Ampli1™ WGA Kit

Balanced, robust whole genome amplification from single cells

The Ampli1™ Whole Genome Amplification (WGA) kit has been developed and optimized for balanced and complete amplification of the total DNA content of a single cell. The output of the Ampli1™ WGA protocol is a well-balanced library of approximately 19 million fragments representing the entire genome.  This DNA library is ideally suited for downstream analysis of both SNPs and CNV in single cells, due to its low rate of preferential amplification.

Single tube protocol ideal for all sample types

The Ampli1™ WGA Kit is designed to provide optimal whole genome amplification—not only from samples containing DNA from a few cells, but from DNA obtained from one single cell. Input DNA may be derived from fresh, fixed, and/or stained cells.

Following cell lysis, DNA is digested with a restriction enzyme and adaptors are ligated onto the DNA fragments. Amplification, performed in the same tube, is mediated by a single highly specific PCR primer for all 19 million fragments.

Reliable, Reproducible, Balanced Single Cell Amplification

• Single-tube, no-precipitation protocol minimizes template loss
• Single, highly specific primer-mediated PCR ensures balanced amplification of both alleles
• Robust protocol generally produces about 2 micrograms dsDNA and 5 micrograms of ssDNA.

• Sanger Sequencing
• Next generation sequencing
• Microsatellite analysis
• Copy number variation (CNV) analysis by RT-PCR or aCGH

Ampli1™ QC Kit 

The Ampli1™ QC Kit provides a useful quality control check of the WGA procedure by utilizing a PCR-based assay to establish DNA integrity. By testing for the presence of one short and three long DNA fragments in the WGA library, the quality of the DNA as starting material for downstream analyses can be assured. Cells with good quality DNA typically produce 3 or 4 PCR bands, while fixation of cells or cells with degraded DNA will show fewer QC bands. It has been proved that the number of the bands revealed is useful to defi ne a “Genome Integrity Index” for predicting success of various downstream analytical methods and for assessing the quality of the starting DNA.

Ampli1™ LowPass Kit

Ampli1™ LowPass kit exploits the deterministic nature of Ampli1™ WGA, to provide a streamlined, single-reaction protocol to generate up to 48 barcoded libraries compatible with IonTorrent PGM™ and S5™ platforms.

Ampli1™ LowPass Kit implements a robust and reproducible method for reduced-representation sequencing in order to assess genome-wide copy-number alterations.

Method performance has been extensively validated by analyzing the Copy Number profiles of single CTCs and WBCs from cancer patients (see figure below for representative data). 

Low-pass Whole Genome Profile (chr 1-22) of single CTC (upper panel) and WBC (lower panel) isolated with DEPArray Technology from a patient with Lung Adenocarcinoma. Ploidy values are indicated in the y-axis; in the x-axis the alternation of different chromosomes are plotted with different colors. Copy Number Alterations in the CTC are indicated in red and blue.

Ampli1™ LowPass Kit Features:

• Accurate characterization of CNA profiles of multiple single tumor cells per single run

• Fast results (6h turnaround time for library preparation)

• Affordable cost for massively parallel single-cell analysis such as multiple tumor cells or CTCs

Ampli1™ ReAmp/ds Kit 

Reamplify the Ampli1™ WGA product obtained from single cells, 

or from a batch of cells, in a reliable and reproducible way. Reamplification will provide additional WGA-amplified DNA from the same cell. For downstream genetic analysis, you may use the Ampli1™ Reamplification product in the same manner as Ampli1™ WGA product.

Using the same kit with a different protocol (supplied) you may also convert ssDNA molecules into dsDNA molecules both in Ampli1™ WGA products and in Ampli1™ reamplification products in order to increase the total dsDNA content. This procedure is recommended for accurate DNA quantitation, high-throughput high dimensional downstream analysis, and NGS applications to ensure high sequencing uniformity.

Ampli1™ Sequencing Kits

Silicon Biosystems has developed Sanger sequencing reagent sets for highly sensitive and specific PCR-based amplification of commonly-examined target genes from DNA libraries obtained with the Ampli1™ WGA kit.

• PIK3CA kit— includes reagents for evaluation of the most common mutations in exons 9 and 20 of the PIK3CA gene.
• EGFR kit—includes reagents for evaluation of the most common mutations in exons 18, 19, 20, and 21 of the EGFR gene.
• KRAS kit—includes reagents for evaluation of somatic mutations in codons 12 and 13 of exon 2 in the KRAS gene.
• BRAF kit—includes reagents for evaluation of V600 mutations of the BRAF gene.

If your research includes analysis of other genes, please contact us for information on obtaining custom primers compatible with the Ampli1™ WGA generated DNA libraries.

To download Material Safety Data Sheets (MSDS), please click here.

The Ampli1™ WGA Kit is for Research Use Only. Not for use in diagnostic procedures. Ampli1™ WGA Kits are protected by U.S. patent 6,673,541 and corresponding patent claims outside the United States.