Full mtGenome reference data: development and characterization of 588 forensic-quality haplotypes representing three U.S. populations.

Though investigations into the use of massively parallel sequencing technologies for the generation of complete mitochondrial genome (mtGenome) profiles from difficult forensic specimens are well underway in multiple laboratories, the high quality population reference data necessary to support full mtGenome typing in the forensic context are lacking. To address this deficiency, we have developed 588 complete mtGenome haplotypes, spanning three U.S. population groups (African American, Caucasian and Hispanic) from anonymized, randomly-sampled specimens. Data production utilized an 8-amplicon, 135 sequencing reaction Sanger-based protocol, performed in semi-automated fashion on robotic instrumentation. Data review followed an intensive multi-step strategy that included a minimum of three independent reviews of the raw data at two laboratories; repeat screenings of all insertions, deletions, heteroplasmies, transversions and any additional private mutations; and a check for phylogenetic feasibility. For all three populations, nearly complete resolution of the haplotypes was achieved with full mtGenome sequences: 90.3-98.8% of haplotypes were unique per population, an improvement of 7.7-29.2% over control region sequencing alone, and zero haplotypes overlapped between populations. Inferred maternal biogeographic ancestry frequencies for each population and heteroplasmy rates in the control region were generally consistent with published datasets. In the coding region, nearly 90% of individuals exhibited length heteroplasmy in the 12418-12425 adenine homopolymer; and despite a relatively high rate of point heteroplasmy (23.8% of individuals across the entire molecule), coding region point heteroplasmies shared by more than one individual were notably absent, and transversion-type heteroplasmies were extremely rare. The ratio of nonsynonymous to synonymous changes among point heteroplasmies in the protein-coding genes (1:1.3) and average pathogenicity scores in comparison to data reported for complete substitutions in previous studies seem to provide some additional support for the role of purifying selection in the evolution of the human mtGenome. Overall, these thoroughly vetted full mtGenome population reference data can serve as a standard against which the quality and features of future mtGenome datasets (especially those developed via massively parallel sequencing) may be evaluated, and will provide a solid foundation for the generation of complete mtGenome haplotype frequency estimates for forensic applications.

Common variant in myocilin gene is associated with high myopia in isolated population of Korcula Island, Croatia.

AIM: To study the association between genetic variants in myocilin and collagen type I alpha 1 genes and high myopia in an isolated island population. METHODS: A total of 944 examinees from the genetic epidemiology study conducted on the island of Korcula, Croatia, were included in the study. We selected 2 short nucleotide polymorphisms (SNP) available in our genome-wide scan set of SNPs that were previously associated with high myopia and used them to replicate previous claims of possible association. RESULTS: Nineteen cases of high myopia, defined as the refraction of

Remarkable effect of water on functionalization of the phenyl ring in methyl-substituted benzene derivatives with F-TEDA-BF4.

Various N-F reagents reacted with hexamethylbenzene (1) forming side chain substituted alkoxides or esters in protic solvents, Ritter type side chain functionalization was observed in acetonitrile in the presence of trifluoroacetic acid, while in aqueous acetonitrile solution phenyl ring transformation took place, starting with ipso attack of water and further rearrangement of the methyl group as the main process. Rearranged 2,3,4,5,6,6-hexamethylcyclohexa-2,4-dienone (7) was transformed to 5-fluoro-2,3,5,6,6-pentamethyl-4-methylenecyclohex-2-en-1-one (8) or 5-hydroxy-2,3,5,6,6-pentamethyl-4-methylenecyclohex-2-en-1-one (9). 1,2,3,4,5,6-Hexamethyl-bicyclo[2.2.0]hexa-2,5-diene reacted with F-TEDA-BF4 in the presence of water and 7 was formed in high yield. Durene (12) followed similar ipso attack of water as 1, but on the other hand 1,2,3,4-tetramethylbenzene displayed different regioselectivity and 2,3,4,5-tetramethylphenol was formed, further transforming to 4-fluoro-2,3,4,5-tetramethylcyclohexa-2,5-dienone. The functionalizations of methylbenzenes obeyed a second-order rate equation v = d[N-F]/dt = k2[N-F][substrate], and DeltaG# values between 77 and 94 kJ/mol were determined. The presence of water did not significantly influence DeltaG# but considerably affected DeltaS# and positive values were found where methyl group migration was the dominant process (9.1 J/(mol K) for 1 and 0.5 J/(mol K) for 12). A higher reactivity of durene than mesitylene (k2(MES)/k2(DUR) = 0.23) was found, supporting the assumption that single electron transfer (SET) is the dominant process in the functionalizations of methyl-substituted benzene derivatives with F-TEDA-BF4.