Variant reporter software v1

Manufactured by Thermo Fisher Scientific

Sourced in United States

Variant Reporter Software v1.1 is a bioinformatics tool designed to analyze and report on genetic variations. The software provides a user-friendly interface for processing and interpreting next-generation sequencing data, focusing on the identification and annotation of genetic variants.

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Lab products found in correlation

Abi prism 377 dna sequencer, by Thermo Fisher Scientific (1 mentions) Genemapper software, by Thermo Fisher Scientific (1 mentions) Bigdyer terminator v3.1 cycle sequencing kit, by Thermo Fisher Scientific (1 mentions) Multiscreen filter plate, by Merck Group (1 mentions) Quantitect reverse transcription kit, by Qiagen (1 mentions) Dna engine tetrad 2 peltier thermal cycler, by Bio-Rad (1 mentions) Pop7 polymer, by Thermo Fisher Scientific (1 mentions) Bigdye xterminator purification kit, by Thermo Fisher Scientific (1 mentions) Bigdye terminator v3.1 kit, by Thermo Fisher Scientific (1 mentions) 3500 genetic analyzer, by Thermo Fisher Scientific (1 mentions) Agencourt ampure xp kit, by Beckman Coulter (1 mentions)

Spelling variants of this product

Variant Reporter software (18 citations) Variant Reporter v1.0 (6 citations) Variant Reporter (4 citations)

3 protocols using variant reporter software v1

Microsatellite and OPA1 Gene Analysis Protocol

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DNA was extracted from blood by a standard salting out method. For amplification of microsatellite markers (D3S3642, D3S3590, D3S2305, D3S3562, D3S2748) PCR primer sequences were retrieved from the Ensembl Genome Browser (http://www.ensembl.org). Forward primers were 5’labeled with 6-carboxyfluorescein (6-FAM) and reverse primers were unlabeled. PCR products were mixed with a fluorescent size marker (Applied Biosystems, Foster City, CA, USA) and analyzed on ABI PRISM 377 DNA sequencer (Applied Biosystems). Fragment lengths were analyzed with the Gene Mapper software (Applied Biosystems).
For the amplification of all OPA1 exons PCR primers were designed with the Primer 3 Plus public domain software (http://primer3plus.com/cgi-bin/dev/primer3plus.cgi) and the OPA1 gene NG_011605.1 reference sequence. The OPA1 exon amplicons were sequenced using the BigDye Termination cycle sequencing kit v3.1 (Applied Biosystems) and analyzed on ABI PRISM 377 DNA sequencer (Applied Biosystems). The results were visualized by the Variant Reporter Software v1.1 (Applied Biosystems). PCR primers and reaction conditions are available upon request.

Ścieżyńska A., Ruszkowska E., Szulborski K., Rydz K., Wierzbowska J., Kosińska J., Rękas M., Płoski R., Szaflik J.P, & Ołdak M. (2017). Processing of OPA1 with a novel N-terminal mutation in patients with autosomal dominant optic atrophy: Escape from nonsense-mediated decay. PLoS ONE, 12(8), e0183866.

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Validating gene fusions by RT-PCR and sequencing

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The putative gene fusions, detected by RNA-Seq, were verified by reverse transcription PCR (RT-PCR), followed by Sanger sequencing. cDNA was synthesized from 2 µg total RNA using a QuantiTect Reverse Transcription kit (Qiagen Inc., Hilden, Germany) with primers that flank the breakpoint of the fusion, in DNA Engine Tetrad 2 Peltier Thermal Cycler (BIO-RAD, Hercules, CA, USA) with the following cycling conditions: one cycle of 5 min at 95 °C, followed by three-step cycles of 30 s at 95 °C, 30 s at 62 °C, 10 min at 72 °C, and a final extension for 20 min at 72 °C. PCR products were purified using a Multiscreen filter plate (Millipore Corp., Bedford, MA, USA) and sequenced in an ABI prism 3730XL Analyzer (Thermo Fisher Scientific, Waltham, MA, USA) using a BigDye (R) Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems Inc., Foster City, CA, USA). The results were accessed by Variant Reporter Software v 1.1 (Applied Biosystems Inc., Foster City, CA, USA).

Lee E., Lee J.W., Lee B., Park K., Shim J., Yoo K.H., Koo H.H., Sung K.W, & Park W.Y. (2020). Genomic profile of MYCN non-amplified neuroblastoma and potential for immunotherapeutic strategies in neuroblastoma. BMC Medical Genomics, 13, 171.

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Genetic Analysis of MC1R Gene

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We used a 3500 Genetic Analyzer (Applied Biosystems) to perform DNA sequencing of the MC1R gene open reading frame (ORF) for all HCAECs and HAoECs. Genomic DNA amplicons of the MC1R ORF were produced by PCR with the following primers: MC1R_Forward(1) (-25) 5'-TCCTTCCTGCTTCCTGGACA-3', MC1R_Reverse(1) (+980) 5'-CACACTTAAAGCCGCGTGCAC-3'. The amplified fragments were purified using the Agencourt AMPure XP kit (Beckman Coulter). Sequencing reactions were carried out using the BigDye Terminator v3.1 Kit (Applied Biosystems) in both strand directions to allow the production of four overlapping fragments. Sequencing primers used were the MC1R_Forward(1), the MC1R_Reverse(1) and: the inner MC1R_Forward(2) (+449) 5'-TGCGCTACCACAGCATCGTG-3', and the inner MC1R_Reverse(2) (+510) 5'-CACCCAGATGGCCGCAAC-3'. Unincorporated fluorescent dideoxynucleotides and salts were removed with the BigDye XTerminator Purification Kit (Applied Biosystems). The purified sequencing reaction products were electrokinetically injected into a 50 cm Capillary Array filled with the POP-7 Polymer (Applied Biosystems). Electropherograms were analysed by the Variant Reporter software v1.1 (Applied Biosystems).

Saporiti F., Piacentini L., Alfieri V., Bono E., Ferrari F., Chiesa M, & Colombo G.I. (2019). Melanocortin-1 Receptor Positively Regulates Human Artery Endothelial Cell Migration. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology, 52(6).

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