Kolorektal Adenokarsinomlu Hastaların Biyopsi ve Rezeksiyon Örneklerinde Rutin Yeni Nesil Dizilemenin Analitik Performansı: İki Merkezli Bir Çalışma

Öz

Biyopsi örnekleri, sınırlı doku hacmi ve daha düşük DNA veriminin oluşturabileceği preanalitik güçlüklere rağmen kolorektal kanserlerin moleküler profillenmesinde giderek daha sık kullanılmaktadır. Bu retrospektif, iki merkezli çalışmada, kolorektal adenokarsinomlu hastalara ait 34 rezeksiyon ve 31 biyopsi örneğinin DNA temelli analitik performansı karşılaştırıldı. Tümör yüzdesi, DNA konsantrasyonu, dizileme kapsamı, ≥500× derinlikte kapsanan hedef baz oranı ve Tier I–II varyant verimi değerlendirildi. Biyopsi örneklerinde medyan tümör yüzdesi (%50’ye karşı %70; p=0,016) ve DNA konsantrasyonu (21,35’e karşı 55,20 ng/µL; p<0,001) rezeksiyon örneklerinden daha düşüktü. Değerlendirilebilir DNA-temelli NGS sonucu, 31 biyopsi örneğinin 30’unda ve 34 rezeksiyon örneğinin tamamında elde edildi ve gruplar arasında istatistiksel olarak anlamlı fark saptanmadı (%96,8’e karşı %100; p=0,477). Medyan dizileme kapsamı (1149,0×’e karşı 1084,5×; p=0,586), ≥500× derinlikte kapsanan hedef baz oranı (%93,87’ye karşı %91,37; p=0,752) ve en az bir Tier I–II varyant saptanma oranı (%100’e karşı %94,1; p=0,494) açısından anlamlı fark bulunmadı. Varyant sayıları, varyant saptanan gen sayıları ve varyant alel frekansı ölçümleri açısından biyopsi ve rezeksiyon örnekleri arasında istatistiksel olarak anlamlı fark bulunmadı. Tümör yüzdesi ve blok yaşı için düzeltme yapıldıktan sonra biyopsi örnekleri daha düşük DNA konsantrasyonu ile bağımsız olarak ilişkiliydi; düzeltilmiş geometrik ortalama oranı 0,45’ti (%95 güven aralığı: 0,30–0,68). Sonuç olarak, daha düşük tümör hücreselliği ve DNA konsantrasyonuna rağmen, bu kohortta uygun şekilde seçilmiş biyopsi örneklerinde yüksek oranda değerlendirilebilir dizileme sonucu ve Tier I–II varyant saptanmış; dizileme kalite ölçütleri ve Tier I–II varyant verimi açısından örnek tipleri arasında istatistiksel olarak anlamlı fark bulunmamıştır.

Anahtar Kelimeler

• Kolorektal Neoplaziler
• Yeni Nesil Dizileme
• Biyopsi
• Örnek İşleme
• Moleküler Tanı Teknikleri

Analytical Performance of Routine Next-Generation Sequencing in Biopsy and Resection Specimens from Patients with Colorectal Adenocarcinoma: A Two-Center Study

Öz

Biopsy specimens are increasingly used for molecular profiling in colorectal cancer, although their limited tissue volume and lower DNA yield may present preanalytical challenges. This retrospective, two-center study compared DNA-based analytical performance between 34 resection and 31 biopsy specimens from patients with colorectal adenocarcinoma. Tumor percentage, DNA concentration, sequencing coverage, the proportion of target bases covered at ≥500×, and Tier I–II variant yield were evaluated. Biopsy specimens had lower median tumor percentages (50% vs. 70%; p=0.016) and DNA concentrations (21.35 vs. 55.20 ng/µL; p<0.001) than resection specimens. An evaluable DNA-based NGS result was obtained in 30 of 31 biopsy specimens and all 34 resection specimens, with no statistically significant difference between the groups (96.8% vs. 100%; p=0.477). No significant differences were observed in median sequencing coverage (1149.0× vs. 1084.5×; p=0.586), the proportion of target bases covered at ≥500× (93.87% vs. 91.37%; p=0.752), or detection of at least one Tier I–II variant (100% vs. 94.1%; p=0.494). Variant counts, numbers of altered genes, and variant allele frequency measures did not differ significantly between biopsy and resection specimens. After adjustment for tumor percentage and block age, biopsy specimens remained independently associated with lower DNA concentration, with an adjusted geometric mean ratio of 0.45 (95% CI: 0.30–0.68). Despite lower tumor cellularity and DNA concentration, appropriately selected biopsy specimens yielded high rates of evaluable sequencing and Tier I–II variant detection in this cohort, with no statistically significant differences in sequencing quality metrics or Tier I–II variant yield between specimen types.

Anahtar Kelimeler

• Colorectal Neoplasms
• Next-Generation Sequencing
• Biopsy
• Specimen Handling
• Molecular Diagnostic Techniques

Etik Beyan

The study was approved by the Pamukkale University Non-Interventional Clinical Research Ethics Committee (Decision no: E-60116787-020-906555, Date: 21.07.2026).

Kaynakça

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