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The human amylase gene locus at chromosome 1p21.1 is structurally complex. This region contains two pancreatic amylase genes, AMY2B, AMY2A, and a salivary gene AMY1. The AMY1 gene harbors extensive copy number variation (CNV), and recent studies have implicated this variation in adaptation to starch-rich diets and in association to obesity for European and Asian populations. In this study, we showed that by combining quantitative PCR and digital PCR, coupled with careful experimental design and calibration, we can improve the resolution of genotyping CNV with high copy numbers (CNs). In two East Asian populations of Chinese and Malay ethnicity studied, we observed a unique non-normal distribution of AMY1 diploid CN genotypes with even:odd CNs ratio of 4.5 (3.3-4.7), and an association between the common AMY2A CN = 2 genotype and odd CNs of AMY1, that could be explained by the underlying haplotypic structure. In two further case-control cohorts (n = 932 and 145, for Chinese and Malays, respectively), we did not observe the previously reported association between AMY1 and obesity or body mass index. Improved methods for accurately genotyping multiallelic CNV loci and understanding the haplotype complexity at the AMY1 locus are necessary for population genetics and association studies.

Introduction Apolipoprotein E (ApoE) is implicated in the pathogenesis of osteoporosis. Objective To investigate possible association of the non-classical APOE gene + 113C/G (rs440446) intron 1 enhancer polymorphism with bone mineral density (BMD) in a homogeneous Chinese population in Singapore. Methods A total of 655 volunteers, males and females, aged between 31 and 72 years, from the public participated. BMD was measured using dual-energy X-ray absorptiometry and APOE + 113C/G (rs440446) genotypes were determined by Sequenom MassARRAY system. To adjust for potential confounders, anthropometric, demographic, and lifestyle determinants were obtained, and serum lipids and E 2 were measured. Results The + 113C/G (rs440446) polymorphism within the APOE gene was associated with BMD in Chinese Singaporean females only. Females with the heterozygous CG genotype were significantly associated with reduced total, lumbar spine, and femoral neck of hip BMD, after multilevel adjustment of confounders. The association was stronger in the spine than in the hip. When females were stratified according to WHO classification for osteoporosis, those with CG and GG genotypes had increased risk (OR 3.50 and 2.22, respectively) of developing osteopenia/osteoporosis in the lumbar spine. Serum lipids did not explain the influence of APOE + 113 C/G (rs440446) on BMD. Conclusion This study demonstrated an association between APOE + 113C/G (rs440446) polymorphism with measures of BMD in Singaporean Chinese females.

MiniSTR loci has demonstrated to be an effective approach to recover genetic information from degraded sample, due to the improved PCR efficiency of their reduced PCR amplicon sizes. This study constructed a partial miniSGM panel and investigated the performance of four miniSTR loci, D2S1338, D16S539, D18S51 and FGA, in three ethnic populations residing in Singapore. The suitability of the miniSTR primers for Singapore populations was assessed for loci D16S539, D18S51 and FGA.

MiniSTR loci has demonstrated to be an effective approach to recover genetic information from degraded sample, due to the improved PCR efficiency of their reduced PCR product sizes. This study investigated the allele frequency of six miniSTR loci, D1S1677, D2S441, D4S2364, D10S1248, D14S1434 and D22S1045, in three Singapore populations. All loci showed a moderate degree of polymorphism with observed heterozygosity >0.6 for all three populations. The allele frequencies, forensic parameters and heterozygosity comparison with other CODIS STR in similar populations are presented.

Systemic lupus erythematosus (SLE) is inherited as a complex polygenic trait. (New Zealand Black (NZB) × New Zealand White (NZW)) F1 hybrid mice develop symptoms that remarkably resemble human SLE, but (NZB × PL/J)F1 hybrids do not develop lupus. Our study was conducted using (NZW × PL/J)F1 × NZB (BWP) mice to determine the effects of the PL/J and the NZW genome on disease. Forty-five percent of BWP female mice had significant proteinuria and 25% died before 12 mo of age compared with (NZB × NZW)F1 mice in which >90% developed severe renal disease and died before 12 mo. The analysis of BWP mice revealed a novel locus (χ2 = 25.0; p < 1 × 10−6; log of likelihood = 6.6 for mortality) designated Wbw1 on chromosome 2, which apparently plays an important role in the development of the disease. We also observed that both H-2 class II (the u haplotype) and TNF-α (TNFz allele) appear to contribute to the disease. A suggestive linkage to proteinuria and death was found for an NZW allele (designated Wbw2) telomeric to the H-2 locus. The NZW allele that overlaps with the previously described locus Sle1c at the telomeric part of chromosome 1 was associated with antinuclear autoantibody production in the present study. Furthermore, the previously identified Sle and Lbw susceptibility loci were associated with an increased incidence of disease. Thus, multiple NZW alleles including the Wbw1 allele discovered in this study contribute to disease induction, in conjunction with the NZB genome, and the PL/J genome appears to be protective.

AIM: To apply an automated system of nucleic acid hybridisation coupled with the enzyme linked immunosorbent assay (ELISA) for the type specific detection of amplification products of dengue viruses. METHODS: Non-structural 3 (NS3) gene targets of reference strains of all four dengue and other flaviviruses, as well as dengue patient viraemic sera, were subjected to reverse transcription and polymerase chain reaction using consensus and dengue type specific primers and digoxigenin-11-dUTP label incorporation. The amplification products were detected by biotinylated type specific primers which served as ELISA capture probes bound to streptavidin coated tubes. RESULTS: Significantly high spectrophotometric absorbance readings were obtained by hybridisation of the consensus and seminested amplification products of all four dengue viruses with their respective capture probes. In contrast, extremely low absorbances were observed for consensus products of Japanese encephalitis, yellow fever, and Kunjin viruses, which served as negative controls. These ELISA data correlated well with agarose gel electrophoresis of dengue type specific amplified products of diagnostic sizes. CONCLUSIONS: The combination of in vitro amplification and antibody based detection offers rapid, type specific, high throughput, and gel-free detection of amplified products of dengue viruses.

Severe myopia (defined as spherical equivalent < −6.0 D) is a predominant problem in Asian countries, resulting in substantial morbidity. We performed a meta-analysis of four genome-wide association studies (GWAS), all of East Asian descent totaling 1603 cases and 3427 controls. Two single nucleotide polymorphisms (SNPs) (rs13382811 from ZFHX1B [encoding for ZEB2] and rs6469937 from SNTB1) showed highly suggestive evidence of association with disease (P < 1 × 10 −7 ) and were brought forward for replication analysis in a further 1241 severe myopia cases and 3559 controls from a further three independent sample collections. Significant evidence of replication was observed, and both SNP markers surpassed the formal threshold for genome-wide significance upon meta-analysis of both discovery and replication stages (P = 5.79 × 10 −10 , per-allele odds ratio (OR) = 1.26 for rs13382811 and P = 2.01 × 10 −9 , per-allele OR = 0.79 for rs6469937). The observation at SNTB1 is confirmatory of a very recent GWAS on severe myopia. Both genes were expressed in the human retina, sclera, as well as the retinal pigmented epithelium. In an experimental mouse model for myopia, we observed significant alterations to gene and protein expression in the retina and sclera of the unilateral induced myopic eyes for Zfhx1b and Sntb1. These new data advance our understanding of the molecular pathogenesis of severe myopia.

Biliary atresia is an important cause of neonatal obstructive jaundice in which there is inflammation, sclerosis and eventual obliteration of the bile duct system. Its onset may be antenatal, affecting the normal development of the biliary system. The intrahepatic biliary system is derived from the ductal plate, a sheath of cuboidal epithelium that appears at the hepatocyte-mesenchymal junction around the portal vein branches at 6 weeks gestation. This epithelial structure is moulded into a network of tubular bile ducts by the proliferating mesenchyme. Certain portions of the ductal plate are selected to become definitive bile ducts, while redundant biliary epithelium is deleted. The molecular dynamics controlling the intra-uterine development of the biliary system in humans are not yet clearly understood. Transforming growth factor-beta 1 is a cytokine that stimulates mesenchymal proliferation and inhibits epithelial growth, and has been shown to be important in organogenesis. In the present study, the pattern of TGF beta 1 peptide immunolocalization was investigated with the aid of computerized image analysis, in normal human bile duct development and in biliary atresia. TGF beta 1 peptide was detected within hepatocytes and ductal plate epithelium from 7 weeks gestation; increased TGF beta 1 immunoreactivity was present within the epithelium of developing bile ducts at 13 weeks gestation, and apical polarization of the cytokine was observed from 16 weeks gestation. In biliary atresia, the TGF beta 1 immunoreactivity pattern within the bile duct structures at the porta hepatis and within intrahepatic portal tracts resembled that of the primitive ductal plate, and there was no significant apical polarization. This may indicate a developmental arrest in the normal ductal plate remodelling process in biliary atresia, and suggests an underlying epithelial-mesenchymal interactive disorder.

MiniSTR loci have been demonstrated to be an effective approach in recovering genetic information from degraded specimen, because of the improved PCR efficiency of their reduced PCR amplicon sizes. This study constructed two miniSTR panels comprising six miniSTR loci, including D2S1776, D3S4529, D6S474, D9S2157, D10S1435 and D12ATA63. The allele frequency distribution, forensic parameters and heterozygosity in three Singapore populations are reported in this paper. All six loci showed relatively high polymorphism with observed heterozygosity0.7. However, many of these six loci also demonstrated significant population differentiation for the three populations.

Amelogenin paralogs on Chromosome X (AMELX) and Y (AMELY) are commonly used sexing markers. Interstitial deletion of Yp involving the AMELY locus has previously been reported. The combined frequency of the AMELY null allele in Singapore and Malaysia populations is 2.7%, 0.6% in Indian and Malay ethnic groups respectively. It is absent among 541 Chinese screened. The null allele in this study belongs to 3 Y haplogroups; J2e1 (85.7%), F* (9.5%) and D* (4.8%). Low and high-resolution STS mapping, followed by sequence analysis of breakpoint junction confirmed a large deletion of 3 to 3.7-Mb located at the Yp11.2 region. Both breakpoints were located in TSPY repeat arrays, suggesting a non-allelic homologous recombination (NAHR) mechanism of deletion. All regional null samples shared identical breakpoint sequences according to their haplogroup affiliation, providing molecular evidence of a common ancestry origin for each haplogroup, and at least 3 independent deletion events recurred in history. The estimated ages based on Y-SNP and STR analysis were approximately 13.5 +/- 3.1 kyears and approximately 0.9 +/- 0.9 kyears for the J2e1 and F* mutations, respectively. A novel polymorphism GA at Y-GATA-H4 locus in complete linkage disequilibrium with J2e1 null mutations is a more recent event. This work re-emphasizes the need to include other sexing markers for gender determination in certain regional populations. The frequency difference among global populations suggests it constitutes another structural variation locus of human chromosome Y. The breakpoint sequences provide further information to a better understanding of the NAHR mechanism and DNA rearrangements due to higher order genomic architecture.

In this study, 12 Y-STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS437, DYS438 and DYS439) were genotyped in the three major ethnic populations in Singapore, namely the Chinese, Malay and Indian. Allele frequency distribution, locus diversity, haplotype diversity and discrimination capacity were estimated. Analysis of molecular variance between the three ethnic populations indicated that 87.71% of the haplotypic variation is found within population and 12.29% is between populations (Fixation Index FST=0.123, p=0.000). Population pairwise comparisons showed significant Phist values between all population pairs, with the lowest (RST=0.05) for Chinese-Malay and the highest (RST=0.19) for Chinese-Indian.

Allele frequency data for 15 Short Tandem Repeat (STR) loci was studied for the three main ethnic groups residing in Singapore, namely Chinese, Malay and Indian. An in-house STR marker panel was employed, consisting all 13 tetranucleaotide STR listed in CODIS (Combined DNA Index System, USA) and two pentanucleaotide STR, Penta D and Penta E. This represents a comprehensive report for allele distribution in the Singapore population for these 15 microsatellite markers commonly used in forensic science.

Microsatellite (short tandem repeat) markers are useful tools for genetic linkage analysis because of their high frequency of occurrence in eukaryotic genomes, ease of typing, and high polymorphism content. To establish a panel of microsatellite markers useful for genome-wide screens in the Chinese population, we determined the heterozygosities and allelic frequencies of a widely used set of 285 markers in 208 individuals of Han Chinese descent. Although the median heterozygosity level in our Chinese population was 0.72, only 63.6% of these markers have a heterozygosity of at least 0.7, compared with 90.8% in the original Caucasian sample. The significant difference in heterozygosity and allelic frequencies between populations suggests that markers should be optimally selected for each study population to maximize information content and power.

Virologic surveillance for dengue through the detection of the prevalent serotype(s) circulating in the human population during inter- and intra-epidemic periods constitutes a reliable sentinel system for dengue outbreaks. We have applied a rapid and sensitive, semi-nested, reverse transcription-polymerase chain reaction (RT-PCR) assay using nonstructural protein 3 gene primers for the type-specific-detection of dengue viruses in artificially infected and in field-caught adult Aedes mosquitoes. In laboratory experiments, the assay was sensitive enough to detect one virus-infected mosquito head in pools of up to 59 uninfected heads. In a prospective field study conducted from April 1995 to July 1996, female adult Ae. aegypti and Ae. albopictus mosquitoes were caught from selected dengue-sensitive areas in Singapore and assayed by RT-PCR. Approximately 20% of 309 mosquito pools were positive for dengue viruses. Of the 23 RT-PCR-positive Ae. aegypti pools (containing 1-17 mosquitoes each), 18 pools (78.3%) were positive for dengue 1 virus. There were 40 RT-PCR-positive Ae. albopictus pools (containing 1-33 mosquitoes each) of which 31 (77.5%) were positive for dengue 1 virus. The predominant virus type responsible for the current dengue epidemic since 1995 was also dengue 1. The geographic locations of the virus-infected mosquitoes correlated with the residences or workplaces of patients within dengue outbreak areas. A total of 43.5% of the positive Ae. aegypti pools and 25.0% of the positive Ae. albopictus pools contained only a single mosquito. Both Aedes species showed similar overall minimum infection rates of 57.6 and 50 per 1,000 mosquitoes. Infected Ae. aegypti were detected as early as six weeks before the start of the dengue outbreaks in 1995 and 1996. However, infected Ae. albopictus appeared later, when the number of cases was increasing. Virologic surveillance by RT-PCR for detecting dengue virus-infected Aedes mosquitoes in the field may serve as an early warning monitoring system for dengue outbreaks.

Trois souches de dengue-1, dont deux recemment isolees au Pakistan et une a Singapour, et deux souches de dengue-2, dont une isolee a Singapour et une au Pakistan, ont ete soumises au sequencage nucleotidique des genes NS3. Les resultats authentifient l'epidemie de dengue de Karachi en 1994 et illustrent les relations genetiques notables entre les souches recemment isolees au Pakistan et a Singapour et les souches de dengue deja connues.

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent. Fil: Corach, Daniel. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Servicio de Huellas Digitales Genéticas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Caputo, Mariela. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Servicio de Huellas Digitales Genéticas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Marino, Miguel Eduardo. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Laboratorio de Analisis de ADN; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Purps, Josephine. Charité-Universitätsmedizin; Alemania Fil: Siegert, Sabine. University of Cologne; Alemania Fil: Willuweit, Sascha. Charité-Universitätsmedizin; Alemania Fil: Nagy, Marion. Charité-Universitätsmedizin; Alemania Fil: Alves, Cíntia. Universidad de Porto; Portugal Fil: Salazar, Renato. Universidad de Porto; Portugal Fil: Angustia, Sheila M. T.. Philippine National Police Crime Laboratory; Filipinas Fil: Santos, Lorna H.. Philippine National Police Crime Laboratory; Filipinas Fil: Anslinger, Katja. Universitat Genzentrum Der Ludwing-maximilians; Alemania Fil: Bayer, Birgit. Universitat Genzentrum Der Ludwing-maximilians; Alemania Fil: Ayub, Qasim. The Wellcome Trust Sanger Institute; Reino Unido Fil: Wei, Wei. The Wellcome Trust Sanger Institute; Reino Unido Fil: Xue, Yali. The Wellcome Trust Sanger Institute; Reino Unido Fil: Tyler Smith, Chris. The Wellcome Trust Sanger Institute; Reino Unido Fil: Baeta Bafalluy, Miriam. Universidad de Zaragoza; España Fil: Martínez Jarreta, Begoña. Universidad de Zaragoza; España Fil: Egyed, Balazs. Eotvos University, Budapest; Argentina Fil: Balitzki, Beate. Universidad de Basilea; Suiza Fil: Tschumi, Sibylle. Universidad de Basilea; Suiza Fil: Ballard, David. King; Reino Unido Fil: Syndercombe Court, Denise. King; Reino Unido Fil: Barrantes, Xinia. Poder Judicial, Forensic Sciences Department; Costa Rica Fil: Bäßler, Gerhard. Landeskriminalamt Baden-Württemberg; Alemania Fil: Berger, Burkhard. Universidad de Innsbruck; Austria Fil: Niederstätter, Haral. Universidad de Innsbruck; Austria Fil: Parson, Walther. Universidad de Innsbruck; Austria. University Park; Estados Unidos Fil: Davis, Carey. Department of Molecular and Medical Genetics; Estados Unidos. Institute of Applied Genetics; Estados Unidos Fil: Furfuro, Sandra. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Laboratorio de Análisis de ADN; Argentina Fil: Locarno, Laura. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Laboratorio de Análisis de ADN; Argentina

We recently cloned the newest human integrin beta subunit, termed beta 7, from a cDNA library constructed from SEA-activated T lymphocytes. In this communication, we report on the structure of the human integrin beta 7 protein complex determined using a rabbit anti-beta 7 peptide antibody raised to an N-terminal 22 amino acid residue sequence deduced from the human beta 7 subunit cDNA. The beta 7 subunit (Mr 116,000) expressed on PHA lymphoblasts associates with a single major alpha subunit (alpha H) that is distinct from the prominent T cell marker, integrin alpha 4. The alpha H subunit (Mr 180,000 nonreduced) displays a distinctive shift in size on reduction to an apparent Mr of 150,000. We show that these structural properties of the integrin beta 7 complex are shared with the cell surface antigen HML-1 found highly expressed on T cells which populate the intestinal epithelium and are proposed to be involved in mucosal immunity. Sequential immunoprecipitation and Western blotting demonstrate identity or close homology between the alpha H beta 7 and HML-1 proteins.