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Alissa

Manufactured by Agilent Technologies
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Alissa is a compact and versatile laboratory instrument designed for high-precision liquid handling. It features automated pipetting and dispensing capabilities to facilitate accurate and efficient sample processing in a variety of applications.

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Lab products found in correlation

Ion ampliseq cancer hotspot panel, by Thermo Fisher Scientific (1 mentions) Ion torrent s5 system, by Thermo Fisher Scientific (1 mentions) Dneasy blood and tissue kit, by Qiagen (1 mentions) Surecall, by Agilent Technologies (1 mentions) Suredesign software, by Agilent Technologies (1 mentions) Miseq platform, by Illumina (1 mentions)

3 protocols using alissa

1

Targeted NGS of Cancer Hotspots

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DNA from the fresh-frozen pulverized tumor tissue was isolated using a DNEasy Blood and Tissue Kit (Qiagen, Venlo, The Netherlands). Targeted next-generation sequencing with a mean coverage of 500X coverage was performed on the Ion Torrent S5 system (ThermoFischer Scientific) using a custom next-generation sequencing (NGS) panel based on the Ion Ampliseq™ Cancer Hotspot Panel targeting mutational hotspots of 64 cancer-related genes. Variants with an allele frequency of at least 5% were reported. Variant call files were generated and analysis was performed using Alissa (Agilent Technologies Alissa Interpret v5.1.7).
Roze J., Sendino Garví E., Stelloo E., Stangl C., Sereno F., Duran K., Groeneweg J., Paijens S., Nijman H., van Meurs H., van Lonkhuijzen L., Piek J., Lok C., Jonges G., Witteveen P., Verheijen R., van Haaften G., Zweemer R, & Monroe G. (2021). In Vitro Systematic Drug Testing Reveals Carboplatin, Paclitaxel, and Alpelisib as a Potential Novel Combination Treatment for Adult Granulosa Cell Tumors. Cancers, 13(3), 368.
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2

Targeted Sequencing of DMD and Related Genes

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A 2.683Mbp custom panel was designed using SureDesign software (Agilent Technologies, Santa Clara, CA). Probes targeted all the DMD exons and the complete 44‐ and 55‐intron sequences. It also contained the SPP1, LTBP4, and ACTN3 DMD modifiers and genes involved in myopathy.26 DNA libraries were prepared according to the SureSelectQXT Target Enrichment for Illumina Multiplexed Sequencing protocol and sequenced on a Miseq platform (Illumina, San Diego, CA) using the V3‐150 cycles cartridges. Files were obtained using the MiSeq Reporter 2.6.2.3 and Illumina RTA 1.18.54. Reads were mapped to the human reference genome (GRCh37/hg19). Data analysis was performed using Alissa and SureCall (Agilent Technologies).
Poyatos‐García J., Martí P., Liquori A., Muelas N., Pitarch I., Martinez‐Dolz L., Rodríguez B., Gonzalez‐Quereda L., Damiá M., Aller E., Selva‐Gimenez M., Vilchez R., Diaz‐Manera J., Alonso‐Pérez J., Barcena J.E., Jauregui A., Gámez J., Aladrén J.A., Fernández A., Montolio M., Azorin I., Hervas D., Casasús A., Nieto M., Gallano P., Sevilla T, & Vilchez J.J. (2022). Dystrophinopathy Phenotypes and Modifying Factors in DMD Exon 45–55 Deletion. Annals of Neurology, 92(5), 793-806.
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3

Oncogenic Variant Analysis in Samples

Cited 1 time
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The exonic and UTR variant analysis was performed using Alissa (Agilent Technologies Alissa Interpret v5.1.4). Variants in the exonic regions, ±100 base pairs into the intronic regions, and in the 5’ and 3’ UTR of Refseq transcripts were retained for analysis. Variants present in the COSMIC Cancer Gene Census (release v89) as somatic mutations in cancer were annotated (Table S2a,b).
To find novel candidate genes in which mutations could contribute to oncogenesis and/or recurrence, we performed a cohort analysis to identify genes with a somatic variant in multiple samples. As this study contained multiple samples from individual patients, this variant list was further filtered to remove any genes in which variation occurred solely within samples of a particular patient. Variants were annotated with the CADD PHRED (Combined Annotation Dependent Depletion) [55 (link)] score and genes with no or only one variant >5 were removed.
Roze J., Monroe G., Kutzera J., Groeneweg J., Stelloo E., Paijens S., Nijman H., van Meurs H., van Lonkhuijzen L., Piek J., Lok C., Jonges G., Witteveen P., Verheijen R., van Haaften G, & Zweemer R. (2020). Whole Genome Analysis of Ovarian Granulosa Cell Tumors Reveals Tumor Heterogeneity and a High-Grade TP53-Specific Subgroup. Cancers, 12(5), 1308.
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