FT-Raman investigation of human dental enamel surfaces

FT-Raman spectra of human enamel surfaces from sound, affected (with 1 cavity) and highly affected (with at least 3 cavities) tooth samples were analyzed by principal component analysis (PCA). Major differences between the unaffected and affected tooth samples seem to arise from the structural changes along the c-axis of hydroxyapatite, the chief crystalline component of human dental enamel. Based on Fisher index calculations, the most discriminative value was obtained for the intensity of the only Raman active nu 2PO43- (E-1) symmetric deformation mode at 428 cm(-1). Moreover, these changes can be observed through the whole tooth enamel surface, establishing a predisposition to caries correlated to chemical and structural composition of tooth enamel. No spectral changes regarding the CO32- substitution were detected by both nondestructive FT-Raman and FTIR (Fourier transform infrared) spectroscopy of the powdered teeth samples. Copyright (C) 2009 John Wiley & Sons, Ltd

Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project

Abstract Background Genotype imputation from single-nucleotide polymorphism (SNP) genotype data using a haplotype reference panel consisting of thousands of unrelated individuals from populations of interest can help to identify strongly associated variants in genome-wide association studies. The Tohoku Medical Megabank (TMM) project was established to support the development of precision medicine, together with the whole-genome sequencing of 1070 human genomes from individuals in the Miyagi region (Northeast Japan) and the construction of the 1070 Japanese genome reference panel (1KJPN). Here, we investigated the performance of 1KJPN for genotype imputation of Japanese samples not included in the TMM project and compared it with other population reference panels. Results We found that the 1KJPN population was more similar to other Japanese populations, Nagahama (south-central Japan) and Aki (Shikoku Island), than to East Asian populations in the 1000 Genomes Project other than JPT, suggesting that the large-scale collection (more than 1000) of Japanese genomes from the Miyagi region covered many of the genetic variations of Japanese in mainland Japan. Moreover, 1KJPN outperformed the phase 3 reference panel of the 1000 Genomes Project (1KGPp3) for Japanese samples, and IKJPN showed similar imputation rates for the TMM and other Japanese samples for SNPs with minor allele frequencies (MAFs) higher than 1%. Conclusions 1KJPN covered most of the variants found in the samples from areas of the Japanese mainland outside the Miyagi region, implying 1KJPN is representative of the Japanese population’s genomes. 1KJPN and successive reference panels are useful genome reference panels for the mainland Japanese population. Importantly, the addition of whole genome sequences not included in the 1KJPN panel improved imputation efficiencies for SNPs with MAFs under 1% for samples from most regions of the Japanese archipelago

Additional file 1: of Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project

Table S1. The imputation coverage (proportion of variants with an imputation r2 ≥ 0.8), with each reference panel across different MAF bins. (XLSX 8 kb