Towards a Universal Law Controlling All Human Cancer Chromosome LOH Deletions, Perspectives in Prostate and Breast Cancers Screening

Background: Global analysis of 3 human genomes of increasing levels of evolution (Neanderthal/Sapiens Build34/Sapiens hg38) reveals 2 levels of numerical constraints controlling, structuring and optimizing these genome's DNA sequences. A global constraint called "HGO" for "Human Genome Optimum" optimizes the genome at its global scale. The same operator applied to each of the 24 individual chromosomes reveals a hierarchical structure of these 24 chromosomes. Methods: We analyze how this HGO genomic optimum is perturbed by hundred single or multiple LOH (Loss of Heterozygosity) deletions relating to different chromosomes and cancers. Results: The generic law highlighted is stated as follows "When an LOH deletion affects a chromosome upstream of the HGO point (chromosomes 4 13). In the chromosomal spectrum, this deletion degrades the genomic optimum of the cancer genome. When an LOH deletion affects a chromosome downstream of the HGO point (chromosomes 19 22) in the chromosomal spectrum, this deletion improves the genomic optimum of the cancer genome. The exhaustive analysis of the 240 LOHs for the following 6 cases: Chromosome 13 (breast cancer), chromosome 5 (breast cancer), chromosome 10 (glioblastoma cancer), chromosome 1 (colorectal cancer), chromosome 1 (neuroblastoma cancer) and chromosome 16 (prostate cancer) obey this law in 227 cases and do not obey this law for 13 cases (success rate of our law=94.58%). In this article we will detail this type of analysis on 153 LOH relating to breast and prostate tumors affecting respectively chromosome 13, chromosome 5 (breast) and chromosome 16 (prostate). In this detailed study, the HGO law described here is verified in 143 cases out of 153 or 93.46% of favorable cases. Conclusion: The main application of this fundamental discovery will be the genomic characterization and classification of tumors, making it possible to predict the dangerousness and even the pathogenicity.


Introduction
Thanks to the CRISPR (Clustered regularly interspaced short palindromic repeats) technology, it is now possible to locally modify the genomes, and particularly the human genome [1]. Almost simultaneously, the fractal and global structures of the human genome were demonstrated [2]. In such a context, apart from ethical questions, can a local technology as powerful as CRISPR be applied, ignoring its possible effect on the possible global and long-range equilibria and balancing at the chromosome scale or even the entire genome scale? For more than 25 years, we have been looking for possible global, even numerical, structures that would organize DNA, genes, chromosomes and even whole genomes [3][4][5][6]. Curiously, the method of numerical analysis of whole genomes as well as the discovery of a global law of impact of the LOH deletions associated with tumors that will be the subject of this article may seem to the reader too simple or even "naive". In effect, these laws are based on a wellknown type of analysis that could be thought to have explored all aspects: the analysis of GC/TA ratios. It has long been known that such ratios [7] characterize the diversity of chromosomes. Under the name of "isochores," Giorgio Bernardi has extensively explored its richness and diversity [8,9]. We have already demonstrated a numerical structure at the scale of each human chromosome as well as on the whole genome [10][11][12][13]. In [10] we have already highlighted this numerical value of 0.6909830056, the HGO in this article: it controls the population of triplet codons analyzing single stranded DNA sequence from the whole human genome. However, it is only by deepening the notion of "fractal periodicity", outlined in [14], and we will highlight in various articles in preparation [15] that we have re-discovered the major role that this GC/TA ratio at the whole chromosome and whole genome scales. Particularly, in 2015, we have demonstrated [14] how a global structure organizes any DNA sequence. This numerical organization is based on the atomic masses of the "G" bases of the double stranded DNA sequence, therefore on the bases C and G of the single stranded DNA sequence.
Here is another reason sufficient to consider the relations and proportions between bases C+G on the one hand, and T+A on the other hand. Comparing the three genomes of reference of Neanderthal [15], Sapiens Build34 of 2003 [16] and Sapiens hg38 of 2013 [17], we will demonstrate in [15] the evidence of "Fractals periods" and "resonance periods" characterizing each of the 24 human chromosomes. It is for these simple reasons that we have decided to focus on these C+G/T+A ratios at the scale of each of the 24 human chromosomes as well as on the whole genome analyzing the 46 chromosomes single stranded DNA sequences.

Analyzed whole human genomes
We analyzed completely and systematically each of the 24 chromosomes of each of the following three reference genomes: For more details, a complete description of method is available in [18,19].

Results
In all that follows, the general methodology will be as follows: we calculate, for the 46 chromosomes constituting each genome studied, only the single-stranded DNA sequences. In these sequences, we count the relative populations of bases T+A on the one hand, and C+G on the other hand.

HGO of the 3 whole genomes: Neanderthal, Sapiens Build34 and Sapiens HG38
The three genomes we compare here are differentiated on the one hand by their respective evolution levels, on the other hand by the sample of individual genomes of which they form the syntheses, and finally by the precision of the sequencing of DNA.
For example, this work by the Craig Venter team demonstrates this level of dispersion between more than 10,000 individual genomes and reference genomes such as HG28 [20].
The detailed data related to the 3 whole genomes shows the various distances and errors between real computed HGOs for each genome and theoretical HGO optimum value= 0.6909830055.
Particularly, it is found that the 3 HGOs calculated for the respective 3 genomes of Neanderthal, Sapiens (2003 Build34 and 2013 hg38 Sapiens) are very close to the ideal theoretical optimal HGO=0.6909830056 (99.67% for the least optimal genome).
It is also observed that female genomes (XX) are more optimal than male genomes (XY).
On the other hand, the genomes of Neanderthal and Sapiens (Build34 of 2003) have very close optimization levels. We believe these results from the fact that the precisions of their respective DNA sequencing are similar. On the contrary, the hg38 genomes of 2013 show the most optimal levels, this is most certainly due to the deeper quality of their DNA sequencing. (Figure 1) summarizes HGO results for these 3 human genomes of varying levels of evolution.
Finally, we note that it is the downstream region (Figure 2) that contributes the most to the superiority of optimality of sapiens hg38 compared to sapiens Build34. However, a more detailed analysis of the upstream and downstream regions shows that when passing from sapiens Build34 2003 to hg38 2013, the notorious optimization obeys the global strategy law of the LOH. Also of note is that 20 out of 24 chromosomes are OK, with the exception of chromosomes 13, X, Y, and 1. The law presented The respective HGOs of 3 human genomes of varying levels of evolution are shown here. Figure 1 Diversity of HGOs of human chromosomes downstream of the numerical attractor HGO=0.6909830056. Figure 2 here states that there is reduction of optimality for upstream chromosomes and improvement of optimality for downstream regions.
It is therefore remarkable that this is the same and only law which seems to simultaneously control two domains as different as: 1) the global strategy of LOH deletions of tumors on the one hand and 2) the difference of evolution of the same genome following two increasing precision levels of DNA sequencing (Build34 2003 and hg38 2013) on the other.
Recall the single stranded C+G, T+A and individual chromosome HGO values: In Table 1, we have sorted the 24 chromosomes by increasing values of CG/TA ratios in the 3 cases of compared genomes.

HGO spectral hierarchy of the 24 Human chromosomes
The following figures 2 and 3 illustrate the hierarchical spectrum of the individual HGOs of each of the 24 chromosomes for each of the three genomes analyzed. It should be noted that the upstream/downstream tipping point lies between chromosomes 14 and 21, which is closely related to the probable mechanisms explaining trisomy21 (whose disorders involve precisely these two chromosomes).
HGO disturbed by 240 LOH deletions related to 5 different chromosomes and 5 different tumors After demonstrating how 3 human genomes with increasing levels of sequencing quality and evolution accuracy seem to "fit" this theoretical value of HGO, we will now analyze how small mutations on one of the chromosomes can "disrupt" this HGO. For this purpose there are a very large number of publications associating such nucleotide regions with deletions of the chromosomal DNA of different tumor cells.
This exhaustive analysis will then reveal the following generic law: "When an LOH deletion affects a chromosome upstream of the HGO point, in the chromosomal spectrum, this deletion degrades the genomic optimum of the cancer genome.
When an LOH deletion affects a chromosome downstream of the HGO point, in the chromosomal spectrum, this deletion improves the genomic optimum of the cancer genome.
The full details of these analyses are available in Table 2, below summarizing these results.
In the Table 2 the shaded areas represent cases of LOH complying with the generic rule, while the unshaded areas represent cases of LOH that do not comply with this rule. In total, 227 cases respect the rule and only 13 cases of LOH do not respect it, a success rate of this law equal to 94.58%. In Bold we represented   Figure 2 and 3 above.
Consequently, these 240 cases are presented in the order of upstream towards downstream with respect to the theoretical HGO.
In particular, this is the case for the first 82 LOHs for breast tumors affecting chromosomes13 and 5, both of which are upstream (Figure 3) on the contrary, all remaining LOHs will be downstream (Figure 2) of the theoretical HGO point, thus downstream.
Thus, Figure 4 and 6 will synthesize the relative positions of all these HGOs. Similarly, the errors or distances (Figure 5 and 7) will also be calculated relative to the respective distances between HGO diversity of human chromosomes upstream of the numerical attractor HGO=0.6909830056. Figure 3 Case of a woman genome, the 82 on the left are for decreased HGO chromosomes: 1/ at the bottom axis level, the theoretical HGO, 2/ in blue, the reference woman HGO value, then, 3/ the 240 LOH cases curve: on the left part of the figure LOH HGO values are principally higher than reference woman HGO, on the right part of the figure LOH HGO values are principally lower than reference woman HGO.

Figure 4
Case of a woman genome, the 82 on the left are for decreased HGO chromosomes: 1/ at the zero axis level, the theoretical HGO, 2/ in blue, the reference woman HGO error, then, 3/ the 240 LOH cases curve: on the left part of the figure LOH HGO errors are principally higher than reference woman HGO error, on the right part of the figure LOH HGO errors are principally lower than reference woman HGO error.

Figure 5
Case of a man genome, the 82 on the left are for decreased HGO chromosomes: 1/ at the bottom axis level, the theoretical HGO, 2/ in blue, the reference man HGO value, then, 3/ the 240 LOH cases curve: on the left part of the figure LOH HGO values are principally higher than reference man HGO, on the right part of the figure LOH HGO values are principally lower than reference man HGO.

Research Journal of Oncology
This article is available in: http://www.imedpub.com/research-journal-oncology/ HGO of the 240 cases of LOH deletions, or of the reference HGOs, with respect to the HGO theoretical.

Detailed results
We have successively demonstrated that, in the Human Genome Evolution and in the precision of sequencing of the genomes, these genomes seemed to "seek" a sort of numerical optimum: HGO ( Figure 1).
Then, we demonstrated how the LOH deletions affecting the tumor cell chromosomes obeyed a generic law based on the chromosome hierarchization illustrated in Figure 2  This is what we are going to demonstrate now in 3 analyses of 153 Breast and Prostate LOH deletions tumors.

First analysis: 40 breast tumors LOH in chromosome 13
Basic data: The article supporting our analysis.
We analyze here 40 LOH associated with Breast cancer of chromosome 13 from the publication [21], of the 46 LOH cases published, only 40 cases of exploitable LOH were identified.
Indeed some LOH are reduced to a single marker that is to say approximately 200000bp, which is too insignificant. For example, the first of the markers in this study is D13S1695: chr13: 32,849,425-33,049,658 200,234 bp. However, such a length of 200234 bp is too insignificant.
Example of LOH effect on the HGO, the case of a single LOH deletion in chromosome 13 breast tumor.
We therefore retain only the LOHs corresponding to regions delimited by 2 markers (for example the first LOH referenced in Table 3), as well as regions comprising at least 2 markers alone (for example the LOH referenced D13S1694 D13S267 in Table 3). To Conclude: Recall that ( Table 4) chromosome 13 is upstream with respect to the tipping point HGO (see manuscript Figure  2). Thus, according to our "global strategy law of LOH by chromosomes", the majority of LOH "should" degrade the value of the HGO: in effect, we observe that 36 out of 40 cases degrade the HGO.

Second analysis: 42 Breast tumors LOH in Chromosome 5
Basic data: The article supporting our analysis, in the analysis from [22]. To conclude: Recall that (table 5) chromosome 5 is upstream with respect to the tipping point HGO (see manuscript Figure  2) Therefore, by virtue of our "global strategy law for LOH by chromosomes", most LOHs "should" degrade the HGO value: in effect, 37 out of 42 cases degrade HGO.

Third analysis: 72 Prostate tumors LOH in Chromosome 16
Basic data: The article supporting our analysis [28].
The chromosome support of our analysis: chr16:1-90,338,345 90,338,345 bp [29] The supporting (figure 10) of our analysis: To conclude: Recall that ( Table 6) chromosome 16 is downstream with respect to the tipping point HGO (see manuscript Figure 3). Therefore, by virtue of our "global LOH strategy law by chromosomes", most LOHs "should" improve the HGO value: in fact, 66 cases out of 72 increase the HGO in the Case of a man genome, the 82 on the left are for decreased HGO chromosomes: 1/ at the zero axis level, the theoretical HGO, 2/ in blue, the reference man HGO error, then, 3/ the 240 LOH cases curve: on the left part of the figure LOH HGO errors are principally higher than reference man HGO error, on the right part of the figure LOH HGO errors are principally lower than reference man HGO error.

Figure 7
Error ideal HGOreference HGO -0 Tumours in group A are indicative of LOH at 13q12-q13, in group B at 13q12-q13 as well as 13q31-q34, and in group C the retinoblastoma gene is involved in the tumours, as well as the two regions depicted in groups A and B.

Figure 11
Effect of LOH of chromosome 5 on the HGO ratio in breast cancers affecting the BRCA1 gene on the same genome according to whether it is female (XX) or male (XY).

Figure 12
case of a Genome (XX) but 71 out of 72 cases increase HGO in the case of a male genome (XY).

First analysis: 40 Breast tumors LOH in Chromosome 13
In the analysis from publication [21], we show that HGO conforms to the above law in 36 of 40 cases (chromosome 13 is in the region upstream of the HGO point, see Figure 2).
In Figure 11, it is interesting to note that the effect on a female genome (XX) is greater than the effect on this same male genome (XY), which is in agreement with the fact that this cancer is almost exclusively feminine. A rapid analysis of the degradations of HGO -for the same LOH -depending on whether the genome is XY (masculine) or XX (feminine) will show that these expected degradations are 1.27 times higher in the case of a female genome (XX). This would reinforce the fact that the female genome is more sensitive to these LOH deletions than the male genome.

Second analysis: 42 Breast tumors LOH in Chromosome 5
In the analysis from publication [22], we show (Figure 12) that the HGO conforms to the above-mentioned law in 37 cases out of 42 (chromosome 5 is located in the region upstream of the HGO point, see Figure 2). The analysis below concerns cases of LOH affecting BRCA1 mutations. It is interesting to observeeven if only visually -that the effect on a female genome (XX) is greater than the effect on the same male genome (XY), which is in agreement with the fact that this cancer is almost exclusively feminine.

Third analysis: 72 Prostate tumors LOH in Chromosome 16
Of 72 cases analyzed from article [28], 71 cases improved HGO while only one did not (Chromosome 16 is located in the region downstream of the HGO point (Figure 3). The evaluation below analyzes the evolution of the HGO according to the 3 grades of pathogenicity of the tumors studied.
Grade A: patients with disease limited to the prostate.
Grade B: patients with local extracapsular extension.
Grade C: patients with regional lymph node involvement or distant metastases.
Between Grade A and Grade B, an average HGO improvement of 4.88% was observed.
The graph below (Figure 13) illustrates this optimization. The HGO of grade C is of the same order as that of grade A, which may be explained by the fact that the LOHs of grades A and B are generally monochromosomes whereas the LOHs of grade C are multichromosomes. There are therefore more complexes to be demonstrated in monochromosome studies.
It is interesting to note that the effect on a female genome (XX) is 4.86 times lower than the effect on the same male genome (XY), which is in agreement with the fact that this cancer is exclusively Increased impact of the HGO optimality between grade A and grade B in prostate cancer involving LOH on chromosome 16.

Conclusion
It is remarkable to discover this strong correlation between the pathogenicity and the aggressiveness of tumors on the one hand, and the categorization and hierarchization of mutations LOH of the mutant genomes at the origin of tumors. The law discovered here is universal, common to all types of cancers and to all chromosomes. Its nature is mathematical, proceeding only from the DNA information of the genomes. The method is exhaustive, systematic, and predictive, making it possible to anticipate the knowledge of the pathogenicity of an existing tumor or even of a mutation before the tumor disappears.
The mutant genome thus constitutes a kind of signature, virtual and numerical image of the tumor. Thus it is remarkable to discover that the LOH genome of a breast tumor, a cancer that is exclusively feminine by its nature, will lead to an overall HGO genomic degradation much greater than the same mutation affecting a male genome.
Conversely, it will be the same, but in the opposite way for a cancer of the prostate which, it is, exclusively masculine.
Finally, in this same prostate cancer, the impact on HGO between grade A and grade B is significant: recall.
Grade A: patients with disease limited to the prostate.
Grade B: patients with local extracapsular extension.
Grade C: patients with regional lymph node involvement or distant metastases.
Between Grade A and Grade B, an average HGO improvement of 4.88% was observed.
To conclude, the most important fact is the universal character of this HGO law, presented here for both breast and prostate cancers, the universal character of this law has been widely generalized experimentally on a large number of cancers differences affecting most chromosomes, this generalization will be described in [28 and 29].