Copy Number Variations (CNVs) Account for 10.8% of Pathogenic Variants in Patients Referred for Hereditary Cancer Testing

BACKGROUND/AIM

Germline copy number variation (CNV) is a type of genetic variant that predisposes significantly to inherited cancers. Today, next-generation sequencing (NGS) technologies have contributed to multi gene panel analysis in clinical practice.

MATERIALS AND METHODS

A total of 2,163 patients were screened for cancer susceptibility, using a solution-based capture method. A panel of 52 genes was used for targeted NGS. The capture-based approach enables computational analysis of CNVs from NGS data. We studied the performance of the CNV module of the commercial software suite SeqPilot (JSI Medical Systems) and of the non-commercial tool panelcn.MOPS. Additionally, we tested the performance of digital multiplex ligation-dependent probe amplification (digitalMLPA).

RESULTS

Pathogenic/likely pathogenic variants (P/LP) were identified in 464 samples (21.5%). CNV accounts for 10.8% (50/464) of pathogenic variants, referring to deletion/duplication of one or more exons of a gene. In patients with breast and ovarian cancer, CNVs accounted for 10.2% and 6.8% of pathogenic variants, respectively. In colorectal cancer patients, CNV accounted for 28.6% of pathogenic/likely pathogenic variants.

CONCLUSION

In silico CNV detection tools provide a viable and cost-effective method to identify CNVs from NGS experiments. CNVs constitute a substantial percentage of P/LP variants, since they represent up to one of every ten P/LP findings identified by NGS multigene analysis; therefore, their evaluation is highly recommended to improve the diagnostic yield of hereditary cancer analysis.

Multimodality treatment for esophageal cancer in Turkey: A single center experience

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Background: Esophagus cancer is an important cause of cancer-related deaths in Turkey as well as in the world. In our study, clinicopathological features and survival results of patients treated for esophageal cancer were presented. Methods: This study retrospectively reviewed esophageal squamous cell carcinoma (SCC) and adenocarcinoma (ADC) patients who were admitted to our center, between 2012 and 2016. Results: A total of 82 patients (56 males) with a median age of 56 years were evaluated. Seventy-one (87%) patients were diagnosed with SCC, 10 (12%) with ADC, 1 with adenosquamous carcinoma. All ADC patients were HER2 negative. The localization of tumors; lower third (55%), middle third (27%) and upper third (18%) of the esophagus. Prior to surgery, neoadjuvant chemoradiotherapy (CRT) was administered in 21 patients (26%); 10 of them receiving carboplatin and paclitaxel (CP), and 11 receiving cisplatin and 5-FU (CF). TNM classification of operated patients were as follows; Stage 1 (n = 5), stage 2 (n = 10), stage 3 (n = 8) and stage 4 (n = 1). Adjuvant chemotherapy (CF) was administered in the other 6 (7%) patients. Definitive CRT was given in 36 patients (44%), with CF being administered in 32 patients, and CP therapy in 4 patients. There were 19 patients (23%) with metastatic diagnosis and 13 of whom were treated with CF, and 4 with docetaxel-cisplatin-5FU combination. With median follow up of 21 months, median overall survival (OS) and time to progression (TTP) were 24 and 17 months, respectively. The median OS and TTP of patients with metastatic disease were 14 and th 9 months, respectively. The median OS and TTP of the patients who underwent surgery were 45 and 34 months, respectively. Conclusions: Our findings in this study regarding the rate of histology, the percentages of patients with metastatic vs. locally advanced disease, and survival rates were similar to the literature.

Clinicopathologic characteristics, treatment outcomes, and prognostic factors of primary thoracic soft tissue sarcoma: A multicenter study of the Anatolian Society of Medical Oncology (ASMO)

Background

Soft tissue sarcomas (STSs) are rare malignant tumors of embryogenic mesoderm origin. Primary thoracic STSs account for a small percentage of all STSs and limited published information is available. This study aimed to identify the prognostic factors for thoracic STSs and evaluate the disease's clinical outcomes.

Methods

The medical records of 109 patients with thoracic STSs who were treated between 2003 and 2013 were retrospectively reviewed. Patients' survival rates were analyzed and potential prognostic factors evaluated.

Results

The median follow-up period was 29 months (range: 1–121 months). STSs were most frequently localized on the chest wall (n = 42; 38.5%) and lungs (n = 42; 38.5%). The most common histological types were malignant fibrous histiocytoma (n = 23; 21.1%), liposarcoma (n = 17; 15.6%), and leiomyosarcoma (n = 16; 14.7%). The median survival time of all patients was 40.3 months (95% confidence interval, 14.22–66.37 months), with one and five-year survival rates of 93.4% and 63.5%, respectively. Univariate analysis of all groups revealed that metastatic stage, unresectability, tumor diameter of >10 cm, tumor location other than the chest wall, and grade 3 diseases were predictable of poor survival. However, only grade 3 diseases and tumor location other than the chest wall were confirmed by multivariate analysis as poor prognostic factors.

Conclusions

Primary thoracic STSs are rarely seen malignant tumors. Our results indicated that patients with low-grade tumors and those localized on the chest wall often experienced better survival outcomes.

KRAS discordance between primary and metastatic tumor in patients with metastatic colorectal carcinoma

PURPOSE

Adding targeted therapies to chemotherapy in metastatic colorectal cancer (CRC) improves response rates and survival. KRAS is a predictive indicator for anti-epidermal growth factor receptor (EGFR) treatments. The most important reasons for KRAS discordance are intratumoral heterogeneity and incorrect mutation analysis. Evaluating the status of KRAS in primary and metastatic lesions becomes even more crucial to ensure efficient usage of anti-EGFR treatments.

METHODS

Patients with metastatic CRC, whose primary disease and liver and/or lung metastases were operated, were retrospectively evaluated, and KRAS assessment was performed on 31 patients who were suitable for DNA analysis. Pyrosequencing with polymerase chain reaction (PCR) was used for KRAS analysis.

RESULTS

The median age of 31 patients diagnosed with rectal cancer (N=13) and colon cancer (N=18) was 63 years (range 33-73). Metastasectomy locations included the liver (N=27), lung (N=3), and both lung and liver (N=1). KRAS discordance was detected in 22% (7/31) of the patients. While 3 patients with detected discordance had mutated KRAS in the primary material, wild type KRAS was detected in their liver or lung lesions. On the other hand, while 4 patients had wild type KRAS in the primary material, mutated KRAS was determined in their liver or lung lesions. The McNemar test revealed no significant discordance between primary and metastatic disease (p=1.00). No progression free survival (PFS) difference was detected between patients with determined discordance and patients with undetermined discordance (10.6 vs 14.7 months, p=0.719).

CONCLUSION

This is the first study to evaluate KRAS discordance between primary and metastasis in CRC patients, who underwent metastasectomy, together with survival data. In the literature and recent studies with large patient numbers in which modern KRAS tests were used, the KRAS discordance rate varies between 3-12%. In our study, a higher KRAS discordance (22%) was detected, and no survival difference was determined between patients with or without discordance. In recent years, the rising interest in borderline resectable disease may bring forward discussions related to which material the KRAS status should be analyzed.

Sequential therapy and prognostic factors in metastatic renal cell carcinoma: single centre experience

PURPOSE

In advanced stage renal cell cancer (RCC), overall survival (OS) of patients has been prolonged due to targeted therapies. To date, there are several prognostic risk models that have been developed for metastatic RCC (mRCC). The purpose of this study was to evaluate the outcomes of the sequential therapy (IFN-α, tyrosine kinase inhibitors/TKIs, m-TOR inhibitor) and prognostic factors in patients with mRCC, especially those with bone metastasis.

METHODS

We retrospectively examined the data of 82 patients with pathologically proven mRCC who were followed-up and treated at the Medical Oncology Clinic of the Dr A.Y Oncology Hospital between 2005 and 2013.

RESULTS

Median OS was 23 months in all patients with mRCC and 20 months in patients treated with TKIs. According to MSKCC and HENG risk classifications, median OS differed between the groups (p=0.02, p<0.001, respectively). Median OS was lower in patients with isolated bone metastasis compared to those with lung metastasis (16 vs 24 months, p=0.25). Median OS improved with increasing number of sequential therapies (p=0.08).

CONCLUSION

This study confirmed the correlation between MSKCC and HENG risk models and survival data. Additionally, it was shown that increase of the number of therapeutic lines in sequential therapy prolonged survival and that bone metastases were negative prognostic factors.