Articles de revues : « Unamplified genomic DNA »

1

Fors, Lance, Kafryn W. Lieder, Stephanie H. Vavra et Robert W. Kwiatkowski. « Large-scale SNP scoring from unamplified genomic DNA ». Pharmacogenomics 1, n^o 2 (mai 2000) : 219–29. http://dx.doi.org/10.1517/14622416.1.2.219.

Texte intégral

Styles APA, Harvard, Vancouver, ISO, etc.

2

Bao, Y. P. « SNP identification in unamplified human genomic DNA with gold nanoparticle probes ». Nucleic Acids Research 33, n^o 2 (19 janvier 2005) : e15-e15. http://dx.doi.org/10.1093/nar/gni017.

Texte intégral

Styles APA, Harvard, Vancouver, ISO, etc.

3

Larsen, Jacob, Anne Marie Ottesen, Maria Kirchhoff, Claes Lundsteen et Jørgen K. Larsen. « High Resolution Comparative Genomic Hybridization Detects 7–8 Megabasepair Deletion in PCR Amplified DNA1 ». Analytical Cellular Pathology 23, n^o 2 (2001) : 61–64. http://dx.doi.org/10.1155/2001/301570.

Texte intégral

Résumé :

We investigated if any change in spatial resolution of comparative genomic hybridization analysis could be detected when using DNA amplified by degenerate oligonucleotide primed PCR (DOP‐PCR) as opposed to the use of unamplified DNA. Five DNA samples from B‐cell leukemias with small 11q deletions were amplified by DOP‐PCR and analysed by means of high resolution comparative genomic hybridization (HR‐CGH) for the evaluation of aberration size detection limit. By means of HR‐CGH, we found the detection limit of DOP‐PCR CGH for deletions to be between 3 Mbp and 7–8 Mbp.

Styles APA, Harvard, Vancouver, ISO, etc.

4

Castro, Alonso, et John G. K. Williams. « Single-Molecule Detection of Specific Nucleic Acid Sequences in Unamplified Genomic DNA ». Analytical Chemistry 69, n^o 19 (octobre 1997) : 3915–20. http://dx.doi.org/10.1021/ac970389h.

Texte intégral

Styles APA, Harvard, Vancouver, ISO, etc.

5

Jung, Ye Lim, Cheulhee Jung, Jung Hun Park, Moon Il Kim et Hyun Gyu Park. « Direct detection of unamplified genomic DNA based on photo-induced silver ion reduction by DNA molecules ». Chemical Communications 49, n^o 23 (2013) : 2350. http://dx.doi.org/10.1039/c3cc38552c.

Texte intégral

Styles APA, Harvard, Vancouver, ISO, etc.

6

Caliskan-Aydogan, Oznur, Saad Asadullah Sharief et Evangelyn C. Alocilja. « Nanoparticle-Based Plasmonic Biosensor for the Unamplified Genomic Detection of Carbapenem-Resistant Bacteria ». Diagnostics 13, n^o 4 (9 février 2023) : 656. http://dx.doi.org/10.3390/diagnostics13040656.

Texte intégral

Résumé :

Antimicrobial resistance (AMR) is a global public health issue, and the rise of carbapenem-resistant bacteria needs attention. While progress is being made in the rapid detection of resistant bacteria, affordability and simplicity of detection still need to be addressed. This paper presents a nanoparticle-based plasmonic biosensor for detecting the carbapenemase-producing bacteria, particularly the beta-lactam Klebsiella pneumoniae carbapenemase (blaKPC) gene. The biosensor used dextrin-coated gold nanoparticles (GNPs) and an oligonucleotide probe specific to blaKPC to detect the target DNA in the sample within 30 min. The GNP-based plasmonic biosensor was tested in 47 bacterial isolates: 14 KPC-producing target bacteria and 33 non-target bacteria. The stability of GNPs, confirmed by the maintenance of their red appearance, indicated the presence of target DNA due to probe-binding and GNP protection. The absence of target DNA was indicated by the agglomeration of GNPs, corresponding to a color change from red to blue or purple. The plasmonic detection was quantified with absorbance spectra measurements. The biosensor successfully detected and differentiated the target from non-target samples with a detection limit of 2.5 ng/μL, equivalent to ~103 CFU/mL. The diagnostic sensitivity and specificity were found to be 79% and 97%, respectively. The GNP plasmonic biosensor is simple, rapid, and cost-effective in detecting blaKPC-positive bacteria.

Styles APA, Harvard, Vancouver, ISO, etc.

7

Storhoff, James J., Adam D. Lucas, Viswanadham Garimella, Y. Paul Bao et Uwe R. Müller. « Homogeneous detection of unamplified genomic DNA sequences based on colorimetric scatter of gold nanoparticle probes ». Nature Biotechnology 22, n^o 7 (30 mai 2004) : 883–87. http://dx.doi.org/10.1038/nbt977.

Texte intégral

Styles APA, Harvard, Vancouver, ISO, etc.

8

Mahon, A. R., M. A. Barnes, F. Li, S. P. Egan, C. E. Tanner, S. T. Ruggiero, J. L. Feder et D. M. Lodge. « DNA-based species detection capabilities using laser transmission spectroscopy ». Journal of The Royal Society Interface 10, n^o 78 (6 janvier 2013) : 20120637. http://dx.doi.org/10.1098/rsif.2012.0637.

Texte intégral

Résumé :

Early detection of invasive species is critical for effective biocontrol to mitigate potential ecological and economic damage. Laser transmission spectroscopy (LTS) is a powerful solution offering real-time, DNA-based species detection in the field. LTS can measure the size, shape and number of nanoparticles in a solution and was used here to detect size shifts resulting from hybridization of the polymerase chain reaction product to nanoparticles functionalized with species-specific oligonucleotide probes or with the species-specific oligonucleotide probes alone. We carried out a series of DNA detection experiments using the invasive freshwater quagga mussel ( Dreissena bugensis ) to evaluate the capability of the LTS platform for invasive species detection. Specifically, we tested LTS sensitivity to (i) DNA concentrations of a single target species, (ii) the presence of a target species within a mixed sample of other closely related species, (iii) species-specific functionalized nanoparticles versus species-specific oligonucleotide probes alone, and (iv) amplified DNA fragments versus unamplified genomic DNA. We demonstrate that LTS is a highly sensitive technique for rapid target species detection, with detection limits in the picomolar range, capable of successful identification in multispecies samples containing target and non-target species DNA. These results indicate that the LTS DNA detection platform will be useful for field application of target species. Additionally, we find that LTS detection is effective with species-specific oligonucleotide tags alone or when they are attached to polystyrene nanobeads and with both amplified and unamplified DNA, indicating that the technique may also have versatility for broader applications.

Styles APA, Harvard, Vancouver, ISO, etc.

9

Brouard, Danny, Olivier Ratelle, A. Guillermo Bracamonte, Maryse St-Louis et Denis Boudreau. « Direct molecular detection of SRY gene from unamplified genomic DNA by metal-enhanced fluorescence and FRET ». Analytical Methods 5, n^o 24 (2013) : 6896. http://dx.doi.org/10.1039/c3ay41428k.

Texte intégral

Styles APA, Harvard, Vancouver, ISO, etc.

10

Martins, R., P. Baptista, L. Silva, L. Raniero, G. Doria, R. Franco et E. Fortunato. « Identification of unamplified genomic DNA sequences using gold nanoparticle probes and a novel thin film photodetector ». Journal of Non-Crystalline Solids 354, n^o 19-25 (mai 2008) : 2580–84. http://dx.doi.org/10.1016/j.jnoncrysol.2007.09.074.

Texte intégral

Styles APA, Harvard, Vancouver, ISO, etc.

11

Bertucci, Alessandro, Alex Manicardi, Alessandro Candiani, Sara Giannetti, Annamaria Cucinotta, Giuseppe Spoto, Maria Konstantaki, Stavros Pissadakis, Stefano Selleri et Roberto Corradini. « Detection of unamplified genomic DNA by a PNA-based microstructured optical fiber (MOF) Bragg-grating optofluidic system ». Biosensors and Bioelectronics 63 (janvier 2015) : 248–54. http://dx.doi.org/10.1016/j.bios.2014.07.047.

Texte intégral

Styles APA, Harvard, Vancouver, ISO, etc.

12

Balderston, Sarah, Jeffrey J. Taulbee, Elizabeth Celaya, Kandace Fung, Amanda Jiao, Kasey Smith, Reza Hajian et al. « Discrimination of single-point mutations in unamplified genomic DNA via Cas9 immobilized on a graphene field-effect transistor ». Nature Biomedical Engineering 5, n^o 7 (5 avril 2021) : 713–25. http://dx.doi.org/10.1038/s41551-021-00706-z.

Texte intégral

Styles APA, Harvard, Vancouver, ISO, etc.

13

Yi, Xinyao, Yonghong Xia, Binrong Ding, Ling Wu, Shengqiang Hu, Zixiao Wang, Minghui Yang et Jianxiu Wang. « Dual-Channel Surface Plasmon Resonance for Quantification of ApoE Gene and Genotype Discrimination in Unamplified Genomic DNA Extracts ». ACS Sensors 3, n^o 11 (17 octobre 2018) : 2402–7. http://dx.doi.org/10.1021/acssensors.8b00845.

Texte intégral

Styles APA, Harvard, Vancouver, ISO, etc.

14

Mariani, Stefano, Simona Scarano, Jolanda Spadavecchia et Maria Minunni. « A reusable optical biosensor for the ultrasensitive and selective detection of unamplified human genomic DNA with gold nanostars ». Biosensors and Bioelectronics 74 (décembre 2015) : 981–88. http://dx.doi.org/10.1016/j.bios.2015.07.071.

Texte intégral

Styles APA, Harvard, Vancouver, ISO, etc.

15

Dester, Emma, Kaily Kao et Evangelyn C. Alocilja. « Detection of Unamplified E. coli O157 DNA Extracted from Large Food Samples Using a Gold Nanoparticle Colorimetric Biosensor ». Biosensors 12, n^o 5 (26 avril 2022) : 274. http://dx.doi.org/10.3390/bios12050274.

Texte intégral

Résumé :

Rapid detection of foodborne pathogens such as E. coli O157 is essential in reducing the prevalence of foodborne illness and subsequent complications. Due to their unique colorimetric properties, gold nanoparticles (GNPs) can be applied in biosensor development for affordability and accessibility. In this work, a GNP biosensor was designed for visual differentiation between target (E. coli O157:H7) and non-target DNA samples. Results of DNA extracted from pure cultures indicate high specificity and sensitivity to as little as 2.5 ng/µL E. coli O157 DNA. Further, the biosensor successfully identified DNA extracted from flour contaminated with E. coli O157, with no false positives for flour contaminated with non-target bacteria. After genomic extraction, this assay can be performed in as little as 30 min. In addition, food sample testing was successful at detecting approximately 103 CFU/mL of E. coli O157 magnetically extracted from flour after only a 4 h incubation step. As a proof of concept, these results demonstrate the capabilities of this GNP biosensor for low-cost and rapid foodborne pathogen detection.

Styles APA, Harvard, Vancouver, ISO, etc.

16

Dester, Emma, Kaily Kao et Evangelyn C. Alocilja. « Detection of Unamplified E. coli O157 DNA Extracted from Large Food Samples Using a Gold Nanoparticle Colorimetric Biosensor ». Biosensors 12, n^o 5 (26 avril 2022) : 274. http://dx.doi.org/10.3390/bios12050274.

Texte intégral

Résumé :

Rapid detection of foodborne pathogens such as E. coli O157 is essential in reducing the prevalence of foodborne illness and subsequent complications. Due to their unique colorimetric properties, gold nanoparticles (GNPs) can be applied in biosensor development for affordability and accessibility. In this work, a GNP biosensor was designed for visual differentiation between target (E. coli O157:H7) and non-target DNA samples. Results of DNA extracted from pure cultures indicate high specificity and sensitivity to as little as 2.5 ng/µL E. coli O157 DNA. Further, the biosensor successfully identified DNA extracted from flour contaminated with E. coli O157, with no false positives for flour contaminated with non-target bacteria. After genomic extraction, this assay can be performed in as little as 30 min. In addition, food sample testing was successful at detecting approximately 103 CFU/mL of E. coli O157 magnetically extracted from flour after only a 4 h incubation step. As a proof of concept, these results demonstrate the capabilities of this GNP biosensor for low-cost and rapid foodborne pathogen detection.

Styles APA, Harvard, Vancouver, ISO, etc.

17

Pan, Xinghua, Alexander Eckehart Urban, Dean Palejev, Vincent Schulz, Fabian Grubert, Yiping Hu, Michael Snyder et Sherman M. Weissman. « A procedure for highly specific, sensitive, and unbiased whole-genome amplification ». Proceedings of the National Academy of Sciences 105, n^o 40 (1 octobre 2008) : 15499–504. http://dx.doi.org/10.1073/pnas.0808028105.

Texte intégral

Résumé :

Highly specific amplification of complex DNA pools without bias or template-independent products (TIPs) remains a challenge. We have developed a method using phi29 DNA polymerase and trehalose and optimized control of amplification to create micrograms of specific amplicons without TIPs from down to subfemtograms of DNA. With an input of as little as 0.5–2.5 ng of human gDNA or a few cells, the product could be close to native DNA in locus representation. The amplicons from 5 and 0.5 ng of DNA faithfully demonstrated all previously known heterozygous segmental duplications and deletions (3 Mb to 18 kb) located on chromosome 22 and even a homozygous deletion smaller than 1 kb with high-resolution chromosome-wide comparative genomic hybridization. With 550k Infinium BeadChip SNP typing, the >99.7% accuracy was compared favorably with results on unamplified DNA. Importantly, underrepresentation of chromosome termini that occurred with GenomiPhi v2 was greatly rescued with the present procedure, and the call rate and accuracy of SNP typing were also improved for the amplicons with a 0.5-ng, partially degraded DNA input. In addition, the amplification proceeded logarithmically in terms of total yield before saturation; the intact cells was amplified >50 times more efficiently than an equivalent amount of extracted DNA; and the locus imbalance for amplicons with 0.1 ng or lower input of DNA was variable, whereas for higher input it was largely reproducible. This procedure facilitates genomic analysis with single cells or other traces of DNA, and generates products suitable for analysis by massively parallel sequencing as well as microarray hybridization.

Styles APA, Harvard, Vancouver, ISO, etc.

18

Lundqvist, M., E. Bengtén, S. Strömberg et L. Pilström. « Ig light chain gene in the Siberian sturgeon (Acipenser baeri). » Journal of Immunology 157, n^o 5 (1 septembre 1996) : 2031–38. http://dx.doi.org/10.4049/jimmunol.157.5.2031.

Texte intégral

Résumé :

Abstract Elasmobranch and teleost fish have their Ig light (L) chain loci organized in multiple clusters (VL-JL-CL). The VL segments of teleosts are in opposite transcriptional orientation to the CL genes, suggesting that in teleosts and elasmobranchs there may have been separate evolutionary events leading to this organization. To address this problem, the IgL locus from the Siberian sturgeon (Acipenser baeri) (representative of a branch between elasmobranchs and teleosts) was investigated. Sequence analysis of cDNA clones shows that sturgeon VL genes are most similar to those of teleosts, but that sturgeon CL genes are more similar to those of the sharks. Southern blot analyses of sturgeon erythrocyte DNA with VL- and CL-specific probes showed that there are more than 20 VL segments in both the tetraploid Siberian sturgeon and the diploid sterlet (Acipenser ruthenus), but only a few CL segments in the genome of the Siberian sturgeon and up to four CL segments in that of the sterlet. Screening of an unamplified genomic library gave more than 300 VL-positive and four CL-positive clones. None of these contained inserts positive for both probes. PCR analysis of a genomic CL clone using IC and CL-specific primers suggested that upstream of the CL segment there are at least seven JL segments. it is concluded that sturgeons have a kappa-like organization of their IgL locus and that the clustered organization of IgL loci in bony fish and sharks arose from two distinct evolutionary events.

Styles APA, Harvard, Vancouver, ISO, etc.

19

Zablocki, Olivier, Michelle Michelsen, Marie Burris, Natalie Solonenko, Joanna Warwick-Dugdale, Romik Ghosh, Jennifer Pett-Ridge, Matthew B. Sullivan et Ben Temperton. « VirION2 : a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature ». PeerJ 9 (30 mars 2021) : e11088. http://dx.doi.org/10.7717/peerj.11088.

Texte intégral

Résumé :

Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity means, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a ‘living document’ to facilitate dissemination of updates to keep pace with the rapid evolution of long-read sequencing technology.

Styles APA, Harvard, Vancouver, ISO, etc.

20

Földes-Papp, Zeno, Masataka Kinjo, Mamoru Tamura, Eckhard Birch-Hirschfeld, Ulrike Demel et Gernot P. Tilz. « A new ultrasensitive way to circumvent PCR-based allele distinction : Direct probing of unamplified genomic DNA by solution-phase hybridization using two-color fluorescence cross-correlation spectroscopy ». Experimental and Molecular Pathology 78, n^o 3 (juin 2005) : 177–89. http://dx.doi.org/10.1016/j.yexmp.2005.01.005.

Texte intégral

Styles APA, Harvard, Vancouver, ISO, etc.

21

Petrone, Joseph R., Alam Muñoz-Beristain, Paula Rios Glusberger, Jordan T. Russell et Eric W. Triplett. « Unamplified, Long-Read Metagenomic Sequencing Approach to Close Endosymbiont Genomes of Low-Biomass Insect Populations ». Microorganisms 10, n^o 3 (26 février 2022) : 513. http://dx.doi.org/10.3390/microorganisms10030513.

Texte intégral

Résumé :

With the current advancements in DNA sequencing technology, the limiting factor in long-read metagenomic assemblies is now the quantity and quality of input DNA. Although these requirements can be met through the use of axenic bacterial cultures or large amounts of biological material, insect systems that contain unculturable bacteria or that contain a low amount of available DNA cannot fully utilize the benefits of third-generation sequencing. The citrus greening disease insect vector Diaphorina citri is an example that exhibits both of these limitations. Although endosymbiont genomes have mostly been closed after the short-read sequencing of amplified template DNA, creating de novo long-read genomes from the unamplified DNA of an insect population may benefit communities using bioinformatics to study insect pathosystems. Here all four genomes of the infected D. citri microbiome were sequenced to closure using unamplified template DNA and two long-read sequencing technologies. Avoiding amplification bias and using long reads to assemble the bacterial genomes allowed for the circularization of the Wolbachia endosymbiont of Diaphorina citri for the first time and paralleled the annotation context of all four reference genomes without utilizing a traditional hybrid assembly. The strategies detailed here are suitable for the sequencing of other insect systems for which the input DNA, time, and cost are an issue.

Styles APA, Harvard, Vancouver, ISO, etc.

22

Hensing, Whitney L., Lorenzo Gerratana, Katherine Clifton, Marko Velimirovic, Ami Shah, Paolo D'Amico, Carolina Reduzzi et al. « Abstract P2-01-01 : Genetic alterations detected by circulating tumor DNA (ctDNA) in HER2-low metastatic breast cancer (MBC) ». Cancer Research 82, n^o 4_Supplement (15 février 2022) : P2–01–01—P2–01–01. http://dx.doi.org/10.1158/1538-7445.sabcs21-p2-01-01.

Texte intégral

Résumé :

Abstract Introduction: Approximately 40-50% of breast cancers are characterized by low HER2 expression (HER2-low), defined as immunohistochemistry (IHC) 1+ or 2+ and HER2 fluorescence in situ hybridization (FISH) unamplified, encompassing a large and heterogeneous subgroup that may confer benefit from novel HER2 directed therapies. Circulating tumor DNA (ctDNA) has emerged as a minimally invasive technique to detect cancer-specific gene aberrations. Genetic alterations in ctDNA of HER2-low MBC have not been well described, and we hypothesized that HER2-low MBC may have a distinct genomic profile, beyond standard histopathologic features. Methods: This retrospective cohort study included patients with MBC treated at Washington University in St. Louis, Northwestern University (Chicago, IL) and Massachusetts General Hospital (Boston, MA) who had undergone ctDNA analysis during the course of treatment using the commercially available Guardant360® assay. HER2 expression was evaluated by IHC/FISH according to ASCO/CAP guidelines on metastatic tissue biopsies (or primary breast tumor tissue if a metastatic site biopsy was not available). Tumors were classified as HER2-low (IHC 1+ or 2+/FISH negative), HER2-0 (IHC 0) or HER2-positive (IHC 3+ or IHC 2+/FISH amplified). Clinicopathologic characteristics and ctDNA genetic alterations for HER2-low MBC were described and compared with the HER2-0 and HER2-positive subgroups. Chi-square and Fisher’s exact tests were used for categorical variables. Logistical regression was performed for multivariable analyses. Results: A total of 991 patients with MBC were analyzed, including 160 (16.1%) HER2-positive, 351 (35.4%) HER2-0, and 480 (48.4%) HER2-low MBC. The majority (89.2%) of HER2-low MBC were estrogen-receptor positive (ER+). Compared with HER2-0 MBC, HER2-low MBC had a significantly higher incidence of PIK3CA mutations (OR 1.54, p=0.027). PDGFRA and MYC amplifications were also more common among HER2-low MBC (2.3% vs 0.28% and 8.1% vs 4.6%, respectively), although not significantly associated with this subtype in multivariable analysis. Within the ER+ MBC cohort, those with HER2-low also had higher rates of PIK3CA mutations (OR 1.66, p=0.012) and MYC amplification (OR 2.29, p=0.034), as compared to HER2-0. Compared with HER2-positive, HER2-low MBC had significantly lower rates of ERBB2 alterations (OR 0.26, p=0.0076 for ERBB2 mutations and OR 0.022, p<0.001 for ERBB2 amplification). ESR1, AKT1, and RB1 mutations were more common in HER2-low compared with HER2-positive MBC (14.0% vs 6.9%; 3.1% vs none; 3.1% vs none, respectively), but were not significant in multivariable analysis. Conclusions: Among patients with ER+ MBC, HER-low had a higher incidence of PIK3CA mutations and MYC amplification compared to HER2-0 MBC, and both of these alterations have been implicated as mechanisms of endocrine resistance. We did not demonstrate a high incidence of ERBB2 alterations in patients with HER2-low MBC. To our knowledge, this is the first study to describe genetic alterations detected by ctDNA in patients with HER2-low MBC. Given the emergence of novel HER2-targeted antibody drug conjugates with clinical activity in HER2-low MBC, these findings may guide combination treatment strategies and patient selection for future studies. Further studies are needed to confirm whether HER2-low MBC represents a truly unique biologic subtype. Citation Format: Whitney L Hensing, Lorenzo Gerratana, Katherine Clifton, Marko Velimirovic, Ami Shah, Paolo D'Amico, Carolina Reduzzi, Qiang Zhang, Charles S Dai, Nusayba A Bagegni, Mateusz Opyrchal, Foluso O Ademuyiwa, Bose Ron, Amir Behdad, Cynthia X Ma, Aditya Bardia, Massimo Cristofanilli, Andrew A Davis. Genetic alterations detected by circulating tumor DNA (ctDNA) in HER2-low metastatic breast cancer (MBC) [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-01-01.

Styles APA, Harvard, Vancouver, ISO, etc.

23

Roux, Simon, Gareth Trubl, Danielle Goudeau, Nandita Nath, Estelle Couradeau, Nathan A. Ahlgren, Yuanchao Zhan et al. « Optimizing de novo genome assembly from PCR-amplified metagenomes ». PeerJ 7 (9 mai 2019) : e6902. http://dx.doi.org/10.7717/peerj.6902.

Texte intégral

Résumé :

Background Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes. Conclusions PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Styles APA, Harvard, Vancouver, ISO, etc.

24

Alkhatabi, Heba A., Azim M. Mohamedali, Austin G. Kulasekararaj, Sneha Shinde, Joop Gaken, Syed A. Mian, Alexander E. Smith et Ghulam J. Mufti. « Utility of Peripheral Blood for Cytogenetic and Mutation Analysis in Myelodysplastic Syndrome ». Blood 120, n^o 21 (16 novembre 2012) : 1707. http://dx.doi.org/10.1182/blood.v120.21.1707.1707.

Texte intégral

Résumé :

Abstract Abstract 1707 With the advent of high throughput and high resolution techniques, >80% of myelodysplastic syndrome (MDS) patients harbour somatic mutations and/or genomic aberrations, which provide diagnostic and prognostic utility; however, frequent bone marrow (BM) aspirates are required. In a significant minority, the BM is hypocellular and fibrotic with suboptimal in vitro growth and, additionally, the procedure causes discomfort particularly in the elderly. This led us to investigate the use of peripheral blood (PB) and serum to identify and monitor BM derived genetic markers using high resolution single nucleotide polymorphism array (SNP-A) karyotyping and 454 parallel sequencing (454-PS) of a 22 gene myeloid panel comprising of all the exons of DNMT3a, RUNX1, CEBPα, TP53, EZH2, TET2 and ZRSR2 and mutations ‘hotposts’ for NPM1, FLT3, ASXL1, IDH1, IDH2, MPL, JAK2, BRAF, cCBL, NRAS, KRAS, C-KIT, SF3B1, SRSF2, and U2AF1. We selected 23 MDS patients with concurrent BM and PB samples and detected 45 mutations in TET2, SF3B1, ASXL1, TP53, DNMT3a, FLT3, U2AF1, NRAS, cCBL, JAK2 and IDH2 in BM and subsequently analysed their PB using 454-PS with independent validation performed by Sanger sequencing (SS). All the mutations identified in BM were detected in PB with the exception of a single NRAS (BM-11%). Nine patients had a single mutation in SF3B1, ASXL1, TP53, TET2, DNMT3a and U2AF1 with the remaining patients having multiple coexisting mutations. Overall there was no significant difference in the mutation burden between the PB (median 25%(1.5%-50%)) and the BM (median 33%(5%-68%)). Concurrent analysis of unamplified and whole genome amplified PB DNA from 3 patients with mutations in TET2, U2AF1, ASXL1 and NRAS showed no difference in their mutation profile. As expected, in three patients post therapy the mutation burden in the PB was lower than in the pre-treatment BM sample. The lower mutation burden and sequence context in the PB contributed significantly to the quality of SS analysis. Prior knowledge of the mutation site resulted in 98% concordance (smallest clone size - 1.5%) between BM and PB, however, a blind approach decreased this to 84% (smallest clone size - 15%). In addition, serum was available from 14 patients (22 known mutations in BM) and SS of serum DNA identified 12 mutations correctly (U2AF1, FLT3, SF3B1, TET2, TP53, ASXL1, DNMT3a and IDH2, 4 as wildtype (TET2, cCBL, ASXL1 and SF3B1) and 6 failed to amplify (ASXL1, TP53 and TET2) without any preference for specific genes and the failure attributed to the quantity of serum DNA. Karyotype aberrations in PB were assessed using Affymetrix SNP 6.0 arrays on 31 MDS patients; normal karyotype (n=11), del5q (n=9), del7q/-7 (n=5), trisomy 8 (n=2), complex (n=2), isodiXq13 (n=1) and t(2:4)(q33;q27). An overall karyotype concordance of 94% was observed in PB with the 2 discordant cases showing normal karyotype in PB and BM by SNP-A but having monosomy 7 (partial cytogenetic remission after 5-azacitidine) and t(2:4)(q33;q27) respectively in their BM by MC. The mean copy number (CN) in the PB was lower than BM (PB vs BM); deletions (CN of 1.8 vs 1.6) and gains(CN of 2.2 vs 2.4), implying a smaller abnormal clone in the PB. Concurrent SNP-A karyotype from BM from 9 patients was concordant with SNP-A karyotype from PB, although a patient with complex karyotype determined by SNP-A in the BM and having 30 aberrations had only 15 aberrations detected in the PB. To determine if the 5q deletion was lineage restricted, we enriched PB for CD3+, CD19+ and CD3-CD19- populations from 4 patients. FISH and SNP-A karyotyping showed the presence of the 5q deletion using both techniques in all three fractions, however at a lower level in PB lymphocytes indicating the presence of a smaller clone. In conclusion, our study showed an excellent concordance between BM and PB, both for karyotype and mutational analyses using high resolution SNP-A karyotyping and 454-PS suggesting its clinical utility as a surrogate for BM, thereby, avoiding the discomfort of repeated BM aspirates and help in monitoring response to therapy more frequently. Disclosures: No relevant conflicts of interest to declare.

Styles APA, Harvard, Vancouver, ISO, etc.

25

Gao, Ge, et David I. Smith. « Clinical Massively Parallel Sequencing ». Clinical Chemistry 66, n^o 1 (30 décembre 2019) : 77–88. http://dx.doi.org/10.1373/clinchem.2019.303305.

Texte intégral

Résumé :

Abstract BACKGROUND The newest advances in DNA sequencing are based on technologies that perform massively parallel sequencing (MPS). Since 2006, the output from MPS platforms has increased from 20 Mb to >7 Tb. First-generation MPS platforms amplify individual DNA molecules to multiple copies and then interrogate the sequence of those molecules. Second-generation MPS analyzes single unamplified molecules to generate much longer sequence reads but with less output than first-generation MPS and lower first-pass accuracy. With MPS technologies, it is now possible to analyze genomes, exomes, a defined subset of genes, transcriptomes, and even methylation across the genome. These technologies have and will continue to completely transform the clinical practice. CONTENT The major first- and second-generation MPS platforms and how they are used in clinical practice are discussed. SUMMARY The ability to sequence terabases of DNA per run on an MPS platform will dramatically change how DNA sequencing is used in clinical practice. Currently, MPS of targeted gene panels is the most common use of this technology clinically, but as the cost for genome sequencing inches downward to $100, this may soon become the method of choice (with the caveat that, at least in the near term, clinical-grade genome sequencing with interpretation may cost much more than $100). Other uses of this technology include sequencing of a mixture of bacterial and viral species (metagenomics), as well as the characterization of methylation across the genome.

Styles APA, Harvard, Vancouver, ISO, etc.

26

Pararajalingam, Prasath, Laura K. Hilton, Krysta M. Coyle, Kostiantyn Dreval, Barbara Meissner, Ari Melnick, Marco A. Marra, David W. Scott et Ryan D. Morin. « Complex Structural Variation Associated with Enhancer Hijacking and Loss of Tumor Suppressors in Mantle Cell Lymphoma ». Blood 138, Supplement 1 (5 novembre 2021) : 675. http://dx.doi.org/10.1182/blood-2021-153162.

Texte intégral

Résumé :

Abstract Mantle cell lymphoma (MCL) is a rare, incurable mature B-cell lymphoma that can have either an aggressive or indolent clinical course. The hallmark aberration of MCL is the t(11;14)(q13;q32) translocation that places CCND1 under control of the immunoglobulin heavy chain (IGH) locus resulting in its constitutive expression. CCND1/IGH translocation occurs in nearly all MCL cases and arises during VDJ recombination. Whole genome sequencing (WGS) of MCLs has shown the prevalence of additional structural variations (SV), particularly in tumors with poor outcome. Complex rearrangements, such as chromothripsis and chromoplexy have been observed in MCL but their role in lymphomagenesis has not been determined. We hypothesized that some of these complex rearrangements afford a selective advantage to the tumor by disrupting tumor suppressor genes or by placing oncogenes in proximity to regulatory elements in cis, thereby resulting in ectopic expression. We performed WGS on tumor DNA extracted from 106 RCHOP-treated MCL patients. Matching ribosomal-depleted RNA-seq data was available for all tumor samples. Gene expression count values were obtained using Salmon and counts were normalized using the DESeq2 method. Structural variants were identified using a consensus between GRIDSS and Manta and these were analyzed to identify the topology of complex rearrangements using JaBbA. This allows the annotation of rearrangements such as chromothripsis and chromoplexy and enables the detection of genes near new regulatory elements through complex (multi-breakpoint) rearrangements. We supplemented this analysis by including 57 published classical and non-nodal leukemic MCL genomes. Chromothripsis and chromoplexy were observed in 8 and 12 tumors, respectively. The majority of the genomes were associated with isolated structural variations such as large deletions, inversions and reciprocal translocations were more common. Six genes (BCL10, TRAF6, TRAF3, MAP3K7, BTK, RELB) coding for canonical and non-canonical NFκB signaling proteins were found rearranged to within 1Mbp of a naïve B-cell super-enhancer region. The TRAF6 rearrangement was part of a chromothripsis and chromoplexy event involving both chr9 and chr11. A separate chromothripsis example involving chr1 placed each of BCL10 and NOTCH2 within 100-200kbp of super-enhancers. A 1Mbp region containing RELB was amplified and inserted into chr19p approximately 150kbp downstream a super-enhancer. An 800kbp deletion brought MAP3K7 to within 400kbp of a super-enhancer. DAZAP1, a gene known to be recurrently mutated in MCL, was translocated upstream to within 300kbp of a super-enhancer by t(5;19)(p13.3;p15.33). TRAF3 was translocated 400kbp upstream a super-enhancer by t(14;20)(q32.32;q13.13). None of the aforementioned SVs were associated with a detectable increase in expression of the affected gene. In contrast, we identified one genome in which the MYC oncogene was relocated 500kbp upstream of a super-enhancer via an unbalanced t(4;8)(q21.23;q24.21) translocation. In this case, MYC expression was in the 95 th percentile of MYC expression across the cohort. Focal deletions and amplifications were also found affecting lymphoma driver genes. Focal amplifications affecting 3q (34 tumors) and 5p (9 tumors), were among the most common recurrent events. These respectively affect the TERC and TERT genes, both involved in telomerase function. All tumors with TERT amplifications also showed TERC amplifications. TERC and TERT were expressed higher on average in amplified tumors than in unamplified tumors. Two tumors showed focal deletions affecting the 3' end of BIRC3. The focal deletion in one tumor was found to span to the 3' end of BIRC2 resulting in a BIRC2/BIRC3 fusion. Aberrant splicing across the two genes was evident in matching tumor RNA-seq data. Complex rearrangements in MCL have been found to link distant super-enhancer elements with a variety of lymphoma oncogenes. We noted a recurrence of such events affecting known regulators of NFκB signaling. We are using nanopore-based long-read PromethION sequencing to validate the structure of the derivative chromosome in these cases. Although these genes were not detectably overexpressed, deregulation of genes may be occurring by other means. The full extent of deregulation of NFκB and other oncogenic pathways will be revealed as complex rearrangements are studied in additional MCL tumors. Disclosures Coyle: Allakos, Inc.: Consultancy. Melnick: Epizyme: Consultancy; Daiichi Sankyo: Research Funding; Sanofi: Research Funding; Janssen Pharmaceuticals: Research Funding; Constellation: Consultancy; KDAC Pharma: Membership on an entity's Board of Directors or advisory committees. Scott: BC Cancer: Patents & Royalties: Patent describing assigning DLBCL COO by gene expression profiling--licensed to NanoString Technologies. Patent describing measuring the proliferation signature in MCL using gene expression profiling. ; AstraZeneca: Consultancy; Abbvie: Consultancy; NanoString Technologies: Patents & Royalties: Patent describing measuring the proliferation signature in MCL using gene expression profiling.; Rich/Genentech: Research Funding; Celgene: Consultancy; Incyte: Consultancy; Janssen: Consultancy, Research Funding. Morin: Epizyme: Patents & Royalties; Celgene: Consultancy; Foundation for Burkitt Lymphoma Research: Membership on an entity's Board of Directors or advisory committees.

Styles APA, Harvard, Vancouver, ISO, etc.

27

Austin, M. D., P. Deshpande, M. Requa, M. Kunkel, H. Sadowski, D. Bozinov, J. Sibert et al. « Single-Molecule Rapid Imaging of Linear Genomes in Nanochannel Array ». MRS Proceedings 1346 (2011). http://dx.doi.org/10.1557/opl.2011.866.

Texte intégral

Résumé :

ABSTRACTHuman genomic structural variation (SV) is significant factor in genome complexity, and thus has substantial implications to the cause, development and progression of genetic diseases. These SVs, ranging in size of 1kbp-1Mbp, are challenging to assess with current technologies. As such, we have developed a commercial system (nanoAnalyzer® 1000) for the rapid linear analysis of genomes at single-molecule level.The core of our system is a nanofluidic chip consisting of an array of channels with a diameter less than 100 nm, nanofabricated on the surface of a silicon substrate. Thousands of unamplified genomic DNA molecules of 100’s kbps to several Mbps can be isolated and linearly streamed into the array for analysis in a parallel fashion. Fluorescently labeled sequence-specific signatures can then be identified and aligned to reference patterns at high resolution with custom software. This automated, multi-color imaging platform will enable a wide range of applications, such as accurate sequencing assembly, discovering genome structural variations, and uncovering epigenomic content. Nanochannel arrays promise to substantially lower the barriers of entry for single-molecule DNA analysis for scientists and clinicians, greatly impacting the advancement of molecular diagnostics, personalized medicine, and biomedical research.

Styles APA, Harvard, Vancouver, ISO, etc.

28

Lu, Hanwen, Ling Wu, Jingrui Wang, Zixiao Wang, Xinyao Yi, Jianxiu Wang et Nan Wang. « Voltammetric determination of the Alzheimer’s disease-related ApoE 4 gene from unamplified genomic DNA extracts by ferrocene-capped gold nanoparticles ». Microchimica Acta 185, n^o 12 (14 novembre 2018). http://dx.doi.org/10.1007/s00604-018-3087-9.

Texte intégral

Styles APA, Harvard, Vancouver, ISO, etc.

Articles de revues sur le sujet « Unamplified genomic DNA »

Créez une référence correcte selon les styles APA, MLA, Chicago, Harvard et plusieurs autres