The Haplotyping problem: an overview of computational models and solutions

  • Authors:

  • Paola Bonizzoni;Gianluca Della Vedova;Riccardo Dondi;Jing Li

  • Affiliations:

  • DISCo, via Bicocca degli Areimboldi 8, University of Milano-Bicocca, 20135 - Milano, Italy;Dip. Statistica, via Bicocca degli Arcimboldi 8, University of Milano-Bicocca, 20135 - Milano, Italy;DISCo, via Bicocca degli Arcimboldi 8, University of Milano-Bicocca, 20135 - Milano, Italy;Department of Computer Science, University of California at Riverside, Riverside CA

  • Venue:
  • Journal of Computer Science and Technology
  • Year:
  • 2003

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Abstract

The investigation of genetic differences among humans has given evidence that mutations in DNA sequences are responsible for some genetic diseases. The most common mutation is the one that involves only a single nucleotide of the DNA sequence, which is called a single nucleotide polymorphism (SNP). As a consequence, computing a complete map of all SNPs occurring in the human populations is one of the primary goals of recent studies in human genomics. The construction of such a map requires to determine the DNA sequences that from all chromosomes. In diploid organisms like humans, each chromosome consists of two sequences called haplotypes. Distinguishing the information contained in both haplotypes when analyzing chromosome sequences poses several new computational issues which collectively form a new emerging topic of Computational Biology known as Haplotyping.This paper is a comprehensive study of some new combinatorial approaches proposed in this research area and it mainly focuses on the formulations and algorithmic solutions of some basic biological problems. Three statistical approaches are briefly discussed at the end of the paper.