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Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs., Genomes vary from one another in multifarious ways, and the totality of this genetic variation underpins the heritability of human traits. Over the past two years, the human reference sequence [...]

The B3 phenotype is the most common B subtype in Korea. The B305 allele (425 T>C, M142T) was first reported in 2 Chinese individuals; however, it has not yet been reported in the Koreans, and the impact of the M142T mutation on the expression of the B3 phenotype has also not been studied. To resolve an ABO discrepancy between a group O neonate and her group O father and A(1)B(3) mother, blood samples from these individuals and other family members were referred to our laboratory for ABO gene analysis. The B305 allele was discovered in the neonate (B305/O01), her mother (A102/ B305), and her maternal aunt (B305/O02), while her father was typed as O01/O02. Transient transfection experiments were performed in HeLa cells using the B305 allele synthesized by site-directed mutagenesis; flow cytometric analysis revealed that this transfect expressed 35.5% of the total B antigen produced by the B101 allele transfect. For comparison, Bx01 allele transfects were also created, and they expressed 11.4% of the total B antigen expressed on the surface of B101 transfects. These experiments demonstrate that the M142T (425 T>C) mutation is responsible for the B subtype phenotype produced by the B305 allele.

Background: Detection of antibodies to extractable nuclear antigens (ENAs) and dsDNA is needed for the diagnosis of and predicting prognosis in systemic autoimmune diseases. Recently introduced line immunoassay (LIA) has the advantage of detecting several autoantibodies simultaneously, and we evaluated its usefulness in the diagnosis of autoimmune diseases in comparison with enzyme-linked immunosorbent assay (ELISA)., Methods: Samples were collected from 437 patients referred by rheumatologists. FANA (fluorescent antinuclear antibody) test and LIA for the detection of 13 different autoantibodies, including 6 ENAs and dsDNA were performed. LIA-positive samples for ENA or dsDNA antibodies were further tested with ELISA. Final diagnosis was made by rheumatologists according to the diagnostic criteria. Agreement of results between LIA and ELISA was analyzed in 53 selected patients with systemic autoimmune diseases., Results: The LIA detected antibodies to ENA and dsDNA in 118 and 22 patients, respectively, and ELISA detected 70.3% (83/118) and 45.5% (10/22) of LIA positive samples. Especially, 60.2% (71/118) of patients with positive ENA antibody on LIA was diagnosed as systemic autoimmune diseases. Patients having strong FANA titer and homogenous/speckled pattern showed higher prevalence of autoantibodies, but a small proportion of FANA negative patients also showed positive reactivity (LIA 10.8%, ELISA 5.2%). LIA showed a good agreement with ELISA for the anti-ENA antibodies (> or =80%), and a lower agreement for the anti-dsDNA antibody (67.9%)., Conclusions: LIA detecting several autoantibodies simultaneously might replace ELISA for anti-ENA antibodies, but not for anti-dsDNA antibodies. When LIA is performed considering clinical manifestations and FANA, it could contribute to the diagnosis of systemic autoimmune disease.

Background: Screening of high-risk patients using bladder tumor markers can offer an advantage of early detection and saving medical costs. For these purpose many tumor markers have been developed to supplement invasive cystoscopy. Our study evaluated the NMP22 point-of-care test (NMP22 POCT), which is one of the tumor makers, comparing with the standard urine cytology for the diagnosis of bladder cancer., Methods: From January to September 2005, 232 patients who had undergone a cystoscopy due to bladder cancer associated symptoms including hematuria and dysuria were enrolled in this study. Urine specimens were collected for NMP22 POCT and cytology. NMP22 POCT and urine cytology were compared for sensitivity and specificity. In addition, we evaluated urine stick test and microscopy to explain some false-positive results in NMP22 POCT., Results: Superficial transitional cell carcinoma was diagnosed in 10 patients. The sensitivity of NMP22 test was 60% (95% confidence interval [CI], 26.2-87.8%), whereas that of cytology was 33.3% (95% CI, 7.5-70.1%); however, the difference was not significant. The specificity of NMP22 test was 69.8% (95% CI, 63.3-75.8%), compared with 99.0% (95% CI, 96.5-99.9%) for cytology (P<0.001). The presence of microscopic RBCs in urine specimen was significantly associated with the lower specificity of NMP22 POCT (P=0.02)., Conclusions: NMP22 POCT was significantly less specific than urine cytology. To be useful as a bladder cancer screening test, the NMP22 test should have a higher specificity.