Slide 1: New study published in Cell advancing functional classification of VUSs
NASDAQ: PHAR | EURONEXT Amsterdam: PHARM % Pharming: [ Webcast New study published in Cell advancing functional classication of VUSs June 30, 2025 at 16:30 CEST / 10:30 EDT Joshua Milner, MD Anurag Relan Columbia University Chief Medical Officer Irving Medical Center Pharming Group N.V. =v
Slide 2: Forward-looking statements
Forward-looking statements This presentation may contain forward-looking statements. Forward-looking statements are statements of future expectations that are based on management’s current expectations and assumptions and involve known and unknown risks and uncertainties that could cause actual resu
Slide 3: Agenda
Agenda Dr. Joshua Milner will: • Present findings of a new study published in Cell titled “Scalable generation and functional classification of genetic variants in inborn errors of immunity to accelerate clinical diagnosis and treatment” • Discuss how this study advances variant of uncertain signifi
Slide 4: Large-scale functional classification of PIK3CD and PIK3R1 variants to improve APDS diagnosis
Large-scale functional classification of PIK3CD and PIK3R1 variants to improve APDS diagnosis Joshua Milner, MD Director, Division of Pediatric Allergy, Immunology and Rheumatology Chief, Allergy, Immunology and Rheumatology Services New York-Presbyterian Morgan Stanley Children Hospital Columbia Un
Slide 5: Two major rate-limiting steps in genetic-based precision medicine
Two major rate-limiting steps in genetic-based precision medicine If genetic testing is performed and a variant is found We often don’t know that there is a genetic disease ClinVar Variant of the immune system right in front of us Distribution in a particular gene, there’s a 50/50 chance we won’t kn
Slide 6: Multiplexed functional assays
Multiplexed functional assays Clinically-relevant, high-throughput methods are required to resolve the VUS problem at scale Multiplexed functional assays simultaneously evaluate the biological effect of thousands of different genetic variants by generating quantitative, functional data on how each v
Slide 7: Activated PI3K δ syndrome (APDS): a genetic disorder of immune dysregulation
Activated PI3K δ syndrome (APDS): a genetic disorder of immune dysregulation caused by gain of PI3K δ function (GOF)
Slide 8: Introducing precise variants in primary human T cells using CRISPR base editing
Introducing precise variants directly in primary human T cells using CRISPR-dependent base editing C>T A>G Porto et al., Nat Rev Drug Disc, 2020 Walsh*, Shah* et al., Nature Biotechnology, 2024
Slide 9: Massively paralleled generation and functional mapping of APDS gene variants
Massively paralleled generation and functional mapping of APDS gene (PIK3CD/PIK3R1) variants Rigor
Slide 10: Clinically-relevant assay discriminates between PI3K δ GOF and LOF
Clinically-relevant assay discriminates between PI3K δ gain-of-function (GOF) and loss-of-function (LOF)
Slide 11: Assay confirms known PIK3CD APDS-causing variants and uncovers new GOF variants
Assay confirms known PIK3CD APDS-causing variants and uncovers new GOF variants
Slide 12: Assay confirms known PIK3R1 APDS-causing variants and uncovers new GOF variants
Assay confirms known PIK3R1 APDS-causing variants and uncovers new GOF variants
Slide 13: Leniolisib normalizes PI3K δ hyperactivity in human T-cells
Leniolisib normalizes PI3K δ hyperactivity in human T-cells and provides validation of study results
Slide 14: Leniolisib normalizes APDS-associated T-cell abnormalities caused by GOF variants
Leniolisib normalizes APDS-associated T-cell abnormalities caused by GOF variants
Slide 15: Finding patients with GOF variants identified in this study
Finding patients with GOF variants identified in this study 1. Patients who underwent genetic testing for IEIs • Data can be utilized by clinical laboratories to reclassify VUS results as APDS 2. General population • Since the study identified many novel unannotated variants, we searched large-scale
Slide 16: GOF variants identified in the study are found in patients with VUS test results
GOF variants identified in the study are found in patients with VUS test results who have APDS symptoms benign pathogenic
Slide 17: Harnessing population databases to estimate genetic prevalence
Harnessing population databases to estimate genetic prevalence The UK Biobank is a large-scale biomedical database and research resource containing in-depth genetic, health, and lifestyle information from participants aged 40–69 at recruitment across the United Kingdom. The All of Us Research Progra
Slide 18: Population databases suggest APDS may be significantly more prevalent
Review of population databases suggests APDS may be significantly more prevalent than previously described Cohort of 633,540 NGS reveals PIK3CD or Screen variant effect individuals from PIK3R1 variant provides evidence to n=123 population database functional classification 12% of these patients had
Slide 19: GOF carriers more likely to exhibit GI, lymphoproliferative, and inflammatory phenotypes
GOF carriers in population databases more likely to exhibit GI, lymphoproliferative, and inflammatory phenotypes p value System Diagnosis Odds Ratio (raw) Gastrointestinal Biliary cirrhosis inf 1.040E-06 Cirrhosis - non-alcoholic 5.37 1.201E-03 Persistent vomiting 9.43 7.930E-06 Autoimmune hepatitis
Slide 20: Toward pathway specific drug indications
Toward pathway specific drug indications Past Now Future? Severe presentation APDS-like presentation Symptoms presentation variants derived from many more carriers of APDS variants Genetic testing Find PIK3CD/R1 variants and pAKT/pS6 testing Variant found, research lab Sequence many investigates, te
Slide 21: Summary
Summary • MAVE study provides functional classification (e.g., GOF or LOF) for >2,000 PIK3CD/PIK3R1 variants • Assay confirmed known PIK3CD/PIK3R1 APDS-causing variants and uncovered many new GOF variants • Leniolisib can restore or improve PI3K δ signaling defects and immune abnormalities caused by
Slide 22: Acknowledgements
Acknowledgements Izar lab Milner Lab Zach Walsh Karan Luthria Josh Milner HTI3 - Human Tissue Immunology and Immunotherapy Initiative Chris Frangieh Edridge D’Souza Jay Levy Neeha Kothapalli Luke Cai Lei Haley Huang Johannes Melms Hsiang-Hsi Ling Ashley Lee Clarissa Heck Ron Gejman R37CA258829 R37CA
Slide 23: Next steps
Next steps Clinical genetic laboratories will utilize this data to independently re-assess PIK3CD/R1 VUSs • These data may impact both patients with exact matches and patients with different genetic changes affecting the same amino acid as a known GOF variant • Expect reassessments to be completed i
Slide 24: Q&A
Q&A