MALDI-TOF mass spectrometry tools for bacterial identification in clinical microbiology laboratory

Carbonnelle, Étienne; Mesquita, Cécile; Bille, Emmanuelle; Day, Nesrine; Dauphin, Brunhilde; Béretti, Jean-Luc; Ferroni, Agnès; Gutmann, Laurent; Nassif, Xavier

doi:10.1016/j.clinbiochem.2010.06.017

Cited by 361 publications

(248 citation statements)

References 44 publications

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“…Briefly, genomic DNA was isolated from 1 ml of whole blood using a genomic DNA isolation kit (Axygen Biosciences, Union City, CA, USA). Genotype of these SNPs was analyzed by using MassARRAY compact analyzer based on the chip-based matrix-assisted laser desorption ionization time-of-flight mass spectrometry platform (Sequenom, San Diego, CA, USA) (Carbonnelle et al, 2011). Multiplex reaction was designed using Assay Designer software (version 3.0, Sequenom, San Diego, CA, USA) and processed by following standard protocols for iPLEX chemistry.…”

Section: Dna Extraction and Genotypingmentioning

confidence: 99%

No Association of XRCC1 and CLPTM1L Polymorphisms with Non-small Cell Lung Cancer in a Non-Smoking Han Chinese Population

Sun¹,

Zhang²,

Kong³

2013

Asian Pacific Journal of Cancer Prevention

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Background: This study aimed to explore potential associations between single nucleotide polymorphisms (SNPs) of the x-ray repair cross-complementing group 1 (XRCC1) and cleft lip and palate transmembrane protein 1-like (CLPTM1L) and non-small cell lung cancer (NSCLC) susceptibility in non-smoker Chinese patients. Methods: A total of 200 NSCLC patients and 200 healthy controls with matched age and gender were recruited for genotyping of XRCC1 SNPs (rs2256507 and rs1001581) and CLPTM1L SNPs (rs401681 and rs4975616). Association of these SNPs with NSCLC risk was evaluated by computing the odds ratio (OR) and 95% confidence interval (CI) from multivariate unconditional logistic regression analyses with adjustment for gender and age. Results: The frequencies of genotype and allele in these four loci (rs2256507, rs1001581, rs401681, and rs4975616) were not significantly different between the cases and controls, or between either of the histological subgroups (adenocarcinoma and squamous cell carcinoma) and controls. Conclusions: Although these SNPs are associated with NSCLC risk in patients with a tobacco-smoking habit, this study demonstrated that XRCC1 and CLPTM1L gene SPNs are not linked with NSCLC risk in non-smoking patients, indicating that molecular mechanisms of NSCLC betwee tobacco smokers and non-smokers may be different. Future studies are needed to uncover the underlying molecular mechanisms for NSCLC in non-smokers.

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Section: Dna Extraction and Genotypingmentioning

confidence: 99%

No Association of XRCC1 and CLPTM1L Polymorphisms with Non-small Cell Lung Cancer in a Non-Smoking Han Chinese Population

Sun¹,

Zhang²,

Kong³

2013

Asian Pacific Journal of Cancer Prevention

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“…[11][12][13][14][15][16] In several recent studies, MALDI-TOF MS has been shown capable of identifying >84% of bacterial species and >95% of bacterial genera in large sets of clinical isolates, with overall analysis costs reduced to 22-32% of that required by conventional bacterial identification methods. 14,17,18 Previously, the identification of Bacillus spp.…”

Section: Introductionmentioning

confidence: 99%

Lipid fingerprinting of Bacillus spp. using online MALDI-TOF mass spectrometry

et al. 2012

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Rapid identification of Bacillus spores has attracted great interest in the medical and forensic communities due to the highly pathogenic nature of certain Bacillus species and its potential application in bioweapons. In this study, we evaluated the feasibility of rapid and reliable identification of several Bacillus spp. (B. subtilis, B. cereus, B. megaterium, B. pumilus, and B. sphaericus) using online MALDI-TOF mass spectrometry combined with lipid profiling. The bacterial cultures in liquid medium were extracted with methanol and chloroform, and the extracts were aerosolized into droplets and immediately analyzed with an online MALDI-TOF mass spectrometer. Results showed that phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and diglycosyldiacylglycerol (DGDG) were present in the mass spectra, as alkali metal adducts. The unique lipid profiles obtained from these Bacillus spp. allowed us to differentiate between them. The reliability and reproducibility of the rapid identification method for Bacillus were tested under different experimental conditions. An alternative online chemotaxonomic method for bacterial identification is demonstrated.

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“…Genomic DNA was extracted from peripheral blood with the AxyPrep Blood Genomic DNA Miniprep kit (Axygen; Corning Life Sciences, Union City, CA, USA). Genotyping was conducted through the Sequenom MassARRAY matrix-assisted laser desorption/ionization-time of flight mass spectrometry platform (Sequenom, San Diego, CA, USA) as previously described (26). Primers (5'-TCC TTA CCG AAT CAC TAC CC-3' and 5'-CCT GCT ATT ACT TCC AAC CC-3') and single base extensions were designed with Assay Designer software (version 3.0; Sequenom) and synthesized by Sangon Biotech Co., Ltd. (Shanghai, China).…”

Section: Methodsmentioning

confidence: 99%

Rs1008805 polymorphism of CYP19A1 gene is associated with the efficacy of hormone therapy in stage I‑II and operable stage III breast cancer

et al. 2017

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Abstract. It has been hypothesized that single nucleotide polymorphisms in CYP19A1 gene may alter aromatase activity and circulating steroid hormone levels in females. Therefore, it is biologically reasonable that CYP19A1 rs1008805 (A/G) polymorphism may be associated with the clinical outcome of hormone therapy. Genotyping for the CYP19A1 rs1008805 polymorphism was performed for 287 females with hormone receptor (HR)-positive early breast cancer, and potential associations were evaluated between CYP19A1 rs1008805 genotypes and disease-free survival (DFS). Based on the analysis of the whole cohort, no significant differences were observed between rs1008805 genotypes and DFS. However, in postmenopausal females, rs1008805 variants were significantly associated with DFS (AA vs. AG vs. GG, 89.2 vs. 58.2 vs. 32.7 months; P=0.019). In addition, when the population was divided into two cohorts, females with the GG variant exhibited a significantly poorer DFS [GG vs. AA or AG, 32.7 vs. 70.6 months; hazard ratio (HR), 3.613; 95% confidence interval (CI), 1.380-9.457; P=0.005]. Furthermore, when adjusted for other patient features in multivariate analyses, GG genotype remained an independent prognostic marker for DFS (HR, 3.439; 95% CI, 1.251-9.456; P=0.017). However, there were no significant differences in DFS between patients harboring the minor allele and those with the homozygous common allele (AG or GG vs. AA, 52.4 vs. 89.2 months; HR, 1.288; 95% CI, 0.705-2.353; P=0.408). There were also no associations between rs1008805 polymorphism and DFS for premenopausal females. In conclusion, the homozygous minor allele (GG) of CYP19A1 rs1008805 was identified to be significantly associated with an inferior clinical outcome of hormone therapy in postmenopausal hormone receptor-positive patients with early breast cancer. If confirmed by further study, genotyping for CYP19A1 rs1008805 polymorphism may provide predictive information to improve the selection of endocrine treatment. IntroductionOver the last three decades, the number of breast cancer cases has increased worldwide (1) to become the most likely cause of cancer mortality and morbidity in females (2). Increased levels of aromatase expression have been observed in breast lesions compared with normal breast tissue (3,4) and alterations in aromatase expression are associated with the pathogenesis of breast cancer (5,6).Approximately two thirds of breast cancer cases overexpress estrogen receptors (ER) and/or progesterone receptors (PgR) (7,8). Consequently, endocrine therapy, including tamoxifen or aromatase inhibitors (AIs), has become an effective treatment for these patients. For decades, 5-year tamoxifen administration was the gold standard for the adjuvant endocrine treatment of breast cancer (9). More recently, postmenopausal patients have also had the option of receiving AIs as an alternative to tamoxifen, or following tamoxifen treatment (10). The presence and intensity of ER and/or PgR are useful predictive markers for the response to hormone therapy in clinica...

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MALDI-TOF mass spectrometry tools for bacterial identification in clinical microbiology laboratory

Cited by 361 publications

References 44 publications

No Association of XRCC1 and CLPTM1L Polymorphisms with Non-small Cell Lung Cancer in a Non-Smoking Han Chinese Population

No Association of XRCC1 and CLPTM1L Polymorphisms with Non-small Cell Lung Cancer in a Non-Smoking Han Chinese Population

Lipid fingerprinting of Bacillus spp. using online MALDI-TOF mass spectrometry

Rs1008805 polymorphism of CYP19A1 gene is associated with the efficacy of hormone therapy in stage I‑II and operable stage III breast cancer

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