer Panel
Targeted Therapies Panel
Immunotherapies Panel
BRCA1/2, HRR gene panel, and HRD tests
TMB, MSI, and PD-L1 IHC for immune checkpoint inhibitors
Tumor agnostic biomarkers panel - NTRK gene fusions, BRAF V600
Time to launch - 4 to 6 months
Activity
Timeline
Notes
1
On Site Installation - Lab Setup, Equipment, Reagents & Consumables
12 weeks
Work will begin after lab facility is identified and available for move in
2
CAP & CLIA certification of lab facilities
12 weeks
Overlap with lab setup
3
Lab Personnel Hiring & Training - Recruitment from India & Egypt
3 to 4 weeks
Human Resources from India will not require additional training. Training will be offered to local talent hired in Egypt
4
Strategic Partnerships with local phlebotomy networks or sample collection centers
4 to 6 weeks
Pre-existing diagnostics chains
5
Regulatory Approvals & License to operate diagnostics lab from Government
4 to 6 weeks
ISO15189 quality systems will be implemented
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Budget Proposal
Category
Description
Budget
1
CAPEX - One Time Upfront Cost
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2
Biosafety Cabinet
Heal Force Biosafety Cabinet - Class II, Type A2, with HEPA filters
$15,000
3
CO2 Incubator
Heal Force CO2 Incubator with automatic controls
$7,500
4
Cryostorage and Biobanking
Antech Liquid Nitrogen Tank, -20C, -80C freezer
$25,000
5
Fluorescent Microscopy for Karyotyping, FISH and IHC
EVOS m5000 model Inverted Cell Culture Microscope with blue, green, red fluorescence filters
$50,000
6
Molecular Biology Lab - Accessories
4C Eppendorf Centrifuge and Pipette set, Vortex, Shaker
$25,000
7
Nanopore Sequencing Devices
GridION pluss P2 Combo
$65,000
8
Agilent Bioanalyzer and TapeStation
For NGS library prep Quality Control
$25,000
9
Nanodrop One Spectrophotometer
Nanoliter measurements
$7,500
10
Invitrogen E-gel System
For DNA QC
$7,500
11
GST, Taxes, Customs Duties
Contingencies - Added 12% extra on total CAPEX
$27,300
12
Travel Expenses
Flight tickets, hotel accomodation etc for three people
$30,000
13
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Total CAPEX
$284,800
14
OPEX for 12 months
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​
15
BSL2 Lab - Consumables
Cell culture dishes, flasks, pipettes, culture media, chamber slides, pipette gun, 5 ml, 10 ml, 25 ml pipettes, 20 micron filters, etc
$15,000
16
Nanopore Sequencing - Flowcells, Sequencing Kits and Barcoding Kits
Official Nanopore Kits + NEB Enzymes + Ampure XP beads
$15,000
17
Nanopore Sequencing - New England Biolabs (NEB)
NEB Enzymes, DNA isolation kits and reagents
$15,000
18
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Total OPEX
$45,000
19
Monthly Recurring Cost
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20
BSL2 Lab Facilities & Utilities (per month)
Rent for 2500 Sqft clean room space at partner location
$3,000
21
Human Resources (per month)
One Senior Scientist - Molecular Biology, three Lab Technicians, One MD Pathologist as Authorized Signatory
$12,000
22
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Total for 12 months
$180,000
23
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Total Project Cost - Initial setup and 12 months
$509,800
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Estimated Sample Volumes - within this budget for first year operations

Medical genetics - 750 samples
Reproductive medicine - 750 samples
MCED - Liquid Biopsy - 1500 men and 1500 women - blood samples
Clinical cancer diagnostics - 1500 samples

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