Dna amplicon

Manufactured by Illumina

DNA Amplicon is a lab equipment product designed for the amplification of DNA segments. It utilizes a process called Polymerase Chain Reaction (PCR) to generate multiple copies of a specific DNA sequence from a small initial amount. The core function of DNA Amplicon is to facilitate the exponential replication of DNA fragments for downstream analysis and applications.

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Lab products found in correlation

Variant interpreter, by Illumina (1 mentions) Basespace, by Illumina (1 mentions) Ampliseq library plus, by Illumina (1 mentions) Quick dna miniprep plus kit, by Zymo Research (1 mentions) Dna rna shield saliva collection kit, by Zymo Research (1 mentions)

2 protocols using dna amplicon

Germline Variant Analysis for Osteogenesis Imperfecta

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Data (VCF files) were obtained using the DNA Amplicon (Illumina) module and analyzed by Evai (Engenome, https://evai.engenome.com/#app/analysis/11919), Variant Interpreter (Illumina, https://variantinterpreter.informatics.illumina.com/registry/cases), and Varsome Clinical (https://varsome.com). Briefly, the DNA Amplicon module was used to align the reads to the reference genome (hg19) and then to run to search for germline variants in the targeted regions. Variant classification is based on the current ACMG standards and guidelines. All variants were reviewed using VARSOME (https://varsome.com), the Osteogenesis Imperfecta Variant Database (oi.gene.le.ac.uk), dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/), and Clinvar (https://www.ncbi.nlm.nih.gov/clinvar/).
The software VarSeq 2.3.0 (Golden Helix) was also used to confirm PVs detected in this study.

Paduano F., Fischetto R., Moretti B., De Vito D, & Tatullo M. (2023). Expanding the genetic and clinical spectrum of osteogenesis imperfecta: identification of novel rare pathogenic variants in type I collagen-encoding genes. Frontiers in Endocrinology, 14, 1254695.

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APOE Genotyping from Saliva

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For APOE genotyping, saliva was collected from participants during the in-person neuropsychological assessment, and DNA was isolated using DNA/RNA Shield Saliva Collection Kits and Quick-DNA miniprep plus kit (Zymo Research Corporation) according to the manufacturer’s suggestions. DNA libraries for sequencing were generated using AmpliSeq^TM custom DNA panel and AmpliSeq^TM Library Plus for Illumina. Multiplexed libraries were sequenced on an Illumina MiSeq paired-end 250 base Nano run. DNA Amplicon (version 2.1.1; Illumina BaseSpace application) was used for variant calling using the BWA aligner to the custom DNA Amplicon manifest.

Sheffler J.L., Arjmandi B., Quinn J., Hajcak G., Vied C., Akhavan N, & Naar S. (2022). Feasibility of an MI-CBT ketogenic adherence program for older adults with mild cognitive impairment. Pilot and Feasibility Studies, 8, 16.

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