Response to Falush: a role for cis-element polymorphisms in HD

Trinucleotide repeats and haplotypes at the huntingtin locus in an Indian sample overlaps with European haplogroup a

Huntington's disease (HD), an autosomal dominant neurodegenerative syndrome, has a world-wide distribution. An estimated 2.5-10/100,000 people of European ancestry are affected with HD, while the Asian populations have lower prevalence (0.6-3.8/100,000). The epidemiology of HD is not well described in India, and the distribution of the pathogenic CAG expansion, and the associated haplotype, in this population needs to be better understood. This study demonstrates a distribution of CAG repeats, at the HTT locus, comparable to the European population in both normal and HD affected chromosomes. Further, we provide an evidence for similarity of the HD halpotype in Indian sample to the European HD haplogroup.

The molecular clock in terms of quantum information processing of coherent states, entanglement and replication of evolutionarily selected decohered isomers

Evolutionary pressures have selected quantum uncertainty limits -ΔxΔp ( x ) ≥ 1/2ħ-to operate on metastable amino DNA protons. This introduces a probability of molecular clock arrangement, keto-amino → enol-imine, where product protons are entangled and participate in coupled quantum oscillation at frequencies of ∼ 10(13) s(-1). The ket "seen by" the transcriptase, reading a coherent enol-imine G'-state, is |φ >= α| + + > +β|+- > +γ|-+ > +δ|-->. The transcriptase implements its measurement and generates an output qubit of observable genetic specificity information in an interval Δt ≪ 10(-13) s. These quantum measurements can specify the relative distribution of coherent G'-C' states at time of measurement. The ensuing quantum entanglement between coherent protons and transcriptase units is utilized as a resource to generate proper decoherence and introduce selected time-dependent substitutions, ts, and deletions, td. Topal-Fresco ts are G'202 → T, G'002 → C, *G020(0) → A and *C202(2) → T, whereas td are exhibited at coherent *A-*T sites. Variation in clock 'tic-rate' is a consequence of clock introduction of initiation codons - UUG, CUG, AUG, GUG - and stop codons, UAA, UAG, UGA. Using approximate quantum methods for times t < ∼ 100 y, the probability, P(t), of keto-amino → enolimine arrangement is P ( ρ )(t) = 1/2(γ ( ρ )/ħ)(2) t (2) where γ ( ρ ) is the energy shift. This introduces a quantum Darwinian evolution model which provides insight into biological consequences of coherent states populating human genes, including inherited (CAG)( n ) repeat tracts.

HTT haplotypes contribute to differences in Huntington disease prevalence between Europe and East Asia

Huntington disease (HD) results from CAG expansion in the huntingtin (HTT) gene. Although HD occurs worldwide, there are large geographic differences in its prevalence. The prevalence in populations derived from Europe is 10-100 times greater than in East Asia. The European general population chromosomes can be grouped into three major haplogroups (group of similar haplotypes): A, B and C. The majority of HD chromosomes in Europe are found on haplogroup A. However, in the East-Asian populations of China and Japan, we find the majority of HD chromosomes are associated with haplogroup C. The highest risk HD haplotypes (A1 and A2), are absent from the general and HD populations of China and Japan, and therefore provide an explanation for why HD prevalence is low in East Asia. Interestingly, both East-Asian and European populations share a similar low level of HD on haplogroup C. Our data are consistent with the hypothesis that different HTT haplotypes have different mutation rates, and geographic differences in HTT haplotypes explain the difference in HD prevalence. Further, the bias for expansion on haplogroup C in the East-Asian population cannot be explained by a higher average CAG size, as haplogroup C has a lower average CAG size in the general East-Asian population compared with other haplogroups. This finding suggests that CAG-tract size is not the only factor important for CAG instability. Instead, the expansion bias may be because of genetic cis-elements within the haplotype that influence CAG instability in HTT, possibly through different mutational mechanisms for the different haplogroups.