Log In Sign up
The largest database of trusted experimental protocols

Ngs analysis

Manufactured by Illumina
Visit Supplier
Sourced in United States

NGS analysis is a core laboratory equipment used for next-generation sequencing (NGS) data analysis. It provides computational tools and algorithms for processing, analyzing, and interpreting NGS data generated from various sequencing platforms.

Automatically generated - may contain errors

Lab products found in correlation

Dnase 1, by Takara Bio (1 mentions) Primescript 2, by Takara Bio (1 mentions) Rneasy plant mini kit, by Qiagen (1 mentions)

4 protocols using ngs analysis

1

Comprehensive Genetic Profiling for Cancer Risk

Check if the same lab product or an alternative is used in the 5 most similar protocols
Both MGPT and TP53 gene-specific tests were performed from DNA isolated from whole blood or saliva samples. NGS analysis (Illumina, San Diego, CA) was performed in all coding domains plus at least five bases into the 5′ and 3′ ends of the introns and untranslated regions (5′UTR and 3′UTR) for all cancer susceptibility genes. EPCAM and GREM1 were only analyzed for gross deletions and duplications, if included on the panel. Depending on the panel ordered by the clinician, 5–49 genes, including TP53, were analyzed. Sanger sequencing was performed for any region with insufficient depth of coverage (<10X), for verification of all variants (other than known benign variants), and for those with decreased mutant to wild-type allele ratios. A targeted chromosomal microarray and/or MLPA was used for the detection of gross deletions and duplications.
A five-tier classification schema—pathogenic; variant, likely pathogenic; variant of unknown significance; variant, likely benign; and benign—was used to classify variants.29 (link)
Weitzel J.N., Chao E.C., Nehoray B., Van Tongeren L.R., LaDuca H., Blazer K.R., Slavin T., Pesaran T., Rybak C., Solomon I., Niell-Swiller M., Dolinsky J.S., Castillo D., Elliott A., Gau C.L., Speare V, & Jasperson K. (2017). Somatic TP53 variants frequently confound germline testing results. Genetics in medicine : official journal of the American College of Medical Genetics, 20(8), 809-816.
+ Open protocol
+ Expand
2

Illumina NGS Analysis of Genome-Edited Gentian Plants

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
The genomic DNA and transcripts in the petals of the genome-edited lines and the WT control underwent an Illumina NGS analysis. Genomic DNA was isolated from the leaves of transgenic and WT gentian plants with the GeneElute Genome DNA Isolation system (Sigma-Aldrich, St Louis, MO, USA). Total RNA was isolated from the petals of transgenic gentian plants with the RNeasy Plant Mini kit (Qiagen, GmbH, Hilden, Germany) and treated with DNase I (TaKaRa) according to the manufacturer’s instructions. The extracted RNA samples were reverse transcribed with PrimeScript II (TaKaRa). The subsequent library preparation, PCR amplification, amplification check, and library quantification check were performed as previously described18 (link). The primer positions and target sites are indicated in Fig. 2b. Additional details regarding the primers (e.g., index) are listed in Supplementary Table S1. A bioinformatics analysis was performed as previously described18 (link). Briefly, the resulting raw sequence reads were pre-processed with the FASTX toolkit, and the read pairs were merged into a single contiguous sequence (fragment) with a fastq-join script28 (link). The unique fragments were then counted.
Tasaki K., Higuchi A., Watanabe A., Sasaki N, & Nishihara M. (2019). Effects of knocking out three anthocyanin modification genes on the blue pigmentation of gentian flowers. Scientific Reports, 9, 15831.
+ Open protocol
+ Expand
3

Comprehensive Genetic Profiling for Cancer Risk

Check if the same lab product or an alternative is used in the 5 most similar protocols
Both MGPT and TP53 gene-specific tests were performed from DNA isolated from whole blood or saliva samples. NGS analysis (Illumina, San Diego, CA) was performed in all coding domains plus at least five bases into the 5′ and 3′ ends of the introns and untranslated regions (5′UTR and 3′UTR) for all cancer susceptibility genes. EPCAM and GREM1 were only analyzed for gross deletions and duplications, if included on the panel. Depending on the panel ordered by the clinician, 5–49 genes, including TP53, were analyzed. Sanger sequencing was performed for any region with insufficient depth of coverage (<10X), for verification of all variants (other than known benign variants), and for those with decreased mutant to wild-type allele ratios. A targeted chromosomal microarray and/or MLPA was used for the detection of gross deletions and duplications.
A five-tier classification schema—pathogenic; variant, likely pathogenic; variant of unknown significance; variant, likely benign; and benign—was used to classify variants.29 (link)
Weitzel J.N., Chao E.C., Nehoray B., Van Tongeren L.R., LaDuca H., Blazer K.R., Slavin T., Pesaran T., Rybak C., Solomon I., Niell-Swiller M., Dolinsky J.S., Castillo D., Elliott A., Gau C.L., Speare V, & Jasperson K. (2017). Somatic TP53 variants frequently confound germline testing results. Genetics in medicine : official journal of the American College of Medical Genetics, 20(8), 809-816.
+ Open protocol
+ Expand
4

NGS-based Pre-S2 Mutant Detection in HBV-related HCC

Cited 2 times
Check if the same lab product or an alternative is used in the 5 most similar protocols
Pre-S2 mutant in the blood of HBV-related HCC patients was detected with a next-generation sequencing (NGS)-based method as described [25 (link)]. Briefly, the HBV pre-S gene (composed of the pre-S1 and pre-S2 gene segments) was amplified from plasma DNA by polymerase chain reaction, followed by NGS analysis (Illumina, San Diego, CA, USA), to determine the percentage of wild-type and three mutant forms of the pre-S gene (including pre-S1, pre-S2, and pre-S1 + pre-S2 deletions). The presence of the deletion spanning the pre-S2 gene segment was defined as the percentage of either pre-S2 or pre-S1 + pre-S2 deletion above a cut-off of 4.643%. This cut-off percentage has been validated to provide highly accurate detection of pre-S gene deletions in the NGS-based pre-S genotyping analysis for the prediction of HCC recurrence [22 (link),25 (link)]. On the basis of the presence and absence of the deletion spanning the pre-S2 gene segment in blood, patients were classified into pre-S2 mutant-positive and -negative groups, respectively. The pre-S genotyping results of the patients enrolled in this study are summarized in Table S1.
Jeng L.B., Li T.C., Hsu S.C., Chan W.L, & Teng C.F. (2021). Association of Low Serum Albumin Level with Higher Hepatocellular Carcinoma Recurrence in Patients with Hepatitis B Virus Pre-S2 Mutant after Curative Surgical Resection. Journal of Clinical Medicine, 10(18), 4187.
+ 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?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!