Ampliseq designer

Manufactured by Thermo Fisher Scientific

Sourced in Sweden

The AmpliSeq Designer is a bioinformatics software tool that assists in the design of targeted amplicon sequencing assays. It allows users to create custom gene panels for various applications, such as genetic analysis, disease research, and clinical diagnostics.

Automatically generated - may contain errors

Lab products found in correlation

13 protocols using ampliseq designer

Ion Torrent Variant Calling Pipeline

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Sequencing reads obtained from Ion Proton were aligned to human reference sequence (human genome build-19) and variant calling was performed using Ion Torrent Variant Caller v5.0 in Torrent Suite software v5.0 (ThermoFisher Scientific). After the reads were aligned to the reference sequence, noisy and low quality reads were removed and sequence variants were detected using Ion Torrent Variant Caller Plugin software v5.0 with optimised parameters (AmpliSeq Designer, ThermoFisher Scientific) for low-frequency variant detection with minimal false-positive calls. Further, variant calls were filtered based on the technical characteristics such as (1) variant quality score, (2) variant coverage and (3) variant allele frequency. Amplicon coverage was determined via Coverage Analysis Plugin software v5.0. ThermoFisher Scientific Alignment reads and variants called, with respect to the reference human genome sequence, were viewed using Integrative Genomic Viewer software (Thorvaldsdóttir et al, 2013 (link)) and to check for strand biases, homopolymer length and sequencing errors. The variant caller plug-in generates a variant caller file or VCF file, which was subsequently imported to Ion Reporter software v5.0 (ThermoFisher Scientific) for variant annotation and filtering.

Chakrabarty S., Varghese V.K., Sahu P., Jayaram P., Shivakumar B.M., Pai C.G, & Satyamoorthy K. (2017). Targeted sequencing-based analyses of candidate gene variants in ulcerative colitis-associated colorectal neoplasia. British Journal of Cancer, 117(1), 136-143.

+ Open protocol

+ Expand

Targeted Sequencing of Pancreatic Cancer Genes

Check if the same lab product or an alternative is used in the 5 most similar protocols

Genetic analysis of the tumor specimens was performed by amplification of the extracted DNA (10 ng) using an Ion AmpliSeq Custom panel (Thermo Fisher) targeting 78 genes (Table S1) and containing 451 primer pairs. The custom panel differed from the ready‐made panel used in our previous study.⁸ It was designed using the AmpliSeq Designer (Thermo Fisher) to cover pancreatic cancer driver genes and actionable targets listed in OncoKB.⁹ OncoKB is a knowledge base for precision medicine used to infer whether an existing molecular‐targeted drug will be effective. Sequencing was performed with an Ion Chef System and an Ion Proton Sequencer (Life Technologies) using an Ion PI Hi‐Q Chef Kit (Life Technologies). Data obtained in the present study were shared with the Japanese Genotype‐Phenotype Archive (JGAS000315/JGAD000426).¹⁰

Takano S., Fukasawa M., Shindo H., Takahashi E., Fukasawa Y., Kawakami S., Hayakawa H., Kuratomi N., Kadokura M., Yamaguchi T., Inoue T., Maekawa S, & Enomoto N. (2022). Next‐generation sequencing of endoscopically obtained tissues from patients with all stages of pancreatic cancer. Cancer Science, 113(3), 1069-1077.

+ Open protocol

+ Expand

Targeted Sequencing of B11, C5, E7

Check if the same lab product or an alternative is used in the 5 most similar protocols

A custom AmpliSeq HD panel was designed to cover specific variants of the B11, C5 and E7 subclones. The panel was designed for ThermoFisher sequencers on the Ampliseq Designer tool and was manufactured by Thermo Fisher.

Mopin A., Leprêtre F., Sebda S., Villenet C., Ben Khoud M., Figeac M., Quesnel B, & Brinster C. (2022). Detection of residual and chemoresistant leukemic cells in an immune-competent mouse model of acute myeloid leukemia: Potential for unravelling their interactions with immunity. PLoS ONE, 17(4), e0267508.

+ Open protocol

+ Expand

Targeted NGS Panel for Comprehensive Cancer Profiling

Check if the same lab product or an alternative is used in the 5 most similar protocols

For targeted NGS, a custom‐made cancer panel was designed using the AmpliSeq designer (Thermo Fisher Scientific, Waltham, MA). This panel comprised 330 amplicons covering 41 genes, multiple hotspot regions in various cancer‐related genes and 154 single nucleotide polymorphisms in multiple tumor suppressor regions to detect copy number variations (Table 2 and Supplementary Table 3).⁵, ⁶, ⁷ NGS was performed with the Ion Torrent platform using supplier's materials and protocols (Thermo Fisher Scientific). Median coverage depths were 1994x for UTUC, 1712x for UCB and 1914x for the adjacent normal tissue. Libraries were made using the Ion AmpliSeq Library Kit plus–384 LV, template was prepared with the Ion 510/520/530 Chef kit and sequencing was performed on a 530‐chip using the Ion S5 system. Data were analyzed using SeqPilot (JSI medical systems). To correct for potential germline mutations, NGS was also performed on DNA isolated from matched nonmalignant kidney tissue. The final tumor cell percentage was calculated based on the DNA quality and quantity and the results of the NGS.

van Doeveren T., Nakauma‐Gonzalez J.A., Mason A.S., van Leenders G.J., Zuiverloon T.C., Zwarthoff E.C., Meijssen I.C., van der Made A.C., van der Heijden A.G., Hendricksen K., van Rhijn B.W., Voskuilen C.S., van Riet J., Dinjens W.N., Dubbink H.J., van de Werken H.J, & Boormans J.L. (2020). The clonal relation of primary upper urinary tract urothelial carcinoma and paired urothelial carcinoma of the bladder. International Journal of Cancer, 148(4), 981-987.

+ Open protocol

+ Expand

Y-SNP Amplification and Sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols

AmpliSeq Designer was employed to conduct single-pool DNA Hotspot designing, and the 74 candidate Y-SNPs were submitted to Thermo Fisher AmpliSeq primer design tool (http://www.ampliseq.com) in a BED file (Thermo Fisher White Glove Approach ID: IAD97812).
Amplification and sequencing primers of the 67 additional Y-SNPs were self-designed by the PSQ Assay Design software (version 1.0, Biotage AB, Sweden). One of each pair of amplification primers was biotinylated at the 5’-end and purified by HPLC to eliminate free biotins (details in Supplementary Table S2).

Qian X., Hou J., Wang Z., Ye Y., Lang M., Gao T., Liu J, & Hou Y. (2017). Next Generation Sequencing Plus (NGS+) with Y-chromosomal Markers for Forensic Pedigree Searches. Scientific Reports, 7, 11324.

+ Open protocol

+ Expand

Comprehensive NGS Assay for CHA

Check if the same lab product or an alternative is used in the 5 most similar protocols

We developed an NGS assay to analyse a panel of 40 genes known to be involved in the pathogenesis of CHA (Table 1). Using Ampliseq Designer software (Thermo Fisher Scientific, S.L.), we selected the regions of interest to be sequenced, including all exons, 30-and 50-untranslated regions, exon-intron boundaries and promoter regions. Additionally, various intronic regions of several genes were included to analyse copy number variation.

Del Orbe Barreto R., Arrizabalaga B., De la Hoz A.B., García-Orad Á., Tejada M.I., Garcia-Ruiz J.C., Fidalgo T., Bento C., Manco L, & Ribeiro M.L. (2016). Detection of new pathogenic mutations in patients with congenital haemolytic anaemia using next-generation sequencing. International journal of laboratory hematology, 38(6).

+ Open protocol

+ Expand

Nrf2 Mutation Analysis in Tumors

Check if the same lab product or an alternative is used in the 5 most similar protocols

To study Nrf2 gene mutations in tumor specimens, single‐nucleotide variants (SNVs), short insertions, and deletions (indels) were assessed by next‐generation sequencing of the coding exons and intron flanking regions according to methods published elsewhere.²³ The associated custom primers were prepared with AmpliSeq Designer (Life Technologies), and the library was constructed and sequenced by an Ion AmpliSeq Library Kit 2.0, Ion PGM IC 200 kit, and Ion PGM (Life Technologies), in accordance with the manufacturer's instructions; these kits analyze a wide range of genes, including those recommended for analysis by the American College of Medical Genetics and Genomics.²⁴ Torrent Suite software were used to analyze the results of sequencing, and Torrent Variant Caller, Ion Reporter (v.5.1.0) was used for variant calling; Ion Torrent sequencer can accurately detect Nrf2 gene mutations.²⁵

Kamai T., Murakami S., Arai K., Ishida K, & Kijima T. (2022). Association of Nrf2 expression and mutation with Weiss and Helsinki scores in adrenocortical carcinoma. Cancer Science, 113(7), 2368-2377.

+ Open protocol

+ Expand

Targeted Sequencing for Germline Mutation Analysis

Cited 2 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

Next-generation sequencing was performed to detect single nucleotide variants (SNVs), short insertions, and deletions (indels). We investigated mutations of the SDHA, SDHB, SDHC, SDHD, fumarate hydratase (FH) and rearranged during transfection (RET) genes by sequencing the coding exons and intron flanking regions in tumor specimens, as described previously [26 (link)]. The custom primers for these regions were designed with Ampliseq Designer (Life Technologies). Library construction and sequencing were performed with an Ion AmpliSeq Library Kit 2.0, Ion PGM IC 200 kit, and Ion PGM (Life Technologies), according to the manufacturer's instructions. Sequencing data were analyzed with Torrent Suite, and variant call was conducted with Torrent Variant Caller, Ion Reporter (v.5.1.0). Ion AmpliSeq panels cover broad research areas for germline analysis, including genes recommended by the American College of Medical Genetics and Genomics [27 (link)]. Then, the accuracy of the Ion Torrent sequencer platform in detecting SDHB gene mutations was confirmed according to a previously published method [28 (link)].

Kamai T., Murakami S., Arai K., Nishihara D., Uematsu T., Ishida K, & Kijima T. (2022). Increased expression of Nrf2 and elevated glucose uptake in pheochromocytoma and paraganglioma with SDHB gene mutation. BMC Cancer, 22, 289.

+ Open protocol

+ Expand

Targeted Sequencing of Nrf2, Keap1, VHL, FH

Check if the same lab product or an alternative is used in the 5 most similar protocols

Tumor tissue samples of the 50 patients were used to investigate mutations of the Nrf2, Keap1, von Hippel-Lindau (VHL), and fumarate hydratase (FH) genes. We performed targeted next-generation sequencing of the coding exons and intron flanking regions of these four genes [19 (link)], using customized primers designed with Ampliseq Designer (Life Technologies). Construction of a library and sequencing were performed with an Ion AmpliSeq Library Kit 2.0, Ion PGM IC 200 kit, and Ion PGM (Life Technologies) according to the directions of the manufacturer. Raw data from each sequencing reaction were analyzed with Torrent Suite version 4.2.1.

Yamaguchi Y., Kamai T., Higashi S., Murakami S., Arai K., Shirataki H, & Yoshida K.I. (2019). Nrf2 gene mutation and single nucleotide polymorphism rs6721961 of the Nrf2 promoter region in renal cell cancer. BMC Cancer, 19, 1137.

+ Open protocol

+ Expand

Targeted Gene Sequencing Panel Design

Check if the same lab product or an alternative is used in the 5 most similar protocols

We utilized the results of several studies to develop a panel of 122 genes for sequencing on an Ion Torrent PGM sequencer (Table 2). An effort was made to select genes from a variety of supercontigs and the final panel contained genes from 78 supercontigs. The sequence for each gene, along with 150bp of flanking sequence on both ends, was copied from VectorBase and formatted as a FASTA file. If there were small (< 100 bp) introns between exons, they were included for sequencing as well. One FASTA file per gene was submitted to Life Technologies’ AmpliSeq Designer (www.Ampliseq.com), where two pools of primers were designed that amplified 200 bp regions of each target gene. The two primer pools amplify overlapping segments of DNA, which increases the chances the entire gene of interest will amplify. For this study, a total of 1255 primer pairs (628 in Pool 1 and 627 in Pool 2) were designed.

Kothera L., Phan J., Ghallab E., Delorey M., Clark R, & Savage H.M. (2019). Using targeted next-generation sequencing to characterize genetic differences associated with insecticide resistance in Culex quinquefasciatus populations from the southern U.S.. PLoS ONE, 14(7), e0218397.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!