Characterization of the Common Genetic Variation in the Spanish Population of Navarre.

Large-scale genomic studies have significantly increased our knowledge of genetic variability across populations. Regional genetic profiling is essential for distinguishing common benign variants from disease-causing ones. To this end, we conducted a comprehensive characterization of exonic variants in the population of Navarre (Spain), utilizing whole genome sequencing data from 358 unrelated individuals of Spanish origin. Our analysis revealed 61,410 biallelic single nucleotide variants (SNV) within the Navarrese cohort, with 35% classified as common (MAF > 1%). By comparing allele frequency data from 1000 Genome Project (excluding the Iberian cohort of Spain, IBS), Genome Aggregation Database, and a Spanish cohort (including IBS individuals and data from Medical Genome Project), we identified 1069 SNVs common in Navarre but rare (MAF ≤ 1%) in all other populations. We further corroborated this observation with a second regional cohort of 239 unrelated exomes, which confirmed 676 of the 1069 SNVs as common in Navarre. In conclusion, this study highlights the importance of population-specific characterization of genetic variation to improve allele frequency filtering in sequencing data analysis to identify disease-causing variants.

Ecotoxicity of binary mixtures of ILs and inorganic salts of electrochemical interest.

The applicability of ionic liquids (ILs) has increased over the last years, and even new opportunities are becoming a reality, i.e. mixtures of pure IL and inorganic salt as electrolytes for smart electrochemical devices, yet the effects on the environment are almost unknown. In this work, the ecotoxicity of two pure protic ILs (Ethylammonium nitrate and Ethylimidazolium nitrate) and two pure aprotic ILs (butylmethylpyrrolidinium bis(trifluoromethylsulfonyl)imide and butyldimethylimidazolium bis(trifluoromethylsulfonyl)imide) and that of their binary mixtures with inorganic salts with common cation was tested towards changes in the bioluminescence of the bacteria Aliivibrio fischeri, using the Microtox® standard toxicity test. EC50 of these mixtures was determined over three standard periods of time and compared with the corresponding values to pure ILs. Results indicate that the aprotic ILs are more toxic than protic and that aromatic are more toxic than non-aromatic. The addition of inorganic mono (LiNO3), di (Ca(NO3)2·4H2O, Mg(NO3)2·6H2O) and trivalent (Al(NO3)3·9H2O) salts in binary mixtures with EAN was analysed first. The latter was found to induce an important increase in toxicity. Finally, mixtures of IL-inorganic lithium salt (LiNO3, for the protic ILs and LiTFSI for the aprotic ILs) toxicity was also studied, which showed toxicity levels strongly dependent on the IL of the mixture.

SMN1 copy-number and sequence variant analysis from next-generation sequencing data.

Spinal muscular atrophy (SMA) is a severe neuromuscular autosomal recessive disorder affecting 1/10,000 live births. Most SMA patients present homozygous deletion of SMN1, while the vast majority of SMA carriers present only a single SMN1 copy. The sequence similarity between SMN1 and SMN2, and the complexity of the SMN locus makes the estimation of the SMN1 copy-number by next-generation sequencing (NGS) very difficult. Here, we present SMAca, the first python tool to detect SMA carriers and estimate the absolute SMN1 copy-number using NGS data. Moreover, SMAca takes advantage of the knowledge of certain variants specific to SMN1 duplication to also identify silent carriers. This tool has been validated with a cohort of 326 samples from the Navarra 1000 Genomes Project (NAGEN1000). SMAca was developed with a focus on execution speed and easy installation. This combination makes it especially suitable to be integrated into production NGS pipelines. Source code and documentation are available at https://www.github.com/babelomics/SMAca.

Glycine-betaine-derived ionic liquids: Synthesis, characterization and ecotoxicological evaluation.

Ionic Liquids (ILs) are generically regarded as environmentally "harmless" and thus, assumed as "non-toxic". However, due to the endless design possibilities, their ecotoxicological profile is still poorly known. An accurate knowledge on the toxicity of a substance is required, under the scope of environmental regulation worldwide, before their application and commercialization. Knowledge on the relationship between the chemical structure and toxic effects is essential for the future design of more biocompatible solvents. Focusing on the use of ILs as base lubricants, lubricant additives, or even as potential working fluids for absorption heat pumps, the knowledge on its environmental impact is of great importance, due to the possibility of spills. In this specific context, four analogues of glycine-betaine-based ILs (AGB-ILs) and four glycine-betaine based ILs (GB-ILs) were synthesized and characterized. Their ecotoxicity was assessed using representatives of two trophic levels in aquatic ecosystems, the bacteria Allivibrio fischeri (commonly used as a screening test organism) and the microalgae Raphidocelis subcapitata (as an alternative test organism that has been proven very sensitive to several IL families). The microalgae were more sensitive than the bacteria, hence, following a precautionary principle, we recommend considering the toxicity towards microalgae as an indicator in future studies regarding the focused ILs. Although four of the studied ILs were derived from a natural amino acid, all were considered hazardous for the aquatic environment, disproving the primary theory that all ILs derived from natural compounds are benign. Furthermore, the modification in the structure of anion and the cation can lead to the increase of toxicity.

Analysis of BRCA1 and mtDNA haplotypes and mtDNA polymorphism in familial breast cancer.

Mitochondrial DNA (mtDNA) defects have been postulated to play an important role in the modulation and/or progression of cancer. In the past decade, a wide spectrum of mtDNA variations have been suggested as potentially sensitive and specific biomarkers for several human cancer types. In this context, single nucleotide polymorphisms (SNPs) described as protective or risk variants have been published, in particular in breast cancer, though not without controversy. Moreover, many mtDNA haplogroups have been associated with different phenotypes and diseases. We genotyped 18 SNPs, 15 of them defining European mtDNA haplogroups, including SNPs described as protective or risk variants, 7 SNPs that determine BRCA1 haplotypes and a BRCA1 intron 7 polymorphism. We included in this study 90 Caucasian unrelated women with breast cancer with familial criteria and 96 controls. Our aim was to clarify the importance of any of these SNPs, mitochondrial haplogroups and BRCA1 haplotypes in the modulation of breast cancer. We detected no significant differences in the distribution of BRCA1 haplotypes between patients and controls. Haplogroup U and the 12308G variant of mtDNA were overrepresented within the control group (p = 0.005 and p = 0.036, respectively) compared to breast cancer. Finally, we identified a significant association between the BRCA1 intron 7 polymorphism and BRCA1 haplotypes. Specifically, (TTC)6/6 and (TTC)6/7 genotypes with the seven polymorphic site cassette of "H2-like" haplotypes, and the (TTC)7/7 genotype associated with the "H1-like" haplotypes (p < 0.001).

Ionic liquids based on phosphonium cations as neat lubricants or lubricant additives for a steel/steel contact.

After doing several miscibility essays with eight ionic liquids (ILs) and four base oils, the ILs tri(butyl)ethylphosphonium diethylphosphate [P4,4,4,2][C2C2PO4] and trihexyl(tetradecyl)phosphonium tris(pentafluoroethyl)trifluorophosphate [P6,6,6,14][(C2F5)3PF3] were selected to be studied as lubricant additives. The neat IL [P4,4,4,2][C2C2PO4], the base oils, and several blends were characterized in terms of density, viscosity, and thermal stability. The tribological performance of the miscible base oil/IL blends (1 wt %) and the neat [P4,4,4,2][C2C2PO4] were evaluated for the lubrication of an AISI 420 steel-100Cr6 steel contact pair. The friction coefficients and wear volumes obtained are also compared with those corresponding to the pure base oils and their mixtures with conventional additive zinc dialkyldithiophosphate (ZDDP). As neat lubricants, [P4,4,4,2][C2C2PO4] showed the best antifriction ability, whereas in terms of wear, better results were obtained with [P6,6,6,14][(C2F5)3PF3]. However, higher improvements in both friction and wear were found for blends containing [P4,4,4,2][C2C2PO4]. XPS analyses of the worn surfaces lubricated with these mixtures indicated the presence of phosphorus in the tribofilm formed on the wear track. However, this compound was slightly detected on tribosamples lubricated with blends containing [P6,6,6,14][(C2F5)3PF3].

Thymidylate synthase polymorphisms in genomic DNA as clinical outcome predictors in a European population of advanced non-small cell lung cancer patients receiving pemetrexed.

BACKGROUND: We studied whether thymidylate synthase (TS) genotype has an independent prognostic/predictive impact on a European population of advanced non-small cell lung cancer (NSCLC) patients receiving pemetrexed. METHODS: Twenty-five patients treated with pemetrexed-based regimens were included. Genomic DNA was isolated prior to treatment. The variable number of tandem repeat (VNTR) polymorphisms, the G > C single nucleotide polymorphisms (SNP) and the TS 6-bp insertion/deletion (6/6) in the 3' untranslated region (UTR) polymorphisms were analyzed and correlated with overall response rate (ORR), progression-free survival (PFS), overall-survival (OS) and toxicity. RESULTS: The genotype +6/+6 predicted a higher ORR among active/former smokers compared to +6/-6 genotype (100% vs. 50%; p = 0.085). Overall, the 3R/3R genotype predicted a higher ORR (100%) over the rest VNTR polymorphisms (p = 0.055). The presence of 3R/3R genotype significantly correlated with a superior ORR in patients without EGFR activating mutations (100%) compared to 2R/2R, 2R/3R and 3R/4R genotype (77.8%, 33.3% and 0% respectively; p = 0.017). After a median follow-up of 21 months, a trend towards a better PFS, although not significant, was found among subjects showing 3R/3R polymorphisms (p = 0.089). A significantly superior OS was found in patients showing 3R/3R genotype rather than other VNTR polymorphisms (p = 0.019). No significant correlation with the toxicity was observed. CONCLUSION: In our series, 3R/3R polymorphism correlated with a superior OS. Also, this polymorphism, when associated to wild type EGFR, was related to a higher ORR to pemetrexed. Toxicity was not significantly correlated with a specific TS genotype.

KRAS mutational status analysis of peripheral blood isolated circulating tumor cells in metastatic colorectal patients.

The present study describes an optimized method for isolating peripheral blood circulating tumor cells (CTCs) and performing KRAS mutation analysis. The approach combines isolation of peripheral blood mononuclear cells and immunomagnetic labeling with CD45 and CD326 human microbeads with KRAS analysis performed with a Therascreen KRAS kit by quantitative PCR. KRAS mutations were detected in the CTCs of patients with metastatic colorectal cancer (mCRC). CTCs may represent an alternative to invasive procedures and their analysis may be representative of the current disease status of the patient. This proposed analysis may be performed in a daily clinical practice.

A novel BRCA1 mutation in a patient with breast and ovarian cancer: A case report.

Germline mutations in the human breast cancer genes BRCA1 and BRCA2 account for a substantial proportion of familial, early-onset breast and ovarian cancers. The present study reports a novel disease-causing BRCA1 mutation, nucleotide 3020insCT/c.2901insCT, in a 55-year-old Spanish female with breast and ovarian cancer. This frameshift mutation creates a premature stop codon at amino acid 1000, leading to a truncated BRCA1 protein. To the best of our knowledge, this mutation has not been previously described in the Breast Cancer Information Core (BIC) database or the published literature.

A novel mutation in BRCA1 linked to breast and ovarian cancer and a genotype-phenotype correlation.

We report a novel BRCA1 germline 4156delAA mutation detected in a 41-year-old woman with breast and ovarian cancer. Genomic DNA was obtained from peripheral blood. Standard polymerase chain reactions and direct sequencing were performed. This mutation originates a premature stop at codon 1354 of BRCA1 protein and has not been documented in any published report to the best of our knowledge. The mutation was not observed in any other family studied. Since this novel mutation was associated with both breast and ovarian cancer, the genotype-phenotype correlation was investigated in a patient base of 30 families.

Comparative disease pattern of a patient with a novel BRCA2 truncation and knockout models for BRCA2.

We report a novel germline 490delCT mutation in BRCA2 gene, detected in a 38-year-old woman with breast cancer. The mutation originates a premature stop at codon 99, leading to a truncated protein, and has not been documented in any published report to the best of our knowledge.

A novel BRCA2 mutation that segregates with breast and prostate cancer in a Spanish family.

We report a novel germline 5369delATTT mutation in BRCA2 gene, detected in a 45-year-old woman with bilateral breast cancer. This deletion was also detected in her father with prostatic cancer and her sister with breast cancer. The mutation originates a premature stop at codon 1723 of BRCA2 protein and has not been documented in any published report to the best of our knowledge.

A novel BRCA1 mutation in a Spanish patient with ovarian cancer.

We report a novel germline 3536delT mutation in BRCA1 gene, detected in a 43-year-old woman with bilateral ovarian adenocarcinoma. The mutation originates a premature stop codon at position 1154 and has not been documented in any published report to the best of our knowledge.

Review: mitochondrial defects in breast cancer.

Mitochondria play important roles in cellular energy metabolism, free radical generation, and apoptosis. Mitochondrial DNA has been proposed to be involved in carcinogenesis because of its high susceptibility to mutations and limited repair mechanisms in comparison to nuclear DNA. Breast cancer is the most frequent cancer type among women in the world and, although exhaustive research has been done on nuclear DNA changes, several studies describe a variety of mitochondrial DNA alterations present in breast cancer. In this review article, we to provide a summary of the mitochondrial genomic alterations reported in breast cancer and their functional consequences.

Polymorphisms in the thymidylate synthase and dihydropyrimidine dehydrogenase genes predict response and toxicity to capecitabine-raltitrexed in colorectal cancer.

Pharmacogenetics is an increasingly useful field where the genetic studies are becoming an important tool for predicting drug toxicity and/or efficacy. Thymidylate synthase (TS) and dihydropyrimidine dehydrogenase (DPD) gene polymorphisms could be highly informative tools in the clinical handling of colorectal cancer patients, who are following fluoropyrimidine based chemotherapy. Fifty-eight patients, with non-resectable metastatic colorectal cancer, were treated with capecitabine and raltitrexed, every three weeks. Patients were divided in a good-response group (complete and partial response) and a poor-response group (stable and progression). A genotype panel TS-DPD was evaluated. Results show that TS genotype analysis clearly differentiates patients with a worst response to a 5-fluorouracil based chemotherapy. DPD genotype was shown to be highly informative for prediction of toxicity of the treatment. These polymorphisms could represent an accurate, rapid and effective determination panel, indicative of resistance and toxicity for patients undergoing fluoropyrimidine based treatment.