Background: Cystic fibrosis (CF) is the most common worldwide, life-shortening multisystem hereditary disease, with an autosomal recessive inheritance pattern caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The national newborn screening (NBS) program for CF has been initiated in Turkey since 2015. If the immunoreactive trypsinogen (IRT) is elevated (higher than 70 μg/L in the second control) and confirmed by sweat test or clinical findings, genetic testing is performed. The aims of this study are to emphasize the effect of NBS on the status of genetic diagnosis centers with the increasing numbers of molecular testing methods, and to determine the numbers and types of CFTR mutations in Turkey. Methods: The next-generation sequencing (NGS) and multiplex ligation-dependent probe amplification (MLPA) results of 1595 newborns, who were referred to Cukurova University Adana Genetic Diseases Diagnosis and Treatment Center (AGENTEM) for molecular genetic testing, were evaluated with positive CF NBS program results since 2017. Results: According to the results; 560 (35.1%) of the 1595 patients carried at least 1 (one) CF-related variant, while 1035 patients (64.9%) had no mutation. Compound heterozygosity for two mutations was the most common in patients, while two detected variants were homozygote in 14 patients. A total of 161 variants were detected in 561 patients with mutations. Fifteen novel variants that have not been previously reported were found. Moreover, p.L997F was identified as the most frequent pathogenic mutation that might affect the IRT measurements used for the NBS. The distribution of mutation frequencies in our study showed a difference from those previously reported; for example, the well-known p.F508del was the third most common (n = 42 alleles), rather than the first. The most striking finding is that 313 cases had a pathogenic variant together with the V470M variant, which might have a cumulative effect on CF perpetuation. Conclusion: This study is the first to determine the mutational spectrum of CFTR in correlation with the NBS program in the Turkish population. NBS for CF raises issues regarding screening in diverse populations, both medical and non-medical benefits, and carrier identification. Through the lens of NBS, we focused on the integrated diagnostic algorithms and their effect on the results of genetic testing.

Background: In terms of precision medicine, not only tumoral tissue samples but also with liquid biopsy for somatic variants detection, have been used routinely. It also helps to overcome the resampling difficulties that require an invasive procedure with the problem of tumor heterogeneity. With the Next Generation Sequencing (NGS) method which is accepted as the gold standard in molecular genetic testing, colorectal cancer patients ccfDNA (Circulating Cell-Free DNA) samples were next generation sequenced via a targeted multigene panel. Methods: In our study, liquid biopsy samples of 63 colorectal cancer patients whom referred to Cukurova University AGENTEM (Adana Genetic Diseases Diagnosis and Treatment Center) were sequenced via GeneReader NGS Systems (Qiagen). The multi-gene panel which includes cancer related actionable 11 genes (KRAS, NRAS, KIT, BRAF, PDGFRA, ALK, EGFR, ERBB2, ERBB3, ESR1 and RAF1) were used to identify the variants of drug sensitivity and resistance. Sequencing data were analyzed by QCI-Analyze and QCI-Interpret bioinformatics tools. Results: Forty-three clinically significant variants detected in 53.96% (n=34) of 63 patients. Total of 43 clinically significant variants in 7 genes (KRAS, NRAS, KIT, BRAF, EGFR, PDGFRA and ERBB2) were detected according to the ACMG (American College of Medical Genetics) and AMP (Association for Molecular Pathology) criteria in which 13.95%, 41.86% and 41.86% prospectively related to drug resistance, treatment sensitivity, and both treatment sensitivity and drug resistance. Moreover, 2.33% were classified as uncertain clinical significance due to data mining. Variants detected upon gene names were listed in Table 1. Conclusion: In terms of identifying potential target therapy options without the need of a invasive intervention becomes available with NGS multigene panel studies within high reliability that also have an effect on the quality of life in colorectal cancer patients. Citation Format: Cem Mujde, Abdullah Hanta, Ozge Sonmezler, Ahmet Rencuzogullari, Ibrahim Boga, Atil Bisgin. The significance of liquid biopsy in colorectal cancer via GeneReader NGS Systems [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1972.

Inflammatory bowel diseases, Familial adenomatous polyposis(FAP) and colorectal cancer(CRC) are associated with alterations of the intestinal microbiota. However, few data are available on the perpetuation of FAP and Ulcerative Colitis(UC) in relation to microbial dysbiosis. This study evaluated the UC and genetically confirmed FAP patients' gut microbial balance in concordance to clinical outcome. Fecal materials (average mass of 0.54 g) were collected from three FAP and five UC patients to compare with healthy individuals as control group. Genomic materials of microbiota were isolated via QIAamp PowerFecal DNA kit according to manufacturer instructions. Next generation sequencing of 16S rRNA was performed by using QIAseq 16S/ITS panel in Illumina Miseq Platform. Data processing and bioinformatics analysis were performed via CLC Genomic Workbench bioinformatics tool. The comparison between FAP subjects, UC patients and control group revealed an alteration in the intestinal microbial composition. More in details, relative abundance of class levels showing statistical significance differences among FAP, UC and control group was given in Table 1, in which the sample groups are reported in column while class levels are in row. Our preliminary data focused on the explanation of how dysbiosis can lead to inflammation and drive processes together with host genetic profile that leads to colorectal carcinogenesis. Citation Format: Atil Bisgin, Abdullah Hanta, Ahmet Rencuzogullari, Ibrahim Boga. Changes of gut microbiota in FAP and UC that might harbor colorectal cancer carcinogenesis [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3346.

Inflammatory bowel diseases, familial adenomatous polyposis (FAP) and colorectal cancer (CRC) are associated with alterations of the intestinal microbiota. However, few data are available on the perpetuation of FAP and ulcerative colitis (UC) in relation to microbial dysbiosis. This study evaluated the UC and genetically confirmed FAP patients’ gut microbial balance in concordance to clinical outcome. Fecal materials (average mass of 0.54 g) were collected from three FAP and five UC patients to compare with healthy individuals as control group. Genomic materials of micro-biota were isolated for next generation sequencing of 16S rRNA that was performed by using QIAseq 16S/ITS panel in Illumina Miseq Platform. Data processing and bioinformatics analysis were performed via CLC Genomic Workbench bioinformatics tool. The comparison between FAP, UC and control group revealed an alteration in the intestinal microbial composition. More in details, relative abundance of class levels showed statistical significance differences among FAP, UC and control groups. Our preliminary data focused on the explanation of how dysbiosis can lead to inflammation and drive processes together with host genetic profile that leads to colorectal carcinogenesis.

E13611 Background: The detection of BRCA1 and BRCA2 mutations both somatic and germ-line became essential for the clinical management strategies of different cancers. Aiming at the identification of common and recurrent mutations that answer the questions about the association between a variant and phenotype, we collected the data of 1126 probands with pathogenic, likely pathogenic variants and variants of uncertain significance (VUS) distributed across 22 Turkish cities. Methods: Peripheral blood samples from 1126 individuals were collected and sequenced via the GeneReader (Qiagen, Hilden, Germany) and MiSeq (Illumina, San Diego, USA) NGS systems for BRCA1/ BRCA2 genes. QCI-Analyze and QCI-Interpret bioinformatics tools were used for bioinformatics analyses. Results: Total of 68 and 108 distinct variants were identified in BRCA1 and BRCA2 genes, respectively. Twenty novel variants were identified in both genes, while BRCA2 had higher heterogeneity. However, there had been no any recurrent mutations identified in any certain geographic region. Among all distinct mutations identified 11.9% were novel, corresponding to 12.8% of all carriers and 28.4% were VUS, corresponding to 32.1% of all carriers. Conclusions: This study presented with three important outcomes. First, a significant molecular heterogeneity in BRCAs among Turkish carriers were confirmed with 15.63% positivity rate. Most notably as the second, this is the first study showing the profiles of recurrent and common mutations that might be unique to Turkish landscape. In conclusion, it is critical to identify all the genetic variants, to aid in diagnosis, prevention, prognosis and treatment. Third and the last, the identification of novel mutations in BRCAs is a vital information that should be shared with mutation databases, in order to use for further clinical interpretation of Turkish population. Key words: Landscape of BRCA1/2, genetic testing, BRCA profiling, population data.