INTRODUCTION: In silico tools capable of predicting the functional consequences of genomic differences between individuals, many of which are AI-driven, have been the most effective over the past two decades for non-synonymous single nucleotide variants (nsSNVs). When appropriately selected for the purpose of the study, a high predictive performance can be expected. In this feasibility study, we investigate the distribution of nsSNVs with an allele frequency below 5%. To classify the putative functional consequence, a tier-based filtration led by AI-driven predictors and scoring system was implemented to the overall decision-making process, resulting in a list of prioritised genes. METHODS: The study has been conducted on breast cancer patients of homogeneous ethnicity. Germline rare variants have been sequenced in genes that influence pharmacokinetic parameters of anticancer drugs or molecular signalling pathways in cancer. After AI-driven functional pathogenicity classification and data mining in pharmacogenomic (PGx) databases, variants were collapsed to the gene level and ranked according to their putative deleterious role. RESULTS: In breast cancer patients, seven of the twelve genes prioritised based on the predictions were found to be associated with response to oncotherapy, histological grade, and tumour subtype. Most importantly, we showed that the group of patients with at least one rare nsSNVs in cystic fibrosis transmembrane conductance regulator (CFTR) had significantly reduced disease-free (log rank, p = 0.002) and overall survival (log rank, p = 0.006). CONCLUSION: AI-driven in silico analysis with PGx data mining provided an effective approach navigating for functional consequences across germline genetic background, which can be easily integrated into the overall decision-making process for future studies. The study revealed a statistically significant association with numerous clinicopathological parameters, including treatment response. Our study indicates that CFTR may be involved in the processes influencing the effectiveness of oncotherapy or in the malignant progression of the disease itself.

• Keywords
• Breast cancer, Cystic fibrosis transmembrane conductance regulator, Gene prioritisation, Machine learning, Survival,
• MeSH
• Adult MeSH
• Gene Frequency MeSH
• Polymorphism, Single Nucleotide MeSH
• Middle Aged MeSH
• Humans MeSH
• Breast Neoplasms * genetics   drug therapy   pathology   MeSH
• Cystic Fibrosis Transmembrane Conductance Regulator * genetics   MeSH
• Aged MeSH
• Feasibility Studies * MeSH
• Artificial Intelligence * MeSH
• Treatment Outcome MeSH
• Check Tag
• Adult MeSH
• Middle Aged MeSH
• Humans MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• CFTR protein, human MeSH Browser
• Cystic Fibrosis Transmembrane Conductance Regulator * MeSH

Breast cancer is the most frequent cancer in the female population worldwide. The role of germline genetic variability in cytochromes P450 (CYP) in breast cancer prognosis and individualized therapy awaits detailed elucidation. In the present study, we used the next-generation sequencing to assess associations of germline variants in the coding and regulatory sequences of all human CYP genes with response of the patients to the neoadjuvant cytotoxic chemotherapy and disease-free survival (n = 105). A total of 22 prioritized variants associating with a response or survival in the above evaluation phase were then analyzed by allelic discrimination in the large confirmation set (n = 802). Associations of variants in CYP1B1, CYP4F12, CYP4X1, and TBXAS1 with the response to the neoadjuvant cytotoxic chemotherapy were replicated by the confirmation phase. However, just association of variant rs17102977 in CYP4X1 passed the correction for multiple testing and can be considered clinically and statistically validated. Replicated associations for variants in CYP4X1, CYP24A1, and CYP26B1 with disease-free survival of all patients or patients stratified to subgroups according to therapy type have not passed a false discovery rate test. Although statistically not confirmed by the present study, the role of CYP genes in breast cancer prognosis should not be ruled out. In conclusion, the present study brings replicated association of variant rs17102977 in CYP4X1 with the response of patients to the neoadjuvant cytotoxic chemotherapy and warrants further research of genetic variation CYPs in breast cancer.

• Keywords
• breast cancer, cytochrome P450, next-generation sequencing, prognosis, response, survival, therapy,
• MeSH
• Genetic Variation * MeSH
• Middle Aged MeSH
• Humans MeSH
• Survival Rate MeSH
• Neoplasm Proteins * genetics   metabolism   MeSH
• Breast Neoplasms * drug therapy   enzymology   genetics   mortality   MeSH
• Neoadjuvant Therapy * MeSH
• Disease-Free Survival MeSH
• Cytochrome P-450 Enzyme System * genetics   metabolism   MeSH
• Check Tag
• Middle Aged MeSH
• Humans MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Clinical Trial MeSH
• Names of Substances
• Neoplasm Proteins * MeSH
• Cytochrome P-450 Enzyme System * MeSH

Breast cancer is the most common cancer in women in the world. The role of germline genetic variability in ATP-binding cassette (ABC) transporters in cancer chemoresistance and prognosis still needs to be elucidated. We used next-generation sequencing to assess associations of germline variants in coding and regulatory sequences of all human ABC genes with response of the patients to the neoadjuvant cytotoxic chemotherapy and disease-free survival (n = 105). A total of 43 prioritized variants associating with response or survival in the above testing phase were then analyzed by allelic discrimination in the large validation set (n = 802). Variants in ABCA4, ABCA9, ABCA12, ABCB5, ABCC5, ABCC8, ABCC11, and ABCD4 associated with response and variants in ABCA7, ABCA13, ABCC4, and ABCG8 with survival of the patients. No association passed a false discovery rate test, however, the rs17822931 (Gly180Arg) in ABCC11, associating with response, and the synonymous rs17548783 in ABCA13 (survival) have a strong support in the literature and are, thus, interesting for further research. Although replicated associations have not reached robust statistical significance, the role of ABC transporters in breast cancer should not be ruled out. Future research and careful validation of findings will be essential for assessment of genetic variation which was not in the focus of this study, e.g., non-coding sequences, copy numbers, and structural variations together with somatic mutations.

• Keywords
• ABC transporter, breast cancer, competitive allele-specific PCR, disease-free survival, next-generation sequencing, therapy response,
• MeSH
• ATP-Binding Cassette Transporters genetics   MeSH
• Alleles MeSH
• Gene Frequency MeSH
• Genetic Variation * MeSH
• Genotype MeSH
• Polymorphism, Single Nucleotide MeSH
• Kaplan-Meier Estimate MeSH
• Humans MeSH
• Quantitative Trait Loci MeSH
• Biomarkers, Tumor * MeSH
• Breast Neoplasms diagnosis   genetics   mortality   therapy   MeSH
• Neoadjuvant Therapy MeSH
• Prognosis MeSH
• Antineoplastic Combined Chemotherapy Protocols therapeutic use   MeSH
• Treatment Outcome MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Check Tag
• Humans MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• ATP-Binding Cassette Transporters MeSH
• Biomarkers, Tumor * MeSH

Mutation spectra of 250 cancer driver, druggable, and actionable genes were analyzed in surgically resected pancreatic ductal adenocarcinoma (PDAC) patients who developed metachronous pulmonary metastases. Targeted sequencing was performed in DNA from blood and archival samples of 15 primary tumors and three paired metastases. Results were complemented with the determination of G12V mutation in KRAS by droplet digital PCR. The median number of protein-changing mutations was 52 per patient. KRAS and TP53 were significantly enriched in fractions of mutations in hotspots. Individual gene mutation frequencies or mutational loads accounting separately for drivers, druggable, or clinically actionable genes, did not significantly associate with patients' survival. LRP1B was markedly mutated in primaries of patients who generalized (71%) compared to those developing solitary pulmonary metastases (0%). FLG2 was mutated exclusively in primary tumors compared to paired metastases. In conclusion, signatures of prognostically differing subgroups of PDAC patients were generated for further utilization in precision medicine.

• Keywords
• adenocarcinoma, metastases, next-generation sequencing, pancreas, pulmonary, survival,
• MeSH
• Adenocarcinoma genetics   pathology   MeSH
• Filaggrin Proteins MeSH
• Gene Frequency genetics   MeSH
• Middle Aged MeSH
• Humans MeSH
• Mutation genetics   MeSH
• Tumor Suppressor Protein p53 genetics   MeSH
• Lung Neoplasms genetics   pathology   MeSH
• Pancreatic Neoplasms genetics   pathology   MeSH
• S100 Proteins genetics   MeSH
• Proto-Oncogene Proteins p21(ras) genetics   MeSH
• Check Tag
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Filaggrin Proteins MeSH
• FLG2 protein, human MeSH Browser
• Tumor Suppressor Protein p53 MeSH
• S100 Proteins MeSH
• Proto-Oncogene Proteins p21(ras) MeSH

The 12 members of the ABCA subfamily in humans are known for their ability to transport cholesterol and its derivatives, vitamins, and xenobiotics across biomembranes. Several ABCA genes are causatively linked to inborn diseases, and the role in cancer progression and metastasis is studied intensively. The regulation of translation initiation is implicated as the major mechanism in the processes of post-transcriptional modifications determining final protein levels. In the current bioinformatics study, we mapped the features of the 5' untranslated regions (5'UTR) known to have the potential to regulate translation, such as the length of 5'UTRs, upstream ATG codons, upstream open-reading frames, introns, RNA G-quadruplex-forming sequences, stem loops, and Kozak consensus motifs, in the DNA sequences of all members of the subfamily. Subsequently, the conservation of the features, correlations among them, ribosome profiling data as well as protein levels in normal human tissues were examined. The 5'UTRs of ABCA genes contain above-average numbers of upstream ATGs, open-reading frames and introns, as well as conserved ones, and these elements probably play important biological roles in this subfamily, unlike RG4s. Although we found significant correlations among the features, we did not find any correlation between the numbers of 5'UTR features and protein tissue distribution and expression scores. We showed the existence of single nucleotide variants in relation to the 5'UTR features experimentally in a cohort of 105 breast cancer patients. 5'UTR features presumably prepare a complex playground, in which the other elements such as RNA binding proteins and non-coding RNAs play the major role in the fine-tuning of protein expression.

• Keywords
• 5′ untranslated region, ABC transporters, ABCA subfamily, bioinformatics, cis-acting elements,
• MeSH
• 5' Untranslated Regions genetics   MeSH
• ATP Binding Cassette Transporter, Subfamily A classification   genetics   metabolism   MeSH
• Biological Transport genetics   MeSH
• Cholesterol metabolism   MeSH
• Introns genetics   MeSH
• Polymorphism, Single Nucleotide genetics   MeSH
• Humans MeSH
• Multigene Family genetics   MeSH
• Open Reading Frames genetics   MeSH
• Protein Biosynthesis genetics   MeSH
• Ribosomes genetics   metabolism   MeSH
• Computational Biology MeSH
• Xenobiotics metabolism   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• 5' Untranslated Regions MeSH
• ATP Binding Cassette Transporter, Subfamily A MeSH
• Cholesterol MeSH
• Xenobiotics MeSH