Single‐nucleotide polymorphisms (SNPs) in CYP2D6, NR0B2, and HNF4A were examined using a custom‐designed Ampliseq panel (ThermoFisher Scientific, Waltham, MA), which is a highly specific, multiplex polymerase chain reaction (PCR)‐based sequence enrichment method using a customizable pool of oligonucleotide primer pairs. The custom Ampliseq panel was designed to target the CYP2D6 gene region (4‐kb upstream of the transcriptional start site to 1‐kb downstream; hg19 chr22:42521501‐42530883), the NR0B2 gene region (2‐kb upstream to 1‐kb downstream; hg19 chr1:27236975‐27242567), and exons, including adjacent intron/putative regulatory regions, of the HNF4A gene. The exon regions that could not be covered by the Ampliseq panel (hg19 chr22:42525025‐42525235 and hg19 chr1:27240340‐27240390) were sequenced using Sanger sequencing. Sequencing was completed using the Ion Torrent next‐generation sequencing platform (ThermoFisher Scientific). Raw data from Ion Torrent sequencing were filtered for quality control and aligned to hg19 genome assembly. SNP calling was completed as previously described.19 Sanger sequencing results for CYP2D6 and NR0B2 were aligned to hg19 chr22:42525025‐42525235 and hg19 chr1:27240340‐27240390 regions, respectively, using novoSNP software.20
Ion torrent next generation sequencing platform
Manufactured by Thermo Fisher Scientific
The Ion Torrent next-generation sequencing platform is a DNA sequencing technology developed by Thermo Fisher Scientific. It utilizes semiconductor-based sequencing to detect the release of hydrogen ions during DNA synthesis, allowing for rapid and scalable DNA sequencing.
Automatically generated - may contain errors
2 protocols using ion torrent next generation sequencing platform
1
Targeted Sequencing of Pharmacogenomic Variants
2
Genomic Surveillance of Influenza A
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Lineage typing and sequence analysis were performed by laboratory staff blinded for epidemiological data. RT-PCR products was used in library preparation performed by AB Library Builder system (Applied Biosystems). Each genome library of about 300-bp fragments was quantified with the Ion Library TaqMan Quantitation Kit (Thermo Fisher Scientific) and template preparation was performed by the Ion Chef system (Thermo Fisher Scientific).
Sequencing was performed using the Ion Torrent next generation sequencing platform with the reference sequence for H3N2 accessed from GenBank. Bioinformatic analysis was performed with the web-based platform INSaFlu and consensus sequences of each InfA genome were obtained [113] . For comparison, samples obtained at primary healthcare centres in the same region, during the same season, were also included. A phylogenetic tree was constructed using the maximum likelihood method in Mega® Version 7. Bootstrap values were obtained from 500 replicates and displayed on nodes if >70%. The modelling process consisted of the following consecutive steps:
(1) Identifying key variables with a potential influence on in-hospital transmission of influenza.
(2) Construction and technical validation of the model.
(3) Selecting the model scenarios of interest.
Sequencing was performed using the Ion Torrent next generation sequencing platform with the reference sequence for H3N2 accessed from GenBank. Bioinformatic analysis was performed with the web-based platform INSaFlu and consensus sequences of each InfA genome were obtained [113] . For comparison, samples obtained at primary healthcare centres in the same region, during the same season, were also included. A phylogenetic tree was constructed using the maximum likelihood method in Mega® Version 7. Bootstrap values were obtained from 500 replicates and displayed on nodes if >70%. The modelling process consisted of the following consecutive steps:
(1) Identifying key variables with a potential influence on in-hospital transmission of influenza.
(2) Construction and technical validation of the model.
(3) Selecting the model scenarios of interest.
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?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!