Neurogenomics 

Principal Investigator: Assist. Prof. Yavuz OKTAY

The Neurogenomics Lab is a research group that develops interdisciplinary approaches to understand the genetic and molecular basis of nervous system diseases. Our work focuses on three main areas: neurogenetic and neurodevelopmental rare diseases, neuropsychiatric disorders, and brain tumors. Using advanced technologies such as functional genomics, epigenomics, cell biology, stem cell models, and statistical genetics, we aim to uncover the cellular and molecular effects of genetic variation.

Our vision is to bridge basic science and clinical applications, developing innovative solutions for the diagnosis, treatment, and prevention of diseases. To this end, our laboratory aims to accelerate knowledge generation through national and international collaborations and to transform the data obtained into tangible outcomes that contribute to public health.

Research Areas

Investigating the mechanisms of action of genetic variants that cause nervous system diseases.

Discovery of novel candidate genes and variants in rare diseases, and their validation using functional methods in patient cells and stem cell models.

Studying genetic and epigenetic alterations associated with neuropsychiatric disorders using statistical genetics and functional genomics approaches.

Investigating genetic predisposition to brain tumors and early oncogenic changes in stem-cell-based models.

Projects

International (Selected)

EU: The European Rare Disease Research Alliance (ERDERA), WP24.2: “Undertaking advocacy and awareness efforts to UCs added value”, 2024 – ongoing, Task Co-leader.

EU: Genome of Europe (GoE) Project, 2024 – ongoing, Researcher.

Medical Research Council (MRC), UK: “MRC Strategic Award for an International Centre for Genomic Medicine in Neuromuscular Diseases (ICGNMD)”, 2020–2024, Co-investigator.

Katip Çelebi-Newton Fund (British Council and TÜBITAK): “An Integrative Approach Towards Improving the Diagnostic Yield of NGS Analysis in Pediatric Neurogenetic Diseases”, 2019–2021, Principal Investigator.

TÜBITAK-RCUK (UK) Bilateral Project: “Novel genomic approaches to study the burden of neurogenetic diseases due to consanguineous marriages in Turkey”, 2016–2020, Researcher.

TÜBITAK, EU-COST: “Development of methods and platforms that enable personalized medicine applications by modeling DNA sequence variants observed in pachygyria patients in iPSCs and zebrafish using genome editing tools”, 2018–2021, Principal Investigator.

TÜBITAK, EU-COST: “Development of third-generation DNA sequencing methods via CRISPR/Cas for the diagnosis and DNA analysis of neurodevelopmental diseases with repeat expansion”, 2019–2021, Principal Investigator.

National (Selected)

TÜBİTAK 1001: “Evaluation of the corrective effects of small molecules identified by multi-omic analyses on mitochondrial defects caused by PTPMT1 deficiency in PTPMT1 knockout neural progenitor cells and zebrafish models”, 2024 – ongoing, Researcher.

TÜBİTAK 1001: “Epigenomic analysis of genomic loci associated with lithium response in bipolar disorder using a colocalization approach”, 2024 – ongoing, Principal Investigator.

TÜBİTAK 1004: Within the “Target-Specific Pan-Cancer Therapies (PAN-TER)” platform: “Development of a next-generation sequencing-based genetic analysis kit for CAR-T cell therapies in acute lymphoblastic leukemia”, 2021 – ongoing, Principal Investigator.

TÜBİTAK 1001: “Functional analysis of a novel missense mutation in the Katanin-Like 2 (KATNAL2) gene, investigated in patient fibroblasts and derived cells”, 2020 – 2023, Researcher.

TÜBİTAK 1001: “Comparison of methylation levels of inflammasome genes in obsessive-compulsive disorder and healthy controls”, 2021 – 2024, Researcher.

TÜBİTAK 1001: “Characterization of persistent epigenomic changes involved in gliomagenesis along the IDH1-TERT-MYC axis”, 2018 – 2023, Principal Investigator.

TÜBİTAK 1001: “Elucidating the molecular mechanisms of SNP Rs55705857 in the 8q24.21 region conferring glioma susceptibility”, 2015 – 2018, Principal Investigator.

Publications

Sönmezler E, Stuani C, Hız Kurul S, Güngör S, Buratti E, Oktay Y. Characterization and Engineered U1 snRNA Rescue of Splicing Variants in a Turkish Neurodevelopmental Disease Cohort. Hum Mutat. 2024.

Yaraş T, Oktay Y, Karakülah G. PGSXplorer: an integrated nextflow pipeline for comprehensive quality control and polygenic score model development. PeerJ. 2025.

Can GŞ, Bakır E, Oktay Y. Functional Annotation of Bipolar Disorder 2 Risk Location Implicates Novel Susceptibility Genes. Neuropsychobiology. 2025.

Falabella M, … Oktay Y, et al. Biallelic PTPMT1 variants disrupt cardiolipin metabolism and lead to a neurodevelopmental syndrome. Brain. 2025.

Cark O, Katkat E, Aydogdu I, Iscan E, Oktay Y, Ozhan G.  tubg1 Somatic Mutants Show Tubulinopathy-Associated Neurodevelopmental Phenotypes in a Zebrafish Model. Mol Neurobiol. 2025.

Ülgen E, Gerlevik U, Gerlevik S, Oktay Y, Sezerman OU, Turcan Ş, Ozduman K. A microdeletion event at 19q13.43 in IDH-mutant astrocytomas is strongly correlated with MYC overexpression. Acta Neuropathol Commun. 2024.

Harwood AJ, Petrakis S, Oktay Y, Pasterkamp RJ. Editorial: Mental health: cell models to mechanisms. Front Cell Dev Biol. 2023.

Lecca M, Pehlivan D, Suñer DH, Weiss K, Coste T, Zweier M, Oktay Y, ……..Lupski JR, Errichiello, E. Bi-allelic variants in the ESAM tight-junction gene cause a neurodevelopmental disorder associated with fetal intracranial hemorrhage. Am J Hum Genet. 2023.

Hız Kurul S*, Oktay Y*, et al. High diagnostic rate of trio exome sequencing in consanguineous families with neurogenetic diseases. Brain. 2022.

Okay K, Varış PÜ, Miral S, Ekinci B, Yaraş T, Karakülah G, Oktay Y. Alternative splicing and gene co-expression network-based analysis of dizygotic twins with autism-spectrum disorder and their parents. Genomics. 2021.

Team

Active Members

Ece Sönmezler Adalı (Postdoctoral Researcher)

Sevcan Mercan (Postdoctoral Researcher) (TÜBİTAK 2218)

Güneş Şayan Can (Doctoral Student)

Ayşe İpek Polat Kalafatçılar (Doctoral Student)

Pınar Gençpınar (Doctoral Student)

Şimal Kayıkçı (Master's Student)

Delfin Alpsoy (Master's Student)

Heval Şeker (Undergraduate Student) (DEU Faculty of Medicine)

Former Members

Ayşe Semra Hız (Doctoral Student / Researcher)

Burcu Ekinci Görgün (Doctoral Student)

Fadime Öztoprak (Doctoral Student)

Aykut Kuruoğlu (Doctoral Student)

Ece Sönmezler Adalı (Doctoral Student)

Tutku Yaraş (Master's Student)

Kaan Okay (Master's Student)

Neşe Direk (Researcher)

Ebru Diler (Bakır) (Master's Student)

Berfin Demirözer (Researcher)

Elmasnur Yılmaz (Master's Student)

Işık Esin Kıroğlu (Master's Student)