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INTRODUCTION

A chromosome is an organized structure of DNA and protein that has many genes, polymorphisms and regulatory elements distributed along its entire length. A ‘normal’ somatic human cell contains 23 pairs of chromosomes, and two sex chromosomes (X,Y) half of which are inherited from the mother and half from the father. At conception chromosomes are ‘constructed’ by an initial process called meiosis when discrete segments from each chromosome pair dissociate and randomly recombine to produce new chromosome structures for subsequent pairing and inheritance. The chromosomal segments between sites of recombination are defined as haplotypes. (Simons, Malcom 1989)

A gene or group of genes located at a specific position (locus) on a chromosome is called an allele. A haplotype is a grouping of alleles which express specific genetic functions. Chromosomes are a paired series of contiguous haplotypes. The distribution of alleles between haplotype pairs is called haplotypic phase. Haplotypic phase is determined by haplotyping which is the identification, by DNAsequencing, of all the elements and their distribution between haplotypes.

Why is haplotyping important?

Haplotypic phase ultimately defines the biological and physiological functions as well as observable characteristics, such as traits of an individual. For example, a certain haplotypic phase could indicate a ‘healthy’ or ‘normal’status of an individual whereas a slightly varied haplotypic phase could confer risk of developing disease. The ability to accurately map the haplotypic phase will have important implications for the general clinical practice of genomics in the fields of disease risk analysis, pharmacogenomics, personalized medicine for life style conditions and transplantation. For example, haplotyping of donor and recipient in a transplant setting will reduce the chance of the tissue being rejected and the need for long-term immunosuppressive therapy.

Haplotyping is the only technique that can determine definitive haplotypes

To date most human genome ‘maps’, including the international Human Genome (HapMap) Project , are comprehensive inventories of genes, mutations, etc but are silent on definitive haplotypes and hence haplotypic phase. These maps have been compiled by analyzing (sequencing) DNA material (diploid DNA) sourced from complex mixtures of chromosomal fragments and processing the sequence data using bioinformatics algorithms. The bioinformatics process attempts to determine haplotypic phase by re-assembling each fragment into its originating contiguous haplotype/chromosome structure. At best diploid DNA/bioinformatics analysis can only ever approximate and ‘infer’ haplotypes and haplotypic phase which does not provide the order of accuracy required for clinical practice.

Haplomics’ IP embodies methods for the determination of definitive haplotypes.

Recent publications and comments

From leading researchers on the subject of haplotypic phase —

Professor Stephen Quake at Stanford University, in a paper published in Nature Biotechnology in December 2010, reported ‘deterministic phasing’ or direct haplotyping of human genomes by sequencing material obtained from isolated single chromosomes.
“...In the context of personalized genomics and medicine, the approaches used in the HapMap project have limited applicability, as materials from family members are not always available and computational approaches using statistical models have inherent statistical uncertainty and are limited to regions with strong linkage disequilibrium.”
http://www.nature.com/nbt/journal/v29/n1/abs/nbt.1739.html

Dr J. Craig Venter, the internationally renowned geneticist, recently stated:
“...the genome revolution is only just beginning. Improving data quality is crucial, because if a human genome cannot be independently assembled then the sequence data cannot be sorted into the two sets of parental chromosomes, or haplotypes. This process — haplotype phasing — will become one of the most useful tools in genomic medicine. Establishing the complete set of genetic information that we received from each parent is crucial to understanding the links between heritability, gene function, regulatory sequences and our predisposition to disease. Fortunately there are some exciting developments on the way that could help, such as new methods from Pacific Biosciences in Menlo Park, California, and Life Technologies that can produce sequence information from a single DNA strand. This approach promises sequence reads, in the range of thousands of base pairs that will result in substantially higher-quality genome sequence data.”

MIT’s Technology Magazine TR10, May/June 2011 – ‘Separating Chromosomes - A more precise way to read DNA will change how we treat disease’
(http://www.technologyreview.com/biomedicine/37204/)

Archon X Prize for Genomics requires that entries from competitors deal with the 'phase' problem as follows —
The "Phase" problem": Whole genome sequencing is required to know which variations or mutations are on which one of the two chromosomes. Variations on the same chromosome are likely to have different functional meaning than if they are on opposite chromosomes. Sequencing a selective part of the genome does not provide full information about this "phase" issue.
http://genomics.xprize.org/archon-x-prize-for-genomics/why-whole-genome-sequencing

10 Technologies Poised to Transform our World,
No 2 - Separating Chromosomes
Innovation News Daily Staff, 21 April 2011
Great strides have been made since the first genome was sequenced, but there are still quite a few mysteries facing researchers. Stephen Quake, a biophysicist at Stanford University, has engineered a way of obtaining that information.
Chromosomes come in pairs; one copy is inherited from your mother and the other from your father. Right now, the standard techniques blend genetic data from the two chromosomes to yield a single sequence. Quake’s alternative is to physically separate chromosomes before genomic analysis. Cells are piped into a microfluidic chip; when Quake spots one that’s preparing to divide (a stage at which the chromosomes are easier to manipulate), he traps the cell in a chamber and bursts its membrane, causing the chromosomes to spill out. Each will end up in a smaller chamber by itself, and there it can undergo normal analysis.
This technology will make it easier to identify the variations between chromosomes, and could have a huge impact on fundamental genomic research and personalized medicine.
http://www.innovationnewsdaily.com/mit-transform-world-tech-1920/2

Dr Malcolm Simons, Unravelling the haplotype could reveal heretofore unknown links between genes and diseases.
http://www.lifescientist.com.au/article/318984/feature_untying_haplomics_knot