Algorithm for Haplotype Construction of Single Nucleotide Polymorphism

Summary The Haplotyper software program utilizes a novel algorithm called Partition-Ligation to reconstruct individual haplotype phase information from unphased genoptype data. The Partition-Ligation method uses an ingenious Markov chain Monte Carlo approach both to construct the partial haplotypes of each segment and to assemble all the segments together. It has the ability to deal with ambiguous or missing genotypes, it has the ability to handle hundreds or thousands of single nucleotide polymorphisms (SNPs), and it is consistently more accurate and faster than competing algorithms. The software is written in C++ , and is under both copyright and patent protection.

Background Haplotype refers to a set of multiple linked SNPs physically located on a single chromosome. Previous studies have shown that the human genome consists of a group of haplotype "blocks", such that there is very limited diversity of haplotypes within each block that can be captured by a subset of common SNPs. Complete knowledge of haplotype phase based on the SNP genotype will be essential for understanding the "block" structure (also known as the "HapMap") of the human genome.

Applications Determination of haplotype has numerous research and clinical applications. For example:

1. Haplotype-based linkage disequilibrium (LD) analysis is a powerful tool in disease gene identification. It offers significant advantages over SNP-based analysis since it captures the local LD information in the phasing process.

2. Haplotype determination can reduce both the length and the expense of clinical trials by helping to define haplotype signatures, which will associate specific haplotypes with higher disease risk or poorer therapeutic effect.

3. In genetic research, haplotypes can predict the activity, transcriptional regulation, as well as posttranslational modification of a gene more accurately than "single-site" genotypes.

4. In evolutionary biology, haplotypes can be used for cladistic analysis in determining the ancestral founder haplotype, for estimating the age of a disease mutation, and for re-constructing a population history (e.g., a population bottleneck, migration, or recent expansion). For Further Information Please Contact the Director of Business Development Vivian Berlin Email: Telephone: (617) 495-0474

Inventor(s): Liu, Jun S.

Type of Offer: Licensing

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