Clinical Genomics — Department of Medical Genetics, Ankara Etlik City Hospital

Capability spectrum

01 Hereditary Cancer Genomics Germline cancer-predisposition testing and interpretation. BRCA1/2 germline analysis and broader multigene hereditary-cancer panels · Syndrome-focused germline testing where the clinical picture indicates a specific condition · Clinical variant interpretation and classification · …
02 Solid Tumor Genomics Somatic molecular profiling for solid tumours. DNA-based somatic next-generation sequencing of solid tumours · RNA-based analysis for clinically relevant gene fusions · Reporting of clinically relevant somatic variants and fusions · …
03 Hematologic Malignancies Genomic and molecular testing for myeloid and lymphoid neoplasms. Myeloid next-generation sequencing panels · Chronic lymphocytic leukaemia panel · IGHV somatic hypermutation status · …
04 Liquid Biopsy Plasma-based circulating tumour DNA and cell-free DNA testing. Targeted plasma next-generation sequencing · ESR1 mutation testing by droplet digital PCR · Cell-free DNA assay development and validation experience · …
05 Rare Disease Genomics Phenotype-driven next-generation sequencing across rare-disease domains. A catalogue of phenotype-driven NGS panels spanning neurological, neuromuscular, cardiovascular, immunological, renal, endocrine, metabolic, dermatological, skeletal, ophthalmic, auditory and multisystem indications · Selection of panel breadth according to the clinical question · Variant interpretation against detailed clinical phenotype · …
06 Cytogenetics & Cytogenomics Conventional and molecular cytogenetic testing. Conventional karyotyping · High-resolution chromosomal microarray · Comprehensive FISH testing · …
07 Molecular Diagnostics Targeted and orthogonal molecular testing beyond next-generation sequencing. MLPA and MS-MLPA for copy-number and methylation-sensitive analysis · Fragment analysis · Repeat-expansion testing · …
08 Prenatal & Reproductive Genetics Genetic testing in prenatal and reproductive settings. Prenatal genetic diagnosis on samples obtained during pregnancy · Prenatal FISH · QF-PCR · …
09 Quality Assurance External quality assessment for selected critical assays. Participation in EMQN external quality assessment (EQA) programmes · QuIP external quality assessment (EQA) for ESR1 digital-PCR testing · Internal quality control and orthogonal confirmation within routine reporting workflows
10 Laboratory Infrastructure Integrated genomic, molecular and cytogenomic infrastructure. NovaSeq 6000 next-generation sequencing · Bio-Rad droplet digital PCR · Multi-capillary Sanger sequencing · …

Targeted NGS panel portfolio

The department maintains 58 phenotype-driven NGS panels. Panel names, gene counts and gene content are reproduced from the department’s current panel source document and are not edited or extended here.

Rare disease panels

54 panels across the rare disease clinical categories

Rare Disease Genomics

Cancer predisposition panels

4 germline panels, presented under hereditary cancer

Hereditary Cancer Genomics

A note on germline and somatic testing

Germline and somatic testing answer different questions and are not interchangeable. Germline testing asks whether a variant is present in every cell and therefore potentially heritable; it informs risk for the patient and for relatives. Somatic testing characterises alterations acquired by a tumour and informs treatment for that tumour.

The distinction matters most for BRCA1 and BRCA2. Tumour BRCA1/2 analysis is performed on tumour tissue and reports the tumour’s status; germline BRCA1/2 testing is performed on a constitutional sample and reports inherited status. A tumour finding does not by itself establish an inherited predisposition, and germline testing is required where one is suspected.