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The Use of Sequence Analysis for Homozygote and Heterozygote Base Variation Discovery

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Molecular Genetic Epidemiology — A Laboratory Perspective

Part of the book series: Principles and Practice ((PRINCIPLES))

Abstract

The fluorescent version of Sanger dideoxy-sequencing has been in use for 15 years for gene discovery and comparative sequencing projects. Only a decade ago, detection of single-base changes, additions or deletions within genes of a given species were only possible provided that the organism was haploid or that the change occurred in the homozygous state. High background and the presence of significant peak height variation within bases of a given sequence read made it difficult to recognize when a base substitution occurred in the heterozygous state. In addition, the lack of efficient software to search for and call hetero- and homozygote single nucleotide polymorphisms (SNPs) provided a major obstacle to scaling up sequencing-based mutation/polymorphism discovery. However, with the advent of new sequencing chemistries, more accurate sequencing enzymes and automation-amenable SNP-scoring software, it is now possible to detect homozygous or heterozygous sequence variations with a high degree of sensitivity and accuracy. Thus, the combination of improved “wet lab” technology and sophisticated bioinformatics tools now allows for a more rigorous quantitative means of determining heterozygous and homozygous sequence polymorphisms.

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  1. Genome Therapeutics Corporation, 100 Beaver Street, Waltham, Massachusetts, 02454, USA

    Hans-Ulrich Thomann, Michael FitzGerald, Heidi Giese & Kristen Wall

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  1. Hans-Ulrich Thomann
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  2. Michael FitzGerald
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  1. Human Genetics Research Division Duthie Building (MP 808), Southampton General Hospital, Tremona Road, Southampton, SO 16 6YD, UK

    Ian N. M. Day

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© 2002 Springer-Verlag Berlin Heidelberg

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Thomann, HU., FitzGerald, M., Giese, H., Wall, K. (2002). The Use of Sequence Analysis for Homozygote and Heterozygote Base Variation Discovery. In: Day, I.N.M. (eds) Molecular Genetic Epidemiology — A Laboratory Perspective. Principles and Practice. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-56207-5_8

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  • DOI: https://doi.org/10.1007/978-3-642-56207-5_8

  • Publisher Name: Springer, Berlin, Heidelberg

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