Survival results according to Oncotype Dx recurrence score in patients with hormone receptor positive HER-2 negative early-stage breast cancer: first multicenter Oncotype Dx recurrence score survival data of Turkey

BackgroundThe Oncotype Dx recurrence score (ODx-RS) guides the adjuvant chemotherapy decision-making process for patients with early-stage hormone receptor-positive, HER-2 receptor-negative breast cancer. This study aimed to evaluate survival and its correlation with ODx-RS in pT1-2, N0-N1mic patients treated with adjuvant therapy based on tumor board decisions.Patients and methodsEstrogen-positive HER-2 negative early-stage breast cancer patients (pT1-2 N0, N1mic) with known ODx-RS, operated on between 2010 and 2014, were included in this study. The primary aim was to evaluate 5-year disease-free survival (DFS) rates according to ODX-RS.ResultsA total of 203 eligible patients were included in the study, with a median age of 48 (range 26-75) and median follow-up of 84 (range 23-138) months. ROC curve analysis for all patients revealed a recurrence cut-off age of 45 years, prompting evaluation by grouping patients as ≤45 years vs. >45 years. No significant difference in five-year DFS rates was observed between the endocrine-only (ET) and chemo-endocrine (CE) groups. However, among the ET group, DFS was higher in patients over 45 years compared to those aged ≤45 years. When stratifying by ODx-RS as 0-17 and ≥18, DFS was significantly higher in the former group within the ET group. However, such differences were not seen in the CE group. In the ET group, an ODx-RS ≥18 and menopausal status were identified as independent factors affecting survival, with only an ODx-RS ≥18 impacting DFS in patients aged ≤45 years. The ROC curve analysis for this subgroup found the ODx-RS cut-off to be 18.ConclusionThis first multicenter Oncotype Dx survival analysis in Turkey demonstrates the importance of Oncotype Dx recurrence score and age in determining treatment strategies for early-stage breast cancer patients. As a different aproach to the literature, our findings suggest that the addition of chemotherapy to endocrine therapy in young patients (≤45 years) with Oncotype Dx recurrence scores of ≥18 improves DFS

Challenges in clinical interpretation of next-generation sequencing data: Advantages and Pitfalls

Next-generation sequencing (NGS) technologies have completely changed the field of genomics by making it possible to rapidly and inexpensively produce genome-scale sequence data with higher precision and resolution. In recent years, rapid technological advancements driven by companies and academic institutions have expanded the range of NGS applications, from research to the clinic. Latest scientific developments have highlighted the effects of NGS technology on complex and Mendelian diseases, particularly cancer. However, the rapid adoption of NGS poses significant challenges in data processing, storage, management, and interpretation, as well as sequencing quality control, making it challenging to integrate the sequence data into clinical practice. Here, we first outline the technical features and performance of the most recent NGS platforms. Furthermore, we summarize the applications of NGS technologies in clinical diagnostics, data interpretation, and valuable bioinformatic tools and databases for analysis. Common issues in NGS processes are also discussed

Bir rekombinant kromozom 4 olgusunun klinik özelliklerinin ayrıntılı tanımlanması

Recombinant chromosome 4 is a very rare chromosomal aberration with eighteen cases reported in the literature up to date. Here we report a five years old male patient with de novo rec(4) dup(4p) del(4q). The physical examination findings were as follows: caput quadratum, flat occiput, low frontal hairline, hypertelorism, ptosis, blepharophimosis, high arched eyebrows, flat nasal root with anteverted nostrils and short nose, long and smooth philtrum, thin upper lip with triangular mouth, microretrognathia, high arched palate, dental anomalies, large low-set ears, short neck, broad chest with widely spaced nipples, micropenis, cryptorchidism. Conventional cytogenetic analysis revealed the karyotype as 46,XY,rec(4)dup(4p14p16.3)del(4q34.3q35). Flourescence insitu hybridization (FISH) analysis with sub-telomeric probes for 4p and 4q showed duplication of 4p and deletion of 4q in recombinant chromosome 4. His parents’ chromosomal analysis and sub-telomeric FISH analysis were both normal. The patient’s final karyotype was reported as 46,XY,rec(4)dup(4p16.3p14)del(4q34.4q35).arr[h g19]4p16.3p14(68,345-36,018)x3,4q34.3q35(177,676,319-190,957,460)x1 detected by Microarray. According the literature all cases with recombinant chromosome 4 have similar clinical findings. Except for our case only one case in the literature has been reported to be de novo. In conclusion, we reported a very rare case of recombinant chromosome 4, which has the largest deletion and duplication in the literature. Further cases with similar findings would help the delineation of the findings associated with this chromosomal abnormality.Rekombinant kromozom 4, literatürde bugüne kadar bildirilen 18 vakayla birlikte ender görülen bir kromozomal anormalidir. Bu yazıda de novo rec (4)dup(4p)del(4q) karyotipine sahip 5 yaşında bir erkek hastayı bildirdik. Hastanın fizik muayenesinde kaput kuadratum, yassı oksiput, düşük frontal saç çizgisi, hipertelorizm, pitozis, blefarofimozis, yüksek kemerli kaşlar, antevert burun delikleri ile düz burun kökü, kısa burun, uzun ve pürüzsüz filtrum, üçgen ince üst dudak, mikroretrognati, yüksek kemerli damak, diş anomalileri, geniş, düşük kulaklar, kısa boyun, geniş aralıklı meme uçları, mikropenis, kriptorşidizm saptanmıştır. Konvansiyonel sitogenetik analiz sonucunda karyotipin 46,XY,rec(4)dup(4p14p16.3)del(4q34.3q35) karyotipi saptanmıştır. 4p ve 4q için subtelomerik problarla yapılan floresan in-situ hibridizasyon (FISH) analizi, rekombinant kromozom 4'te 4p'nin duplikasyonunu ve 4q'nun delesyonunu göstermiştir. Yapılan microarray analizi sonrası hastanın son karyotipi 46,XY, rec (4) dup (4p16.3p14) del (4q34.4q35) .arr [hg19] 4p16.3p14 (68.345-36.018) x3,4q34.3q35 (177,676,319-190,957,460) olarak rapor edilmiştir. Literatüre göre rekombinant kromozom 4 olan tüm olgular benzer klinik bulgulara sahiptir. Bizim olgumuz dışında literatürde sadece bir olgunun de novo olduğu bildirilmiştir. Sonuç olarak, bu yazıda nadir bir rekombinant kromozom 4 olgusu bildirilmiştir. Benzer bulgulara sahip bildirilecek diğer vakalar, nadir görülen bu rekombinasyonun daha iyi tanımlanmasına yardımcı olacaktır

Whole exome sequencing of consanguineous families of clinically diagnosed with neurodevelopmental disorders

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