SoftGenetics - Software PowerTools for Genetic Analysis


Trisomy Analysis

GeneMarker® software accepts all major CE output files, including: ABI-PRISM® (*.FSA,*AB1,*.ABI), SCF, MegaBace® (*.RSD,*.ESD), Beckman-Coulter files (*.CEQ) for aneuploidy/trisomy analysis. Aneuploidy occurs from non-disjunction during meiosis I or meiosis II during gametogenesis and results in an abnormal number of chromosomes in the gametes; resulting in trisomy or monosomy. Most common forms of trisomy involve trisomy of chromosome 21 (Down Syndrome), others include: trisomy 18 (Edwards Syndrome), trisomy 13 (Patau Syndrome). Aneuploidy of sex chromosomes may result in extra X chromosome(s); Klinefelter syndrome (men),Triple X syndrome (women); while monosomy X gives rise to women with Turner syndrome. GeneMarker software is a biologist-friendly alternative to GeneMapper®, Genotyper™, GeneScan®, CEQ™ Fragment Analysis Software. GeneMarker software provides accurate size and allele calls with a linked trisomy application for complete data analysis from QF-PCR results Aneufast, CyberGene®, Devyser®, Elucigene QST*R® kits or custom-chemistries. The program's Customized report follows Best Practice Guidelines. ChimerMarker software automates MCC testing prior to aneuploidy or trisomy analysis.

Reporting options include:

  1. Use of peak height or peak area ratios
  2. Identification of peak ratios that are consistent with designated triallelic (trisomy) range
  3. Identification of peak ratios that are consistent with intermediate (inconclusive) ranges
  4. Linear correction of data to resolve PCR bias
  5. Display of ratio plots for population or individual sample<
  6. Conclusion/Authorization table
  7. Header automatically populated with info on sample ID, analysis parameters and analyst name/affiliation


Patient Report: Highlighted samples are consistent with user specified triallelic range and samples marked with a ‘?' are consistent with user specified intermediate (inconclusive) ranges.


GeneMarker software has been designed to accurately detect trisomies using short tandem repeat markers derived from PCR DNA fragments.Trisomy individuals will either show three fragments of equal intensity or two fragments at a 2:1 or 1:2 ratio.


Ratio 1:2


Ratio 2:1


Ratio 1:1:1


The GeneMarker software Trisomy tool offers two answers to the 2:1 trisomy detection question.


First, in the Ratio Plot in the bottom left corner of the analysis window, the peak intensity ratio of all markers are plotted. A linear regression line is run through the center of the data points and is used to correct for intensity drop due to fragment size increase. The Ratio Plot can be viewed as a linear regression plot or corrected for slope. This method of data correction aids in the detection of 2:1 ratio trisomies.


Report option provides display of ratio plots corrected for slope

The second aid in trisomy determination is the trisomy score. First a t‐value is determined and defined as the difference between the sample and the expected value divided by the standard deviation. There are two possible t‐values for every marker, one is the tvalue for heterozygote and the second is for a trisomy. T‐Score is the ratio of the heterozygote t-value divided by the trisomy t‐value. Therefore, as the T‐Score increases, the confidence of the trisomy call also increases. A T‐Score greater than 5.0 is a confident trisomy call. A T-Score less than 0.3 indicates a confident heterozygous call. Click here to Download Trisomy Application Note discussing linear regression and t-Score calculation/interpretation.


Download Trisomy Application Note (PDF)
Download Aneuploidy Analysis Application Note (PDF)


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SoftGenetics - Software PowerTools for Genetic Analysis

SoftGenetics - Software PowerTools for Genetic Analysis


















SoftGenetics - Software PowerTools for Genetic Analysis





SoftGenetics - Software PowerTools for Genetic Analysis

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