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Low-cost generation of clinical-grade , layperson-friendly pharmacogenetic passports using oligonucleotide arrays

AMERICAN JOURNAL OF HUMAN GENETICS 2025年第5期112卷 1015-1028页

作者： Lanting, Pauline Warmerdam, Robert Slager, Jelle Brugge, Harm Ochi, Taichi Benjamins, Marloes Lopera-Maya, Esteban Jankipersadsing, Soesma Gelderloos-Arends, Jody Teuben, Daphne Hendriksen, Dennis Charbon, Bart Johansson, Lennart Munnink, Thijs Oude de Boer-Veger, Nienke Wilffert, Bob Swertz, Morris Touw, Daan Deelen, Patrick Knoers, Nine Dekens, Jackie Franke, Lude Univ Groningen Univ Med Ctr Groningen Dept Genet Groningen Netherlands Univ Groningen Univ Med Ctr Groningen Dept Clin Pharm & Pharmacol Groningen Netherlands Oncode Inst Utrecht Netherlands Univ Groningen Groningen Res Inst Pharm Unit PharmacoTherapy Epidemiol & Econ Groningen Netherlands Serv Apotheek Boterdiep Groningen Netherlands Genom Coordinat Ctr Groningen Netherlands Univ Groningen Univ Med Ctr Groningen Ctr Dev & Innovat Groningen Netherlands

Pharmacogenomic (PGx) information is essential for precision medicine, enabling drug prescriptions to be personalized according to an individual's genetic background. Almost all individuals will carry a genetic marker that affects their drug response, so the ideal drug prescription for these individuals will differ from the population-level guidelines. Currently, PGx information is often not available at first prescription, reducing its effectiveness. In the Netherlands, pharmacogenetic information is most often obtained using dedicated single-gene assays, making it expensive and time consuming to generate complete multi-gene PGx profiles. We therefore hypothesized that we could also use genome-wide oligonucleotide genotyping arrays to generate comprehensive PGx information (PGx passports), thereby decreasing the cost and time required for PGx testing and lowering the barrier to generating PGx information prior to first prescription. Taking advantage of existing genetic data generated in two biobanks, we developed and validated Asterix, a low-cost, clinical-grade PGx passport pipeline for 12 PGx genes. In these biobanks, we performed and clinically validated genetic variant calling and statistical phasing and imputation. In addition, we developed and validated a CYP2D6 copy-number-variant-calling tool, forgoing the need to use separate PCR-based copy-number detection. Ultimately, we returned 1,227 PGx passports to biobank participants via a layperson-friendly app, improving knowledge of PGx among citizens. Our study demonstrates the feasibility of a low-cost, clinical-grade PGx passport pipeline that could be readily implemented in clinical settings to enhance personalized healthcare, ensuring that patients receive the most effective and safe drug therapy based on their unique genetic makeup.

关键词： pharmacogenetics pharmacogenomics PGx profile PGx passport clinical pharmacogenomics layperson communication oligonucleotide array

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Rapid detection of dermatophytes and Candida albicans in onychomycosis specimens by an oligonucleotide array

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BMC INFECTIOUS DISEASES 2014年第1期14卷 1-7页

作者： Han, Huan Wen Hsu, Mark Ming-Long Choi, Jong Soo Hsu, Chao-Kai Hsieh, Hsin Yi Li, Hsin Chieh Chang, Hsien Chang Chang, Tsung Chain Natl Cheng Kung Univ Coll Engn Inst Biomed Engn Tainan 70101 Taiwan ESkin Clin Tainan Taiwan Yeungnam Univ Coll Med Dept Dermatol Taegu South Korea Natl Cheng Kung Univ Hosp Dept Dermatol Tainan 70428 Taiwan Natl Cheng Kung Univ Coll Med Dept Med Lab Sci & Biotechnol Tainan 70101 Taiwan

Background: Onychomycosis is a fungal infection of nails, leading to the gradual destruction of the nail plate. Treatment of onychomycosis may need long-time oral antifungal therapy that can have potential side effects, thus accurate diagnosis of the disease before treatment is important. Culture for diagnosis of onychomycosis is time-consuming and has high false-negative rates. To expedite the diagnosis, an oligonucleotide array, based on hybridization between immobilized oligonucleotide probes and PCR products, for direct detection of dermatophytes and Candida albicans in clinical specimens was evaluated. Methods: Species-specific oligonucleotide probes designed from the internal transcribed spacer (ITS) regions of the rRNA gene were immobilized on a nylon membrane. The assay procedures consisted of PCR amplification of the ITS using universal primers, followed by hybridization of the digoxigenin-labeled amplicons to probes on the array. Thirty two nail samples (29 patients) were analyzed by the array, and the results were compared with those obtained by culture. array-positive but culture-negative samples were confirmed by cloning and re-sequencing of the amplified ITS and by reviewing patient's clinical data. The total recovery of culture and confirmed array-positive but culture-negative results was considered 100% and was used for performance evaluation of both methods. Results: Concordant results were obtained in 21 samples (10 positives and 11 negatives) by both methods. Eleven samples were array-positive but culture-negative;among them, 9 samples were considered true positives after discrepant analysis. Comparing with culture, the array had significantly higher sensitivity [100% (95% CI 82.2% - 100%) vs 52.6% (28.9% - 75.5%), p <0.001] and negative predictive value [100% (71.3% - 100%) vs 59.1% (36.4% - 79.3%), p <0.05), while no significant differences were observed in specificity (84.6% vs 100%, p =0.48) and positive predictive value (90.5% vs 100%, p =1.0

关键词： Onychomycosis oligonucleotide array Molecular diagnosis Internal transcribed spacer Dermatophytes

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Pivotal role of biallelic frequency analysis in identifying copy number alterations using genome-wide methods in tumors with a high level of aneuploidy

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JOURNAL OF APPLIED GENETICS 2025年 1-6页

作者： Rymuza, Julia Woroniecka, Renata Grygalewicz, Beata Bujko, Mateusz Maria Sklodowska Curie Natl Res Inst Oncol Dept Mol & Translat Oncol Warsaw Poland Maria Sklodowska Curie Natl Res Inst Oncol Cytogenet Lab Warsaw Poland

Chromosome number abnormalities is one of the hallmarks of cancer. DNA copy number alterations (CNA) are studied using various genome-wide methods. In our study, we investigated CNA in human pituitary tumors using three platforms CytoSNP-850 K microarrays, low-pass whole-genome sequencing (average x 7 coverage, LPWGS), and Infinium Methylation EPIC array. Virtual karyotypes based on each dataset were generated using open-source software packages for each sample. Concordant CNA profiles were found for most of tumor. Surprisingly, substantial discrepancies between results from SNP arrays and LPWGS/EPIC arrays were identified in 20% of tumors, for which discrimination of true karyotype was required. B-allelic frequency data from SNP arrays was crucial to adjust normal ploidy level as ultimately verified with FISH. The discrepancy between virtual karyotypes was more pronounced the more CNAs were found. When CNAs covered around half of genome, the level of normal/diploid copy number was incorrectly set with methods, based solely on signal intensity/read-counts coverage. To conclude, CNA analyses with methods such as LPWGS and methylation arrays in highly aneuploid tumors are prone to a bias from improper normal ploidy level setting. These methods are commonly used therefore, we aimed to aware the scientific community about this underestimated methodological problem.

关键词： DNA copy number variations Aneuploidy Genomic instability Cancer Cytogenetic analysis oligonucleotide array Sequence analysis Whole genome sequencing

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Species identification and antifungal susceptibility of uncommon blood yeast isolates

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JOURNAL OF MICROBIOLOGY IMMUNOLOGY AND INFECTION 2022年第1期55卷 130-137页

作者： Li, Ming-Chi Tang, Hung-Jen Wu, Chi-Jung Wang, Shin-Wei Su, Shu-Li Liu, Wei-Lun Ko, Wen-Chien Chen, Yee-Chun Natl Cheng Kung Univ Natl Cheng Kung Univ Hosp Dept Internal Med Coll Med Tainan Taiwan Natl Cheng Kung Univ Dept Publ Hlth Coll Med Tainan Taiwan Chi Mei Med Ctr Dept Med Tainan Taiwan Chia Nan Univ Pharm & Sci Dept Hlth & Nutr Tainan Taiwan Natl Inst Infect Dis & Vaccinol Natl Hlth Res Inst Tainan Taiwan Natl Cheng Kung Univ Natl Cheng Kung Univ Hosp Dept Pathol Coll Med Tainan Taiwan Natl Cheng Kung Univ Natl Cheng Kung Univ Hosp Coll Med Diagnost Microbiol & Antimicrobial Resistance Lab Tainan Taiwan Fu Jen Catholic Univ Fu Jen Catholic Univ Hosp Dept Emergency & Crit Care Med New Taipei Taiwan Fu Jen Catholic Univ Sch Med Coll Med New Taipei Taiwan Natl Cheng Kung Univ Dept Med Coll Med Tainan Taiwan Natl Taiwan Univ Hosp & Coll Med Div Infect Dis Dept Internal Med Taipei Taiwan Natl Taiwan Univ Dept Med Coll Med Taipei Taiwan

Background/Purpose: Accurate identification of Candida species is increasingly important in the era of emergence of Candida auris. We aimed to compare the identification performance of two matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems (Vitek MS and Bruker biotyper MS) and an oligonucleotide array for uncommon blood yeast isolates and demonstrate the susceptibilities among those isolates. Method: Candida species isolates from blood culture other than Candida albicans, Candida parapsilosis, Candida tropicalis, Candida glabrata, and Candida krusei identified by biochemical methods were collected from multiple hospitals and further identified by an oligonucleotide array based on the internal transcribed spacer-1 (ITS-1) and ITS-2 sequences of the rRNA genes, Vitek MS and Bruker biotyper MS. The minimal inhibitory concentrations (MICs) of these clinical isolates were determined by the Sensititre YeastOne (SYO) system. Results: Among 136 isolates, Candida guilliermondii was most common (52, 38.2%), followed by C. lusitaniae (13, 9.6%) and C. haemulonii (12, 8.8%). The oligonucleotide array, Vitek MS and Bruker biotyper MS correctly identified 89.7% (122), 90.4% (123), and 92.6% (126) of these isolates, respectively. Elevated minimal inhibitory concentrations (MICs) of fluconazole were observed for C. haemulonii (MIC90: 256 mg/L), and C. guilliermondii (MIC90: 16 mg/L) with 28.4% of uncommon Candida isolates with MIC >= 8 mg/L. Conclusions: For uncommon Candida species, the unmet need for current databases of two commercial MALDI-TOF MS systems is highlighted, and the oligonucleotide array may serve as a supplement. Copyright (C) 2021, Taiwan Society of Microbiology. Published by Elsevier Taiwan LLC.

关键词： MALDI-TOF oligonucleotide array Susceptibility Uncommon Candida Yeast

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Combination of an Immunomagnetic Separation Method and a Chromogenic oligonucleotide array for the Detection of Beer-Spoilage Lactic Acid Bacteria

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Proceedings. Annual meeting - American Society of Brewing Chemists 2013年第1期71卷 57-62页

For the brewing industry, the possibility of beer spoilage by lactic acid bacteria (LAB) or by wild yeasts is always a concern. Contamination by certain LAB, such asLactobacillus brevis, L. casei, L. plantarum, Pediococcus claussenii, P. damnosus,andP. inopinatus,may result in the deterioration of beer quality. Thus, monitoring of these spoilage organisms during the brewing process is critical to quality control. When concentrations of spoilage organisms in the brewing samples are low and, thus, difficult to detect, collection and concentration of these spoilage organisms prior to the application of diagnostic methods are important. Although the membrane filtration method can be used even if filters of the correct pore sizes are chosen, it is still possible that some LAB cells will go through the membrane filters. Another drawback of membrane filtration is membrane fouling, which restricts the beer volume to be filtered. In this study, polyclonal antibodies against beer-spoilage bacteria were prepared by rabbit immunization. The antibodies were then conjugated to magnetic beads for the capture and concentration of major beer-spoilage LAB. The captured cells were subsequently discriminated to species level by a commercially available oligonucleotide array. The combination of immunomagnetic separation with an oligonucleotide array allowed the simultaneous and sensitive detection of several major beer-spoilage LAB species in the brewing samples within 8 hr. This method is accurate and time-saving and can be used for routine monitoring and control of the spoilage organisms during the beer brewing *** la industria de elaboración de la cerveza, la posibilidad de deterioro de la cerveza por las bacterias ácido lácticas (BAL) o por levaduras silvestres es siempre una preocupación. La contaminación por ciertas BAL, tales comoLactobacillus brevis, L. casei, L. plantarum, Pediococcus claussenii, P. damnosus,yP. inopinatus,puede resultar en el deterioro de la ca

关键词： Beer-spoilage bacteria Detection Immunomagnetic separation Lactic acid bacteria oligonucleotide array las bacterias de deterioración de cerveza detección separación inmunomagnética bacterias del ácido láctico matriz de oligonucleótidos

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Feasibility of diagnosing renal allograft dysfunction by oligonucleotide array: Gene expression profile correlates with histopathology

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TRANSPLANT IMMUNOLOGY 2011年第3期24卷 172-180页

作者： Mao, You-ying Yang, Hao Wang, Minmin Peng, Wenhan He, Qiang Shou, Zhang-fei Jiang, Hua Wu, Jianyong Fang, Yong-qi Dong, Hai-tao Chen, Jiang-hua Zhejiang Univ Coll Med Affiliated Hosp 1 Kidney Dis Ctr Hangzhou 310003 Zhejiang Peoples R China Zhejiang Univ Sch Agr & Biotechnol Bioinformat & Gene Network Res Grp Hangzhou Peoples R China Minist Publ Hlth Key Lab Combined Multi Organ Transplantat Hangzhou Peoples R China State Adm tradit Chinese Med Grade Lab 3 Kidney Dis Immunol Lab Hangzhou Zhejiang Peoples R China

Background: Effective non-invasive monitoring method to tell histopathology is a big challenge in renal transplantation. Methods: We used 70-mer long oligonucleotide array with 449 immune related genes to determine gene expression profiles of peripheral blood mononuclear cells (PBMCs) under different immune status including stable renal function (TX), acute tubular necrosis (ATN), biopsy conformed acute rejection (AR), clinical rejection with pathology of borderline changes (BL), clinical rejection without biopsy proven/presumed rejection (PR) and renal dysfunction without rejection (NR). Results: Distinct molecular expression signatures in each group were found to correlate with histopathology. And we concluded that B cell chemokine CXCL13 and mast cell may play a role in renal allograft rejection through significant difference analysis and functional pathway analysis. Conclusions: It provides a potential non-invasive method for monitoring renal allograft function and immune status of renal transplant recipients. (C) 2010 Elsevier B.V. All rights reserved.

关键词： Renal transplant Acute allograft rejection oligonucleotide array Gene expression Immune status

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Link between nasal carriage of Staphylococcus aureus and infected diabetic foot ulcers

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DIABETES & METABOLISM 2017年第2期43卷 167-171页

作者： Dunyach-Remy, C. Courtais-Coulon, C. DeMattei, C. Jourdan, N. Schuldiner, S. Sultan, A. Carriere, C. Alonso, S. Sotto, A. Lavigne, J. -P. Montpellier Univ Fac Med Natl Inst Hlth & Med Res U1047 F-30908 Nimes 02 France Univ Hosp Caremeau Dept Microbiol Pl Prof Robert Debre F-30029 Nimes 9 France Univ Hosp Caremeau Dept Biostat Epidemiol Publ Hlth & Med Informat F-30029 Nimes 9 France Univ Hosp Caremeau Dept Endocrinol F-30029 Nimes 9 France Univ Hosp Nimes Dept Diabetol F-30240 Le Grau Du Roi France Univ Hosp Lapeyronie Dept Endocrinol F-34295 Montpellier 5 France Univ Hosp Arnaud de Villeneuve Dept Bacteriol F-34295 Montpellier 5 France Nimes Univ Hosp Caremeau Dept Infect Dis F-30029 Nimes 9 France

Aims. Nasal carriage of Staphylococcus aureus in diabetic patients may be a risk factor for diabetic foot lesion infections. The aims of this study were to compare the genotypic profiles of S. aureus strains isolated from nares and diabetic foot ulcers (DFUs) using microarray technology. Methods. Patients were included if they were admitted for diabetic foot infection (DFI) at any of three diabetology departments of Montpellier and Nimes University Hospitals between 1 September 2010 to 30 June 2012. All S. aureus isolates were analyzed using oligonucleotides arrays;S. aureus resistance and virulence genes were determined and each isolate was affiliated to a clonal complex. Results. The prevalence of S. aureus nasal carriage among the 276 included patients was 39.5% (n = 109), while 36.6% (n = 101) had S. aureus at both sites (nares and foot wounds) and, of these patients, 65.3% of patients harboured the same strain at both sites. In addition, the spread of the methicillin-resistant S. aureus (MRSA) ST398 clone in DFI and its tropism for bone were also further confirmed. Conclusion. These findings appear to provide new arguments in favour of the systematic detection of nasal S. aureus carriage to anticipate the management of DFI. (C) 2016 Elsevier Masson SAS. All rights reserved.

关键词： Clonal complexes Diabetic foot ulcer Infection Nasal carriage oligonucleotide array Staphylococcus aureus

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Rapid identification of allergenic and pathogenic molds in environmental air by an oligonucleotide array

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BMC INFECTIOUS DISEASES 2011年第1期11卷 91-91页

作者： Hung, Wen-Tsung Su, Shu-Li Shiu, Lin-Yi Chang, Tsung C. Natl Cheng Kung Univ Coll Med Dept Med Lab Sci & Biotechnol Tainan 70101 Taiwan Environm Protect Adm Environm Anal Lab Zhongli Taiwan

Background: Airborne fungi play an important role in causing allergy and infections in susceptible people. Identification of these fungi, based on morphological characteristics, is time-consuming, expertise-demanding, and could be inaccurate. Methods: We developed an oligonucleotide array that could accurately identify 21 important airborne fungi (13 genera) that may cause adverse health problems. The method consisted of PCR amplification of the internal transcribed spacer (ITS) regions, hybridization of the PCR products to a panel of oligonucleotide probes immobilized on a nylon membrane, and detection of the hybridization signals with alkaline phosphatase-conjugated antibodies. Results: A collection of 72 target and 66 nontarget reference strains were analyzed by the array. Both the sensitivity and specificity of the array were 100%, and the detection limit was 10 pg of genomic DNA per assay. Furthermore, 70 fungal isolates recovered from air samples were identified by the array and the identification results were confirmed by sequencing of the ITS and D1/D2 domain of the large-subunit RNA gene. The sensitivity and specificity of the array for identification of the air isolates was 100% (26/26) and 97.7% (43/44), respectively. Conclusions: Identification of airborne fungi by the array was cheap and accurate. The current array may contribute to decipher the relationship between airborne fungi and adverse health effect.

关键词： Internal Transcribe Spacer oligonucleotide array Multiple Probe Trichoderma Viride Airborne Fungus

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Microfluidic cartridge with integrated array of amorphous silicon photosensors for chemiluminescence detection of viral DNA

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Sensing and Bio-Sensing Research 2016年 7卷 127-132页

作者： Zangheri, M. Mirasoli, M. Nascetti, A. Caputo, D. Bonvicini, F. Gallinella, G. de Cesare, G. Roda, A. Department of Chemistry Giacomo Ciamician University of Bologna Italy Aerospace Engineering School Sapienza University of Rome Italy Department of Information Electronics and Communication Engineering Sapienza University of Rome Italy Department of Pharmacy and Biotechnology University of Bologna Italy

Portable and simple analytical devices based on microfluidics with chemiluminescence detection are particularly attractive for point-of-care applications, offering high detectability and specificity in a simple and miniaturized analytical format. Particularly relevant for infectious disease diagnosis is the ability to sensitively and specifically detect target nucleic acid sequences in biological fluids. To reach the goal of real-life applications for such devices, however, several technological challenges related to full device integration are still to be solved, one key aspect regarding on-chip integration of the chemiluminescence signal detection device. Nowadays, the most promising approach is on-chip integration of thin-film photosensors. We recently proposed a portable cartridge with microwells aligned with an array of hydrogenated amorphous silicon (a-Si:H) photosensors, reaching attomole level limits of detection for different chemiluminescence model reactions. Herein, we explore its applicability and performance for multiplex and quantitative detection of viral DNA. In particular, the cartridge was modified to accommodate microfluidic channels and, upon immobilization of three oligonucleotide probes in different positions along each channel, each specific for a genotype of Parvovirus B19, viral nucleic acid sequences were captured and detected. With this system, taking advantage of oligoprobes specificity, chemiluminescence detectability, and photosensor sensitivity, accurate quantification of target analytes down to 70 pmol L^-1 was obtained for each B19 DNA genotype, with high specificity and multiplexing ability. Results confirm the good detection capabilities and assay applicability of the proposed system, prompting the development of innovative portable analytical devices with enhanced sensitivity and multiplexed capabilities. © 2016 The Authors.

关键词： Amorphous silicon photosensors Chemiluminescence Integrated analytical system Nucleic acids detection oligonucleotide array Point-of-care

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Changing Interpretation of Chromosomal Microarray Over Time in a Community Cohort With Intellectual Disability

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AMERICAN JOURNAL OF MEDICAL GENETICS PART A 2014年第2期164卷 377-385页

作者： Palmer, Emma Speirs, Helen Taylor, Peter J. Mullan, Glenda Turner, Gill Einfeld, Stewart Tonge, Bruce Mowat, David Sydney Childrens Hosp Dept Med Genet Randwick NSW Australia Univ NSW Sch Womens & Childrens Hlth Sydney NSW Australia Univ NSW Ramaciotti Ctr Gene Funct Anal Sydney NSW Australia South Eastern Area Lab Serv Sydney NSW Australia Hunter Area Hlth Serv Newcastle NSW Australia Univ Sydney Sydney NSW 2006 Australia Univ Sydney Brain & Mind Res Inst Ctr Disabil Res & Policy Sydney NSW 2006 Australia Monash Univ Sch Psychol & Psychiat Clayton Vic Australia

Chromosomal microarray (CMA) is the first-line diagnostic test for individuals with intellectual disability, autism, or multiple congenital anomalies, with a 10-20% diagnostic yield. An ongoing challenge for the clinician and laboratory scientist is the interpretation of variants of uncertain significance (VOUS)usually rare, unreported genetic variants. Laboratories differ in their threshold for reporting VOUS, and clinical practice varies in how this information is conveyed to the family and what follow-up is arranged. Workflows, websites, and databases are constantly being updated to aid the interpretation of VOUS. There is a growing literature reporting new microdeletion and duplication syndromes, susceptibility, and modifier copy number variants (CNVs). Diagnostic methods are also evolving with new array platforms and genome builds. In 2010, high-resolution arrays (Affymetrix 2.7M Oligo and SNP, 50kB resolution) were performed on a community cohort of 67 individuals with intellectual disability of unknown aetiology. Three hundred and one CNVs were detected and analyzed using contemporary resources and a simple scoring system. Thirteen (19%) of the arrays were assessed as potentially pathogenic, 4 (6%) as benign and 50 (75%) of uncertain clinical significance. The CNV data were re-analyzed in 2012 using the contemporary interpretative resources. There was a statistically significant difference in the assessment of individual CNVs (P<0.0001). An additional eight patients were reassessed as having a potentially pathogenic array (n=21, 31%) and several additional susceptibility or modifier CNVs were identified. This study highlights the complexity involved in the interpretation of CMA and uniquely demonstrates how, even on the same array platform, it can be subject to change over time. (c) 2013 Wiley Periodicals, Inc.

关键词： aberrations chromosome intellectual disability diagnostic test oligonucleotide array

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