Haplotype Analysis and Automated Phase Assignment Pedigrees from Familial DNA Fragment Data

Familial DNA fragment data is used for haplotype analysis in areas such as genetic disorder research and preimplantation studies. Importing ABI®PRISM, Beckman-Coulter® or MegaBASE® CE data to into GeneMarker software provides user friendly, accurate genotyping with a linked Haplotype Analysis application (avoids potential errors from data transfer from one software to another), combining allele call information from multiple PCR reactions for each individual (an alternative to Cyrillic©). Pedigrees are automatically drawn and allele calls of children and parents are used to assign a first-orderapproximation phase. Whenever the alleles are informative for phase assignment a pattern/color bar is assigned to indicate most probable phase, flags allele conflicts, detects potential uniparental disomy, allows analyst to review, edit for cross-over , save and print pedigrees.

Features of GeneMarker® Software's Haplotype Analysis Application
1. Follows Bennett et al. nomenclature for pedigrees
2. X-linked and autosomal pedigree formats based on parent/child(ren) allele calls
3. Edit family and individual information
4. Displays markers, allele calls, personal information in pedigree
5. Control ordering of markers in pedigree by customizing panels
6. Automatically makes first order phase assignment
7. Edit capability for reassigning phase or edit crossover
8. Save pedigree and re-open for adding data and editing
9. Allele conflicts flagged; detects potential uniparental disomy

Results (figure 1) X-Linked and Autosomal Linkage Examples

X-linked Example:
Personal information Phase assignment Carrier status Standard symbols for male, female, Miscarriage (SAB)
(left)

Autosomal linkage Example:
Phase assignment Cross-over in child 1 Standard symbols for male, female, deceased, pregnancy
(right)

Download Haplotype Analysis Application Note (PDF)

Application Notes

  • Complete Genotype with Merge Project Tool (PDF)
  • Automatic Phase Determination of Disease Haplotype from Family Genotyping Data (PDF)
  • Kinship Analysis and Duplicate Sample Identification of Animal Microsatellite Markers with GeneMarker® Software (PDF)
  • GeneMarker® Software for Multiplex Ligation-dependent Probe Amplification (MLPA™) (PDF)
  • Methylation Specific Multiplex Ligation-dependent Probe Amplification (MS-MLPA®) with GeneMarker® Software (PDF)
  • GeneMarker® Software for Trisomy Analysis (PDF)
  • Loss of Heterozygosity Detection with GeneMarker® Software (PDF)
  • Software for Amplified Fragment Length Polymorphism (AFLP®) (PDF)
  • GeneMarker® Software for Terminal-Restriction Fragment Length Polymorphism (T-RFLP) Data Analysis (PDF)
  • Microsatellite Analysis with Linked Pedigree Tool (PDF)
  • GeneMarker® software for SNPlex™analysis (PDF)
  • GeneMarker® Software for SNPWave™Analysis (PDF)
  • Clustering Algorithms for Genetic Analysis with GeneMarker® SoftwareNote (PDF)
  • Analysis of MegaBACE™ Data with GeneMarker® Software Application Note (PDF)
  • Capillary Tilling Application Note (PDF

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