ATM mutations improve radio-sensitivity in wild-type isocitrate dehydrogenase-associated high-grade glioma: retrospective analysis using next-generation sequencing data

Background: To identify the relationship between somatic ataxia-telangiectasia mutated (ATM) mutation and improved radio-sensitivity, we retrospectively reviewed the next-generation sequencing data from patients diagnosed with glioma isocitrate dehydrogenase (IDH) -wildtype high quality.
Methods: We included 39 individuals (IDH) -wildtype high-grade glioma (diffuse astrocytoma n = 2, n = 10 anaplastic astrocytoma and glioblastoma n = 27) had no gross tumor resection and radiation therapy undergo the median total dose of 60 Gy in 30 fractions. ATM gene mutation status was obtained through generation sequencing using TruSight cancer panel 170. Tumor progression was defined by Response Assessment in Neuro-Oncology (Rano) criteria as well as neurological and clinical findings.
Results: Among the 39 samples, ATM mutations (mut ATM (+)) was detected in 26% of cases (n = 10).
No significant differences were observed in the patient or tumor characteristics. Among the 10 patients in the ATM mut (+), there are 6 patients with glioblastoma and four patients with anaplastic astrocytoma. Most mutations are missense mutations (n = 8, 80%). With a median follow-up of 16.5 mo (interquartile range, 11.4 to 19.8), ATM mut (+) exhibited one year of control in the field of 100% compared with 44.1% in ATM mut (-) group (p = 0.002). There was no difference in the rate of out-of-field control or overall survival between the two groups (p = 0.861 and p = 0.247, respectively).
Conclusions: Our results indicate that ATM mutations may be involved in the increase in radio-sensitivity with good control in the field despite the aggressive nature of IDH-wildtype high-grade glioma. Further studies are needed to uncover the potential role of ATM as a candidate biomarker and therapeutic target in high-grade glioma.

Whole-genome sequencing and Mycobacterium tuberculosis: Challenges in sample preparation and analysis of sequencing data
The number of patients with tuberculosis (TB) caused by resistant strains are still alarming. Therefore, it is necessary to determine the resilience of faster and more accurate, than with the currently used phenotypic and genotypic methods.
In recent years, technological advances have been made and the method of whole genome sequencing (WGS) has been introduced as part of routine clinical laboratory diagnostics. Comparing various mycobacterial genome variation with reference genome leads to a consistent evaluation of molecular epidemiology and resistance of Mycobacterium tuberculosis (M. tuberculosis) to a variety of anti-TB drugs.
The quality of sequencing data obtained is closely related to the type of samples and the methods used for DNA extraction and sequencing library preparation. In addition, the correct interpretation of the results is also affected by bioinformatics data processing. A large number of bioinformatics pipeline that is currently available, the sensitivity varies due to the different size of the database containing the relevant mutation. This review focuses on the individual steps in the workflow including sequencing and factors that may affect the interpretation of the final results.
comparative analysis suggests that miR-375 and miR-7 expression was substantially higher in the case of the control of non-Nen Nen. Correlation analysis showed that NENs from diverse anatomical sites have convergent program miRNA expression, may reflect the morphological and functional similarities.
PCR Clean-up Kit, |
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PC200 | GeneOn | 200 preps | EUR 226.8 |
PCR Clean-up Kit, |
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PC50 | GeneOn | 50 preps | EUR 112.8 |
TuMinute PCR Clean-Up Kit |
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P-1005-1 | EpiGentek | 50 Samples | EUR 90.2 |
TuMinute PCR Clean-Up Kit |
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P-1005-2 | EpiGentek | 100 Samples | EUR 171.6 |
TuMinute PCR Clean-Up Kit |
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P-1005 | EpiGentek |
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MicroElute PCR Clean Up Kit (50prep) |
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FAMPK-001 | Favorgen | 50 preps | EUR 151.2 |
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PCR Clean-Up Mini Kit (50prep) |
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PCR Clean-Up Mini Kit (300prep) |
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AxyPrep Mag PCR clean up -50mL |
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AXY1046 | Scientific Laboratory Supplies | EACH | EUR 1511.64 |
AXYPREP MAG PCR CLEAN UP KIT- 1 ML - (SAMPLE SIZE) |
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Description: Bioscience Mag Beads; Magnetic PCR Clean Up |
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Description: Bioscience Mag Beads; Magnetic PCR Clean Up |
AXYPREP MAG PCR CLEAN UP KIT- 50 ML - 1110 PREPS |
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MAG-PCR-CL-50 | CORNING | 1/pk | EUR 694.8 |
Description: Bioscience Mag Beads; Magnetic PCR Clean Up |
FavorPrep Genomic DNA Clean-Up Kit (50prep) |
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FAGDC-001 | Favorgen | 50 preps | EUR 154.8 |
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AxyPrep Mag PCR clean up Kit-1mL |
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AXY1040 | Scientific Laboratory Supplies | EACH | EUR 79.8 |
AxyPrep Mag PCR clean up Kit-5mL |
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AXY1044 | Scientific Laboratory Supplies | EACH | EUR 320.34 |
96-well PCR Clean-Up Kit (1 prep) |
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FACKE-96001 | Favorgen | 1 prep | EUR 189.6 |
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Eppendorf DNA LoBind tubes 0.5ml PCR clean |
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E0030108035 | Scientific Laboratory Supplies | PK250 | EUR 27.36 |
Eppendorf DNA LoBind tubes 1.5ml PCR clean |
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E0030108078 | Scientific Laboratory Supplies | PK250 | EUR 18.02 |
DNA Library Prep Kit for IIlumina Sequencing |
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K1475-12 | Biovision | 12 Rxns | EUR 576 |
96-well GE/PCR Clean Up Purification Kit (1 plates) |
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FAPKE-96001 | Favorgen | 1 prep | EUR 175.2 |
96-well GE/PCR Clean Up Purification Kit (2 plates) |
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FAPKE-96002 | Favorgen | 2 preps | EUR 225.6 |
96-well GE/PCR Clean Up Purification Kit (4 plates) |
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FAPKE-96004 | Favorgen | 4 preps | EUR 328.8 |
Gel Permeation Clean Up Calibration Standard |
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GPC-CAL-91 | Scientific Laboratory Supplies | 5ML | EUR 92.34 |
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N411-01 | Vazyme | 5 ml | EUR 259.2 |
VAHTS DNA Clean Beads |
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N411-02 | Vazyme | 60 ml | EUR 634.8 |
VAHTS DNA Clean Beads |
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N411-03 | Vazyme | 450 ml | EUR 3055.2 |
Eppendorf tubes 5mL screw cap DNA LoBind PCR clean |
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E0030122348 | Scientific Laboratory Supplies | PK200 | EUR 68.4 |
Genorise® Customized PCR primers for cloning and sequencing |
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GR108023 | Genorise Scientific | 2 nmol | EUR 78 |
Chymotrypsin for Sequencing grade |
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C4001-010 | GenDepot | 4x25ug | EUR 375.6 |
Chymotrypsin for Sequencing grade |
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C4001-100 | GenDepot | 100ug | EUR 343.2 |
Trypin for Mass & Sequencing |
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T9600-025 | GenDepot | 25ug | EUR 174 |
Trypin for Mass & Sequencing |
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T9600-100 | GenDepot | 100ug | EUR 262.8 |
Trypin for Mass & Sequencing |
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T9600-112 | GenDepot | 12x100ug | EUR 1988.4 |
Trypin for Mass & Sequencing |
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T9600-400 | GenDepot | 4x100ug | EUR 781.2 |
Zenoquick DNA Clean & Concentrator-5 |
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Z2001-050 | GenDepot | 50 prpe | EUR 216 |
Genorise® Gel DNA Purification Mini Kit-PCR Clean Kit- 50 |
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GR101080 | Genorise Scientific | 50 | EUR 177.6 |
Genorise® Gel DNA Purification Mini Kit-PCR Clean Kit- 100 |
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GR101080-100 | Genorise Scientific | 100 | EUR 320.4 |
Genorise® Gel DNA Purification Mini Kit-PCR Clean Kit- 200 |
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GR101081 | Genorise Scientific | 200 | EUR 572.4 |
Genorise® Gel DNA Purification Mini Kit-PCR Clean Kit- 500 |
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GR101081-500 | Genorise Scientific | 500 | EUR 1288.8 |
EpiQuik DNA Clean and Concentrator Kit |
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P-1068-050 | EpiGentek | 50 preparations | EUR 88 |
EpiQuik DNA Clean and Concentrator Kit |
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P-1068-100 | EpiGentek | 100 preparations | EUR 167.2 |
EpiQuik DNA Clean and Concentrator Kit |
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P-1068 | EpiGentek |
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epTIPS Reloads 0.1-10ul PCR-clean |
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E0030073754 | Scientific Laboratory Supplies | PK960 | EUR 80.94 |
epTIPS Reloads 0.1-20ul PCR-clean |
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E0030073770 | Scientific Laboratory Supplies | PK960 | EUR 83.22 |
epTIPS Reloads 0.5-20ul PCR-clean |
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E0030073797 | Scientific Laboratory Supplies | PK960 | EUR 77.52 |
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E0030073819 | Scientific Laboratory Supplies | PK960 | EUR 72.96 |
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E0030073835 | Scientific Laboratory Supplies | PK960 | EUR 72.96 |
epTIPS Reloads 50-1000ul PCR-clean |
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E0030073851 | Scientific Laboratory Supplies | PK960 | EUR 72.96 |
epTIPS Reloads 50-1250ul PCR-clean |
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E0030073878 | Scientific Laboratory Supplies | PK960 | EUR 88.92 |
epTIPS Reloads 250-2500ul PCR-clean |
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E0030073894 | Scientific Laboratory Supplies | PK480 | EUR 58.94 |
Tubes 5mL screw cap PCR clean |
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E0030122313 | Scientific Laboratory Supplies | PK200 | EUR 61.56 |
Micro test tubes 3810X PCR clean |
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E0030125215 | Scientific Laboratory Supplies | PK1000 | EUR 43.32 |
100 BP DNA LADDER, 500UL PER KIT |
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M-DNA-100BP | CORNING | 1/pk | EUR 87.6 |
Description: Bioscience Mol Bio; DNA Ladder |
1 KB DNA LADDER, 500UL PER KIT |
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M-DNA-1KB | CORNING | 1/pk | EUR 84 |
Description: Bioscience Mol Bio; DNA Ladder |
Eppendorf Protein LoBind tubes 0.5ml PCR clean |
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E0030108094 | Scientific Laboratory Supplies | PK100 | EUR 14.58 |
Eppendorf Protein LoBind tubes 1.5ml PCR clean |
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E0030108116 | Scientific Laboratory Supplies | PK100 | EUR 10.93 |
Eppendorf Protein LoBind tubes 2.0ml PCR clean |
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E0030108132 | Scientific Laboratory Supplies | PK100 | EUR 17.4 |
PCR Tubes (50) |
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PCR-50 | BioAssay Systems | 50 | EUR 15 |
Description: To be used with the PractiChrom kits in conjuction with the PiCO Explorer. Quantity: 50 PCR tubes. |
Automatic FillDrain for Clean Steam for Rodwell autoclaves |
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AUT1351 | Scientific Laboratory Supplies | EACH | EUR 2211.6 |
SEPTA MAT, FOR 96 WELL PCR PLATES, SILICONE, GREY, NONSTERILE, FOR ABI MULTI-CAPILLARY SEQUENCING INSTRUMENTS, BULK |
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AM-96-SEPTA-3100 | CORNING | 10/pk | EUR 639.6 |
Description: Sealing Products; Sealing mats - Axygen |
Tips PCR Clean 50uL 103 mm dark green 10x96 |
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E0030073649 | Scientific Laboratory Supplies | EACH | EUR 90.06 |
epT.I.P.S. G Reloads 384 PCR clean 0.1 - 20uL 42mm |
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E0030076001 | Scientific Laboratory Supplies | PK3840 | EUR 531.24 |
epT.I.P.S. G Reload 384 PCR clean 0.5 - 100uL 52.8mm |
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E0030076010 | Scientific Laboratory Supplies | PK3840 | EUR 531.24 |
epT.I.P.S. Reload 384 IVD PCR clean 0.1 - 20uL 42mm |
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E0030076060 | Scientific Laboratory Supplies | PK3840 | EUR 539.22 |
epT.I.P.S. Reload 384 IVD PCR clean 0.5 - 100uL 53mm |
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E0030076079 | Scientific Laboratory Supplies | PK3840 | EUR 539.22 |
Combitips Adv. PCR Clean 1.0ml 4 packs of 25 |
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E0030089790 | Scientific Laboratory Supplies | PK100 | EUR 123.12 |
Combitips Adv. PCR Clean 2.5ml 4 packs of 25 |
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E0030089804 | Scientific Laboratory Supplies | PK100 | EUR 123.12 |
Combitips Adv. PCR Clean 10ml 4 packs of 25 |
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E0030089820 | Scientific Laboratory Supplies | PK100 | EUR 123.12 |
Combitips Adv. PCR Clean 25ml 4 packs of 25 |
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E0030089839 | Scientific Laboratory Supplies | PK100 | EUR 144.78 |
Combitips Adv. PCR Clean 50ml 4 packs of 25 |
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E0030089847 | Scientific Laboratory Supplies | PK100 | EUR 156.18 |
Eppendorf Conical Tubes 25mL with snap cap PCR clean |
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E0030118413 | Scientific Laboratory Supplies | PK200 | EUR 64.98 |
Eppendorf tubes 5mL screw cap protein LoBind PCR clean |
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E0030122356 | Scientific Laboratory Supplies | PK200 | EUR 92.34 |
Eppendorf Conical Tubes 25mL with screw cap PCR clean |
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E0030122429 | Scientific Laboratory Supplies | PK200 | EUR 69.54 |
Eppendorf Safe-Lock micro test tubes 0.5ml PCR clean |
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E0030123301 | Scientific Laboratory Supplies | PK500 | EUR 50.62 |
Eppendorf Safe-Lock micro test tubes 1.5ml PCR clean |
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E0030123328 | Scientific Laboratory Supplies | PK1000 | EUR 50.62 |
Eppendorf Safe-Lock micro test tubes 2.0ml PCR clean |
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E0030123344 | Scientific Laboratory Supplies | PK1000 | EUR 69.54 |
sequencing unit 33x45 cm |
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ESEQ1100-SYS | Consort | ea | EUR 1842 |
sequencing system 20x50 cm |
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ESEQ1200-SYS | Consort | ea | EUR 1842 |
lyophilised real-time PCR Master Mix with SYBR® Green fluorescent DNA stain |
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M-PCR-173L | MiTeGen | 960 reactions x 20 µl | EUR 789.36 |
Description: lyophilised real-time PCR Master Mix with SYBR® Green fluorescent DNA stain |
lyophilised real-time PCR Master Mix with SYBR® Green fluorescent DNA stain |
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M-PCR-173S | MiTeGen | 192 reactions x 20 µl | EUR 197.34 |
Description: lyophilised real-time PCR Master Mix with SYBR® Green fluorescent DNA stain |
Taq DNA Polymerase (PCR) |
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G008 | ABM | 5000 U (1.0 ml) | EUR 246 |
Taq DNA Polymerase (PCR) |
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G009 | ABM | 1000 U (200 ul) | EUR 104.4 |
HotStart DNA Polymerase (PCR) |
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G011 | ABM | 250 U (50 ul) | EUR 98.4 |
HotStart DNA Polymerase (PCR) |
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G039 | ABM | 1000 U (200 ul) | EUR 189.6 |
Taq DNA Polymerase (PCR) |
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G126 | ABM | 10000 U (2 x 1.0 ml) | EUR 370.8 |
TaqFast DNA Polymerase (PCR) |
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G277 | ABM | 250 U (50 ul) | EUR 87.6 |
TaqFast DNA Polymerase (PCR) |
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G278 | ABM | 1000 U (200 ul) | EUR 160.8 |
Bloodirect DNA Polymerase (PCR) |
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G462 | ABM | 100 U (100 ul) | EUR 73.2 |
Bloodirect DNA Polymerase (PCR) |
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G463 | ABM | 400 U (400 ul) | EUR 104.4 |
96 WELL CLEAR PCR PLATE FOR ABI |
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PCR-96-AB-C | CORNING | 10/pk | EUR 200.4 |
Description: PCR Plates & Tubes; A354 PCR Plate-Axygen |
96 WELL PCR MICROPLATES FOR MEGA BASE |
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PCR-96-MB-C | CORNING | 10/pk | EUR 174 |
Description: PCR Plates & Tubes; A354 PCR Plate-Axygen |
MULTIPLEX KIT PCR MASTITIS PCR kit |
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PCR-MPX218-48D | Bioingentech | 50T | EUR 543.6 |
MULTIPLEX KIT PCR MASTITIS PCR kit |
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PCR-MPX218-96D | Bioingentech | 100T | EUR 686.4 |
CONNECTION KIT FOR START-UP |
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STARTKIT1 | Scientific Laboratory Supplies | EACH | EUR 229.14 |
MULTIPLEX KIT PCR Babesia & Theileria PCR kit |
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PCR-MPX401-48D | Bioingentech | 50T | EUR 543.6 |
MULTIPLEX KIT PCR Babesia & Theileria PCR kit |
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PCR-MPX401-96D | Bioingentech | 100T | EUR 686.4 |
SYBR® Green Fluorescent DNA StainDNA intercalation dye for real-time PCR analysis** shipped ice packs - must be shipped via overnight service |
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M-PCR-378 | MiTeGen | 500 µl | EUR 63.63 |
Description: SYBR® Green Fluorescent DNA StainDNA intercalation dye for real-time PCR analysis** shipped ice packs - must be shipped via overnight service |
ep LoRetention PCR clean 0.1-10ul 10 x 96 reloads |
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E0030072006 | Scientific Laboratory Supplies | PK960 | EUR 88.92 |
ep LoRetention PCR clean 0.5-20ul 10 x 96 reloads |
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E0030072014 | Scientific Laboratory Supplies | PK960 | EUR 85.5 |
ep LoRetention PCR clean 2-200ul 10 x 96 reloads |
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E0030072022 | Scientific Laboratory Supplies | PK960 | EUR 80.94 |
ep LoRetention PCR clean 50-1000ul 10 x 96 reloads |
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E0030072030 | Scientific Laboratory Supplies | PK960 | EUR 80.94 |
0.2ML CLEAR STRIP CAPS FOR REAL TIME PCR |
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PCR-2CP-RT-C | CORNING | 125/pk | EUR 267.6 |
Description: PCR Plates & Tubes; PCR Strip Tubes and Strip Caps - Axygen |
lyophilised real-time PCR Master Mix for dual labeled probes |
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M-PCR-156L | MiTeGen | 960 reactions x 20 µl | EUR 900.68 |
Description: lyophilised real-time PCR Master Mix for dual labeled probes |
lyophilised real-time PCR Master Mix for dual labeled probes |
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M-PCR-156S | MiTeGen | 192 reactions x 20 µl | EUR 225.3 |
Description: lyophilised real-time PCR Master Mix for dual labeled probes |
Lancer Clean Detergent |
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CLE1136 | Scientific Laboratory Supplies | 10L | EUR 72.96 |
SequaGel Sequencing System 1L Kit |
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NAT1136 | Scientific Laboratory Supplies | 1KIT | EUR 127.68 |
SequaGel Sequencing System 2.2L Kit |
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NAT1138 | Scientific Laboratory Supplies | EACH | EUR 217.74 |
EpiNext Bisulfite Sequencing Kit (Illumina) |
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P-1056-12 | EpiGentek | 12 Reactions | EUR 625.9 |
EpiNext Bisulfite Sequencing Kit (Illumina) |
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P-1056-24 | EpiGentek | 24 Reactions | EUR 1225.4 |
EpiNext Bisulfite Sequencing Kit (Illumina) |
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P-1056 | EpiGentek |
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ranavirus PCR kit |
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PCR-V337-48D | Bioingentech | 50T | EUR 543.6 |
ranavirus PCR kit |
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PCR-V337-96D | Bioingentech | 100T | EUR 686.4 |
Ruminococcus PCR kit |
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PCR-V619-48D | Bioingentech | 50T | EUR 510.96 |
Description: An conventional PCR kit for detection of Ruminococcus |
Ruminococcus PCR kit |
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PCR-V619-96D | Bioingentech | 100T | EUR 625.8 |
Description: An conventional PCR kit for detection of Ruminococcus |
Bifidobacterium PCR kit |
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PCR-V621-48D | Bioingentech | 50T | EUR 510.96 |
Description: An conventional PCR kit for detection of Bifidobacterium |
Bifidobacterium PCR kit |
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PCR-V621-96D | Bioingentech | 100T | EUR 625.8 |
Description: An conventional PCR kit for detection of Bifidobacterium |
Halobacillus PCR kit |
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PCR-A635-48D | Bioingentech | 50T | EUR 543.6 |
Halobacillus PCR kit |
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PCR-A635-96D | Bioingentech | 100T | EUR 686.4 |
Enterovirus PCR kit |
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PCR-H433-48R | Bioingentech | 50T | EUR 987.6 |
Enterovirus PCR kit |
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PCR-H433-96R | Bioingentech | 100T | EUR 1030.8 |
Mengovirus PCR kit |
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PCR-H453-48R | Bioingentech | 50T | EUR 987.6 |
Mengovirus PCR kit |
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PCR-H453-96R | Bioingentech | 100T | EUR 1335.6 |
Astrovirus PCR kit |
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PCR-H491-48R | Bioingentech | 50T | EUR 987.6 |
Astrovirus PCR kit |
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PCR-H491-96R | Bioingentech | 100T | EUR 1335.6 |
Calicivirus PCR kit |
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PCR-H493-48R | Bioingentech | 50T | EUR 987.6 |
Calicivirus PCR kit |
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PCR-H493-96R | Bioingentech | 100T | EUR 1335.6 |
Adenovirus PCR kit |
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PCR-H501-48D | Bioingentech | 50T | EUR 543.6 |
Adenovirus PCR kit |
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PCR-H501-96D | Bioingentech | 100T | EUR 686.4 |
Polyomavirus PCR kit |
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PCR-H515-48D | Bioingentech | 50T | EUR 543.6 |
Polyomavirus PCR kit |
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PCR-H515-96D | Bioingentech | 100T | EUR 686.4 |
Ruminococcus PCR kit |
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PCR-H619-48D | Bioingentech | 48T | EUR 543.6 |
Ruminococcus PCR kit |
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PCR-H619-96D | Bioingentech | 96T | EUR 686.4 |
Bifidobacterium PCR kit |
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PCR-H621-48D | Bioingentech | 48T | EUR 543.6 |
Bifidobacterium PCR kit |
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PCR-H621-96D | Bioingentech | 96T | EUR 686.4 |
Sapovirus PCR kit |
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PCR-H630-48R | Bioingentech | 50T | EUR 987.6 |
Sapovirus PCR kit |
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PCR-H630-96R | Bioingentech | 100T | EUR 1335.6 |
Parechovirus PCR kit |
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PCR-H642-48R | Bioingentech | 50T | EUR 813.6 |
Parechovirus PCR kit |
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PCR-H642-96R | Bioingentech | 100T | EUR 1335.6 |
Metapneumovirus PCR kit |
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PCR-H643-48R | Bioingentech | 50T | EUR 987.6 |
Metapneumovirus PCR kit |
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PCR-H643-96R | Bioingentech | 100T | EUR 1335.6 |
Entamoeba PCR kit |
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PCR-H683-48D | Bioingentech | 50T | EUR 543.6 |
Entamoeba PCR kit |
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PCR-H683-96D | Bioingentech | 100T | EUR 686.4 |
Acanthamoeba PCR kit |
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PCR-H684-48D | Bioingentech | 50T | EUR 543.6 |
Acanthamoeba PCR kit |
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PCR-H684-96D | Bioingentech | 100T | EUR 686.4 |
Echovirus PCR kit |
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PCR-H722-48D | Bioingentech | 50T | EUR 543.6 |
Echovirus PCR kit |
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PCR-H722-96D | Bioingentech | 100T | EUR 686.4 |
PCR DNA Extraction and Purification |
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EP10013 | Neuromics | 100 Tests | EUR 356.4 |
Taq Plus DNA Polymerase (PCR) |
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G012 | ABM | 250 U (50 ul) | EUR 87.6 |
Taq Plus DNA Polymerase (PCR) |
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G040 | ABM | 1000 U (200 ul) | EUR 127.2 |
Precision™ DNA Polymerase (PCR) |
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G078 | ABM | 500 U (100 ul) | EUR 133.2 |
Bestaq™ DNA Polymerase (PCR) |
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G456 | ABM | 250 U (50 ul) | EUR 104.4 |
Bestaq™ DNA Polymerase (PCR) |
|||
G457 | ABM | 1000 U (200 ul) | EUR 189.6 |
Using machine learning approach, we identified 17 miRNAs to distinguish 15 Nen type of pathological and then build a classifier multilayer, correctly identified 217 (98%) of the 221 samples and overturning a histological diagnosis.