Join HT in funding a breakthrough in clinical genomics

Haploid Technologies (HT) has developed a groundbreaking new technology that enables precise assignment of phase across multiple genetic mutations — a critical advancement in genomic analysis

This unique innovation has the potential to transform clinical medicine by improving diagnostic accuracy, guiding targeted therapies, and deepening our understanding of complex genetic disorders.

The method can be used in one of two ways. In cases where alleles have been well established and sequenced, they can be used to determine haplotypes such as the HLA system. In cases where alleles have been defined by linkage disequilibrium between single-nucleotide polymorphisms (SNPs), by next-generation sequencing or by 3rd generation sequencing, it can be used to determine both alleles present in an individual by the sequencing of both chromosomes separately, with theoretically 100% accuracy.

Technical synopsis in brief

In the absence of reliable definitive techniques for assigning haplotypes outside single-family studies, we at Haploid Technologies (HT) believe the only method for assigning haplotypes over megabases of DNA with certainty, and without relying on statistical probability, involves the separation of the two homologous chromosomes from the 23 pairs of chromosomes within a single cell.

To achieve that aim, we have developed a nanotechnologically designed cartridge which traps and then lyses a single metaphase cell, which releases the 46 (23 pairs) of chromosomes as singular entities, two of which are labelled (chromosomes of interest). By selecting appropriate polymerase chain reaction (PCR) primers, the gene of interest can be haplotyped by sequencing (single chromosome sequencing). This method allows for haplotypes of megabase pair length.

This has not been achieved before, and such a technique would be applicable to any gene(s) and any disease and therefore of profound importance in the era of molecular and personalised medicine. We believe our technology will revolutionise both the research and treatment of a range of human diseases, including cancers.

The cartridge and methodology are the subject of granted and patent rights in various jurisdictions handled by HT’s patent advisors. Full details of the technology are available on request to parties interested in funding this project further, under a confidentiality agreement.

Current methods of establishing the genetic phase

The conventional method for phase (haplotypes) is by family segregation studies. Providing an individual proband’s parents are different for the gene sequences under study, then a phase can be established, which can be two single-nucleotide polymorphisms on one allele, or one on each of the inherited alleles.

In the absence of family studies, determining haplotypes becomes an exercise in probability, based on linkage disequilibrium (LD), which makes the assumption that because the SNPs are in positive LD, they must be on the same allele. This does not apply, however, to all racial groups or to disease patients.

The role of next-generation sequencing

Next-generation sequencing (NGS)

NGS can be divided into two phases of development, short-read sequencing and long-range sequencing (LRS), as developed by Oxford Nanopore and Pac-Bio. Both approaches to LRS have the potential to provide haplotyping over long DNA distances, but at the present time are restricted to approximately 75kb length of DNA or RNA (1,2) and rely on heterozygote differences between common areas of overlapping sequences. If this is a newly discovered sequence, it could lead to errors in haplotyping. No such problems exist with single chromosome sequencing, and there is no limit to the length of DNA which can be tiled.

Below are four examples of where we feel HT’s technology will be of particular use.

Four examples of situations where SCS can be used to assign a phase to alleles or polymorphisms:

Bone marrow transplantation

Immediate application is in the field of bone marrow transplantation. This is an area of clinical medicine where HLA haplotype matching has been shown to have a distinct effect in terms of patient survival using unrelated donors and where alleles are fully defined. The haplotypes which are matched are called HLA and are found on a 3-megabase stretch of DNA on the short arm of human chromosome 6. Those donor/recipient pairs who are haplotype matched have been shown to have significantly lower life-threatening graft versus host disease (GVHD) than those pairs which are matched at individual HLA loci, but not haplotype matched.

Our customer market surveys indicate a keen interest in this technology amongst both clinicians and laboratory-based scientists involved in bone marrow transplantation.

Immunotherapy

The 2018 Nobel Prize for Medicine was awarded to James Allison and Tasuku Honjo “For their discovery of cancer therapy by inhibition of negative immune regulation”.

The main ones to be considered are PD-1 and CTLA-4, and their respective ligands, PDL-1 and PDL-2, and B7.1 and B7.2. All have been shown to be polymorphic. SCS has a role in assisting in the definition of alleles coding for these molecules.

CYP genes

The CYP genes (previously called P450 genes) are a family of genes which code for detoxifying enzymes involved in metabolism, which number 57 genes in the human, representing 18 families and 44 sub-families.

The CYP genes are located on many chromosomes in humans, and the products function as oxygenase enzymes, being particularly active in drug metabolism. The majority of drugs metabolised by the liver involve either CYP1, 2, or 3.

The CYP genes are located on many chromosomes in humans, and the products function as oxygenase enzymes, being particularly active in drug metabolism. The majority of drugs metabolised by the liver involve either CYP1, 2, or 3.

The majority of CYP alleles have been defined by LD or NGS. SCS has a role in defining the alleles of the genes, with no limit on the size of the genes, and with greater precision than is available now.

Genes involved in the development of human cancer

Many human cancers share genes which are involved in tumour development, including tumour suppressor genes, e.g. BRCA1 and BRCA2 genes, oncogenes, kinases, cell surface receptors, and phosphatase genes. Again, great reliance has been placed on LD to define alleles. SCS has an exciting role to play in this field in defining alleles of these genes, which have been shown to be polymorphic.