The importance of establishing genetic phase in clinical medicine

Abstract

Haplotyping or determination of genetic phase has always played a pivotal role in MHC (HLA studies) both in helping to understand inheritance patterns in diseases such as type 1 diabetes (T1D) and in ensuring better matching in transplantation scenarios such as haematopoietic stem cell transplantation (HSCT), using donors genetically related to the patient. In recent years the need to establish genetic phase in a number of clinical scenarios has become apparent. These include:1. Genetic phasing for hematopoietic stem cell transplants using unrelated donors, where the HLA haplotypes are not known but where haplotype-matched recipients fare better clinically than allele matched, but haplotype mismatched patients.2. The use of checkpoint inhibitors is one of the most innovative and exciting developments in cancer treatment in years. An example is the use of the monoclonal ipilimumab to block the CTLA-4 receptor which is known to contain polymorphic sites.Until the phase of these polymorphisms is known it will not be possible to determine how effectively this monoclonal will perform in individual patients.3. The role of miRNA single strand molecules and their effect on gene expression. Thousands of non-coding genes have been identified and have been shown to be polymorphic, as have their target genes. Genetic phasing of polymorphism both in the miRNA source genes and their targets is clearly a fertile area of research 4. In areas such a drug metabolism where the polymorphic family of CYP genes is responsible for the metabolism of the majority of prescription drugs, determining phase of SNPs is critical to understanding drug metabolism and efficacy. 5. In multigenic disease studies combinations of single nucleotide polymorphisms (SNPs) in participating genes require accurate phasing in order to fully appreciate their role in the disease process. In addition, the level of expression of genes (point 3) is also important in understanding disease processes at the functional level. This review outlines the techniques that are currently available for approximating phase and discusses the clinical relevance of establishing genetic phase in areas of clinical medicine outlined in points 1-3.

Human leukocyte antigen super-locus: nexus of genomic supergenes, SNPs, indels, transcripts, and haplotypes

“…The diversity of the variable long-range haplotype segments within heterozygote individuals has provided problems and challenges for assigning SNPs to loci, and assembling structural variants of numerous duplicated genes particular in regard to associating them as genetic markers or causative agents for many of the immune-related phenotypes and diseases 18 . In recent years, more attention is being given to gaining a better understanding of MHC haplotypes by phased long-range sequencing as an extension of genotyping and identifying genic and non-genic alleles for associating them with disease, bone marrow transplantation, and for ascertaining the effects of immunotherapy 26 . Reliable MHC linkage mapping and haplotyping usually are dependent on pedigree studies of particular genotyped markers to evaluate their linkage or segregation in meiosis 18 or on phased genomic sequences 26 , such as those that have been sequenced or genotyped using multilocus HLA-captured haplotype phasing 27 , 28 , de novo assembled trios 29 , MHC homozygous cell-lines 11 , sperm 30 or single chromosomes 31 .…”

“…In recent years, more attention is being given to gaining a better understanding of MHC haplotypes by phased long-range sequencing as an extension of genotyping and identifying genic and non-genic alleles for associating them with disease, bone marrow transplantation, and for ascertaining the effects of immunotherapy 26 . Reliable MHC linkage mapping and haplotyping usually are dependent on pedigree studies of particular genotyped markers to evaluate their linkage or segregation in meiosis 18 or on phased genomic sequences 26 , such as those that have been sequenced or genotyped using multilocus HLA-captured haplotype phasing 27 , 28 , de novo assembled trios 29 , MHC homozygous cell-lines 11 , sperm 30 or single chromosomes 31 . Because of the complexity of the MHC as a HLA super-locus with a myriad of interconnected gene systems and sub-genomic regions, it is a gradual and continuing difficult process to build up the genetic, molecular and functional knowledge about the architectural and functional organisation of haplotypes in this region and their overall contribution to health and disease 1 , 2 , 25 , 26 , 32 , 33 .…”

“…Haplotypes at the genomic sequence level are blocks of phased coding and non-coding nucleotide sequences of multiple loci that are in the same orientation ( cis ) as their mode of gene transcription and regulation 26 . The characterisation and understanding of MHC haplotypes in modern disease and population genetics began in 1967 with the introduction of the word ‘haplotype’ by Ruggero Ceppellini to describe alleles in the HLA system 45 , and expanded in the 1990s with the pedigree studies of the research groups of Alper 9 , 18 , and Dawkins 10 , 46 , 47 .…”

“…Although this question is not resolved fully, available data suggest that many inherited haplotypes are not completely identical and that de novo mutations, SNPs and/or indels, in MHC genomic sequence comparisons do exist between the same conserved haplotypes 83 – 86 . The identification of variants between the same haplotypes might have importance in assisting with optimal donor-recipient selection for allogeneic stem cell transplantation and with reducing acute and chronic graft-versus-host disease 26 .…”

Cross-ethnic analysis of common gene variants in hemostasis show lopsided representation of global populations in genetic databases

“…Second, there are also other circumstances where genetic phasing plays a role. For example, hematopoietic stem cell transplants using haplotype matched recipients perform better clinically than those using allele matched but haplotype mis-matched patients [ 36 ]. To mention another example that applies methods akin to our own work, an interesting new proposal appeared recently in the field of pre-implantation genetic diagnosis (PGD) for molecular disorders.…”