Detection by low-pass whole-genome sequencing with Ion Reporter™ Software

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Preimplantation aneuploidy detection

Copy number variations (CNVs) represent a class of variation in which segments of the genome have been duplicated (gains) or deleted (losses). While smaller inherited de novo CNVs (up to ~10 Mb) have been associated with many disease conditions, including cancer and inherited genetic disorders, larger chromosomal imbalances from 10s of Megabases up to whole chromosomes are commonly associated with human reproductive viability.  These large genomic imbalances can now be detected using Low-Pass Whole Genome Sequencing and Ion Reporter Software using DNA from just a single cell.

Most normal human somatic cells contain a diploid (2N) set of autosomes (non-sex chromosomes) and a pair of sex chromosomes. Cells that do not contain an exact diploid set are called aneuploid (Figure 1). Common types of aneuploidy that survive to term are monosomy (the loss of one chromosome) of the X chromosome in females—Turner syndrome (45, X)—and some trisomies, three copies of a given chromosome in a diploid cell. Live births are possible with trisomies of chromosomes 13 (Patau syndrome), 18 (Edwards syndrome), and 21 (Down syndrome), as with the presence of extra sex chromosomes, such as in Klinefelter syndrome (47, XXY) and Triplo-X syndrome (47, XXX).

Detect duplications or deletions of entire chromosomes within a day, using Ion Reporter™ Software, at significantly lower cost than karyotyping.

Figure 1. Monosomy of chromosome 13 and trisomy
of chromosome 14 and 15, as shown in
Ion Reporter™ Software.

Rapid and simple workflow for aneuploidy detection


  1. Perform low-pass whole-genome sequencing
  2. Analyze with aneuploidy workflow
  3. Visualize aneuploidy using customized IGV Karyotype View
  4. Create your interpretive report

Low-pass whole-genome aneuploidy workflow features:

  • Uses as little as a single cell’s DNA as input, followed by whole-genome amplification that is robust at as low as 0.01x coverage
  • Compares samples are to a built-in bioinformatics baseline normal control. Detects gains or losses of whole chromosomes (aneuploidy) and subchromosomal regions (≥10 Mb)
  • Delivers DNA ploidy results using low-pass coverage. Achieved 100% sensitivity and 100% specificity relative to microarray-based truth data on same samples, as described in the aneuploidy application note.

Read the application note


1 Run
Ion Reporter Software

Ion Proton™ & Ion PGM™ Sequencers

2 Analyze
Proton or PGM

Ion Reporter™ Software

3 Visualize

Broad's IGV

Broad's IGV

4 Report

Interpretive Report

*Renewal includes access to software updates

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