Application Note

Learn how next-generation sequencing on an Ion PGM™ System can be used to detect aneuploidy in preimplantation embryos, or for genetic analysis of cancer cells.

Introduction to CNV Analysis for Aneuploidy

View the CNV analysis workflow for aneuploidy on the Ion PGM™ System

Informatics Solutions

Empower your data analysis with push-button variant detection and annotation.

The Ion PGM™ System enables aneuploidy assessment for preimplantation genetic research or for quickly assessing large chromosome dupications or deletions in cell characterization, with flexible, user-defined workflows that can be tuned to your required sensitivity and specificity, and multi-plex solutions that can help reduce costs without compromising results.

CNV Aneuploidy Analysis Workflow for the Ion PGM™ System

1 Select
2 Construct
Construct library for RNA-Seq
3 Prepare
Prepare Template for RNA-Seq
4 Run
Run Sequence for RNA Sequencing
5 Analyze
Analyze data for RNA Sequencing

Introduction to CNV Analysis for Aneuploidy

Copy number variation (CNV) analysis is a next-generation sequencing method that can be used to analyze chromosomal aberrations like aneuploidy. Why use Ion PGM next-generation sequencing for preimplantation genetic analysis? Traditional techniques for preimplantation genetic research include karyotyping and microarray analysis. Karyotyping can require more sample material than can be obtained from some specimens, for example, blastomere or trophectoderm stage embryos. In addition, karyotyping methods require chromosomes from metaphase cells. Microarray and comparative genomic hybridization techniques are available, yet take longer to yield results than is available for time-sensitive samples. With next-generation sequencing on the Ion PGM™ System, researchers benefit from a simple, rapid technique that is designed to reliably deliver easy-to-interpret data so you can move on to other research questions. Now you don’t have to be an expert in cytogenetics or molecular genetics techniques to get accurate results.

Select Cell

Ion Torrent™ semiconductor sequencing and Ion Reporter™ Software deliver the power to identify aneuploidies and subchromosomal events as small as 10 megabases (Mb) across all 23 pairs of chromosomes via a simple, rapid, integrated workflow (see workflow figure above). Through the use of whole genome amplification (WGA), gDNA from a small number of cells—even a single cell—can be used in the Ion PGM™ sequencing workflow to enable low-pass sequencing of the entire genome with sufficient coverage for the detection of gross chromosomal and sub-chromosomal aneuploidies. In this application note we describe how researchers can leverage the Ion PGM™ System along with Ion Reporter™ Software to accurately identify aneuploidies in ≤10 hours from DNA sequence data generated from multiplexed analysis of ≥10 samples with low initial input DNA amounts.

The aneuploidy detection solution described here leverages library construction and template preparation solutions that ensure a robust workflow with ease of use for routine applications. For example, the automatable enzymatic shearing protocol of the Ion Xpress™ Plus gDNA Fragment Library Kit removes the need for a physical shearing device to save time and cost while delivering superior coverage uniformity for low-pass whole-genome sequencing data. Workflow simplicity and automated template preparation can be accomplished with either the Ion OneTouch™ 2 System or the Ion Chef™ System*† . The Ion Chef™ System incorporates automated chip loading to further reduce sources of variability and ensure reproducible sequencing results.

See our application note for further details.

CNV Analysis for Aneuploidy Screening Informatics Solutions

Torrent Suite™ Software coordinates all the experiment planning and data processing steps necessary to complete your targeted sequencing workflow. New product templates enable users to plan targeted runs simply and quickly. Raw data are processed on the Ion PGM™ Sequencer and transferred to the PGM™ Torrent Server for base calling and variant calling. This entire process takes just a few hours, and further analysis can be performed using Ion Reporter™ Software, or third-party software solutions such as the Ingenuity® Variant Analysis™ Knowledge Module for Ion Reporter™ Software.

Ion Reporter™ Software comprises a suite of bioinformatics tools that streamline and simplify analysis of semiconductor sequencing data. Data generated on the Ion PGM™ System are automatically uploaded from the Torrent Browser to the hosted Ion Reporter™ Software environment for read mapping, annotation and reporting of common and rare variants, and multi-sample analysis—all with version control and audit traceability.

For Research Use Only. Not for use in diagnostic procedures.