PostGenetic Medicine; Personalized Medicine plus targeting "non-coding DNA Diseases" (PostGene Diseases)

For 50 years since the unravelling of DNA it has been assumed that the genomics of health and disease will reside in protein-coding genes.

Preoccupation with genes, expected to number 100,000+ and so suffice as a total explanation of genetic phenomena, maintained dismissal of the rest of the genome to non-protein coding, “irrelevant”, “Junk” DNA.

Among considerations which should have cautioned against consigning 95+% of the genome to the “junk heap” were:

• Expression of genes has been known since the early 1980’s to be influenced by ‘enhancers’ and other regulatory elements, often located way into the intergenic “Junk” boondocks;

• The coinheritance of “Junk” DNA markers with traits of interest in families that are widely separated in geography and even ethnicity;

• The implausible assumption that evolution, in general, and natural selection, in particular, would act only on protein-coding genes, like atolls, in isolation from surrounding vast genomic seas.

Some 15 years ago it began to be recognised that functions were attributable to both unique and repeat non-protein coding DNA, and that previous concepts of genomic information limited to gene-based dogma had to be reviewed.

(Simons & Pellionisz, Genomics, morphogenesis and biophysics: Triangulation of Purkinje cell development - Introduction, para.1. Cerebellum, 13 January 2006: see below and in full)

As recently as 2003, Gibbs¹ recorded the assertion by Mattick³ that “"the failure to recognize the importance of introns (i.e. non-protein-coding sequences between coding exons) may well go down as one of the biggest mistakes in the history of molecular biology'”. Mattick might have extended his assertion beyond “Junk” sequences within genes to the much more extensive sequences between genes.

The realization that all “Junk” DNA occurred as non-random chromosomal segments, or haplotypes, and that these haplotypes remained unrearranged in individuals widely separated in geography and even ethnicity, was a clear indication that preservation of genomic structure reflected function involving “Junk” DNA both within and between genes.

In this first year of the 2nd century post definition of ‘gene (See below Haplotypy -Chronology) our thesis is that genetic attention must be expanded to the remaining 98.7% of the genome. Many diseases, some seemingly monogenic, others undoubtedly complex, involve genetic and epigenetic phenomena that are not confined to protein-coding genic sequences.

We have established the International Post Genetics Society (IPGS) to promote awareness of “Junk” DNA’s central role in an integrative view of the genome, broader than genes alone.

The IPGS will also serve to inform government and the private sector of the utility of total genome information in postgenetic medicine, biotechnology, nanotechnology and information technology.

Genomics, morphogenesis and biophysics: Triangulation of Purkinje cell [Excerpts]
[full preview] [clickable refs]

Malcolm J Simons* and András J Pellionisz**

* Haplomic Technologies Pty. Ltd., Victoria, Australia
** HelixoMetry, Sunnyvale, California, USA

Excerpts

In ways that are largely unknown, genomic information is presumed to specify the development of cellular systems, distributed as well as discrete. For most of the half century since the discovery of DNA structure it has been assumed that the projected 100,000+ genes were sufficiently responsible for the genesis of dispersed cell systems and of organelles and organs. It has been a major surprise to find that the number of genic units in humans is only of the order of 20,000, and possibly an even greater challenge to comprehend that a similar number is present in most eukaryotic species whose genomes have been sequenced.

While recognising that alternative splicing is exhibited by many genes, augmenting the number of protein varieties, it is becoming widely appreciated, even in generalist publications, that previous concepts of genomic information limited to gene-based dogma need to be reviewed^1,2. It is fast becoming recognised that there is genetics beyond genes in which the information content of introns and other non-coding sequences can be expected to contribute important roles. As recently as 2003, Gibbs1 recorded the assertion by Mattick3 that “"the failure to recognize the importance of introns 'may well go down as one of the biggest mistakes in the history of molecular biology'”. One of us (MJS) did not make this mistake. By 1989, 11 years before essential completion of the Human Genome sequencing project in 2000, patents were filed based on the discovery that intron/non-coding sequence variation was sufficiently non-random for haplotype analysis in unrelated subjects4,5,6. Recognition of the utility of linkage disequilibrium-based haplotype structure was a paradigm shift from previous linkage-based pedigree analysis. The central issue was that if the so-called Junk DNA had structure then, under Darwinian Theory, it could be expected to have function. Proof of application was provided for the most polymorphic and complex component of the genome, the major histocompatibility complex (#6p21.3), in the context of HLA genetic tissue typing7,8. The non-random haplotypic structure of non-coding DNA has been the basis for genome-wide gene discovery by haplotype mapping for more than a decade, and underpins the current international HapMap project. Also in 1989, the second author (AJP), working in a totally different field, and unknown to MJS, recognised that attention would need to be given to the wider genome to understand genetically determined, fractal geometrical development of P-cells9, suggesting that a key to fractal geometry of the P-cell may lie in the genome, while cautioning that an understanding may lie “far in the future9”.

Reference Excerpts

1. Gibbs, WW (2003) The unseen genome: Gems among the junk. Scientific American, November, 289(5): 48-53
2. Battistutti, WB (2004) Cross-talking between cells - the future of functional genomics? Business Briefings, London: The Future of Drug Discovery, 54-58
3. Mattick J (2003) In: "Genius of Junk" (Producer Sonia Pemberton, Australian Broadcasting Company), full transcript at http://www.abc.net.au/catalyst/stories/s898887.htm#transcript
4. Simons MJ (1993) Intron sequence analysis method for detection of adjacent and remote locus alleles as haplotypes US Patent # 5,192,659
5. Simons, MJ (1997) Intron sequence analysis method for detection of adjacent and remote locus alleles as haplotypes, US Patent # 5,612,179
6. Simons, MJ (1998) Genomic mapping method by direct haplotyping using intron sequence analysis, US Patent # 5,851,762
7. Simons MJ, Limm TM, Naughton MJ, Quinn DL, McGinnis MD, Ashdown ML. (1993) Strategy for definition of DR/DQ haplotypes in the 4AOHW cell panel using noncoding sequence polymorphisms. Hum Immunol. 38(1):69-74.
8. Limm TM, Ashdown MJ, Naughton MJ, McGinnis MD, Simons MJ (1993) HLA-DQA1 allele and suballele typing using noncoding sequence polymorphisms. Application of 4AOHW cell panel typing. Hum Immunol. 38(1):57-68.
9. Pellionisz, AJ (1989) Neural Geometry: Towards a fractal model of neurons. In: Models of brain function, ed. By Cotterill, RMJ, Cambridge University Press; 453-464

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Haplotypy - Some Landmarks [MJS]

1856< Mendel Discovered Trait inheritance due to discrete ‘units’
1905 Bateson Introduced the terms 'Gene, allelomorph, homozygote, heterozygote’
1953 Watson, Crick (Franklin, Wilkins) DNA structure
1967 Ceppellini 'Haplotype' (contraction of haploid genotype) Original definition as cis-phase alleles at >2 linked loci
1974 Southern Genotyping by Restriction Fragment Length Polymorphism (RFLP)
1985 Mullis Polymerase Chain Reaction for DNA analysis
1988 Li, Gyllensten, Cui, Saiki, Erlich, Arnheim Haploid typing using haploid sperm PCR
1989 Simons 'Haplotype' defined as chromosome segment between sites of recombination (Mendelian ‘unit’), incorporating Ceppelini’s definition of cis-phase alleles at >2 linked loci. Use of non-coding ('Junk' DNA) for linkage disequilibrium-based surrogate allele and haplo-typing, and for fine gene mapping by haplotype heterogeneity restriction (Assigned to Genetic Technologies)
1989 Ruano, Kidd 'Haplotype' redefined differently from Ceppelini/Simons as 2< cisphase SNPs, Haplotyping by allele-specific PCR
1990 Stephens, Rogers, Ruano Haplotyping by single-molecule-dilution (Assigned to Genaissance)
2001 Vogelstein Haploid (monochromosome) typing by Human-Rodent Hybrid Conversion Technology (Assigned to GMP Genetics)
2002 Dapprich Haplotyping by Specific Extraction (Assigned to GenoVision)
2003 Ding, Cantor Haplotyping by single molecule dilution (M1PCR - Assigned to Sequenom)
2003 Simons et alii Proof of Concept of non-coding sequence-based surrogate Allele and Haplotyping (1)
2005 Anantharaman, Mysore, Mishra Haplotyping by Optical PCR Mapping (restriction fragment alignment)
2005 Simons Haploid (single chromosome) PCR Typing (Assigned to Haplomic Technologies) Haplotyping (diploid or haploid) by ‘overlapping’ high density SNP microarray (Assigned to Haplomic Technologies)

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(1) Intron-based Gene allele and haplotype Diagnostic - Proof of Principle, extracted from ‘Full Article’ at http://www.simonsjunkdna.com

The intention of the Intron Diagnostic patent (US Patent No. 5,612,179), to describe those situations where a non-coding sequence variant is in Linkage Disequilibrium with a coding locus allele such that the former is characteristic of the latter, is clearly illustrated in the proof of principle experiment of HLA Class II typing in the 4th Asia-Oceania Histocompatibility Workshop (4AOHW).

Non-coding SNPs were shown to surrogately mark HLA-DQA1 coding locus alleles (as assigned at 1994) (34,35), and to define HLA-DR/DQ haplotypes (36).

34. Limm TM, Ashdown ML, Naughton MJ, McGinnis MD, Simons MJ. HLA-DQA1 allele and suballele typing using noncoding sequence polymorphisms. Application to 4AOHW cell panel typing. Human Immunology 1993 Sep; 38(1): 57-68.
35. Amos DB, van Rood, JJ. Editorial. (“An approach pioneered by Malcolm Simons is presented in this issue. ..although simple and inexpensive, it performed perfectly in the preceding fourth AOH workshop”). Human Immunology 1993 Sep; 38(1): 1-2.
36. Simons M.J, Limm T.M, Naughton M.J, Quinn D.L, McGinnis M.D, Ashdown M.L. Strategy for Definition of DR/DQ Haplotypes in the 4AOHW Cell Panel Using Noncoding Sequence Polymorphisms. Human Immunology 1993 Sep; 38(1): 69-74.