Exome Chip Analysis of 14,026 Koreans Reveals Known and Newly Discovered Genetic Loci Associated with Type 2 Diabetes Mellitus

BACKGROUND

Most loci associated with type 2 diabetes mellitus (T2DM) discovered to date are within noncoding regions of unknown functional significance. By contrast, exonic regions have advantages for biological interpretation.

METHODS

We analyzed the association of exome array data from 14,026 Koreans to identify susceptible exonic loci for T2DM. We used genotype information of 50,543 variants using the Illumina exome array platform.

RESULTS

In total, 7 loci were significant with a Bonferroni adjusted P=1.03×10-6. rs2233580 in paired box gene 4 (PAX4) showed the highest odds ratio of 1.48 (P=1.60×10-10). rs11960799 in membrane associated ring-CH-type finger 3 (MARCH3) and rs75680863 in transcobalamin 2 (TCN2) were newly identified loci. When we built a model to predict the incidence of diabetes with the 7 loci and clinical variables, area under the curve (AUC) of the model improved significantly (AUC=0.72, P<0.05), but marginally in its magnitude, compared with the model using clinical variables (AUC=0.71, P<0.05). When we divided the entire population into three groups-normal body mass index (BMI; <25 kg/m2), overweight (25≤ BMI <30 kg/m2), and obese (BMI ≥30 kg/m2) individuals-the predictive performance of the 7 loci was greatest in the group of obese individuals, where the net reclassification improvement was highly significant (0.51; P=8.00×10-5).

CONCLUSION

We found exonic loci having a susceptibility for T2DM. We found that such genetic information is advantageous for predicting T2DM in a subgroup of obese individuals.

Arterial Ischemic Stroke Secondary to Cardiac Disease in Neonates and Children

OBJECTIVE

We describe the risk factors for peri-procedural and spontaneous arterial ischemic stroke (AIS) in children with cardiac disease.

METHODS

We identified children with cardiac causes of AIS enrolled in the International Pediatric Stroke Study registry from January 2003 to July 2014. Isolated patent foramen ovale was excluded. Peri-procedural AIS (those occurring during or within 72 hours of cardiac surgery, cardiac catheterization, or mechanical circulatory support) and spontaneous AIS that occurred outside of these time periods were compared.

RESULTS

We identified 672 patients with congenital or acquired cardiac disease as the primary risk factor for AIS. Among these, 177 patients (26%) had peri-procedural AIS and 495 patients (74%) had spontaneous AIS. Among non-neonates, spontaneous AIS occurred at older ages (median 4.2 years, interquartile range 0.97 to 12.4) compared with peri-procedural AIS (median 2.4 years, interquartile range 0.35 to 6.1, P < 0.001). About a third of patients in both groups had a systemic illness at the time of AIS. Patients who had spontaneous AIS were more likely to have a preceding thrombotic event (16 % versus 9 %, P = 0.02) and to have a moderate or severe neurological deficit at discharge (67% versus 33%, P = 0.01) compared to those with peri-procedural AIS.

CONCLUSIONS

Children with cardiac disease are at risk for AIS at the time of cardiac procedures but also outside of the immediate 72 hours after procedures. Many have acute systemic illness or thrombotic event preceding AIS, suggesting that inflammatory or prothrombotic conditions could act as a stroke trigger in this susceptible population.

Prognostic significance of glycaemic control in patients with HBV and HCV-related cirrhosis and diabetes mellitus

AIMS

Diabetes mellitus (DM) is frequently observed in patients with cirrhosis, particularly that due to hepatitis C virus (HCV) infection. However, no studies have focused on the clinical significance of glycaemic control in cirrhotic patients because of their short life expectancy and poor hepatic function. The aim of this study was to evaluate the prognostic impact of glycaemic control in patients with hepatitis B virus (HBV) and HCV-related cirrhosis and DM.

METHODS

A total of 434 patients with HCV-related (HCV group, n = 88) or HBV-related (HBV group, n = 346) cirrhosis were studied retrospectively. We determined the prevalence of DM and treatment methods for hyperglycaemia and status of glycaemic control, and the patients' outcome.

RESULTS

The prevalence of DM was 43.2% (38/88) in the HCV group and 19.7% (68/346) in the HBV group. Patients in the HCV group were older with a female preponderance. DM was detected before the diagnosis of cirrhosis or simultaneously in 92% and 79% in the HCV and HBV groups, respectively. Most patients were treated with insulin or oral hypoglycaemic agents. However, blood glucose levels were maintained within the normal range in 34.2% of the HCV group and in 23.5% of the HBV group. Forty-six patients died during the observation period in both groups. Hepatic failure was the most common cause of death, and sepsis and variceal bleeding were more frequent in the HCV group than in the HBV group. Multivariate analysis showed that Child-Pugh class was the most important factor for survival in both groups. In the HCV group, the status of glycaemic control was a significant independent factor of survival (P = 0.018). In the HBV group, age and the development of spontaneous bacterial peritonitis were significant.

CONCLUSION

DM is more frequent in patients with HCV-related cirrhosis than in patients with HBV. Strict control of blood glucose levels could improve survival in HCV patients. A precise assessment of the risks and benefits of glycaemic control is required to reduce the mortality and morbidity of patients with cirrhosis and DM.

Temporal aspects of the fine-scale genetic structure in a population of Cinnamomum insularimontanum (Lauraceae)

Cinnamomum insularimontanum Hayata (Lauraceae) is an insect-pollinated, broad-leaved evergreen tree with bird-dispersed seeds. We used allozyme loci, Wright's fixation index, spatial autocorrelation statistics (Moran's I), and coancestry measures to examine changes in genetic structure among four age-classes within a recently founded study population (60 x 100 m area) in southern Korea. There were no significant differences in expected heterozygosity among age classes. However, significant genetic differentiation among age classes was detected (P<0.0001). Fixation indices within age classes showed significant deficits of observed heterozygosity, which may be caused by partial selfing. The homogeneity of genetic structure among four age-classes may reflect similar spatial patterns of seed immigration from surrounding populations occurring year after year. Finally, the average Moran's I and coancestry estimates indicated essentially random spatial distributions of alleles for each of the four age-classes and between seedlings and 2-4 year juveniles vs adult trees. These findings are very similar to those observed in the same study area for another member of the Lauraceae, Neolitsea sericea, which has a very similar life history and ecological characteristics (ie, bird-dispersed fruits, insect pollination, and a similar age structure). Together, these results suggest that the fleshy drupes of lauraceous species represent an adaptation to aid in the independent dispersal of seed by birds, which in turn may increase the genetic diversity of founders colonizing new habitats.

Successful treatment of Boerhaave's syndrome with endoscopic insertion of a self-expandable metallic stent: report of three cases and a review of the literature

Boerhaave's syndrome is a rare but life-threatening condition which presents a diagnostic as well as therapeutic challenge. Early diagnosis and prompt surgical repair are critical for survival; however late recognition of esophageal rupture is not unusual. A variety of nonsurgical approaches have been proposed, particularly in the case of delayed diagnosis. In recent years, the insertion of a metallic stent has been described as a promising modality in the treatment of spontaneous esophageal rupture. We report three cases of Boerhaave's syndrome treated with self-expandable metallic stents and review previously published cases.

High levels of allozyme variation within populations and low allozyme divergence within and among species of Hemerocallis (Liliaceae)

Thirty populations from five species of Hemerocallis in Korea were analyzed by starch gel electrophoresis to measure genetic diversity and to determine genetic population structure and the amount of genetic divergence within and between species at 12 isozyme loci. In addition, Moran's I spatial autocorrelation statistics were used to examine the spatial distribution of allozyme polymorphisms in populations of H. thunbergii and H. hakuunensis. Populations of five Korean species maintain high levels of genetic variation and little differentiation among populations and species. Mean expected heterozygosities range from 0.165 in H. hongdoensis, an island endemic, to 0.265 in H. taeanensis, and a total of 81 alleles across the 12 loci were detected in the five species. G(ST) values for each of the five species were low, ranging from 0.051 in H. taeanensis to 0.078 in H. hakuunensis. Mean intraspecific Nei's genetic identities (I) between populations of the five species were all above 0.97. However, a considerable level of heterozygote deficiencies within populations was detected, ranging from 0.242 to 0.411 measured as F(IS) statistics. This deficiencies may be due to inbreeding, limited pollen and seed dispersal, or from the pooling of subpopulations that differ in allele frequencies. A small spatial scale population substructuring (<12 m) was found in H. thunbergii and H. hakuunensis. A group of populations from each of the five previously designated Hemerocallis species (based on their morphology, ecology, and phenology) agrees with our allozyme data, though pairwise comparisons among species had high I values (from 0.862, H. middendorffii vs. H. hongdoensis, to 0.969, H. thunbergii vs. H. taeanensis). This is attributed to the presence of the same high-frequency alleles in different species at seven loci. In addition, no "diagnostic allele" that appears in all populations of one species, but is absent in other species, was detected at the 12 isozyme loci. These all suggest that species of Hemerocallis in Korea may have recently derived from an ancestor or progenitor harboring high levels of genetic diversity.

Spatial genetic structure in a Neolitsea sericea population (Lauraceae)

Neolitsea sericea (Bl.) Koidz. (Lauraceae) is a dioecious, insect-pollinated, and broad-leaved evergreen tree with bird-dispersed seeds. We used allozyme loci, F-statistics, and spatial autocorrelation statistics (Moran's I ) to examine the changes in genetic structure among five age classes within a study population (60 m x 100 m area) in southern Korea. No significant differences in expected heterozygosity were found among the age classes. The mean F-values averaged over loci were similar among age classes and showed overall conformance of heterozygosities with Hardy-Weinberg proportions. Differences in allelic frequencies among age classes were small (mean G(ST)=0.012), and statistically significant only for one locus (Pgd-2). The mean Moran's I-values for each of five age classes indicated essentially random spatial distribution. The homogeneity of genetic structure and genetic diversity among the five age classes may reflect the occurrence of similar reproductive events, year after year. The results may reflect the attractive red drupes of N. sericea in that they cause various frugivorous birds to disperse the seed long distances and independently, which in turn may help N. sericea maintain higher levels of genetic diversity within populations.

Allozyme Variation and Genetic Relationships among Species of Cimicifuga (Ranunculaceae) from Korea

Allozyme investigation of the five Cimicifuga taxa in Korea was conducted to assess genetic and clonal diversity within populations and genetic divergence among populations and taxa. Levels of allozyme variation maintained in Korean Cimicifuga taxa were comparable to those for most herbaceous perennials. In general, samples excluding copies of the same multilocus genotype maintained higher levels of genetic diversity than the total samples within populations. Copies of homozygous genotypes at several loci resulting from clonal spread lead to decreased levels of genetic diversity within populations, indicating that clonal reproduction found in Cimicifuga affects population genetic structure. In general, more widely distributed species such as C. dahurica and C. japonica harbored higher levels of allozyme diversity than the other taxa examined. Although two varieties of C. heracleifolia are geographically and reproductively isolated, the genetic and clonal structure of var. bifida seems to resemble var. heracleifolia, indicating that the two varieties may have had a similar evolutionary history. However, the allozyme data strongly indicate that the two morphological types (Groups I and II) of C. simplex should be treated as separate species.

Spatial distribution of allozyme polymorphisms following clonal and sexual reproduction in populations of Rhus javanica (Anacardiaceae)

Rhus javanica L. (Anacardiaceae), a dioecious tree with both sexual reproduction and clonal growth, is widely distributed in warm temperate, subtropical, and tropical regions in east Asia. We used allozyme loci and spatial autocorrelation statistics to examine clonal structure and the spatial distribution of allozyme polymorphisms in two Korean populations. Populations of the species maintain moderate levels of allozyme variability (mean He=0.175, GST=0.060), and high levels of multilocus genotypic diversity (mean DG=0.971). Clone-pair distances ranged from 1.4 m to 57.4 m, and had high mean values of 24.0 m and 25.6 m in the two study populations. Approximate genetic patch widths were inferred to be 23-25 m. The results indicated that within populations there is moderate (one study population) or no (other study population) spatial genetic structure among sexually reproduced individuals, and vegetatively reproduced genotypes also are almost randomly distributed. The spatial genetic structure among sexually reproduced trees in the one case is probably caused by limited pollen dispersal in that population, and the lack of structure in the other probably results from the short time elapsed since founding. It appears that clonal reproduction also does not contribute substantially to genetic isolation by distance neither among the sexually reproduced individuals nor the total population. Ramets often establish long distances from their progenitors and thus do not substantially increase the degree of local consanguineous matings.

Clonal and spatial genetic structure in Eurya emarginata (Theaceae)

Eurya emarginata (Thunb.) Makino (Theaceae) is a dioecious, insect-pollinated tree, which combines sexual reproduction and clonal spread. It is narrowly distributed in coastal areas from southern China, along southern Korea, and extending to central and southern Japan. We used allozyme loci and spatial autocorrelation statistics to examine the clonal structure and the spatial distribution of allozyme polymorphisms of sexually reproduced individuals in a study population (70 m x 120 m area) in Korea. The population maintains moderate levels of allozyme variability (mean He=0.133), and multilocus genotypic diversity is high (mean DG=0. 992). The frequency of clones was 0.377 (90/239), and the mean clone-pair distance was very large (35.06 m +/- 1.91 m [SE]), indicating that clones can form at long distances away from their ancestors. In addition, it was found that genetic patch width was at least 24 m. However, join-count statistics for the total number of unlike joins showed that, contrary to expectation for such species, clonal reproduction does not contribute substantially to genetic isolation by distance neither among the sexually reproduced individuals nor the whole population. In contrast, limits to seed and pollen dispersal create substantial levels of genetic structure.