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 research of 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 >10 Mb up to whole chromosomes are commonly associated with human reproductive viability.  These large genomic imbalances can now be detected by Low-Pass Whole Genome Sequencing using Ion ReproSeq PGS kits 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 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. Other chromosome imbalances include 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. Using Ion Reporter 5.4 or later, obtain enhanced interpretation of results including mosaicism detection, gender masking, and improved data plotting. 

Rapid and simple workflow for aneuploidy detection


  1. Perform low-pass whole-genome sequencing using Ion ReproSeq PGS kits for the Ion S5 System or Ion PGM System
  2. Analyze with aneuploidy workflow
  3. Visualize aneuploidy using customized Ion Reporter Genomic Viewer (IRGV) Karyotype View
  4. Create your interpretive report

Low-pass whole-genome aneuploidy workflow features:

  • Compares samples to a built-in bioinformatics baseline normal control. Detects gains or losses of whole chromosomes (aneuploidy) and subchromosomal regions
  • Delivers DNA ploidy results using low-pass coverage. Demonstrated 100% sensitivity and 100% specificity relative to microarray-based data on same samples, as described in the aneuploidy application note.

Read the application note


1 Run
Ion Reporter Software

Ion S5, Ion Proton & Ion PGM sequencers

2 Analyze
Proton or PGM

Ion Reporter Software

3 Visualize

Broad's IGV

Built-in IRGV browser

4 Report

Interpretive report

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