GeneSpring Analysis Platform
GeneSpring GT Analytical Tool
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Note: This is a review of the published article listed below. All information, quotes, figures, methods, and findings mentioned in this review are from that article, and are the property of its authors and/or the publication in which the article originally appeared.
As microarray technology has evolved and scientists attempt to characterize the genetic effects on phenotypes, cutting edge analytical platforms offer the tools necessary to process and evaluate meaningful biological patterns. In particular, genotyping tools make it possible to identify the genetic causes of a diverse range of human diseases with varying modes of inheritance. With the ability to simultaneously analyze hundreds of millions of variations measurements, Agilent’s GeneSpring GT enables you to quickly identify genotype-phenotype relationships using using a comprehensive set of linkage and association algorithms. Using GeneSpring GT, Antony Shrimpton and a collaborative group of researchers (2004) identified a HOX gene mutation in a family with isolated congenital vertical talus and Charcot-Marie-Tooth disease. Due to reduced call rates from genomic DNA damage the group was unable to use their standard Merlin software for nonparametric linkage analysis. However, the researchers were able to perform several methods of whole-genome parametric linkage analysis in GeneSpring GT (Varia [Silicon Genetics]), including one based on individual markers and one based on a haplotype map deduced from the data. Successful analysis with GeneSpring GT enabled the researchers to define a 7-Mb critical region on chromosome 2q31, which led to candidate-gene sequencing of six HOX genes and detection of a single missense mutation in the HOXD10 gene.
Figure 1. Whole-genome haplotype–based parametric linkage map at LOD > 1.88.
Figure 2. Analytical options with GeneSpring GT.
A, Pedigree showing individuals from whom DNA was isolated (bars below symbol). Individuals marked with an asterisk (*) were included in the original 10K Array linkage study. The bars represent the 2q31 chromosomal section between markers D2S124 and D2S1391. B, Critical-region haplotypes in affected individuals, in more detail. All 16 affected individuals—but no unaffected individuals—contain the same chromosomal section distal to D2S1267 and proximal to D2S2978 (boxed). V=CVT; M=CMT; B=CVT and CMT; N=unaffected. An asterisk (*) indicates a presumed 5–6 reversion mutation.
Original Research Paper:
Title: A HOX gene mutation in a family with isolated congenital vertical talus and Charcot-Marie-Tooth disease.
Authors: Shrimpton AE, Levinsohn EM, Yozawitz JM, Packard DS Jr, Cady RB, Middleton FA, Persico AM, Hootnick DR.
Journal: Am J Hum Genet. 2004 Jul;75(1):92-6.
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GeneSpring GT: a desktop analysis workbench for analyzing high-volume, high-density genotyping data.
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For research use only and not for use in diagnostic procedures.