A second generation human haplotype map of over 3.1 million SNPs

We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r(2) of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r(2) of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62863/1/nature06258.pd

The Genetic and Environmental Foundation of the Simple View of Reading in Chinese.

The Simple View of Reading (SVR) in Chinese was examined in a genetically sensitive design. A total of 270 pairs of Chinese twins (190 pairs of monozygotic twins and 80 pairs of same-sex dizygotic twins) were tested on Chinese vocabulary and word reading at the mean age 7.8 years and reading comprehension of sentences and passages one year later. Results of behavior-genetic analyses showed that both vocabulary and word reading had significant independent genetic influences on reading comprehension, and the two factors together accounted for most but not all of the genetic influences on reading comprehension. In addition, sentence comprehension had a stronger genetic correlation with word reading while passage comprehension showed a trend of stronger genetic overlap with vocabulary. These findings suggest that the genetic foundation of the SVR in Chinese is largely supported in that language comprehension and decoding are two core skills for reading comprehension in nonalphabetic as well as alphabetic written languages

Generalist genes and cognitive abilities in Chinese twins.

This study considered how far nonverbal cognitive, language and reading abilities are affected by common genetic influences in a sample of 312 typically developing Chinese twin pairs aged from 3 to 11 years. Children were individually given tasks of Chinese word reading, receptive vocabulary, phonological memory, tone awareness, syllable and rhyme awareness, rapid automatized naming, morphological awareness and orthographic skills, and Raven's Colored Progressive Matrices. Factor analyses on the verbal tasks adjusted for age indicated two factors: Language as the first factor and Reading as the second factor. Univariate genetic analyses indicated that genetic influences were substantial for nonverbal cognitive ability and moderate for language and reading. Multivariate genetic analyses showed that nonverbal cognitive ability, language and reading were influenced by shared genetic origins, although there were specific genetic influences on verbal skills that were distinct from those on nonverbal cognitive ability. This study extends the Generalist Genes Hypothesis to Chinese language and reading skills, suggesting that the general effects of genes could be universal across languages

Genetic and environmental overlap between Chinese and English reading-related skills in Chinese children.

This twin study examined the relative contributions of genes and environment on 2nd language reading acquisition of Chinese-speaking children learning English. We examined whether specific skills-visual word recognition, receptive vocabulary, phonological awareness, phonological memory, and speech discrimination-in the 1st and 2nd languages have distinct or overlapping genetic and environmental origins. A sample of 279 Chinese twin pairs with a mean age of 6 years was tested. Univariate twin analyses were used to identify sources of individual variations in reading abilities and related cognitive-linguistic skills in Chinese and English, respectively. They were used to show both similar and distinctive patterns in these skills across Chinese and English. Bivariate Cholesky decomposition analyses indicated genetic overlaps between all parallel Chinese and English variables, as well as shared environmental overlaps in receptive vocabulary and phonological awareness. The phenotypic correlations between 1st and 2nd language skills previously observed in cross-linguistic studies could be explained by the shared genetic and environmental influences found in this twin study. (PsycINFO Database Record (c) 2014 APA, all rights reserved)

The Norman Transcript

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Genetic analysis of CYP2D6 locus of Hong Kong Chinese psychiatric patients

The genetically determined polymorphism of debrisoquine hydroxylase (cytochrome P4502D6, CYP2D6) shows marked interethnic differences due to the different distribution of the alleles of the CYP2D6 gene in different populations. Differences are not only in the incidence of poor metabolizers (PM) of debrisoquone, but also in the enzyme activity within the extensive metabolizer (EM) phenotype. The distribution of the debrisoquine metabolic ratios (MR) is shifted towards higher values among Oriental EMs compared to Caucasian EMs due to the high prevalence of the CYP2D6*10 allele [nomenclature according to Daly et al., 1996] in this population [Wang et al., 1993]. The prevalence of the different alleles of the CYP2D6 gene may be different within different Oriental populations or in particular patient groups. The genotype of 54 patients with diagnosis of major depression according to DSM IV was assessed for the prevalence of the alleles CYP2D6*10, CYP2D6*4, and CYP2D6*8 (the prevalence of which in Chinese is not known). Mutation 2938C→T indicative of CYP2D6*2 (allele L) was also assessed in five patients homozygous for CYP2D6*10 and was found to be absent. Genotyping was performed according to published methods. The CYP2D6*8 and CYP2D6*4 alleles were absent in the present population studied as expected. The CYP2D6*10 allele frequency was 0.6 in the present study, similar to that found among Singaporean Chinese, higher than that found among the Japanese, Koreans, and Chinese living in Sweden (0.51), and lower than that among Taiwanese (0.7) [Wang et al., 1993; Yokota et al., 1993; Lee and Jeyaseelan, 1994; Roh et al., 1996]. Genotyping a healthy Hong Kong Chinese population and testing for other variants of the CYP2D6 gene is in progress. This is the first CYP2D6 genotyping study conducted on a Hong Kong Chinese population. It will contribute to previous data on differences among EMs of different Oriental origins.link_to_subscribed_fulltex

Using a three-item questionnaire to determine zygosity in Chinese young twins: A validation study

Using questionnaire method to determine zygosity is common in twin research due to its low cost and time saving advantage. A recent study1 by the authors show that a simple 3-item parent questionnaire can achieve accuracy of over 90% in zygosity classification in a Chinese school-aged twin sample. The three questions asked (1) parental perception of their twins’ zgyosity, (2) twins’ resemblance and (3) whether twins were confused by strangers. The current study attempted to replicate the effectiveness of this 3-item questionnaire in an independent validation sample. Three methods were employed to evaluate parental report accuracy, namely summed score, logistic regression, and decision tree. All three methods yielded similarly high classification accuracy in both the original sample and the validation sample. Furthermore, the current study explored the possibility to improve the questionnaire by adding additional physical characteristics items, such as twins’ similarity in hair texture. How parental responses were affected by the advice of medical professionals and information about the placenta was also discussed. 1. Ho, C. S. H., Zheng, M., Chow, B. W. Y., Wong, S. W.,Lim, C. K., & Waye, M. M. (2017). Adequacy of using a three-item questionnaire to determine zygosity in Chinese young twins. Behavior Genetics, 47(2), 244-254

Radiation hybrid mapping of human cytosolic malate dehydrogenase (hcMDH) to the short arm of chromosome 2

Compartmentalization of human cytosolic malate dehydrogenase, hcMDH, together with its isozyme partner-mitochondrial form, hmMDH, plays an important role in the aerobic metabolism of the malate-aspartate shuttle and the citric acid cycle. However, they share few structural homology at the molecular level. The pseudogenes of mMDH has been reported in mice but hcMDH has no pseudogenes as shown by Southern blot analysis. A single band only was detected for the EcoRI digestion with 9.4 kb long of human genomic DNA and HindIII cutting with 2.8kb long. hcMDH gene was mapped to chromosome 2 by somatic cell hybrid analysis and further localised to 268.72cR from the top telomere of Chromosome 2 (near 2p15) by radiation hybrid mapping. The genes falling into this region may be related to dilated cardiomyopathy (DCM), several types of cancers and immunoregulation mechanism of cancers.link_to_subscribed_fulltex